Accelerated Communication
Received: 12 December 2008; Revised: 29 January 2009; Accepted: 2 February 2009
10.1002/pro.90 About DOI
A novel topology for representing protein folds |
| Mark R. Segal * |
| Division of Biostatistics, University of California, San Francisco, California 94107 |
| email: Mark R. Segal (mark@biostat.ucsf.edu) |
*Correspondence to Mark R. Segal, 185 Berry Street, Lobby 5, Suite 5700, San Francisco, CA 94107
Funded by:
UCSF Center for Bioinformatics and Molecular Biostatistics
| Keywords |
| topology folding rate contact order primary sequence three dimensional structure |
| Abstract |
| Various topologies for representing 3D protein structures have been advanced for purposes ranging from prediction of folding rates to ab initio structure prediction. Examples include relative contact order, Delaunay tessellations, and backbone torsion angle distributions. Here, we introduce a new topology based on a novel means for operationalizing 3D proximities with respect to the underlying chain. The measure involves first interpreting a rank-based representation of the nearest neighbors of each residue as a permutation, then determining how perturbed this permutation is relative to an unfolded chain. We show that the resultant topology provides improved association with folding and unfolding rates determined for a set of two-state proteins under standardized conditions. Furthermore, unlike existing topologies, the proposed geometry exhibits fine scale structure with respect to sequence position along the chain, potentially providing insights into folding initiation and/or nucleation sites. |
Received: 12 December 2008; Revised: 29 January 2009; Accepted: 2 February 2009
| Digital Object Identifier (DOI) |
10.1002/pro.90 About DOI
