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

Institute of Physics P.O. Box 57 11001 Belgrade Serbia
The European Physical Journal D (Impact Factor: 1.4). 01/2009; 51(1):41-49. DOI: 10.1140/epjd/e2008-00195-x

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.