Sections

Introduction

This application allows one to generate an unfolded state ensemble using a self-avoiding statistical coil model that is based on backbone conformational preferences from a coil library, a subset of protein data bank.

The model reproduces two apparently contradicting behaviors observed in the chemically denatured state of a variety of proteins: random coiling scaling of the radius of gyration and the presence of significant amounts local backbone structure (NMR residual dipolar couplings, RDCs).  The agreement with the NMR data substantially improves when the backbone conformational preferences include correlations arising from the chemical and conformational identity of neighboring residues. Although the unfolded ensembles match the experimental observables, they do not display evidence of native-like topology. By providing an accurate representation of the unfolded state, our statistical coil model can be used to improve thermodynamic and kinetic modeling of protein folding. To read more about our statistical coil model for the unfolded state published in [download pdf] PNAS 2005 .

Credits and Acknowledgment

This service is the result of a collaboration between the Physical Sciences Division, Karl F. Freed , Biological Science Division, Tobin R. Sosnick , and Department of Computer Science, Dave Angulo, at the The University of Chicago. Website developed and maintained by Abhishek Jha , Dr. Andres Colubri, Jonathan Gemmell and Tim Wake.

This work is supported by grants from Burroughs Wellcome Fund Interfaces Fellowships and NIH, NSF.

Questions and Suggestions: Please feel free to contact us at ajha@uchicago.edu with any questions or suggestions.

Note:
We used OOPS , a project of the Protein Library for this project.