title: A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular dynamics simulations.
abstract: The psychrophilic and mesophilic endonucleases A (EndA) from Aliivibrio salmonicida (VsEndA) and Vibrio cholera (VcEndA) have been studied experimentally in terms of the biophysical properties related to thermal adaptation. The analyses of their static X-ray structures was no sufficient to rationalize the determinants of their adaptive traits at the molecular level. Thus, we used Molecular Dynamics (MD) simulations to compare the two proteins and unveil their structural and dynamical differences. Our simulations did not show a substantial increase in flexibility in the cold-adapted variant on the nanosecond time scale. The only exception is a more rigid C-terminal region in VcEndA, which is ascribable to a cluster of electrostatic interactions and hydrogen bonds, as also supported by MD simulations of the VsEndA mutant variant where the cluster of interactions was introduced. Moreover, we identified three additional amino acidic substitutions through multiple sequence alignment and the analyses of MD-based protein structure networks. In particular, T120V occurs in the proximity of the catalytic residue H80 and alters the interaction with the residue Y43, which belongs to the second coordination sphere of the Mg2+ ion. This makes T120V an amenable candidate for future experimental mutagenesis.
authors.affiliation: The Centre for Theoretical and Computational Chemistry, Department of Chemistry, Faculty of Science and Technology, The Arctic University of Norway, Tromsø, Norway.
authors.forename: Davide
authors.initials: D
authors.lastname: Michetti
authors.affiliation: The Centre for Theoretical and Computational Chemistry, Department of Chemistry, Faculty of Science and Technology, The Arctic University of Norway, Tromsø, Norway.
authors.forename: Bjørn Olav
authors.initials: BO
authors.lastname: Brandsdal
authors.affiliation: The Centre for Theoretical and Computational Chemistry, Department of Chemistry, Faculty of Science and Technology, The Arctic University of Norway, Tromsø, Norway.
authors.forename: Davide
authors.initials: D
authors.lastname: Bon
authors.affiliation: The Centre for Theoretical and Computational Chemistry, Department of Chemistry, Faculty of Science and Technology, The Arctic University of Norway, Tromsø, Norway.
authors.forename: Geir Villy
authors.initials: GV
authors.lastname: Isaksen
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom.
authors.forename: Matteo
authors.initials: M
authors.lastname: Tiberti
authors.affiliation: Computational Biology Laboratory, Danish Cancer Society Research Centre, Strandboulevarden 49, Copenhagen, Denmark.|Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza 2, Milan, Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Papaleo
mesh_terms: D044165:Aliivibrio salmonicida / Q000201:enzymology / Q000235:genetics; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites / Q000235:genetics; D003080:Cold Temperature; D004706:Endodeoxyribonucleases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004795:Enzyme Stability; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D008565:Membrane Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D009154:Mutation; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D055672:Static Electricity; D013816:Thermodynamics; D014734:Vibrio cholerae / Q000201:enzymology / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D008565:Membrane Proteins; D004706:Endodeoxyribonucleases; C064668:endA protein, bacteria