# HELP!Energetic frustration and the nature of the transition state in protein folding

1. Apr 16, 2003

### Entropia

The following is the abstract to an article by Joan Emma Shea et al published in journal of chemical physics volume 113 number 17, 1 nov 2000

"The amino acid sequence and the folding motif are essential in determining the protein folding mechanism. The interplay between energetic (sequence-dependent) and topological (motif dependent) frustrations is investigated for two model beta-barrel proteins of the same native fold but with different interaction Hamiltonians. The nature of the folding transition state ensemble for both models is probed. The extent of structure in the transition state is determined by performing point mutations and recording their effect on stability of the transition state through their phi values. The transition state shows more strctural heterogeneity for the more frustrated sequence, a reflection of the increased roughness of the funneled energy landscape which restricts the number of pathways to thenative state. The validity of the psi analysis approach was assessed to be critically dependent on the degree of frustration of the model. The interpretation of psi alues as a measure of the strcture of the transition state breaks down for sequences with higher levels of frustration (lower cooperativity) in which a Kramer's description of the folding reaction is no longer appropriate."

*what on earch is meant by "frustrations"???

*what are beta barrel proteins?

*what is meant by "probed" when it was aid "the nature of the folding transition state ensemble for both models is probed" ??

*what are point mutations?

*what is meant by "the transition state shows more structural heterogeneity for the more frustrated sequence" ?

*what is "Kramer's description"?

I need to present this article on friday... i need help ASAP!!

thnx!!

2. Apr 16, 2003

### Mike H

Proteins have a number of constraints upon them, especially energetic and structural, in attempting to fold properly. "Frustration" refers to the phenomenon where a protein is unable to satisfy all constraints. So, just based on the abstract, there would seem to be an interplay between the protein trying to satisfy its structural constraints vs. its energetic constraints.

A beta barrel protein is a protein whose predominant (for the most part, only) secondary structure motif is beta-strands which make up a "barrel" in 3-D.

I would suspect that what the paper by Shea was interested in looking at was the transition state - that is, they "probed" what the transition state ensemble looked like via computational methods. It's important to remember that while you may have a single folded protein at the end, you have an entire ensemble of unfolded proteins and an ensemble of partially folded proteins, not just one or two structures in the latter two cases.

Point mutations refer to single amino acid residue changes which are typically done to investigate how structure & function changes. For example, if you suspected two cysteine residues of forming a disulfide bridge which played a role in the protein's folded state, you might change one to an alanine which would (in principle) change the behavior of the protein. If you were investigating enzymatic function, for instance, and you had the idea that a certain lysine residue helped stabilize a transition state, you might change it to a nonpolar hydrophobic amino acid or a negatively charged carboxylate-containing amino acid to see how enzymatic function was changed, if at all.

As I haven't read the paper (although I probably should), I would think that "the transition state shows more structural heterogeneity for the more frustrated sequence" means that the protein which finds it harder to satisfy all of its constraints - the more frustrated protein - has greater variability in its ensemble of transition state structures.

As for "Kramer's description," am not totally sure on what it refers to without having read the paper. Although I suspect it's probably referring to one of those kinetic theories which I can't remember for the life of me. Is it referenced in Shea's paper? If so, you'd probably want to take a look at it.

Last edited: Apr 17, 2003
3. Apr 17, 2003

### Entropia

Mike H! Again you satisfy my curiosities... and this time saved my a!!!

Thank you soooooooo much.

Well, if you (or anybody else for that matter) happen to read that article within the next 24 hours or so...

if anybody has any tips on how i ought to present this to a group of undergrads whom have not had p-chem yet.... im all ears (or eyes, since i'll be reading the posts)

4. Apr 17, 2003

### Mike H

I would suspect most undergrads have some idea of what an electrostatic interaction (ionic bond) is, some idea of what hydrogen bonding is, and some vague conception of what hydrophobic interactions are as well as steric conflicts (if they've had some organic they should be a bit more familiar with the latter two concepts than someone with just some introductory general chemistry). Mention about how there's a tradeoff in energetics - if all the hydrophobic side chains are going to be most likely "buried" you may not get as many salt bridges (ionic bonds) and hydrogen bonding as you would otherwise, but you get a better result (thermodynamically) from hydrophobic residue burial. As for sterics, if they know some conformational analysis, this should be easy as they're familiar with dihedral angles between four atoms. Throw in a comment about how there is often some rigidity in the protein backbone (the partial double bond character in the amide bond is where you see this introduced) and that there are preferred conformations in terms of angles for certain dihedral angles in the protein backbone. You may want to build a short stretch of a protein backbone or two with modeling kits and demonstrate the idea visually.

I sadly won't be able to read the paper any time soon, so will have to go with my intuition on this one. Of course, you should understand I have enough trouble reading papers I'm supposed to read for class or research on time to begin with, so heh.