Format

Send to

Choose Destination
See comment in PubMed Commons below
PLoS One. 2012;7(7):e39993. doi: 10.1371/journal.pone.0039993. Epub 2012 Jul 9.

Analysis of conformational variation in macromolecular structural models.

Author information

1
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India. sandeep@mbu.iisc.ernet.in

Abstract

Experimental conditions or the presence of interacting components can lead to variations in the structural models of macromolecules. However, the role of these factors in conformational selection is often omitted by in silico methods to extract dynamic information from protein structural models. Structures of small peptides, considered building blocks for larger macromolecular structural models, can substantially differ in the context of a larger protein. This limitation is more evident in the case of modeling large multi-subunit macromolecular complexes using structures of the individual protein components. Here we report an analysis of variations in structural models of proteins with high sequence similarity. These models were analyzed for sequence features of the protein, the role of scaffolding segments including interacting proteins or affinity tags and the chemical components in the experimental conditions. Conformational features in these structural models could be rationalized by conformational selection events, perhaps induced by experimental conditions. This analysis was performed on a non-redundant dataset of protein structures from different SCOP classes. The sequence-conformation correlations that we note here suggest additional features that could be incorporated by in silico methods to extract dynamic information from protein structural models.

PMID:
22808083
PMCID:
PMC3392262
DOI:
10.1371/journal.pone.0039993
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Public Library of Science Icon for PubMed Central
    Loading ...
    Support Center