Normal mode analysis of protein structure dynamics based on residue contact energy

Abstract

Normal mode analysis is one of the important methods in the study of protein structural dynamics. NMA makes the harmonic approximation to the potential energy around an equilibrium configuration. Conventional normal mode methods consider residues as uniform particles and inter-particle force constants are all the same. However, the amino acid properties, such as hydrophobicity, hydrophilicity, and residue charge, etc., play key roles in the mutual interactions. The potential energy between different residue pairs should depend on amino acid types. In this work, an amino acid type related force field model is proposed based on residue contact energy. The Atom Distance criteria (ADC) model is used to judge residue contact relationship, rather than a constant cutoff distance between two Ca atoms. The elastic network is facilitated with more realistic force distribution so that structural vibration frequency/mode analysis are much more accurate. Numerical examples show that this new method can improve the calculation of crystal structure B-factor greatly.