Insights into the fold organization of TIM barrel from interaction energy based structure networks.

ABSTRACT: There are many well-known examples of proteins with low sequence similarity, adopting the same structural fold. This aspect of sequence-structure relationship has been extensively studied both experimentally and theoretically, however with limited success. Most of the studies consider remote homology or "sequence conservation" as the basis for their understanding. Recently "interaction energy" based network formalism (Protein Energy Networks (PENs)) was developed to understand the determinants of protein structures. In this paper we have used these PENs to investigate the common non-covalent interactions and their collective features which stabilize the TIM barrel fold. We have also developed a method of aligning PENs in order to understand the spatial conservation of interactions in the f

SUBMITTER: Vijayabaskar MS 

PROVIDER: S-EPMC3355060 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature