Protein Secondary Structure Question

[chez_butt23]

Homework Statement

15) How is it possible that many different linear sequences of amino acids can form the same secondary structure (alpha helices, beta sheets, random coils, etc.)?


I understand that alpha-helices, beta-sheets, etc. appear in tons of proteins and peptides, but I do not understand why this is so. I know that the reason alpha-helices exist is due to hydrophobic amino acids being "protected" from water as well as hydrogen bonding between every fourth amino acid. However, I do not understand why they appear so often, as the common amino acids have such different properties. Please help!

Thank you

 

[hjelmgart]

Hmm, in my opinion there are always several reasons (which was typic in my protein physics course, lol).

You are on to some of it. The hydrogen bonds make most secondary structures energetically stable. This thing about forming structures, is almost always about energy.

But what defines the structure depends on the amino acids and their structure. I've completely forgot the names (lol), but you can most surely find a long list, that will tell you, which amino acids favors beta sheets, and which favors alpha helices.

Some specific amino acids are only found in the beginning or the end of the secondary structure, because it may be good at starting the bend, which leads to the helix structure. Well you hopefully relate all this to some courses?

But overall it may be a quite short answer. It is simply energetically favorable for a sequence of amino acids to form secondary structures. Which structure it forms, depends on the individual amino acids, their location with respect to each other, and of course the amount of amino acids in the sequence :-)

You also mention something about hydrophobic amino acids, which is somewhat correct, however, it is more often associated with the tertiary stucture, as it is here the different secondary structures are positioned or even bended in an energetically favorable manner, which for instance can protect the hydrophobic proteins from water. Well you definitely need illustrations to clearly understand this, I guess.

 

[Yanick]

The short answer, in fact, is that no one is quite sure how primary structure (the linear AA sequence) results in the higher order structuring of a protein. The descriptions you will find in intro biochem texts is mostly of observations in known structures. In other words it is an empirical observation which we do not yet have the capability to predict ab initio. Although it seems that we should be able to because we can describe the interactions, the system is simply too complicated for us to look at a sequence and tell you with certainty what the higher order structure will be. So far, AFAIK, we are relegated to guessing by comparison with protein which share common motifs and who's structure has been solved.

Also keep in mind that each "typical" structure has many variants in nature. Beta shets can bend around a long axis and become a beta barrel, for instance. Alpha helices can vary as well, the typical one is just that, typical/common however many variations exist.

In addition, many proteins in nature require help to adopt the proper structure. There are chaperone protein which aid a newly synthesized protein in folding and there are 'clean up' mechanisms which aid in removing 'bad' proteins.

Its all very complicated and one should not get the impression that just because we can describe the interactions we assume to be the driving force of higher order structure in proteins, it means we can predict what any given protein will do under any circumstances.

Rational protein design is a huge field with the potential for large impacts on many different areas.

 

[Ygggdrasil]

The simple answer is that many secondary structural elements (such as alpha helices and beta sheets) are stabilized primarily by hydrogen bonding between the amide bonds in the polypeptide backbones. Because these interactions do not involve the variable side chains, their formation does not depend strongly on protein sequence.

Of course, as Yanick mentioned, certain sequences have greater proclivities toward forming different secondary structures, but these rules are fairly complicated.