Calculation of nuclear magnetic resonance order parameters in proteins by normal mode analysis. II. Contribution from localized high frequency motions

Abstract

Nuclear magnetic resonance (NMR) order parameter S̃ 2 for spin pairs in protein is an important quantity for deducing protein static and dynamic three-dimensional structures from NMR experimental data. In the previous paper it has been shown that contribution from low frequency motions to the order parameter can be calculated reliably from normal mode analysis carried out in dihedral angle space for spin pairs for which a number of intervening dihedral angles (NIVDA) is 10 or less. However, it has been known that for spin pairs with NIVDA=0, high frequency motions also affect the value of the order parameter. In this paper we show that the effect of high frequency motions can be accounted for by a correction term to be added to the value obtained from normal mode analysis in dihedral angle space. A factor of the correction term determined by high frequency motions can be calculated by the usual normal mode analysis for a small peptide fragment which has the same local conformation as in protein.