Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs.

ABSTRACT:

Background

Mapping protein primary sequences to their three dimensional folds referred to as the 'second genetic code' remains an unsolved scientific problem. A crucial part of the problem concerns the geometrical specificity in side chain association leading to densely packed protein cores, a hallmark of correctly folded native structures. Thus, any model of packing within proteins should constitute an indispensable component of protein folding and design.

Results

In this study an attempt has been made to find, characterize and classify recurring patterns in the packing of side chain atoms within a protein which sustains its native fold. The interaction of side chain atoms within the protein core has been represented as a contact network based on the surface complementarity

SUBMITTER: Basu S 

PROVIDER: S-EPMC3123238 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature