We have now concluded our discussion of the complement system - a biochemical cascade which complements other activities of the immune system. As part of the cascade, proteins are produced which perform these complementary roles and/or go on to react with other proteins to continue the cascade. The complement system produces chemotactic factors, which effectively "summon" immunocompetent cells - which can destroy the initiating pathogens - to the site of the infection. It can also mark pathogens as targets for macrophages and it produces the membrane attack complex, which destroys pathogens through lysis. Finally, it cleans up any neutralised antigen:antibody complexes.
This is all achieved through three different pathways: the classical pathway, the alternative pathway and the lectin pathway. All three of them are different ways of cleaving the important protein C3, which produces C3a and C3b. C3b - which is, additionally, an important opsonin - goes on to form C5-convertase, which cleaves C5 into C5a and C5b. C5b - through a series of intermediate complexes - forms the membrane attack complex, in conjunction with other complement components. This destroys cells through lysis. As a reminder, many of the intermediate products of these pathways, such as C4a, are important anaphylatoxins, which stimulate the release of histamine from mast cells. C5a is, additionally, a chemotactic factor and C3a may be involved in the production of the cytokine ASP.
Due to the dangers that the complement system can pose to the body, it needs to be highly regulated and this need underlies the reality of numerous, complex pathways - for it is important that the complement system only be activated when necessary, but it is equally important for it to be able to be activated quickly.
Friday, 2 May 2014
Complement system
We come, now, to the complement system - the other prong of the innate immune system (although it has a relationship with the adaptive immune system, too). The complement system complements the activities of immunocompetent cells and of antibodies. The complement system is made up of proteins produced predominantly by the liver which are generally present in the blood plasma, but in inactive states. These proteins take part in a biochemical cascade initiated by means of three possible pathways - the classical complement pathway, the alternative complement pathway, and the lectin pathway - each of which we will look at. As we have already seen to an extent, this cascade serves a number of important functions:
Since the complement system can cause severe damage to the body it's defending, it is of critical importance that it be well regulated. The primary way of doing this is through complement control proteins, which we will talk about very soon, as they're very relevant and have an important role to play in the effective functioning of the system itself, as well.
Before we talk about the complement system, however, we have to discuss antibodies in a lot more detail. We've already made reference to them, but it is time to consider them properly. We will have more to say about them when we look at adaptive immunity; but, for now, we need only understand what they are and what they do.
Antibodies (which have the abbreviation Ab and are also referred to as immunoglobulin (or Ig)) are proteins which play a critical role in the immune system by instigating immunocompetent cells to attack a pathogen, or by directly interfering with the pathogen's ability to invade the body. Importantly, antibodies are capable of engendering particular responses to particular pathogens, which is obviously important for the effective and efficient removal of a threat.
Antibodies function by binding to antigens (antibody generators). An antigen is any substance which binds with an antibody. This is getting to be quite circular and we need to be more specific. An antigen is any substance which is able to be bound by the antigen-binding site of an antibody. Antigen-binding sites are referred to as paratopes and they are highly variable; each antibody will have a slightly different paratope. Each paratope will bind to a particular epitope,1 which is the part of an antigen which actually binds to an antibody. The analogy which is so often used is that of a lock and key. Estimates for the number of different antibodies produced by the human body reach 10 billion, which gives a vast range of paratopes. This, of course, means that there are a vast number of possible epitopes. Antibodies work because of their huge diversity. Billions are produced meaning that vast numbers of different substances can bind to them and can, therefore, be recognised. The definition of an antigen then becomes any substance which the immune system can recognise. In the earlier terminology an antigen was specifically any substance recognised by an antibody; however, we now tend to use the term "antigen" to refer, also, to substances which bind to receptors on cells of the immune system. Antigens tend to be proteins, polysaccharides and, in some cases, lipids. This is because antibodies are generally required to recognise the kind of things which these make up: things like bacterial or viral coats, capsules, cell walls, flagella, fimbrae and toxins. Because these molecules are very large, they may have multiple epitopes. A final, more rounded definition of an antigen, then, is any substance which exhibits one or more epitopes and is, therefore, recognisable by the immune system.
It is worth recognising a distinction, at this point, between antigenicity - the ability to bind to products of the immune response - and immunogenicity - the ability to engender an immune response. Not all antigens are immunogenic, although all immunogenic substances are antigenic, for - if they could not be recognised by the immune system, they could not engender an immune response. This difference is very important. Many of the body's own components have antigens and it is obviously very important that they aren't immunogenic. Unfortunately, in some individuals some of them are, or may become so, and this is what causes autoimmune diseases, such as diabetes - where a self-antigen is recognised and produces an immune response. This is also what is involved in transplant rejection, where a part of another's body is transplanted, recognised as a threat by its antigens, and attacked.
A related problem is allergens which are harmless substances (such as peanuts) which are incorrectly perceived as a threat. They are, then, immunogenic, despite their not being a threat. This occurs as a result of the way paratopes are constructed (more on that later) which is essentially arbitrary. Certainly, the paratope can't tell what it's binding to, it just binds to it. There are mechanisms to subdue the production of low-quality antibodies (which bind poorly to their epitope) and of antibodies which would produce an autoimmune response. However, the construction of paratopes is not guided, the B-cell which produces them is not an intelligence and cannot 'design' an antibody for a particular antigen. It just produces antigens and the immune system relies on the huge variety to recognise as many threats as possible. However, don't get me wrong, as I said above, the impetus of natural selection has furnished us with B-cells which produce antibodies capable of binding to the sort of chemicals which make up (or are produced by) pathogens and there are mechanisms to reduce the risk of an autoimmune response. However, sometimes antibodies will be produced which cause a response to the wrong thing and sometimes things will slip through the net (or, at least, take a long time to be recognised).
There is a lot more to say, and most of it will be said when we turn to the adaptive immune system, to which it is more relevant. Now, however, we need only understand that antibodies bind to antigens. Vast numbers are produced, allowing a vast range of substances to be recognised, allowing a response to be produced to most foreign substances which shouldn't be in the body. There are a number of different responses which can be occasioned, but one of them is the activation of the complement system (which can also be activated by other means). We now return, then, to the complement system.
So, the complement system begins with the activation of C3, which we have already talked about (Inflammation (part 3)). C3 is present in the blood in an inactive state, as we saw earlier, and it needs to be activated as the first stage of the complement system. To reiterate, the complement system is a danger to the body and hence must only be activated in response to a threat. However, it is also a very useful defence. Therefore, the entire basis of the complement system is inactive proteins, which are constantly in circulation, awaiting activation. The genius of the convoluted chain of events I am about to describe is that they ensure that the complement system is only operative when it is required. However, the constant circulation of the components means they can be present in good quantities all over the body, so that the complement system can be readily and quickly activated. The inactive components are harmless and it is their need to be activated that allows them to circulate quite safely until they are needed. The perfect trade-off between a prompt and destructive defence mechanism, and the need to protect the body from its own defences.
C3 is activated by cleavage - the large molecule that is the protein C3 must be split into two smaller proteins - C3a and C3b.
These proteins are useful in themselves (see Inflammation (part 3)) - C3b opsonises pathogens and C3a triggers the degranulation of mast cells, such that they release histamine. C3b is also involved in the rest of the cascade and is necessary for bringing about the other effects of the complement system.
So, the trigger for the complement system is the cleavage of C3. This is what all three of the pathways achieve. The classical pathway achieves the cleavage of C3 by producing a particular C3-convertase, which, in this case, is a complex of two proteins - C4b and C2a (the complex of these two is referred to as C4b2a).
There are actually two different molecules which can cleave C3 and activate the complement pathway, and both of them are C3-convertases (this is because C3-convertase is a description - both of them are convertases which cleave C3 - it is not a name). However, the classical pathway makes use of C4b2a to cleave C3. This, then, is what the classical pathway needs to produce, in the first place. The starting point is another complex of proteins called C1-complex. C1-complex is a complex of 5 molecules: 1 × C1q, 2 × C1r and 2 × C1s. This is denoted C1qr2s2, which we refer to as C1-complex.
The C1q has good affinity for two of the five different types of antibody (specifically IgM and IgG - more on these later). Recall that antibodies can occasion a number of different responses. The "choice" of response is influenced by which of the five isotypes is involved. Only two are involved in the classical complement pathway. This is noteworthy, as this is one of the ways in which specific, appropriate responses can be produced to specific pathogens. So, C1q binds to antigen:antibody complexes - specifically complexes of antigens and IgM or IgG. C1q can also bind to certain molecules on the surface of some pathogens. In either case, this binding causes a conformational change in C1q, which activates the two C1r molecules - forming a catlytically active molecule referred to as C1r*. This then cleaves and activates the two C1s molecules, forming C1s*.
If you're interested in a slightly less stylised and simplified diagram, you may prefer this alternative diagram:
After undergoing this activation, the C1s cleaves another complement component C4. This cleavage produces two smaller molecules - C4a and C4b.
C4a, like C3a, is an anaphylatoxin, meaning it stimulates histamine release from mast cells. Meanwhile, C4b binds to the membrane of the pathogen, before binding to our next complement component C2. This causes the activated C1s to cleave C2 into C2a and C2b.
We now have the components for C3-convertase. The C2a binds with the C4b, forming C4b2a.
C4b2a cleaves C3 into C3a and C3b. We know that C3a is an anaphylatoxin and that C3b opsonises pathogens. C3b also binds with C4b2a, giving C4b2a3b - C5-convertase.
C5 is another complement component and - you will be amazed to hear - is cleaved by C5-convertase into C5a and C5b. In another turn-up for the books, C5a is an anaphylatoxin, while C5b is involved in the membrane attack complex (Inflammation (part 3)).
C5b binds with C6, forming a complex. This complex then binds with C7, forming a complex which binds with C8. This complex catalyses the polymerisation of C9 and these polymers also bind with this same complex, giving C5b-C6-C7-C8-C9{n}. This is the membrane attack complex. When C7 binds to the C5bC6 complex it alters the configuration of the proteins and exposes a hydrophobic site of the C7 (i.e. a site which is repelled by water). The cell membrane of the pathogens affected by the MAC are composed of phospholipid bilayers which have a hydrophobic tail. They also have a hydrophilic head, which has good affinity for water. Since the hydrophobic tails are repelled by water, they aggregate when exposed to it, forming the lipid bilayer cell membrane. This consists of a two-layered sheet with all of the tails in the centre and all of the heads on the outside. This is highly impermeable to water-soluble molecules and allows the cell to regulate the passage of substances into and out of it. The hydrophobic site of the C7 is able to insert into this bilayer.
