Structural Investigation of Supercooled Water Confined in Antifreeze Proteins: Models’ Performance Evaluation between Coarse Grained and Atomistic Simulation Models
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 experimentally analyze 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, M. primoryensis andC. Fumiferana were collected on the Protein Data Bank using high resolution of X-ray diffraction because the β-helix/helix in AFPs’ structure play an important role to face ice-binding residues with ice cluster, as receptor and ligand interactions. In results, the root mean square deviations have shown high identity of RMSF between AA-MD and CG-MD simulation in 1HG7 and 3P4G, exceptionally, 1N4I and 3ULT that can be further studied in detail using all-atoms molecular dynamics simulation (AA-MD).
KeywordsAntifreeze protein Coarse-Grained simulation helix/beta-helix MARTINI force field AA-MD
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