Structural investigation of supercooled water confined in antifreezed proteins

Abstract

Antifreeze proteins (AFPs) play an important role as inhibitors of ice crystal growth in the body fluid of living organisms. Nonetheless, the exact mechanism of ice growth inhibition is still poorly understood to analyze experimentally in the molecular-scale which strongly requires computer simulation for AFPs’ binding site to certain planes of ice crystal. In this research, Coarse-Grained simulation using MARTINI force field was utilized to evaluate stability of helix/β-helix restraints of M. Americanus, L. Perenne, Leucosporidiumand T. ishikariensis which were collected on Protein Data Bank using high resolution of X-ray diffraction because the β-helix/helix in AFPs’ structures play an important role to face ice-binding residues with ice cluster, as receptor and ligand interactions. As results, the root mean square deviations have shown the unstable regions in AFPs of M. Americanus, L. Perenne, Leucosporidium derived from free movement of the tails, exceptionally, the unfolded β-helix region in T. ishikariensis antifreeze protein creates a very long β-sheet tail that is presumably decreasing in the affinity of AFP for ice leads to reduce thermal hysteresis activity which can be further studied in detail using all-atoms molecular dynamics simulation (AA-MD). Keywords: Antifreeze protein, Coarse-Grained simulation, helix/beta-helix, MARTINI force field, AA-MD.