When the C8 binds to the complex of C5b, C6 and C7, a hydrophobic area is also exposed, which can also insert into the bilayer. The hydrophobic area of C8 (C8 alpha-gamma - C8 is composed of a complex of C8-beta and C8 alpha-gamma) also polymerises C9. Hydrophobic sites of C9 are similarly exposed and associate with the lipid bilayer. Brilliantly, the C9 has this external face which is hydrophobic and a hydrophilic internal face, allowing water to enter the cell. When enough of these pores are opened, the cell is simply flooded with water and, ultimately, falls apart.
This, then, is the complement system. This is what it does and how it does it. Well, it's one way it can do what it does. There are two other pathways and we continue onto the alternative pathway. The alternative pathway is based on the properties of C3. C3 is a little unstable in aqueous solutions and this means that it undergoes occasional hydrolysis. Hydrolysis is a simple process where water cleaves chemical bonds. In this case, it is an internal thioester bond that is cleaved. A thioester has the functional group C-S-CO-C, i.e. a radical bonded to a sulfur atom, bonded to a carbon atom, itself double bonded to an oxygen atom and bonded to a radical. The generic structural formula, then, looks like this:
Anyway, this thioester bond is able to be cleaved by hydrolysis, forming C3(H2O):
This is constantly happening spontaneously, but at a low level. The cleavage brings about a change in the shape of the molecule, which means that it can now bind with a plasma protein called factor B:
After this has happened, another protein called factor D can cleave factor B into Ba and Bb. The Bb remains bound to the C3(H2O), forming C3(H2O)Bb:
This is a fluid-phase C3-convertase, which is capable of cleaving C3 into C3a and C3b, in order to activate the complement system. Because this is constantly taking place, the process needs to be regulated. The C3(H2O) and the C3b that is produced by C3-convertase are inactivated by factor H and factor I (examples of complement control proteins), preventing the spontaneous activation of the entire complement system.
However, naturally, if there are pathogens present, the activation of the complement system is desirable. In this case, it is often true that the C3 will be cleaved by hydrolysis caused by a reaction with a hydroxyl or amino group of a cell surface molecule on a pathogen. This will leave C3b bound to the surface. Alternatively, the C3(H2O)Bb discussed earlier may cleave C3 and produce C3b, which will then bind to the surface of a pathogen. Once the C3b has bound to a pathogen, it is protected from being inactivated by Factor H.
In either case, C3b - now bound to the surface of a pathogen - can bind with factor B, forming C3bB. The factor B can then be cleaved by factor D, leaving us with the C3bBb complex bound to the surface of the pathogen. This is very similar to what happened before:
C3bBb is an unstable molecule; however it can bind with factor P (also called properdin), forming C3bBbP:
This is a stable C3-convertase, which can cleave C3 and produce more C3b, which binds to the same cell surface. Gradually, the amount of C3b will build up, "decorating" the cell and opsonising it. Many pathogens have no way of preventing this; however, the body's own cells possess complement regulatory proteins, such as CD35, CD46, CD55 and CD59. These inhibit this activity, preventing the body's own cells from activating the complement system. Furthermore, factor H can deactivate C3b on self cells, which is achieved by binding to glycosaminoglycans (GAGs). These are present on self cells, but not present on many pathogens. Therefore, the alternative complement pathway is halted when activated C3b binds to self cells, but not to pathogens.
Now, assuming the C3 convertase C3bBbP is bound to a pathogen, which needs to be eliminated, it will now be able to bind to another molecule of C3b which has been produced. This forms C3bBbC3b (sometimes shortened to C3b2Bb) - the C5-convertase of the alternative pathway. This cleaves C5 into C5a and C5b:
C5b can then bind with C6 and, eventually, the MAC will be formed and will be able to destroy pathogens by lysis.
To summarise, then, the alternative pathway is constantly being activated. However, if there are no pathogens around, it is quickly halted by complement control proteins. If, on the other hand, there are pathogens present, the cascade is not halted and the full complement system is initiated and takes effect. Once the pathogens are destroyed, there is nothing to sustain the complement system and it is halted.
Finally, we move on to the lectin pathway, which is very similar to the classical pathway. However, rather than C1-complex, the lectin pathway begins with a protein called mannose-binding lectin (MBL). Alternatively, a group of molecules called ficolins may also initiate this pathway. MBL binds with sugars, such as mannose and glucose, which are present on the surface of many pathogens, including salmonella and listeria. MBL is present in the blood in a complex with MASPs (MBL-associated serine proteases). There are three such MASPs, conveniently named MASP-1, MASP-2 and MASP-3. When MBL, in such a complex, binds with an appropriate sugar (say, for example, mannose), the MASP-1 and MASP-2 are activated and begin to cleave C4 and C2. Thus, we get C4a, C4b, C2a and C2b, whence we get C4b2a, whence we get C3a and C3b, whence we get the rest of the complement system. A similar process occurs with ficolins.
This, then, is the complement system - the second of the two major components of the innate immune system. As I highlighted above, the complement system does "interface" with the adaptive immune system and can be initiated by that system. It is, however, a much older and more primitive defence. Its response is also non-specific and the alternative pathway can be activated "automatically" and is not reliant upon antibodies. The key point to stress, though, is that it does not adapt over the course of the lifetime of an individual
1Some paratopes can bind to more than one epitope
- Some of the proteins serve as chemotactic factors for immunocompetent cells involved in the inflammatory response
- Some proteins opsonise pathogens, "marking" them as targets for phagocytosis
- As we saw above, the membrane attack complex destroys pathogens through the process called lysis
- Finally, "clearing up" antigen-antibody complexes (more on these shortly) is the last role that the complement system plays
Since the complement system can cause severe damage to the body it's defending, it is of critical importance that it be well regulated. The primary way of doing this is through complement control proteins, which we will talk about very soon, as they're very relevant and have an important role to play in the effective functioning of the system itself, as well.
Before we talk about the complement system, however, we have to discuss antibodies in a lot more detail. We've already made reference to them, but it is time to consider them properly. We will have more to say about them when we look at adaptive immunity; but, for now, we need only understand what they are and what they do.
Antibodies (which have the abbreviation Ab and are also referred to as immunoglobulin (or Ig)) are proteins which play a critical role in the immune system by instigating immunocompetent cells to attack a pathogen, or by directly interfering with the pathogen's ability to invade the body. Importantly, antibodies are capable of engendering particular responses to particular pathogens, which is obviously important for the effective and efficient removal of a threat.
Antibodies function by binding to antigens (antibody generators). An antigen is any substance which binds with an antibody. This is getting to be quite circular and we need to be more specific. An antigen is any substance which is able to be bound by the antigen-binding site of an antibody. Antigen-binding sites are referred to as paratopes and they are highly variable; each antibody will have a slightly different paratope. Each paratope will bind to a particular epitope,1 which is the part of an antigen which actually binds to an antibody. The analogy which is so often used is that of a lock and key. Estimates for the number of different antibodies produced by the human body reach 10 billion, which gives a vast range of paratopes. This, of course, means that there are a vast number of possible epitopes. Antibodies work because of their huge diversity. Billions are produced meaning that vast numbers of different substances can bind to them and can, therefore, be recognised. The definition of an antigen then becomes any substance which the immune system can recognise. In the earlier terminology an antigen was specifically any substance recognised by an antibody; however, we now tend to use the term "antigen" to refer, also, to substances which bind to receptors on cells of the immune system. Antigens tend to be proteins, polysaccharides and, in some cases, lipids. This is because antibodies are generally required to recognise the kind of things which these make up: things like bacterial or viral coats, capsules, cell walls, flagella, fimbrae and toxins. Because these molecules are very large, they may have multiple epitopes. A final, more rounded definition of an antigen, then, is any substance which exhibits one or more epitopes and is, therefore, recognisable by the immune system.
It is worth recognising a distinction, at this point, between antigenicity - the ability to bind to products of the immune response - and immunogenicity - the ability to engender an immune response. Not all antigens are immunogenic, although all immunogenic substances are antigenic, for - if they could not be recognised by the immune system, they could not engender an immune response. This difference is very important. Many of the body's own components have antigens and it is obviously very important that they aren't immunogenic. Unfortunately, in some individuals some of them are, or may become so, and this is what causes autoimmune diseases, such as diabetes - where a self-antigen is recognised and produces an immune response. This is also what is involved in transplant rejection, where a part of another's body is transplanted, recognised as a threat by its antigens, and attacked.
A related problem is allergens which are harmless substances (such as peanuts) which are incorrectly perceived as a threat. They are, then, immunogenic, despite their not being a threat. This occurs as a result of the way paratopes are constructed (more on that later) which is essentially arbitrary. Certainly, the paratope can't tell what it's binding to, it just binds to it. There are mechanisms to subdue the production of low-quality antibodies (which bind poorly to their epitope) and of antibodies which would produce an autoimmune response. However, the construction of paratopes is not guided, the B-cell which produces them is not an intelligence and cannot 'design' an antibody for a particular antigen. It just produces antigens and the immune system relies on the huge variety to recognise as many threats as possible. However, don't get me wrong, as I said above, the impetus of natural selection has furnished us with B-cells which produce antibodies capable of binding to the sort of chemicals which make up (or are produced by) pathogens and there are mechanisms to reduce the risk of an autoimmune response. However, sometimes antibodies will be produced which cause a response to the wrong thing and sometimes things will slip through the net (or, at least, take a long time to be recognised).
There is a lot more to say, and most of it will be said when we turn to the adaptive immune system, to which it is more relevant. Now, however, we need only understand that antibodies bind to antigens. Vast numbers are produced, allowing a vast range of substances to be recognised, allowing a response to be produced to most foreign substances which shouldn't be in the body. There are a number of different responses which can be occasioned, but one of them is the activation of the complement system (which can also be activated by other means). We now return, then, to the complement system.
So, the complement system begins with the activation of C3, which we have already talked about (Inflammation (part 3)). C3 is present in the blood in an inactive state, as we saw earlier, and it needs to be activated as the first stage of the complement system. To reiterate, the complement system is a danger to the body and hence must only be activated in response to a threat. However, it is also a very useful defence. Therefore, the entire basis of the complement system is inactive proteins, which are constantly in circulation, awaiting activation. The genius of the convoluted chain of events I am about to describe is that they ensure that the complement system is only operative when it is required. However, the constant circulation of the components means they can be present in good quantities all over the body, so that the complement system can be readily and quickly activated. The inactive components are harmless and it is their need to be activated that allows them to circulate quite safely until they are needed. The perfect trade-off between a prompt and destructive defence mechanism, and the need to protect the body from its own defences.
