Classical Molecular Dynamics for the Study of Biological Systems

Dr. Marc Ma , Assistant Professor
Department of Computer Science, NJIT


Abstract

Classical molecular dynamics (MD) can be used to model biological systems by solving Newton's equations of motion, which are believed to govern the motion of atoms and molecules at the atomic scale. MD simulations have shown to be critically important in explaining the puzzling fact that the water-conducting channels (aquaporins) in cell membranes only conduct water and other small molecules but not protons (the naked hydrogens with positive charge) and folding pathways of some small peptides. In this presentation, I will outline a recent initiative that my group is working on in the study of pre-chemistry structural changes of an enzyme that catalyzes the reaction that changes GTP to the cyclic GMP (cGMP). The MD approach in this particular study is likely to enable us to study the mechanisms allosteric activation of catalytic reaction and perform reliable in silico screening of the candidates for the best vasodilation drugs.