BIOPHYSICAL THEORY AND MODELING |
Deciphering protein dynamics from NMR data using explicit structure sampling and selection
Yiwen Chen 1, Sharon L Campbell 1 and Nikolay V Dokholyan 1*
1 The University of North Carolina at Chapel Hill
* To whom correspondence should be addressed. E-mail: dokh{at}med.unc.edu.
Submitted on January 9, 2007
Revised on February 28, 2007
Accepted on 5 June 2007
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Abstract |
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Perhaps one of the most prominent realizations of recent years is the critical role that protein dynamics plays in many facets of cellular function. While characterization of protein dynamics is fundamental to our understanding of protein function, the ability to explicitly detect an ensemble of protein conformations from dynamics data is a paramount challenge in structural biology. Here, we report a new computational method, "Sample and Select" (SAS), for determining the ensemble of protein conformations consistent with NMR dynamics data. This method can be generalized and extended to different sources of dynamics data, enabling broader applicability in deciphering protein dynamics at different time-scales. The structural ensemble derived from SAS will provide structural and dynamic information that should aid in understanding and manipulating protein function.
Key Words:
NMR dynamics data, NMR relaxation, molecular dynamics simulation, order parameter, protein dynamics
