Are Protein Folds Atypical?

Preprint

6 September 1997

preprint
Published by arXiv in arXiv

https://doi.org/10.48550/arXiv.cond-mat/9709083

Abstract

Protein structures are a very special class among all possible structures. It was suggested that a ``designability principle'' plays a crucial role in nature's selection of protein sequences and structures. Here we provide a theoretical base for such a selection principle, using a novel formulation of the protein folding problem based on hydrophobic interactions. A structure is reduced to a string of 0's and 1's which represent the surface and core sites, respectively, as the backbone is traced. Each structure is therefore associated with one point in a high dimensional space. Sequences are represented by strings of their hydrophobicities and thus can be mapped into the same space. A sequence which lies closer to a particular structure in this space than to any other structures will have that structure as its ground state. Atypical structures, namely those far away from other structures in the high dimensional space, have more sequences which fold into them, and are thermodynamically more stable. We argue that the most common folds of proteins are the most atypical in the space of possible structures.

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All Related Versions

Version 1, 1997-09-06, ArXiv
Published version: Proceedings of the National Academy of Sciences, 95 (9), 4987.

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