title: Effect of glycosylation on hydration behavior at the ice-binding surface of the Ocean Pout type III antifreeze protein: a molecular dynamics simulation.
abstract: Antifreeze proteins (AFPs), found in certain vertebrates, plants, fungi and bacteria have the ability to permit their survival in subzero environments by thermal hysteresis mechanism. However, the exact mechanism of ice growth inhibition is still not clearly understood. Here, four long explicit molecular dynamics (MD) simulations have been carried out at two different temperatures (277 and 298 K) with and without glycan to study the conformational rigidity of the Ocean pout type III antifreeze protein in aqueous medium and the structural arrangements of water molecules hydrating its ice-binding surface. It is found that irrespective of the temperature the ice-binding surface (IBS) of the protein is relatively more rigid than its non ice-binding surface (NonIBS) in its native and glycosylated form. Hydrophilic residues N14, T18 and Q44 are essential to antifreeze activity. Radial distribution, density distribution function and nearest neighbor orientation plots with respect to individual two surfaces confirm that density of water molecule near these binding surface in native and glycosylated form are relatively more than the nonbinding surface. The glycosylated form shows a strong peak than the native one. From rotational auto correlation function of water molecules around ice-binding sites, it is prominent that with increase in temperature, strong interaction between the water oxygen and the hydrogen bond acceptor group on the protein-binding surface decreases. This provides a possible molecular reason behind the ice-binding activity of ocean pout at the prism plane of ice.
authors.affiliation: a Department of Chemistry , University of Calcutta , 92, A. P. C. Road, Kolkata 700009 , India.
authors.forename: Swagata
authors.initials: S
authors.lastname: Halder
authors.affiliation: a Department of Chemistry , University of Calcutta , 92, A. P. C. Road, Kolkata 700009 , India.
authors.forename: Chaitali
authors.initials: C
authors.lastname: Mukhopadhyay
mesh_terms: D000818:Animals; D021343:Antifreeze Proteins, Type III / Q000737:chemistry*; D001665:Binding Sites; D029941:Fish Proteins / Q000737:chemistry*; D006031:Glycosylation; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D056004:Molecular Dynamics Simulation; D010473:Perciformes / Q000502:physiology; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D054730:Protein Interaction Domains and Motifs; D055672:Static Electricity; D013696:Temperature; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D021343:Antifreeze Proteins, Type III; D029941:Fish Proteins; D014867:Water
keywords: antifreeze glycoprotein; density distribution function; electrostatic–van der Waals interaction; glycosylation; ice-binding surface; nearest neighbor orientation; survival of hydrogen bond