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Molecular Dynamics (MD) method is a computer simulation for studying the physical movements of atoms and molecules of a N-body system by solving classical equations of motion. Here, this method is used to investigate the structural changes of a vital molecular bond in the body. This bond is created by the interaction of P-selectin, expressed on activated endothelium, and its counterpart P-selectin glycoprotein ligand-1 (PSGL-1) which is expressed on leukocytes. Frequent association and dissociation of these bonds allow the leukocyte to roll on the endothelium layer which is a pivotal step in inflammatory responses. Understanding the mechanism underlying the dissociation process of this bond is helpful in pathological researches. Here this process is simulated with MD method using the program NAMD and Visual Molecular Dynamics (VMD). The results indicate that the hydrogen bonds between ion Ca2+ and residue fucose of glycan group of PSGL-1 and also between sulfated tyrosine residues are the most effective bonds in binding.

Keywords: Molecular Dynamics, NAMD, Leukocyte, P-selectin/PSGL-1 bond dissociation, non-bonded energy

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