C3 is activated by cleavage - the large molecule that is the protein C3 must be split into two smaller proteins - C3a and C3b.
 |
| Figure 1.24: A highly simplified graphical representation of C3. This is C3 in its normal, inactivate state. It is a large protein composed of two smaller proteins C3a and C3b. The separation of these from one another is what is achieved by cleavage |
These proteins are useful in themselves (see Inflammation (part 3)) - C3b opsonises pathogens and C3a triggers the degranulation of mast cells, such that they release histamine. C3b is also involved in the rest of the cascade and is necessary for bringing about the other effects of the complement system.
So, the trigger for the complement system is the cleavage of C3. This is what all three of the pathways achieve. The classical pathway achieves the cleavage of C3 by producing a particular C3-convertase, which, in this case, is a complex of two proteins - C4b and C2a (the complex of these two is referred to as C4b2a).
 |
| Figure 1.25: The C3-convertase C4b2a |
There are actually two different molecules which can cleave C3 and activate the complement pathway, and both of them are C3-convertases (this is because C3-convertase is a description - both of them are convertases which cleave C3 - it is not a name). However, the classical pathway makes use of C4b2a to cleave C3. This, then, is what the classical pathway needs to produce, in the first place. The starting point is another complex of proteins called C1-complex. C1-complex is a complex of 5 molecules: 1 × C1q, 2 × C1r and 2 × C1s. This is denoted C1qr2s2, which we refer to as C1-complex.
 |
| Figure 1.26: C1-complex: C1qr2s2 |
The C1q has good affinity for two of the five different types of antibody (specifically IgM and IgG - more on these later). Recall that antibodies can occasion a number of different responses. The "choice" of response is influenced by which of the five isotypes is involved. Only two are involved in the classical complement pathway. This is noteworthy, as this is one of the ways in which specific, appropriate responses can be produced to specific pathogens. So, C1q binds to antigen:antibody complexes - specifically complexes of antigens and IgM or IgG. C1q can also bind to certain molecules on the surface of some pathogens. In either case, this binding causes a conformational change in C1q, which activates the two C1r molecules - forming a catlytically active molecule referred to as C1r*. This then cleaves and activates the two C1s molecules, forming C1s*.
 |
| Figure 1.27: As we've been going along, I've been making self-deprecating remarks about my own diagrams. This isn't just for the purposes of humour or anything like that, I want to stress that they're for illustration only. They're a bit like the tube map - they don't really show what the things they represent actually look like, they use straight lines and bright colours in the hope of providing a useful guide. This time, though, I really need to emphasise this again. I have chosen to leave my diagrams the way they are because I think it is clearer and because I'm bad at drawing. However, C1-complex looks nothing like this. Still, I hope the diagram above gives a flavour for what is going on. The change in the colour of C1q indicates the conformational change in C1q as a result of binding with the antigen:antibody complex. I have chosen to take this as an example and I have chosen to use an IgG antibody purely as an example. As I explained above, there are other possible alternatives |
If you're interested in a slightly less stylised and simplified diagram, you may prefer this alternative diagram:
 |
| Figure 1.28: An alternative diagram of the same process, showing a more accurate rendering of C1-complex. This is taken from a Wikipedia image and was authored by "Tossh_eng." I have only included the relevant part of a much larger image available here. We will come to the processes shown in the rest of that image in due course |
After undergoing this activation, the C1s cleaves another complement component C4. This cleavage produces two smaller molecules - C4a and C4b.
 |
| Figure 1.29: Here, C4 is shown in its normal, inactive state, composed of two proteins - C4a and C4b. I have tried to show it moments before it is cleaved by activated C1s. This cleavage, of course, will separate C4a from C4b |
C4a, like C3a, is an anaphylatoxin, meaning it stimulates histamine release from mast cells. Meanwhile, C4b binds to the membrane of the pathogen, before binding to our next complement component C2. This causes the activated C1s to cleave C2 into C2a and C2b.
 |
| Figure 1.30: Again, I am attempting to show the process moments before the cleavage takes place. You can see that C2 is shown in its inactive state, that it has bound with C4b - which has now bound to the membrane - and that it is about to be cleaved by activated C1s. Note, also, that C4a has now moved away from where this is all taking place |
We now have the components for C3-convertase. The C2a binds with the C4b, forming C4b2a.
 |
| Figure 1.31: You may recognise the C3-convertase C4b2a from before |
C4b2a cleaves C3 into C3a and C3b. We know that C3a is an anaphylatoxin and that C3b opsonises pathogens. C3b also binds with C4b2a, giving C4b2a3b - C5-convertase.
 |
| Figure 1.32: This time I have chosen to show unactivated C3 moments before it is cleaved on the left. On the right is the result of this cleavage - C3a goes off to fulfil its role as an anaphylatoxin, while C3b binds with the C3-convertase (C4b2a) to form C5-convertase (C4b2a3b) |
C5 is another complement component and - you will be amazed to hear - is cleaved by C5-convertase into C5a and C5b. In another turn-up for the books, C5a is an anaphylatoxin, while C5b is involved in the membrane attack complex (Inflammation (part 3)).
 |
| Figure 1.33 |
C5b binds with C6, forming a complex. This complex then binds with C7, forming a complex which binds with C8. This complex catalyses the polymerisation of C9 and these polymers also bind with this same complex, giving C5b-C6-C7-C8-C9{n}. This is the membrane attack complex. When C7 binds to the C5bC6 complex it alters the configuration of the proteins and exposes a hydrophobic site of the C7 (i.e. a site which is repelled by water). The cell membrane of the pathogens affected by the MAC are composed of phospholipid bilayers which have a hydrophobic tail. They also have a hydrophilic head, which has good affinity for water. Since the hydrophobic tails are repelled by water, they aggregate when exposed to it, forming the lipid bilayer cell membrane. This consists of a two-layered sheet with all of the tails in the centre and all of the heads on the outside. This is highly impermeable to water-soluble molecules and allows the cell to regulate the passage of substances into and out of it. The hydrophobic site of the C7 is able to insert into this bilayer.
When the C8 binds to the complex of C5b, C6 and C7, a hydrophobic area is also exposed, which can also insert into the bilayer. The hydrophobic area of C8 (C8 alpha-gamma - C8 is composed of a complex of C8-beta and C8 alpha-gamma) also polymerises C9. Hydrophobic sites of C9 are similarly exposed and associate with the lipid bilayer. Brilliantly, the C9 has this external face which is hydrophobic and a hydrophilic internal face, allowing water to enter the cell. When enough of these pores are opened, the cell is simply flooded with water and, ultimately, falls apart.
 |
| Figure 1.34: A very highly stylised diagram of the MAC, giving a broad idea of how it works and the proteins involved. I would imagine there would be more units of C9 and it should not be presumed that the proteins would join together in this way. This is merely the principle |
This, then, is the complement system. This is what it does and how it does it. Well, it's one way it can do what it does. There are two other pathways and we continue onto the alternative pathway. The alternative pathway is based on the properties of C3. C3 is a little unstable in aqueous solutions and this means that it undergoes occasional hydrolysis. Hydrolysis is a simple process where water cleaves chemical bonds. In this case, it is an internal thioester bond that is cleaved. A thioester has the functional group C-S-CO-C, i.e. a radical bonded to a sulfur atom, bonded to a carbon atom, itself double bonded to an oxygen atom and bonded to a radical. The generic structural formula, then, looks like this:
 |
| Figure 1.35: The structural formula of a thioester. (Image courtesy of Ben Mills and "Vladsinger," via Wikipedia) |
Anyway, this thioester bond is able to be cleaved by hydrolysis, forming C3(H2O):
 |
| Figure 1.36: A very unrealistic representation of C3(H2O), purely for diagrammatic purposes |
This is constantly happening spontaneously, but at a low level. The cleavage brings about a change in the shape of the molecule, which means that it can now bind with a plasma protein called factor B:
 |
| Figure 1.37 |
After this has happened, another protein called factor D can cleave factor B into Ba and Bb. The Bb remains bound to the C3(H2O), forming C3(H2O)Bb:
 |
| Figure 1.38: The Factor B is cleaved by Factor D |
This is a fluid-phase C3-convertase, which is capable of cleaving C3 into C3a and C3b, in order to activate the complement system. Because this is constantly taking place, the process needs to be regulated. The C3(H2O) and the C3b that is produced by C3-convertase are inactivated by factor H and factor I (examples of complement control proteins), preventing the spontaneous activation of the entire complement system.
However, naturally, if there are pathogens present, the activation of the complement system is desirable. In this case, it is often true that the C3 will be cleaved by hydrolysis caused by a reaction with a hydroxyl or amino group of a cell surface molecule on a pathogen. This will leave C3b bound to the surface. Alternatively, the C3(H2O)Bb discussed earlier may cleave C3 and produce C3b, which will then bind to the surface of a pathogen. Once the C3b has bound to a pathogen, it is protected from being inactivated by Factor H.
In either case, C3b - now bound to the surface of a pathogen - can bind with factor B, forming C3bB. The factor B can then be cleaved by factor D, leaving us with the C3bBb complex bound to the surface of the pathogen. This is very similar to what happened before:
 |
| Figure 1.39 |
C3bBb is an unstable molecule; however it can bind with factor P (also called properdin), forming C3bBbP:
 |
| Figure 1.40 |
This is a stable C3-convertase, which can cleave C3 and produce more C3b, which binds to the same cell surface. Gradually, the amount of C3b will build up, "decorating" the cell and opsonising it. Many pathogens have no way of preventing this; however, the body's own cells possess complement regulatory proteins, such as CD35, CD46, CD55 and CD59. These inhibit this activity, preventing the body's own cells from activating the complement system. Furthermore, factor H can deactivate C3b on self cells, which is achieved by binding to glycosaminoglycans (GAGs). These are present on self cells, but not present on many pathogens. Therefore, the alternative complement pathway is halted when activated C3b binds to self cells, but not to pathogens.
Now, assuming the C3 convertase C3bBbP is bound to a pathogen, which needs to be eliminated, it will now be able to bind to another molecule of C3b which has been produced. This forms C3bBbC3b (sometimes shortened to C3b2Bb) - the C5-convertase of the alternative pathway. This cleaves C5 into C5a and C5b:
 |
| Figure 1.41: Again I show unactivated C5 moments before it is cleaved on theleft. On the right is the result of this cleavage |
C5b can then bind with C6 and, eventually, the MAC will be formed and will be able to destroy pathogens by lysis.
To summarise, then, the alternative pathway is constantly being activated. However, if there are no pathogens around, it is quickly halted by complement control proteins. If, on the other hand, there are pathogens present, the cascade is not halted and the full complement system is initiated and takes effect. Once the pathogens are destroyed, there is nothing to sustain the complement system and it is halted.
