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Variable pH based molecular dynamics simulation of type II antifreeze protein

Raghunath Satpathy, Rashmiranjan Behera and Rajesh K Guru

Anti-freeze proteins( AFPs) in case of cold adapted organisms helps to avoid or reduce damage to the organism caused by freezing stress. Without the AFPs, water molecules will add to an ice lattice that results ice crystal growth and there by causes heavy damage to the tissue. Due to this property of these proteins are commercially used for cryopreservation purpose. Here in this work effect on physiological pH on the structure and function of the type II antifreeze protein has been established. The crystallography structure of the protein was obtained from Protein Data Bank. Molecular dynamics simulation of the protein was performed at 1 nano second (1000 pico seconds) in a series of physiological pH environment ranges from 2-11.The constant physiological condition was chosen for the simulation as protein in water at -5 degree Celsius and the salt concentration 0.15M.The results indicates the stability of the protein within a suitable pH range between 4 and 6.