title: Distinct molecular features facilitating ice-binding mechanisms in hyperactive antifreeze proteins closely related to an Antarctic sea ice bacterium.
abstract: Antifreeze proteins or ice-binding proteins (IBPs) facilitate the survival of certain cellular organisms in freezing environment by inhibiting the growth of ice crystals in solution. Present study identifies orthologs of the IBP of Colwellia sp. SLW05, which were obtained from a wide range of taxa. Phylogenetic analysis on the basis of conserved regions (predicted as the 'ice-binding domain' [IBD]) present in all the orthologs, separates the bacterial and archaeal orthologs from that of the eukaryotes'. Correspondence analysis pointed out that the bacterial and archaeal IBDs have relatively higher average hydrophobicity than the eukaryotic members. IBDs belonging to bacterial as well as archaeal AFPs contain comparatively more strands, and therefore are revealed to be under higher evolutionary selection pressure. Molecular docking studies prove that the ice crystals form more stable complex with the bacterial as well as archaeal proteins than the eukaryotic orthologs. Analysis of the docked structures have traced out the ice-binding sites (IBSs) in all the orthologs which continue to facilitate ice-binding activity even after getting mutated with respect to the well-studied IBSs of Typhula ishikariensis and notably, all these mutations performing ice-binding using 'anchored clathrate mechanism' have been found to prefer polar and hydrophilic amino acids. Horizontal gene transfer studies point toward a strong selection pressure favoring independent evolution of the IBPs in some polar organisms including prokaryotes as well as eukaryotes because these proteins facilitate the polar organisms to acclimatize to the adversities in their niche, thus safeguarding their existence.
authors.affiliation: a Department of Biophysics, Molecular Biology and Bioinformatics , University of Calcutta , 92, A.P.C. Road, Kolkata 700009 , India.
authors.forename: Rachana
authors.initials: R
authors.lastname: Banerjee
authors.forename: Pratim
authors.initials: P
authors.lastname: Chakraborti
authors.forename: Rupa
authors.initials: R
authors.lastname: Bhowmick
authors.forename: Subhasish
authors.initials: S
authors.lastname: Mukhopadhyay
mesh_terms: D000595:Amino Acid Sequence; D000864:Antarctic Regions; D021301:Antifreeze Proteins / Q000737:chemistry* / Q000235:genetics*; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics*; D016000:Cluster Analysis; D003062:Codon; D019143:Evolution, Molecular; D046448:Ice Cover / Q000382:microbiology*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D011487:Protein Conformation; D012641:Selection, Genetic; D016415:Sequence Alignment
chemical_list: D021301:Antifreeze Proteins; D001426:Bacterial Proteins; D003062:Codon
keywords: antifreeze proteins; horizontal gene transfer; ice-recrystallization inhibition; molecular docking; phylogenetic analysis