Exploring Amino Acid Substitution in Similar Properties

[YChromatic]

Is it true that an amino acid tends to substitute another if they share similar properties ?

Thanks

 

[bobze]

What do you mean "substitute another"?

 

[Andy Resnick]

I'd be interested in hearing from an expert on this- my understanding is that a mutation that exchanges (say) a hydrophobic group for another (like leucine for valine) doesn't change the protein function much. Switching a lysine for cysteine *does* impair function considerably.

That is, my understanding is that amino acid substitutions range from benign to advserse based on the hydrophobicity- is that the only criterion? Cysteine also engages in disulfide bonds... like I said, I'd be interested in hearing from an expert.

 

[Ygggdrasil]

As with everything in biology, there's no simple answer. It really depends on where the amino acid is on the protein. There are some cases where you can substitute two amino acids with very dissimilar properties and the protein will still function fine. These amino acids are usually very far away from regions of the protein involved in its function (binding sites, active sites, etc.). It would not be so surprising if a lysine to cysteine mutant does not dramatically alter a proteins function. This would tell you, however, that the lysine is not a key residue in stabilizing the protein's structure or enabling its function. In other cases, you could make very conservative substitutions and completely destroy the function of the protein (often these are amino acids in the active sites of proteins). For example, something as subtle as a leucine to valine mutation could subtly alter the shape of an enzyme's active site and, for example, prevent it from binding a certain inhibitor (such cases are common in the development of drug resistance).

However as a general rule, substituting one amino acid for another with similar properties will be less likely to cause problems. Hydrophobicity is one criteria to consider but it is not the only one. For example, substituting a small amino acid like alanine with a large amino acid like phenylalanine could definitely cause problems (for example, if the alanine packs tightly against another region of the protein, the large phenylalanine could sterically hinder packing).

 

[bobze]

I'd be interested in hearing from an expert on this- my understanding is that a mutation that exchanges (say) a hydrophobic group for another (like leucine for valine) doesn't change the protein function much. Switching a lysine for cysteine *does* impair function considerably.

That is, my understanding is that amino acid substitutions range from benign to advserse based on the hydrophobicity- is that the only criterion? Cysteine also engages in disulfide bonds... like I said, I'd be interested in hearing from an expert.

Like Yggg pointed out, its complicated. Soluble proteins have polar residues on their surface, so changing to a insoluble or less soluble one can cause problems.

Even if there is little change in hydrophobicity steric interactions can still play a problem. For instance, collage uses glycine every 4th residue (Gly-x-y) because of its small size, it allows tight packing of tropocollagen helix. Even if you change it to another fairly small amino acid, with similar polar properties (like alanine or valine) the steric hindrance keeps the helix from correctly packing and you end up with http://en.wikipedia.org/wiki/Ehlers%E2%80%93Danlos_syndrome" .

This is why in genetics or biochemistry we consider all changes of amino acids from mutation to be missense mutations. Only when retrospectively considering the impacts they have on fitness can we consider it a 'silent' (to natural selection) mutation.

 

[Andy Resnick]

Thanks, guys. My only knowledge is in terms of site-directed mutagenesis, and there seems to be an agreed-upon set of substitutions that are used to establish, for example, binding site activity or more generally, protein function- like this:

http://www.ncbi.nlm.nih.gov/pubmed/12220194

 

[nobahar]

As a kind of addendum. How far along generally are folding algorithms, are there any good mathematical theories to predict protein folding. I would be very suprised if you couldn't predict folding. But there are some proteins that have to be folded in certain environments, or 'assissted' in folding (such as the use of chaperones). I have never understood why it is necessary. Surely when you transfer the protein to another environment (presumably one in which it would not have folded correctly, hence the need for chaperones) wouldn't it's shape alter? Or is it such features as disulfide bridges that help preserve the shape? Since hydrophobic/philic interactions, and ionic interactions, are subject to change based on the environment much more than covalent bonds are. But since sometimes 'assistance' is required, that means that either predicting shape is going to be based on probabilities or the protein is fairly rigid and retains it shape under some degree of environmantal pressure to change.

 

[Andy Resnick]

The only quantitative work I have seen on protein folding has been very... qualitative.

http://www.sciencemag.org/cgi/content/abstract/296/5574/1832 (and the citing articles listed below)

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682736/

 

[bobze]

As a kind of addendum. How far along generally are folding algorithms, are there any good mathematical theories to predict protein folding. I would be very suprised if you couldn't predict folding.

The problem as of now, is proteins have too many interactions between the numerous residues and the environments they exist into accurately (at least as of yet) predict protein folding. I'm sure, it could be done to some degree (in fact it is, with things like alpha helices and beta sheets) for smaller proteins (such as one that's really just an alpha helix), but larger proteins have tertiary and even quaternary structure.

But there are some proteins that have to be folded in certain environments, or 'assissted' in folding (such as the use of chaperones). I have never understood why it is necessary.

Because proteins start folding while they are synthesize. Think about it like a growing piece of yarn. When the yarn is short, interactions will be taking place on what is available. Though you may want a certain interaction taking place with the finished product that is 'blocked' because of early folding. Enter a chaperon.

Chaperons have lots of jobs, not just folding but bond rearrangement as well. For instance, you may want a cysteine disulfide bonded with another certain cysteine, even though there are others that could potentially form. So you have protein disulfide isomerases to rearrange those bonds.

Other chaperons simply aid in certain types of post-translational modification folding. Like oxidative folding, etc

Surely when you transfer the protein to another environment (presumably one in which it would not have folded correctly, hence the need for chaperones) wouldn't it's shape alter? Or is it such features as disulfide bridges that help preserve the shape? Since hydrophobic/philic interactions, and ionic interactions, are subject to change based on the environment much more than covalent bonds are.

