A Computational Method to Identify Residues Important in Creating a Protein Promoting Vibration in Enzymes

Abstract

In this paper, we present a computational method to screen a large set of protein residues to identify those residues the motions of which help create a protein promoting vibration and are therefore important for catalysis. The method is illustrated for the case of horse liver alcohol dehydrogenase (HLADH). In this system, the protein promoting vibration is the relative motion between hydride donor and acceptor, that is, the benzyl alcohol substrate and the nicotinamide adenine dinucleotide (NAD+) cofactor, respectively. The resulting subset of screened residues compares favorably with existing experimental data and also suggests additional residues as objects for potential study. The method presented in this paper employs correlated motion as the basis for identifying residues important in catalysis. As such, the success of the method in the case of HLADH further supports the importance of protein dynamics in certain enzyme systems.