Finally, we move on to the lectin pathway, which is very similar to the classical pathway. However, rather than C1-complex, the lectin pathway begins with a protein called mannose-binding lectin (MBL). Alternatively, a group of molecules called ficolins may also initiate this pathway. MBL binds with sugars, such as mannose and glucose, which are present on the surface of many pathogens, including salmonella and listeria. MBL is present in the blood in a complex with MASPs (MBL-associated serine proteases). There are three such MASPs, conveniently named MASP-1, MASP-2 and MASP-3. When MBL, in such a complex, binds with an appropriate sugar (say, for example, mannose), the MASP-1 and MASP-2 are activated and begin to cleave C4 and C2. Thus, we get C4a, C4b, C2a and C2b, whence we get C4b2a, whence we get C3a and C3b, whence we get the rest of the complement system. A similar process occurs with ficolins.
This, then, is the complement system - the second of the two major components of the innate immune system. As I highlighted above, the complement system does "interface" with the adaptive immune system and can be initiated by that system. It is, however, a much older and more primitive defence. Its response is also non-specific and the alternative pathway can be activated "automatically" and is not reliant upon antibodies. The key point to stress, though, is that it does not adapt over the course of the lifetime of an individual
1Some paratopes can bind to more than one epitope
Thursday, 1 May 2014
Summary
And that's it - that's inflammation. So, to summarise:
Cells, such as macrophages and dendritic cells, recognise generic pathogen molecules called PAMPs, and molecules released by damaged cells (perhaps as the result of an infection) called DAMPs. This is achieved by the PAMPs and DAMPs binding with receptors on these cells called PRRs. When these cells recognise pathogens, they release cell derived inflammatory mediators, which initiate and/or take part in the inflammatory response. Alongside these mediators, we also have plasma derived mediators. These work in combination with the cell derived mediators. The systems which the plasma derived mediators are part of are not activated by cells. We will discuss the processes involved in the next subsection, but, suffice it to say that it is largely done by the mediators themselves, or other molecules present in the blood. These mediators recruit immunocompetent cells which, hopefully, remove the pathogen (or whatever initiated the response); or serve to contain the pathogen. (Some also have a direct effect on the pathogen.) This is done, for the most part, by inducing vasodilation and increasing vascular permeability (which increases the presence of immunocompetent cells in the required area and allows them to pass out of the blood and into the interstitial fluid), or by inducing chemotaxis (which almost "summons" immunocompetent cells). These cells then get to work removing the pathogens and when they have done so, healing or repair can begin. Because these mediators are quickly degraded in the body, they do not survive for very long. Also, as part of the inflammatory response, molecules which inhibit certain aspects of the response are released. Therefore, to sustain the immune response, a sustained presence of a pathogen is required. Otherwise, it will "fizzle out" naturally. Where the response is sustained - because of a difficult to remove initiator, or because the response has been wrongly initiated (say by one's own cells), or because of a defect - chronic inflammation results, which can be harmful.
Cells, such as macrophages and dendritic cells, recognise generic pathogen molecules called PAMPs, and molecules released by damaged cells (perhaps as the result of an infection) called DAMPs. This is achieved by the PAMPs and DAMPs binding with receptors on these cells called PRRs. When these cells recognise pathogens, they release cell derived inflammatory mediators, which initiate and/or take part in the inflammatory response. Alongside these mediators, we also have plasma derived mediators. These work in combination with the cell derived mediators. The systems which the plasma derived mediators are part of are not activated by cells. We will discuss the processes involved in the next subsection, but, suffice it to say that it is largely done by the mediators themselves, or other molecules present in the blood. These mediators recruit immunocompetent cells which, hopefully, remove the pathogen (or whatever initiated the response); or serve to contain the pathogen. (Some also have a direct effect on the pathogen.) This is done, for the most part, by inducing vasodilation and increasing vascular permeability (which increases the presence of immunocompetent cells in the required area and allows them to pass out of the blood and into the interstitial fluid), or by inducing chemotaxis (which almost "summons" immunocompetent cells). These cells then get to work removing the pathogens and when they have done so, healing or repair can begin. Because these mediators are quickly degraded in the body, they do not survive for very long. Also, as part of the inflammatory response, molecules which inhibit certain aspects of the response are released. Therefore, to sustain the immune response, a sustained presence of a pathogen is required. Otherwise, it will "fizzle out" naturally. Where the response is sustained - because of a difficult to remove initiator, or because the response has been wrongly initiated (say by one's own cells), or because of a defect - chronic inflammation results, which can be harmful.
Inflammation (part 3)
This, then, is the "nuts and bolts" behind the initiation of the inflammatory response. The PAMPs of pathogens bind with the PRRs of cells in the immune system, which will either lead to the release of molecules which initiate or mediate an inflammatory response; or it will simply result in the destruction on the pathogen in and of itself. (Alternatively, DAMPs released by damaged cells can initiate the response.) But what happens when pathogens are recognised? We know broadly what happens when a pathogen is recognised (vascular changes (such as vasodilation) and cellular changes (such as recruitment of immunocompetent cells) take place). It is time to consider how those changes are brought about. These changes, as we have seen, are brought about by specific chemicals released by cells of the immune system when they are activated. We now turn to these mediators and what they do.
One of the most crucial inflammatory modulators is histamine, which looks like this:
Histamine is released by mast cells, basophils and platelets, where it is stored in granules prior to release. The role of histamine in inflammation is vasodilation and it is also responsible for the increase in permeability of the endothelium. This, you will recall, is important for allowing antibodies - which can clear the infection - and clotting factors - which can contain it - to reach the required location. It also has a role to play in recruiting leukocytes.
Histamine works by binding with certain G protein-coupled receptors called histamine receptors. There are four such receptors, imaginatively named H1 histamine receptor, H2 histamine receptor, etc. This induces a signal transduction cascade which brings about the required response.
Naturally, histamine is not the only compound involved in this process. Indeed, numerous cytokines involved in various elements of the inflammatory response (some of which we will soon see) have vasoactive properties. Lysosome granules, which are enzymes used to break down molecules as part of the response (either as a direct defence mechanism, or to break down molecules involved in initiating the response, in order to regulate it, or to instigate another aspect of the response), are a good example.
Another important group of molecules (specifically, they are fatty acids) are the prostaglandins, which - as we have already seen - are partly responsible for the experience of pain. There are numerous different prostaglandins and they perform many roles, not all of which are related to the immune response. Some of them are also involved in increasing vascular permeability. Others of them cause the aggregation (and others, still, cause the disaggregation) of platelets. This is important in the process of clotting, which helps to contain the infectious agent and keep it from spreading.
All of this is achieved by the binding of specific prostaglandins to specific receptors. We know of ten prostaglandin receptors, all of which are G-protein coupled receptors. Naturally, the receptors are selective with regards to the prostaglandins they bind with. This accounts for the range of effects of the prostaglandins. Different cell types will exhibit different (combinations of) prostaglandin receptors, which - of course - bind with particular prostaglandins, stimulating particular cells to produce particular responses.
A class of mediators which we have mentioned quite frequently, but only briefly touched on, are cytokines, which are vital in cell signalling processes. Each cytokine has a specific role to play, but they may serve to promote inflammation, or as anti-inflammatories. Due to the dangers of inflammation mentioned above, it is important that it be somewhat limited. Indeed, most of the body's immune responses involve impressive feedback systems and processes which are self-limiting. Also, the mediators we are looking at are quickly degraded, hence inflammation is usually self-regulating and clears up when the stimulus is removed. It is the failure of this which precipitates chronic inflammation. Now, cytokines are involved in upregulation and/or downregulation of certain genes. In a fascinating process, which is another example of where complex feedback mechanisms are employed, they serve to increase production of other cytokines, inhibit their own effects, change cell behaviour to more effectively combat disease and attract cells which can help fight the infection.
Two of the most notable cytokines released (primarily by macrophages) are interleukin-1 (IL-1) and tumour necrosis factor alpha (TNF-α). TNF-α causes fever, cell death and inflammation. It also inhibits the growth of malignant tumours and viral replication. An important cytokine,1 TNF-α looks like this:
The receptors which TNF can bind to are TNFR1 (TNF receptor type 1) and TNFR2. These receptors can actually initiate three signalling pathways, one of which is the NF-κB pathway.
IL-1 cytokines are deeply involved in producing fever. IL-1 also leads to vasodilation and enables immunocompetent cells, which can help the immune response, to reach the site of infection.
IL-1 looks like this:
Another important cytokine is IFN-γ (interferon gamma), which looks like this:
Released by natural killer cells (and T-cells, to which we will come), IFN-γ activates macrophages, can inhibit viral replication and combat tumours. IFN-γ binds to a heterodimeric receptor - interferon-gamma receptor (IFNGR) - composed of two macromolecules - interferon gamma receptor 1 (IFNGR1) and interferon gamma receptor 2 (IFNGR2).
We also have to consider another member of the interleukin group - interleukin 8 (IL-8), which is a chemokine (a chemotactic cytokine, or a cytokine which induces chemotaxis). IL-8 is also predominantly released by macrophages. IL-8 induces chemotaxis in a number of cells, but primarily in neutrophils (as we have, in fact, mentioned already). As well as this, it is important in phagocytosis, inducing changes in the cells which are conducive to phagocytosis, such as increasing the concentration of Ca2+ within the cell. It also promotes angiogenesis - the creation of new blood vessels from old ones.
Another mediator which we have mentioned before is leukotriene B4 - an eicosanoid (signalling molecules derived from fatty acids (by oxidation)) like the prostaglandins. Leukotriene B4 is released by leukocytes and actually affects leukocytes themselves. It is important in their activation and in mediating their adhesion to the endothelium and their migration across it. It is, too, an important chemotactic factor of neutrophils. The structural formula of leukotriene B4 is given below:
The final cell derived mediator - that is, the final mediator released by cells - which we shall consider is simple nitric oxide. Nitric oxide is released by macrophages, as well as endothelial cells and some neurons. Its role is vasodilation and it also reduces platelet aggregation, in order to regulate the response. As well as this it aids leukocyte recruitment and can destroy microbes when it is sufficiently concentrated.
This, then, is the cellular side of things; but, when discussing mediation, we again need to consider the exudate - the fluid containing substances such as clotting factors and antibodies which carries them into the interstitial fluid - as well. Contained within the exudate are numerous plasma derived mediators of inflammation, which we consider here. These mediators can be categorised as belonging to four systems:
The complement system is actually the subject of our next "section," for want of a better word, coming up in the post after next. For now, we will consider three elements of it - the first of which is C3 (complement component 3). In order to function as part of the complement system, C3 actually needs to be cleaved into two smaller proteins - C3a and C3b. This is done by a protease called C4b2a which is a type of C3-convertase. C3a induces mast cells to release histamine, while C3b is an opsonin - these bind to pathogens and "mark" them for phagocytosis.