No, because the idea is, once you get the protein in the correct shape that other interactions (say polar interactions on the outside of a soluble protein) maintain its shape. This is especially true of soluble proteins which tend to have very hydrophobic interiors, such that hydrophobic interactions greatly aid maintaining shape by increasing entropy of the protein-aqueous environment.

But since sometimes 'assistance' is required, that means that either predicting shape is going to be based on probabilities or the protein is fairly rigid and retains it shape under some degree of environmantal pressure to change.

Don't forget that biochemistry and these complex molecules aren't rigid in nature. They often exist in multiple confirmations in cells in some sort of equilibrium. Some proteins don't even have "shape", like elastin--Others alternate between tertiary structures and others still use the 'unstableness' of their tertiary structure as a kind of biological clock.

 

[nobahar]

Thanks for the links Andy, although I don't think I'll be able to follow them (the first one sounded very confusing!).
Thanks for the reply bobze, that was very informative. I never considered any of those points, which is a little worrying! Also, the multiple structures equilibrium sounds very interesting, something which, as far as I can recall, I have never heard of.

 

[Ygggdrasil]

As a kind of addendum. How far along generally are folding algorithms, are there any good mathematical theories to predict protein folding. I would be very suprised if you couldn't predict folding.

There are two general approaches to predicting protein structure. The first approach is inspired by the central principle underlying biology: evolution. For these approaches, you look for proteins that are similar in sequence to your target protein with the assumption that proteins with similar sequences were likely to have evolved from a common ancestor and likely have the same or similar structure. By comparing the search hits to databases of known protein structures, one can model the structure of the target by threading it through the structures of the closely matching hits creating what is called a homology model.

The other general approach is based more in physics/chemistry. Here, you start with a "force field" which defines the energies of the interactions between the different chemical groups in a protein. You then use Monte-Carlo methods to search for the lowest energy configuration of the amino acid chain, which you assume to be the folded state of the protein. This is challenging, however, because the energy landscape over which you need to search is very rough and contains many local minima which can complicate the Monte-Carlo simulations. This approach, however, has been used successfully to predict the structures of small proteins from first principles, an impressive feat in itself.

Obviously these two approaches can be combined to be even more successful: the homology modeling can create a good initial guess of the protein structure which can then be refined via Monte-Carlo methods.

A problem with these approaches, however, is that they do not give you much information about the actual mechanism of protein folding (this is especially true for the biology-inspired approach, some have used Monte-Carlo simulations to try to gain some insight into protein folding). To computationally simulate protein folding, you need to perform molecular dynamics calculations. Here, you take the protein you want to study and calculate the forces between all of the atoms in the system using your force field, write out Newton's equations for each atom in your system, let the atoms move slightly, recalculate all the forces, and repeat. The step sizes between recalculating the forces need to be very small (~ one femtosecond) or else the atoms in the simulation basically explode (bonds start breaking and atoms fly all over the place). Obviously, this approach is very computationally intensive for systems as large as proteins. Until very recently, computers were limited to simulating at most a few nanoseconds-to-microseconds of time whereas proteins fold on the millisecond or longer timescale. Recently, a research group specifically designed a supercomputer to perform long molecular dynamics simulations and were able to achieve 1 ms long simulations, long enough to observe the folding of a small protein (Shaw et al. 2010 Atomic-Level Characterization of the Structural Dynamics of Proteins. Science, 330: 341-346. http://dx.doi.org/10.1126/science.1187409, free news writeup: http://pubs.acs.org/cen/news/88/i42/8842notw1.html ).

But there are some proteins that have to be folded in certain environments, or 'assissted' in folding (such as the use of chaperones). I have never understood why it is necessary. Surely when you transfer the protein to another environment (presumably one in which it would not have folded correctly, hence the need for chaperones) wouldn't it's shape alter? Or is it such features as disulfide bridges that help preserve the shape? Since hydrophobic/philic interactions, and ionic interactions, are subject to change based on the environment much more than covalent bonds are. But since sometimes 'assistance' is required, that means that either predicting shape is going to be based on probabilities or the protein is fairly rigid and retains it shape under some degree of environmantal pressure to change.

One thing to keep in mind that the cell is a very crowded environment. Furthermore, the free energy of folding of most proteins is very small, on the order of the energy of only a handful of hydrogen bonds. At physiological temperature, protein structures "breath", thermal energy can cause them to transiently open up slightly. This "breathing" can expose the hydrophobic core of the proteins and if they collide with another "breathing" protein, the hydrophobic cores can stick together and you can get some misfolded proteins. Chaperon proteins are required to identify and refold these proteins or target them for degradation. Chaperons are also required to keep other proteins from disturbing the folding of newly synthesized proteins as they come off the ribosome and before they have a chance to fold.

 

[Andy Resnick]

Has anyone made any progress on transmembrane proteins? For example, when and how are they inserted into the bilipid layer?

 

[Ygggdrasil]

Transmembrane proteins are inserted into the bilayer by a protein channel called the translocon. Many groups have been studying the mechanisms of translocation and the factors regulating transmembrane protein insertion, notably Tom Rapoport at Harvard and Gunar Von Heijne at Stockholm University. Below is a link to a review by Rapoport on the mechanisms of protein translocation:

http://www.nature.com/nature/journal/v450/n7170/abs/nature06384.html

For a more general view of membrane protein folding, here is another useful review from Nature:

http://www.nature.com/nature/journal/v438/n7068/abs/nature04395.html