Eur. Phys. J. D 51, 41-49 (2009)
https://doi.org/10.1140/epjd/e2008-00195-x

Semistiff polymer model of unfolded proteins and its application to NMR residual dipolar couplings

¹ Frankfurt Institute for Advanced Studies, Ruth-Moufang-Str. 1, 60438 Frankfurt am Main, Germany
² Institute of Physics, P.O. Box 57, 11001 Belgrade, Serbia

Corresponding author: ^a solovyov@fias.uni-frankfurt.de

Received: 14 March 2008
Revised: 15 September 2008
Published online: 15 October 2008

Abstract

We present a new statistical model of unfolded proteins in which the stiffness of polypeptide backbone is taken into account. We construct and solve a mean field equation which has the form of a diffusion equation and derive the distribution function for conformations of unfolded polypeptides. Accounting for the stiffness of the protein backbone results in a more accurate description of general properties of a polypeptide chain, such as its gyration radius. We then use the distribution function of a semistiff protein within a previously developed theoretical framework [J. Biomol. NMR 39, 1 (2007)] to determine the nuclear magnetic resonance (NMR) residual dipolar couplings (RDCs) in unfolded proteins. The calculated RDC profiles (dependence of the RDC value on the residue number) exhibit a more prominent bell-like shape and a better agreement with experimental data as compared to the previous results obtained with the random flights chain model.