The second element we shall consider is C5a. We have already seen that this is a chemotactic factor and it also induces mast cells to release histamine.
The final element that we will consider here, and perhaps my favourite, is the membrane attack complex, which really does seem like something out of a military. The membrane attack complex is a combination of C5b (obviously this is short for complement component 5b), C6, C7, C8, and multiple units of C9. Pleasingly, "unit" really is the word used in the associated Wikipedia article. The complex formed of these proteins creates pores in the cell membrane of invading pathogens. These holes allow molecules to move in and out of the cell - they are very much physical wounds of the cell. Enough of them will utterly destroy the cell in a process called lysis.
Next we turn to the kinin system and bradykinin. Bradykinin is very important in vasodilation and increasing vascular permeability. Not a whole lot is known about it, let alone the "kinin system" to which it belongs. However, we do know that this is the bugger that's responsible for a large amount of the pain we feel from inflammation. Just look at it:
Turning, now, to the coagulation system, we look at thrombin. Thrombin cleaves the protein fibrinogen - a soluble protein which is part of the blood plasma - into fibrin. Fibrin is insoluble and aggregates, forming a clot and preventing the spread of the infection. Thrombin also works to produce chemokines and nitric oxide.
Alongside this, we have the fibrinolysis system. The primary component of this is an enzyme called plasmin and plasmin breaks down the fibrin clots, regulating the immune response. One does not want to overdo it with clots, they can be very damaging and, in extreme cases, can be deadly. Plasmin is, then, very important. Additionally, the products of breaking down fibrin can have some effects on vascular permeability. Plasmin is also involved in the cleaving of C3 (see above) and it activates Factor XII.
Factor XII is the final component and it is produced by the liver. Factor XII is a protein which usually circulates in the blood flow in its inactive state. When it is activated, it, in turn, participates in the activation of the kinin, fibrinolysis and coagulation systems.
1Technically, it is an adipokine, a specific type of cytokine distinguished by being secreted by adipose tissue.
One of the most crucial inflammatory modulators is histamine, which looks like this:
 |
| Figure 1.18: The structural formula of 2-(1H-imidazol-4-yl)ethanamine (histamine). (Image courtesy of "NEUROtiker," via Wikipedia) |
Histamine is released by mast cells, basophils and platelets, where it is stored in granules prior to release. The role of histamine in inflammation is vasodilation and it is also responsible for the increase in permeability of the endothelium. This, you will recall, is important for allowing antibodies - which can clear the infection - and clotting factors - which can contain it - to reach the required location. It also has a role to play in recruiting leukocytes.
Histamine works by binding with certain G protein-coupled receptors called histamine receptors. There are four such receptors, imaginatively named H1 histamine receptor, H2 histamine receptor, etc. This induces a signal transduction cascade which brings about the required response.
Naturally, histamine is not the only compound involved in this process. Indeed, numerous cytokines involved in various elements of the inflammatory response (some of which we will soon see) have vasoactive properties. Lysosome granules, which are enzymes used to break down molecules as part of the response (either as a direct defence mechanism, or to break down molecules involved in initiating the response, in order to regulate it, or to instigate another aspect of the response), are a good example.
Another important group of molecules (specifically, they are fatty acids) are the prostaglandins, which - as we have already seen - are partly responsible for the experience of pain. There are numerous different prostaglandins and they perform many roles, not all of which are related to the immune response. Some of them are also involved in increasing vascular permeability. Others of them cause the aggregation (and others, still, cause the disaggregation) of platelets. This is important in the process of clotting, which helps to contain the infectious agent and keep it from spreading.
All of this is achieved by the binding of specific prostaglandins to specific receptors. We know of ten prostaglandin receptors, all of which are G-protein coupled receptors. Naturally, the receptors are selective with regards to the prostaglandins they bind with. This accounts for the range of effects of the prostaglandins. Different cell types will exhibit different (combinations of) prostaglandin receptors, which - of course - bind with particular prostaglandins, stimulating particular cells to produce particular responses.
A class of mediators which we have mentioned quite frequently, but only briefly touched on, are cytokines, which are vital in cell signalling processes. Each cytokine has a specific role to play, but they may serve to promote inflammation, or as anti-inflammatories. Due to the dangers of inflammation mentioned above, it is important that it be somewhat limited. Indeed, most of the body's immune responses involve impressive feedback systems and processes which are self-limiting. Also, the mediators we are looking at are quickly degraded, hence inflammation is usually self-regulating and clears up when the stimulus is removed. It is the failure of this which precipitates chronic inflammation. Now, cytokines are involved in upregulation and/or downregulation of certain genes. In a fascinating process, which is another example of where complex feedback mechanisms are employed, they serve to increase production of other cytokines, inhibit their own effects, change cell behaviour to more effectively combat disease and attract cells which can help fight the infection.
Two of the most notable cytokines released (primarily by macrophages) are interleukin-1 (IL-1) and tumour necrosis factor alpha (TNF-α). TNF-α causes fever, cell death and inflammation. It also inhibits the growth of malignant tumours and viral replication. An important cytokine,1 TNF-α looks like this:
 |
| Figure 1.19: Crystal structure of tumour necrosis factor alpha. (Image courtesy of Ramin Herati, via Wikipedia) |
The receptors which TNF can bind to are TNFR1 (TNF receptor type 1) and TNFR2. These receptors can actually initiate three signalling pathways, one of which is the NF-κB pathway.
IL-1 cytokines are deeply involved in producing fever. IL-1 also leads to vasodilation and enables immunocompetent cells, which can help the immune response, to reach the site of infection.
IL-1 looks like this:
 |
| Figure 1.20: Crystal structure of interleukin-1 alpha (IL-1α) (the interleukin-1 family actually consists of 11 cytokines, but these are beyond the scope of this text). (Image courtesy of "Boghog2," via Wikipedia) |
Another important cytokine is IFN-γ (interferon gamma), which looks like this:
 |
| Figure 1.21: Crystallographic structure of interferon gamma. (Image courtesy of "K.murphy," via Wikipedia) |
Released by natural killer cells (and T-cells, to which we will come), IFN-γ activates macrophages, can inhibit viral replication and combat tumours. IFN-γ binds to a heterodimeric receptor - interferon-gamma receptor (IFNGR) - composed of two macromolecules - interferon gamma receptor 1 (IFNGR1) and interferon gamma receptor 2 (IFNGR2).
We also have to consider another member of the interleukin group - interleukin 8 (IL-8), which is a chemokine (a chemotactic cytokine, or a cytokine which induces chemotaxis). IL-8 is also predominantly released by macrophages. IL-8 induces chemotaxis in a number of cells, but primarily in neutrophils (as we have, in fact, mentioned already). As well as this, it is important in phagocytosis, inducing changes in the cells which are conducive to phagocytosis, such as increasing the concentration of Ca2+ within the cell. It also promotes angiogenesis - the creation of new blood vessels from old ones.
Another mediator which we have mentioned before is leukotriene B4 - an eicosanoid (signalling molecules derived from fatty acids (by oxidation)) like the prostaglandins. Leukotriene B4 is released by leukocytes and actually affects leukocytes themselves. It is important in their activation and in mediating their adhesion to the endothelium and their migration across it. It is, too, an important chemotactic factor of neutrophils. The structural formula of leukotriene B4 is given below:
 |
| Figure 1.22: 5,12-dihydroxyicosa-6,8,10,14-tetraenoic acid (leukotriene B4). (Image courtesy of "Calvero," via Wikipedia) |
The final cell derived mediator - that is, the final mediator released by cells - which we shall consider is simple nitric oxide. Nitric oxide is released by macrophages, as well as endothelial cells and some neurons. Its role is vasodilation and it also reduces platelet aggregation, in order to regulate the response. As well as this it aids leukocyte recruitment and can destroy microbes when it is sufficiently concentrated.
This, then, is the cellular side of things; but, when discussing mediation, we again need to consider the exudate - the fluid containing substances such as clotting factors and antibodies which carries them into the interstitial fluid - as well. Contained within the exudate are numerous plasma derived mediators of inflammation, which we consider here. These mediators can be categorised as belonging to four systems:
- The complement system.
- The kinin system.
- The coagulation system.
- The fibrinolysis system.
The complement system is actually the subject of our next "section," for want of a better word, coming up in the post after next. For now, we will consider three elements of it - the first of which is C3 (complement component 3). In order to function as part of the complement system, C3 actually needs to be cleaved into two smaller proteins - C3a and C3b. This is done by a protease called C4b2a which is a type of C3-convertase. C3a induces mast cells to release histamine, while C3b is an opsonin - these bind to pathogens and "mark" them for phagocytosis.
The second element we shall consider is C5a. We have already seen that this is a chemotactic factor and it also induces mast cells to release histamine.
The final element that we will consider here, and perhaps my favourite, is the membrane attack complex, which really does seem like something out of a military. The membrane attack complex is a combination of C5b (obviously this is short for complement component 5b), C6, C7, C8, and multiple units of C9. Pleasingly, "unit" really is the word used in the associated Wikipedia article. The complex formed of these proteins creates pores in the cell membrane of invading pathogens. These holes allow molecules to move in and out of the cell - they are very much physical wounds of the cell. Enough of them will utterly destroy the cell in a process called lysis.
Next we turn to the kinin system and bradykinin. Bradykinin is very important in vasodilation and increasing vascular permeability. Not a whole lot is known about it, let alone the "kinin system" to which it belongs. However, we do know that this is the bugger that's responsible for a large amount of the pain we feel from inflammation. Just look at it:
 |
| Figure 1.23: The structural formula of bradykinin. (Image courtesy of "Yikrazuul," via Wikipedia) |
Turning, now, to the coagulation system, we look at thrombin. Thrombin cleaves the protein fibrinogen - a soluble protein which is part of the blood plasma - into fibrin. Fibrin is insoluble and aggregates, forming a clot and preventing the spread of the infection. Thrombin also works to produce chemokines and nitric oxide.
Alongside this, we have the fibrinolysis system. The primary component of this is an enzyme called plasmin and plasmin breaks down the fibrin clots, regulating the immune response. One does not want to overdo it with clots, they can be very damaging and, in extreme cases, can be deadly. Plasmin is, then, very important. Additionally, the products of breaking down fibrin can have some effects on vascular permeability. Plasmin is also involved in the cleaving of C3 (see above) and it activates Factor XII.
Factor XII is the final component and it is produced by the liver. Factor XII is a protein which usually circulates in the blood flow in its inactive state. When it is activated, it, in turn, participates in the activation of the kinin, fibrinolysis and coagulation systems.
1Technically, it is an adipokine, a specific type of cytokine distinguished by being secreted by adipose tissue.
A return to chemotaxis
We can briefly return, at this point, to chemotaxis - since we are now in a better position to understand it. In the case of neutrophils, a similar signalling process will take place in response to chemotactic factors binding to ligands on the cell surface. The process isn't well-understood, but in the case of chemotaxis I believe that G protein-coupled receptors (GPCRs) are used, rather than toll-like receptors. The principles are very much the same, however. In this case, signalling is initially effected by a class of protein called G proteins (or guanosine nucleotide-binding proteins). When unactivated, these proteins are bound to the GPCRs. When a ligand binds to the GPCR, it brings about a conformational change, which leads to the activation of the G protein. This is a very cursory overview and the way it is done is not fully understood, but we should be aware that there are a number of steps which I am not treating here. Ultimately, however, the activated G protein can then take part in chemical reactions such as those described earlier, which results in the polymerisation of actin filaments and, finally, a pseudopod.
Cell signalling
(In this post I include a lot of diagrams. This blog layout allows you to click on the images and enlarge them, but you may find it more convenient to open them in new tabs, otherwise you have to hit 'back' and reload the page again, which can be a nuisance.)
This, then, is how the cells of the immune system effect an inflammatory response. I will now give a detailed discussion of what happens when a ligand such as peptidoglycan binds to TLR 1. In fact, I will take the case of TLR 1:TLR 2 signalling (remember TLR 1 can either act as a homodimer or a heterodimer with TLR 2). Again, this is not strictly necessary for understanding inflammation and can be read separately. I hope, however, that this will be a means of understanding cell signalling in general, as well as the specific processes by which a macrophage recognises a pathogen and participates in the inflammatory response (here, by releasing cytokines). Throughout, I will make use of my own fairly ugly and very simplistic diagrams. I have taken a lot of license with them and they are for purely illustrative purposes - mostly to help with keeping track of the proteins.
So, the story begins with a pathogen entering the body, perhaps through an open wound, perhaps through ingestion, perhaps by other means. Forming part of the cell wall of our pathogen is peptidoglycan:
Our pathogen, once in the body, can be recognised by macrophages, which are found all over the body, ready to respond to pathogens, damaged cells and so on. Expressed on the surface of macrophages are many PRRs, including TLR 1 and TLR 2:
When a PAMP like peptidoglycan binds with TLR 1 and TLR 2, it initiates a signalling pathway called the MyD88-dependent pathway. The simultaneous binding of peptidoglycan to TLR 1 and (in our case) TLR 2, brings about a conformational change in these receptors which leads to a change in a specific domain of each receptor called the TIR domain (Toll/Interleukin-1R domain). The precise mechanisms by which this happens are not only very complicated, but not really relevant. In brief, intricate chemical interactions between the TLRs and peptidoglycan result in a physical change in the TLRs. The TIR domain is changed and can now interact with other proteins in the cell, which it couldn't have interacted with before:
So, with the TIR domain now changed in both receptors, these receptors are able to associate with a protein in the cell called TIRAP (TIR Adaptor Protein). The TIR domain of TIRAP binds with the newly altered TIR domains of the receptors:
MyD88 is now recruited - it can now interact with the complex formed by the TIR domain of the receptors and TIRAP:
The proteins MyD88 and TIRAP are adaptor proteins. As we have just seen, the TLR 1 and TLR 2 undergo a conformational change when they bind with a PAMP. This changes the TIR domain of those receptors which attracts and binds with TIRAP, which leads to the recruitment of MyD88. The adaptor MyD88 has another domain called the death domain (DD). This serves as the adaptor. The TIR domain allows the MyD88 to interact with the TLRs, while the death domain interacts with the kinases1 we discuss next. Once MyD88 has bound to the activated receptor it recruits another protein called IRAK4 (interleukin-1 receptor-associated kinase 4):
With this completed, the next stage is the recruitment of another protein - IRAK1 - which is also recruited through death domain interaction. IRAK4 undergoes phosphorylation, which is the process of transferring phosphate groups from one molecule to another. It is extremely important in the behaviour of proteins, for it transfers energy and also affects the structure of the protein. IRAK4 is phosphorylated and it phosphorylates IRAK1, which I believe then hyperautophosphorylates:2
IRAK1 is now competent for binding with another protein called TRAF6 (TNF receptor associated factor 6). This it does and it is also ubiquitinated, which is where a chain of ubiquitin molecules are added to a protein (in this case IRAK1). Ubiquitin is a small regulatory protein involved in numerous processes such as these, which changes the behaviour of proteins. I believe TRAF6 may also be phosphorylated.
As I understand it, IRAK1 dissociates from the complex that's bound to the TLR - along with TRAF6 - and is transferred to a new complex:
The new complex in question is a complex of TAK1 (transforming growth factor beta-activated kinase 1), TAB1 (TAK1-Binding protein 1) and TAB2, which are associated to the membrane. TAB2 facilitates the binding of our complex of IRAK1 and TRAF6 to TAK1:
TAK1, TAB1 and TAB2 are now phosphorylated. This causes dissociation, leaving IRAK1 bound to the membrane, while the complex of TAK1, TAB1, TAB2 and TRAF6 'breaks away.' This complex moves to the cytosol, which is a part of the cell, where TAK1 is activated. It is polyubiquitinated:
After all this, we begin to see the immensely beautiful and complex process of numerous chemical reactions which eventually transduces a signal and produces a response. Finally, we have the components which now activate MAP kinases and NF-κB. For the purposes of my example, I am going to consider precisely how NF-κB (which is involved in the production of cytokines, in this case) works.
As I have said, NF-κB is involved in the production of cytokines. When it is activated, it binds to particular DNA sequences (sc. response elements (RE)). More proteins and RNA polymerase are recruited and, by means of transcription and translation - which we will come to when we consider how the HIV virus works - cytokines are ultimately produced. This is the function of NF-κB here. When it is not activated, it is "stored" in the cytoplasm, where it is bound to proteins called IκBs (inhibitors of κB). There are four such proteins, but the best known is IκBα, which we may take as an example. Very simply, the IκB forms a complex with NF-κB, which keeps the NF-κB unactivated until such times as it is needed to bring about a change in the cell, so that it - for example - produces cytokines. Until it is needed, it is held in a kind of IκB storage:
The IκBs can be induced to released NF-κB by IKK (IκB kinase). IKK is composed of two heterodimers - IKKα and IKKβ - and a regulatory protein IKKγ (or NEMO (NF-κB essential modulator)):
IKK ubiquitinates IκB:
Which causes structures called proteasomes to degrade (or proteolyze) the IκB. A proteasome is an enzyme which degrades proteins by breaking peptide bonds. With the IκB degraded, NF-κB is released and goes on to induce the production of cytokines, as I described above:
So, to tie it all together. In our case - in the case of a macrophage with activated TLR 1 & TLR 2 receptors - the release of NF-κB is achieved by the TAK1 when it has been polyubiquitinated. At last we have all the pieces in place. The TAK1, which has been "prepared" by being polyubiquitinated, can now phosphorylate IKKβ. When this has happened, the IKKβ ubiquitinates IκB, releasing NF-κB by the mechanism described:
It is worth taking a moment just to appreciate a few things. Firstly, the NF-κB is held in what I have dubbed a kind of "storage," ready to be activated, but inactive when all is well. When PAMPs are recognised (and, therefore, when pathogens are present), the NF-κB is released, by means of the process I have outlined. This will lead to the production of cytokines, which should help to remove the pathogen. NF-κB is only released when pathogens are present and the more pathogens there are, the more PAMPs will bind with receptors on macrophages and the stronger the response will be. Once there are no pathogens left, there will be nothing to bind with the PRRs on the macrophages and so NF-κB will not be released and cytokines will not be produced.
The next thing to point out is this: When a PAMP binds with a receptor it brings about a change in the receptor which recruits adaptor proteins. These allow the signal (the recognition of the PAMP) to be transduced, as proteins already present in the cell can now be recruited and begin to interact. This couldn't have happened before, as the TIR domain of the TLRs cannot interact with the kinases such as IRAK4 which are involved in the signalling pathway. And so we see that the recognition of a pathogen is necessary for a response to take place, which is important as you would not want your immune system constantly activated - it would be bad for your own cells.
The process is also wonderfully intricate and this, too, is important as there are actually multiple pathways, and multiple responses which can be elicited, depending on the cell, the receptor and the signal. I have chosen one very specific event to walk you through, by way of example. However, these complex interactions allow complex responses to take place.
N.B.: Once again, the diagrams provided are for illustration only. I have tried to make them accurate but information is, understandably, scanty. The relative positions and interactions of the proteins shown in the diagrams should not be taken as necessarily representative. Whilst I don't wish to excuse myself of any shoddy research, I would also just like to emphasise that this discussion is purposed towards giving a deeper understanding of cell signalling, by means of considering a specific pathway, in a specific case. Through this, I hope to illuminate the discussion of inflammation. I may have unintentionally abbreviated or passed over some steps and various intricacies.
1An enzyme which transfers phosphate groups to other molecules, i.e. an enzyme which phosphorylates
2What it says on the tin: IRAK1 phosphorylates itself. A lot
This, then, is how the cells of the immune system effect an inflammatory response. I will now give a detailed discussion of what happens when a ligand such as peptidoglycan binds to TLR 1. In fact, I will take the case of TLR 1:TLR 2 signalling (remember TLR 1 can either act as a homodimer or a heterodimer with TLR 2). Again, this is not strictly necessary for understanding inflammation and can be read separately. I hope, however, that this will be a means of understanding cell signalling in general, as well as the specific processes by which a macrophage recognises a pathogen and participates in the inflammatory response (here, by releasing cytokines). Throughout, I will make use of my own fairly ugly and very simplistic diagrams. I have taken a lot of license with them and they are for purely illustrative purposes - mostly to help with keeping track of the proteins.
