The amino acid alphabet and the architecture of the protein sequence-structure map. I. Binary alphabets.

ABSTRACT: The correspondence between protein sequences and structures, or sequence-structure map, relates to fundamental aspects of structural, evolutionary and synthetic biology. The specifics of the mapping, such as the fraction of accessible sequences and structures, or the sequences' ability to fold fast, are dictated by the type of interactions between the monomers that compose the sequences. The set of possible interactions between monomers is encapsulated by the potential energy function. In this study, I explore the impact of the relative forces of the potential on the architecture of the sequence-structure map. My observations rely on simple exact models of proteins and random samples of the space of potential energy functions of binary alphabets. I adopt a graph perspective and study the d

SUBMITTER: Ferrada E 

PROVIDER: S-EPMC4256021 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature