Research article
Probing the folding of mini-protein Beta3s by two-dimensional infrared spectroscopy; simulation study
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* Corresponding authors: Shaul Mukamel smukamel@uci.edu - Jin Wang jin.wang.1@stonybrook.edu
1 Graduate Program in Biochemistry and Structural Biology, State University of New York at Stony Brook, New York, 11794-3400, USA
2 Department of Chemistry, University of California, Irvine, CA, 92697-2025, USA
3 Department of Chemistry, State University of New York at Stony Brook, New York, 11794-3400, USA
4 Department of Physics, State University of New York at Stony Brook, New York, 11794-3400, USA
PMC Biophysics 2010, 3:8 doi:10.1186/1757-5036-3-8
Published: 19 March 2010Abstract
We propose to use infrared coherent two-dimensional correlation spectroscopy (2DCS) to characterize the folding mechanism of the mini-protein Beta3s. In this study Beta3s was folded by molecular dynamics (MD) simulation and intermediate conformational ensembles were identified. The one and two-dimensional correlation spectrum was calculated for the intermediate and native states of the mini-protein. A direct structure-spectra relationship was determined by analysis of conformational properties and specific residue contributions. We identified the structural origin of diagonal and off-diagonal peaks in the 2DCS spectra for the native and intermediate conformational ensembles in the folding mechanism. This work supports the implementation of computational techniques in conjunction with experimental 2DCS to study the folding mechanism of proteins. In addition to exploring the folding mechanism the work presented here can be applied in combination with experiment to refine and validate current molecular dynamics force fields.
PACS Codes: 87.15.Cc, 87.15.hm, 87.15.hp