Implications from a network-based topological analysis of ubiquitin unfolding simulations.

ABSTRACT:

Background

The architectural organization of protein structures has been the focus of intense research since it can hopefully lead to an understanding of how proteins fold. In earlier works we had attempted to identify the inherent structural organization in proteins through a study of protein topology. We obtained a modular partitioning of protein structures with the modules correlating well with experimental evidence of early folding units or "foldons". Residues that connect different modules were shown to be those that were protected during the transition phase of folding.

Methodology/principal findings

In this work, we follow the topological path of ubiquitin through molecular dynamics unfolding simulations. We observed that the use of recurrence quantification analysis

SUBMITTER: Krishnan A 

PROVIDER: S-EPMC2364640 | biostudies-literature | 2008 May

REPOSITORIES: biostudies-literature