So, the story begins with a pathogen entering the body, perhaps through an open wound, perhaps through ingestion, perhaps by other means. Forming part of the cell wall of our pathogen is peptidoglycan:
 |
| Figure 1.3: A highly stylised representation of a bacterium. Obviously, the 'P's are for 'Peptidoglycan' |
Our pathogen, once in the body, can be recognised by macrophages, which are found all over the body, ready to respond to pathogens, damaged cells and so on. Expressed on the surface of macrophages are many PRRs, including TLR 1 and TLR 2:
 |
| Figure 1.4 |
When a PAMP like peptidoglycan binds with TLR 1 and TLR 2, it initiates a signalling pathway called the MyD88-dependent pathway. The simultaneous binding of peptidoglycan to TLR 1 and (in our case) TLR 2, brings about a conformational change in these receptors which leads to a change in a specific domain of each receptor called the TIR domain (Toll/Interleukin-1R domain). The precise mechanisms by which this happens are not only very complicated, but not really relevant. In brief, intricate chemical interactions between the TLRs and peptidoglycan result in a physical change in the TLRs. The TIR domain is changed and can now interact with other proteins in the cell, which it couldn't have interacted with before:
 |
| Figure 1.5: I use cyan to indicate that the receptors are activated. Note, also, my simplistic representation of the change in the TIR domain (represented by triangles rather than semi-circles) |
So, with the TIR domain now changed in both receptors, these receptors are able to associate with a protein in the cell called TIRAP (TIR Adaptor Protein). The TIR domain of TIRAP binds with the newly altered TIR domains of the receptors:
 |
| Figure 1.6 |
MyD88 is now recruited - it can now interact with the complex formed by the TIR domain of the receptors and TIRAP:
 |
| Figure 1.7 |
The proteins MyD88 and TIRAP are adaptor proteins. As we have just seen, the TLR 1 and TLR 2 undergo a conformational change when they bind with a PAMP. This changes the TIR domain of those receptors which attracts and binds with TIRAP, which leads to the recruitment of MyD88. The adaptor MyD88 has another domain called the death domain (DD). This serves as the adaptor. The TIR domain allows the MyD88 to interact with the TLRs, while the death domain interacts with the kinases1 we discuss next. Once MyD88 has bound to the activated receptor it recruits another protein called IRAK4 (interleukin-1 receptor-associated kinase 4):
 |
| Figure 1.8: The squares on the side of MyD88 represent the death domain interactions. IRAK4 cannot bind directly to the TIR domains of TLR 1 or TLR 2 because it is not the right shape, with its square death domains. Note how the MyD88 serves as the adaptor, it can bind to both the TIR domains of TLR 1 and TLR 2 (in combination with TIRAP) and to IRAK4. This is just like a travel adaptor for an electrical appliance. I cannot, however, stress enough what a gross over-simplification this is. In reality, the domains of proteins are highly complex chemical structures which fit together in really rather astonishing ways |
With this completed, the next stage is the recruitment of another protein - IRAK1 - which is also recruited through death domain interaction. IRAK4 undergoes phosphorylation, which is the process of transferring phosphate groups from one molecule to another. It is extremely important in the behaviour of proteins, for it transfers energy and also affects the structure of the protein. IRAK4 is phosphorylated and it phosphorylates IRAK1, which I believe then hyperautophosphorylates:2
 |
| Figure 1.9: Note my crude representation of the phosphorylation of IRAK1 by means of the ellipses. Phosphorylation is, as we've seen, the transfer of phosphate groups - PO43- - which is the reason behind the 'PO4's |
IRAK1 is now competent for binding with another protein called TRAF6 (TNF receptor associated factor 6). This it does and it is also ubiquitinated, which is where a chain of ubiquitin molecules are added to a protein (in this case IRAK1). Ubiquitin is a small regulatory protein involved in numerous processes such as these, which changes the behaviour of proteins. I believe TRAF6 may also be phosphorylated.
As I understand it, IRAK1 dissociates from the complex that's bound to the TLR - along with TRAF6 - and is transferred to a new complex:
 |
| Figure 1.10: The 'U's in circles obviously represent ubiquitin |
The new complex in question is a complex of TAK1 (transforming growth factor beta-activated kinase 1), TAB1 (TAK1-Binding protein 1) and TAB2, which are associated to the membrane. TAB2 facilitates the binding of our complex of IRAK1 and TRAF6 to TAK1:
 |
| Figure 1.11: Don't worry too much about my phosphate groups, my diagrams are very rough and meant only to help in keeping track of things. I'm not much of an artist |
TAK1, TAB1 and TAB2 are now phosphorylated. This causes dissociation, leaving IRAK1 bound to the membrane, while the complex of TAK1, TAB1, TAB2 and TRAF6 'breaks away.' This complex moves to the cytosol, which is a part of the cell, where TAK1 is activated. It is polyubiquitinated:
 |
| Figure 1.12 |
After all this, we begin to see the immensely beautiful and complex process of numerous chemical reactions which eventually transduces a signal and produces a response. Finally, we have the components which now activate MAP kinases and NF-κB. For the purposes of my example, I am going to consider precisely how NF-κB (which is involved in the production of cytokines, in this case) works.
As I have said, NF-κB is involved in the production of cytokines. When it is activated, it binds to particular DNA sequences (sc. response elements (RE)). More proteins and RNA polymerase are recruited and, by means of transcription and translation - which we will come to when we consider how the HIV virus works - cytokines are ultimately produced. This is the function of NF-κB here. When it is not activated, it is "stored" in the cytoplasm, where it is bound to proteins called IκBs (inhibitors of κB). There are four such proteins, but the best known is IκBα, which we may take as an example. Very simply, the IκB forms a complex with NF-κB, which keeps the NF-κB unactivated until such times as it is needed to bring about a change in the cell, so that it - for example - produces cytokines. Until it is needed, it is held in a kind of IκB storage:
 |
| Figure 1.13: The normal state of NFκB - it is unactivated and in a complex with IκBα |
The IκBs can be induced to released NF-κB by IKK (IκB kinase). IKK is composed of two heterodimers - IKKα and IKKβ - and a regulatory protein IKKγ (or NEMO (NF-κB essential modulator)):
 |
| Figure 1.14: IKK |
IKK ubiquitinates IκB:
 |
| Figure 1.15 |
Which causes structures called proteasomes to degrade (or proteolyze) the IκB. A proteasome is an enzyme which degrades proteins by breaking peptide bonds. With the IκB degraded, NF-κB is released and goes on to induce the production of cytokines, as I described above:
 |
| Figure 1.16: Note that the faded yellow of my IκBα is supposed to represent the fact that it has been degraded |
So, to tie it all together. In our case - in the case of a macrophage with activated TLR 1 & TLR 2 receptors - the release of NF-κB is achieved by the TAK1 when it has been polyubiquitinated. At last we have all the pieces in place. The TAK1, which has been "prepared" by being polyubiquitinated, can now phosphorylate IKKβ. When this has happened, the IKKβ ubiquitinates IκB, releasing NF-κB by the mechanism described:
 |
| Figure 1.17 |
It is worth taking a moment just to appreciate a few things. Firstly, the NF-κB is held in what I have dubbed a kind of "storage," ready to be activated, but inactive when all is well. When PAMPs are recognised (and, therefore, when pathogens are present), the NF-κB is released, by means of the process I have outlined. This will lead to the production of cytokines, which should help to remove the pathogen. NF-κB is only released when pathogens are present and the more pathogens there are, the more PAMPs will bind with receptors on macrophages and the stronger the response will be. Once there are no pathogens left, there will be nothing to bind with the PRRs on the macrophages and so NF-κB will not be released and cytokines will not be produced.
The next thing to point out is this: When a PAMP binds with a receptor it brings about a change in the receptor which recruits adaptor proteins. These allow the signal (the recognition of the PAMP) to be transduced, as proteins already present in the cell can now be recruited and begin to interact. This couldn't have happened before, as the TIR domain of the TLRs cannot interact with the kinases such as IRAK4 which are involved in the signalling pathway. And so we see that the recognition of a pathogen is necessary for a response to take place, which is important as you would not want your immune system constantly activated - it would be bad for your own cells.
The process is also wonderfully intricate and this, too, is important as there are actually multiple pathways, and multiple responses which can be elicited, depending on the cell, the receptor and the signal. I have chosen one very specific event to walk you through, by way of example. However, these complex interactions allow complex responses to take place.
N.B.: Once again, the diagrams provided are for illustration only. I have tried to make them accurate but information is, understandably, scanty. The relative positions and interactions of the proteins shown in the diagrams should not be taken as necessarily representative. Whilst I don't wish to excuse myself of any shoddy research, I would also just like to emphasise that this discussion is purposed towards giving a deeper understanding of cell signalling, by means of considering a specific pathway, in a specific case. Through this, I hope to illuminate the discussion of inflammation. I may have unintentionally abbreviated or passed over some steps and various intricacies.
1An enzyme which transfers phosphate groups to other molecules, i.e. an enzyme which phosphorylates
2What it says on the tin: IRAK1 phosphorylates itself. A lot
Inflammation (part 2)
This post picks up from where the first Inflammation post left off.
As I have already suggested, chemicals released in the inflammatory response can cause damage to cells and the response can also lead to the formation of oedemas. Of course, the response can also be initiated by tissue damage in the first place. Ideally, when any pathogens or foreign bodies - and/or dead or damaged cells - have been removed in the way I described earlier, the healing process will begin. Some cells, such as epithelial cells, are easily capable of regenerating. Some structures, such as the skin, are easy to reconstruct. Some cells, however, such as liver cells, do not generally regenerate - but can be made to - and some do not regenerate at all. Again, some structures, such as glands, are not easy to reconstruct. In the case of cells which can easily regenerate, they will do so and, where simple structures need to be reconstructed, they are rebuilt quite happily.
Where, however, there is substantial damage, or the damaged area is difficult to heal, a repair process will take place. In this case, scar tissue is built which "patches up" the damage. It is often imperfect. New blood vessels are constructed first from endothelial cells and fibroblasts form loose connective tissue. What results is granulation tissue. The new blood vessels establish blood flow to the growing tissue and collagen is formed from the fibroblasts. Ultimately, one is left with a scar, primarily formed of this collagen. It functions much like a patch on clothes and, much like a patch on clothes, it is not usually a perfect substitute. Improper repair can cause organ dysfunction, as in cirrhosis of the liver.
A second non-optimal result is suppuration, which is the formation of pus - which consists largely of dead and otherwise spent neutrophils and bacteria, fluid (from the blood vessels) and debris (from the cells). It occurs as a result of a pathogen or foreign body which is hard to remove and, hence, the neutrophils, bacteria, etc. remain and collect as pus. This pus will accumulate and an abscess will eventually develop, which is simply the accumulated pus enclosed by a membrane. Difficult to treat, due to the membrane, they may need to be surgically removed. Some, however, such as boils, will simply burst. Which is nice. At least, it's nice after a manner of speaking. When the abscess does burst, or when it's removed, the surrounding tissue is repaired as normal.
With this - and the brief foray into chemotaxis - concluded we have a good overview of what inflammation is and what it does. The question we must answer is how all of this is achieved. Those cells which initiate the inflammatory response are macrophages, dendritic cells, histiocytes, Kupffer cells and mastocytes. These cells possess cell surface receptors called pattern recognition receptors (PRRs). These are proteins, such as TLR 1 (toll-like receptor 1):
Which bind specifically with pathogen-associated molecular patterns (PAMPs) and damage-associated molecular patterns (DAMPs). PAMPs are molecules which are conserved in many different pathogens, but are peculiar to pathogens. That is to say that PAMPs are generic pathogen molecules - most pathogens will have them and they can be recognised by the PRRs. Remember that inflammation is non-specific, it is a response to pathogens in general and this is the how and the why. Generic pathogen molecules can be recognised and the response is always the same. DAMPs, meanwhile, are molecules which are released when cells are damaged. The principle is, again, the same. A cell such as a macrophage, which possesses PRRs, will recognise a DAMP as coming from a damaged cell and will respond to it. The response is generic.
I will take macrophages as an example. Macrophages have TLR 1 as one of their PRRs and so do neutrophils. Not all of the cells involved in the immune response will have TLR 1 and TLR 1 is only one PRR among many. Nevertheless, I will use it as an example. TLR 1, in combination with TLR 2, can recognise the polymer peptidoglycan, which forms the cell wall of many bacteria. Peptidoglycan is found in large numbers of pathogens, but not natively in the body. As such, the ability to recognise peptidoglycan is very useful. It is peculiar to pathogens and so its presence is always indicative of pathogens. It is also common and so a good number of pathogens can be recognised simply by the presence of peptidoglycan. As such, natural selection has furnished us with cells with receptors on them that are good at recognising peptidoglycan (and other such PAMPs).
Suppose, then, that peptidoglycan binds with TLR 1. (From this example we can understand the general principle which underlies all such processes. It will not be necessary to consider every cell, every receptor, every PAMP, etc. but it is necessary to appreciate that each receptor will be different and work in its own way.) TLR 1 actually functions either as a homodimer1 - which is to say that two TLR 1 molecules together recognise a PAMP - or as a heterodimer2 with TLR 2. The shape and chemical composition of TLR 1 (and TLR 2) is crucial and it is this which allows it to "recognise" PAMPs; this is why particular receptors only bind to certain, specific molecules and bind to them well. Thus each receptor is specific in what it recognises, meaning that the right cells recognise the right molecules (and, therefore, pathogens) and the right response is elicited. In our case, the result of peptidoglycan binding to TLR 1 - either in combination with another TLR 1 receptor, or with TLR 2 - is a conformational change of the receptors, which activates a signalling pathway.
Cell signalling is an extremely important and fundamental process which allows collections of individual cells to function as part of a larger whole - such as a muscle, or an organ - and, ultimately, as part of a complex organism. It is a means of communication and coordination, and it is the means by which our cells are made to do what is required of them. Cells communicate with each other either by cell-to-cell contact (juxtacrine signalling); or by releasing signalling molecules,3 which may be used for communication with nearby cells (paracrine signalling), or with many cells around the body and/or cells which are far away (endocrine signalling). This signalling is achieved by ligands binding to cell surface receptors. Again, when the ligand binds to the receptor, it brings about a change in the conformation of the receptor. In some cases this, in itself, brings about the required response of the cell. In other cases, signal transduction takes place. The conformational change in a receptor will initiate a series of chemical reactions inside the cell which, ultimately, brings about the required response.
In our case, when peptidoglycan binds with TLR 1, signal transduction also takes place. Here, however, the signal is not from the body, but from a pathogen. In the case of PRRs, signalling pathways are employed to elicit an immune response to a pathogen, rather than to coordinate some bodily function, such as stimulating the ovaries to release an egg, or stimulating blood vessels to dilate. In our case, the response elicited is the release of cytokines.
Once again I will now briefly pause my discussion of inflammation for a slight tangent, where cell signalling will be discussed more deeply. Once again, feel free to skip straight on to the rest of the discussion.
1A dimer is a large macromolecule formed from two macromolecules joined together. In the case of homodimers, these two component molecules are the same
2Naturally, in the case of heterodimers, the two component molecules are different
3The three primary types of signalling molecules are hormones, neurotransmitters and cytokines
As I have already suggested, chemicals released in the inflammatory response can cause damage to cells and the response can also lead to the formation of oedemas. Of course, the response can also be initiated by tissue damage in the first place. Ideally, when any pathogens or foreign bodies - and/or dead or damaged cells - have been removed in the way I described earlier, the healing process will begin. Some cells, such as epithelial cells, are easily capable of regenerating. Some structures, such as the skin, are easy to reconstruct. Some cells, however, such as liver cells, do not generally regenerate - but can be made to - and some do not regenerate at all. Again, some structures, such as glands, are not easy to reconstruct. In the case of cells which can easily regenerate, they will do so and, where simple structures need to be reconstructed, they are rebuilt quite happily.
Where, however, there is substantial damage, or the damaged area is difficult to heal, a repair process will take place. In this case, scar tissue is built which "patches up" the damage. It is often imperfect. New blood vessels are constructed first from endothelial cells and fibroblasts form loose connective tissue. What results is granulation tissue. The new blood vessels establish blood flow to the growing tissue and collagen is formed from the fibroblasts. Ultimately, one is left with a scar, primarily formed of this collagen. It functions much like a patch on clothes and, much like a patch on clothes, it is not usually a perfect substitute. Improper repair can cause organ dysfunction, as in cirrhosis of the liver.
A second non-optimal result is suppuration, which is the formation of pus - which consists largely of dead and otherwise spent neutrophils and bacteria, fluid (from the blood vessels) and debris (from the cells). It occurs as a result of a pathogen or foreign body which is hard to remove and, hence, the neutrophils, bacteria, etc. remain and collect as pus. This pus will accumulate and an abscess will eventually develop, which is simply the accumulated pus enclosed by a membrane. Difficult to treat, due to the membrane, they may need to be surgically removed. Some, however, such as boils, will simply burst. Which is nice. At least, it's nice after a manner of speaking. When the abscess does burst, or when it's removed, the surrounding tissue is repaired as normal.
With this - and the brief foray into chemotaxis - concluded we have a good overview of what inflammation is and what it does. The question we must answer is how all of this is achieved. Those cells which initiate the inflammatory response are macrophages, dendritic cells, histiocytes, Kupffer cells and mastocytes. These cells possess cell surface receptors called pattern recognition receptors (PRRs). These are proteins, such as TLR 1 (toll-like receptor 1):
 |
| Figure 1.2: A rendering of toll-like receptor 1 (TLR 1). (Image courtesy of "Yookji," via Wikipedia) |
Which bind specifically with pathogen-associated molecular patterns (PAMPs) and damage-associated molecular patterns (DAMPs). PAMPs are molecules which are conserved in many different pathogens, but are peculiar to pathogens. That is to say that PAMPs are generic pathogen molecules - most pathogens will have them and they can be recognised by the PRRs. Remember that inflammation is non-specific, it is a response to pathogens in general and this is the how and the why. Generic pathogen molecules can be recognised and the response is always the same. DAMPs, meanwhile, are molecules which are released when cells are damaged. The principle is, again, the same. A cell such as a macrophage, which possesses PRRs, will recognise a DAMP as coming from a damaged cell and will respond to it. The response is generic.
I will take macrophages as an example. Macrophages have TLR 1 as one of their PRRs and so do neutrophils. Not all of the cells involved in the immune response will have TLR 1 and TLR 1 is only one PRR among many. Nevertheless, I will use it as an example. TLR 1, in combination with TLR 2, can recognise the polymer peptidoglycan, which forms the cell wall of many bacteria. Peptidoglycan is found in large numbers of pathogens, but not natively in the body. As such, the ability to recognise peptidoglycan is very useful. It is peculiar to pathogens and so its presence is always indicative of pathogens. It is also common and so a good number of pathogens can be recognised simply by the presence of peptidoglycan. As such, natural selection has furnished us with cells with receptors on them that are good at recognising peptidoglycan (and other such PAMPs).
Suppose, then, that peptidoglycan binds with TLR 1. (From this example we can understand the general principle which underlies all such processes. It will not be necessary to consider every cell, every receptor, every PAMP, etc. but it is necessary to appreciate that each receptor will be different and work in its own way.) TLR 1 actually functions either as a homodimer1 - which is to say that two TLR 1 molecules together recognise a PAMP - or as a heterodimer2 with TLR 2. The shape and chemical composition of TLR 1 (and TLR 2) is crucial and it is this which allows it to "recognise" PAMPs; this is why particular receptors only bind to certain, specific molecules and bind to them well. Thus each receptor is specific in what it recognises, meaning that the right cells recognise the right molecules (and, therefore, pathogens) and the right response is elicited. In our case, the result of peptidoglycan binding to TLR 1 - either in combination with another TLR 1 receptor, or with TLR 2 - is a conformational change of the receptors, which activates a signalling pathway.
Cell signalling is an extremely important and fundamental process which allows collections of individual cells to function as part of a larger whole - such as a muscle, or an organ - and, ultimately, as part of a complex organism. It is a means of communication and coordination, and it is the means by which our cells are made to do what is required of them. Cells communicate with each other either by cell-to-cell contact (juxtacrine signalling); or by releasing signalling molecules,3 which may be used for communication with nearby cells (paracrine signalling), or with many cells around the body and/or cells which are far away (endocrine signalling). This signalling is achieved by ligands binding to cell surface receptors. Again, when the ligand binds to the receptor, it brings about a change in the conformation of the receptor. In some cases this, in itself, brings about the required response of the cell. In other cases, signal transduction takes place. The conformational change in a receptor will initiate a series of chemical reactions inside the cell which, ultimately, brings about the required response.
In our case, when peptidoglycan binds with TLR 1, signal transduction also takes place. Here, however, the signal is not from the body, but from a pathogen. In the case of PRRs, signalling pathways are employed to elicit an immune response to a pathogen, rather than to coordinate some bodily function, such as stimulating the ovaries to release an egg, or stimulating blood vessels to dilate. In our case, the response elicited is the release of cytokines.
Once again I will now briefly pause my discussion of inflammation for a slight tangent, where cell signalling will be discussed more deeply. Once again, feel free to skip straight on to the rest of the discussion.
1A dimer is a large macromolecule formed from two macromolecules joined together. In the case of homodimers, these two component molecules are the same
2Naturally, in the case of heterodimers, the two component molecules are different
3The three primary types of signalling molecules are hormones, neurotransmitters and cytokines
Subscribe to:
Posts (Atom)