Computational study on ice growth inhibition of Antarctic bacterium antifreeze protein using coarse grained simulation

citation_title=Antifreeze proteins: Structures and mechanisms of function; citation_author=Yeh Y.; citation_author=Feeney R. E.; citation_journal_title=Chem. Rev.; citation_year=1996; citation_volume=96; citation_pages=601-618;

citation_title=Antifreeze proteins: Computer simulation studies on the mechanism of ice growth inhibition; citation_author=Nada H.; citation_author=Furukawa Y.; citation_journal_title=Polym. J.; citation_year=2012; citation_volume=44; citation_pages=690-698;

citation_title=Hyperactive antifreeze proteins from longhorn beetles: Some structural insights; citation_author=Kristiansen E.; citation_author=Wilkens E.; citation_author=Vincents B.; citation_author=Friis D.; citation_author=Lorentzen A. B.; citation_author=Jenssen H.; citation_author=Lobner-Olesen A.; citation_author=Ramlov H.; citation_journal_title=Insects Physiol.; citation_year=2012; citation_volume=58; citation_pages=1502-1510;

citation_title=Chemical and physical properties of freezing point depressing glycoproteins from Antarctic fishes; citation_author=DeVries A. L.; citation_author=Komatsu S. K.; citation_author=Feeney R. E.; citation_journal_title=Biol. Chem.; citation_year=1970; citation_volume=245; citation_pages=2901-2908;

citation_title=Fish antifreeze proteins: Physiology and evolutionary biology; citation_author=Davies P. L.; citation_author=Hew C. L.; citation_author=Fletcher G. L.; citation_journal_title=Can. J. Zool.; citation_year=1980; citation_volume=66; citation_pages=2611-2617;

citation_title=Hyperactive antifreeze protein in a fish; citation_author=Marshall C. B.; citation_author=Fletcher G. L.; citation_author=Davies P. L.; citation_journal_title=Nature (London); citation_year=2004; citation_volume=429; citation_pages=153

citation_title=Presence of cystine-containing antifreeze proteins in the spruce budworm, Choristoneura fumiferana; citation_author=Hew C. L.; citation_author=Kao M. H.; citation_author=So Y.-P.; citation_author=Lim K.-P; citation_journal_title=Can. J. Zool.; citation_year=1983; citation_volume=61; citation_pages=2324-2328;

citation_title=Isolation and characterization of freezing-point depressing peptides from larvae of Tenebrio molitor; citation_author=Schneppenheim R.; citation_author=Theede H.; citation_journal_title=Comp. Biochem. Physiol., Part B: Biochem. Mol. Biol.; citation_year=1980; citation_volume=67; citation_pages=561-568;

citation_title=Anti-freeze proteins in Alaskan insects and spiders; citation_author=Duman J. G.; citation_author=Bennett V.; citation_author=Sformo T.; citation_author=Hochstrasser R.; citation_author=Barnes B. M.; citation_journal_title=Insects Physiol.; citation_year=2004; citation_volume=50; citation_pages=259-266;

citation_title=Antifreeze proteins in higher plants; citation_author=Atıcı O.; citation_author=Nalbantoglu B.; citation_journal_title=Phytochemistry; citation_year=2003; citation_volume=64; citation_pages=1187-1196;

citation_title=Antifreeze proteins in overwintering plants: A tale of two activities; citation_author=Griffith M.; citation_author=Yaish M. W. F.; citation_journal_title=Trends Plant Sci.; citation_year=2004; citation_volume=9; citation_pages=399-405;

citation_title=Long-range protein-water dynamics in hyperactive insect antifreeze proteins; citation_author=Meister K.; citation_author=Ebbinghaus S.; citation_author=Xu Y.; citation_author=John G. D.; citation_author=DeVries A.; citation_author=Gruebele M.; citation_author=David M. L.; citation_author=Havenith M.; citation_journal_title=Proc. Natl. Acad. Sci. U.S.A.; citation_year=2012; citation_volume=110; citation_pages=1617-1622;

citation_title=The mechanism of the type III antifreeze protein action: A computational study; citation_author=Yang C.; citation_author=Kim A. S.; citation_journal_title=Biophys. Chem.; citation_year=2004; citation_volume=109; citation_pages=137-148;

citation_title=A hyperactive, Ca2+ - dependent antifreeze protein in an Antarctic bacterium; citation_author=Jack A. G.; citation_author=Peter L. D.; citation_author=Johanna L.-P.; citation_journal_title=FEMS Microbiol. Lett.; citation_year=2005; citation_volume=245; citation_pages=67-72;

citation_title=Antifreeze proteins of bacteria; citation_author=Chattopadhyay M. K.; citation_journal_title=Resonance; citation_year=2007; citation_volume=12; citation_pages=25-30;

citation_title=Structure and function of antifreeze proteins; citation_author=Davies P. L.; citation_author=Baardsnes J.; citation_author=Kuiper M. J.; citation_author=Walker V. K.; citation_journal_title=Philos. Trans. R. Soc. Lond. B; citation_year=2002; citation_volume=357; citation_pages=927-935;

citation_title=Anchored clathrate waters bind antifreeze proteins to ice; citation_author=Christopher P. G.; citation_author=Robert L. C.; citation_author=Peter L. D.; citation_journal_title=Proc. Natl. Acad. Sci. U.S.A.; citation_year=2011; citation_volume=108; citation_pages=7363-7367;

citation_title=A Ca2+-dependent bacterial antifreeze protein domain has a novel β-helical ice-binding fold; citation_author=Christopher P. G.; citation_author=Jack A. G.; citation_author=Christopher P. H.; citation_author=Robert L. C.; citation_author=Johanna L.-P.; citation_author=Peter L. D.; citation_journal_title=Proc. Natl. Acad. Sci. U.S.A.; citation_year=2008; citation_volume=411; citation_pages=171-180;

citation_title=Ice-binding site of snow mold fungus antifreeze protein deviates from structural regularity and high conservation; citation_author=Kondo H.; citation_author=Hanada Y.; citation_author=Sugimoto H.; citation_author=Hoshino T.; citation_author=Christopher P. G.; citation_author=Peter L. D.; citation_journal_title=Proc. Natl. Acad. Sci. U.S.A.; citation_year=2012; citation_volume=109; citation_pages=9360-9365;

citation_title=Thermal hysteresis protein activity in bacteria, fungi and phylogenetically diverse plants; citation_author=John G. D.; citation_author=Olsen T. M.; citation_journal_title=Cryobiology; citation_year=1993; citation_volume=30; citation_pages=322-328;

citation_title=VMD-visual molecular dynamics; citation_author=Humphrey W.; citation_author=Dalke A.; citation_author=Schulten K.; citation_journal_title=Mol. Graphics; citation_year=1996; citation_volume=14; citation_pages=33-38;

citation_title=The MARTINI force field: Coarse grained model for biomolecular simulation; citation_author=Siewert J. M.; citation_author=Risselada H. J.; citation_author=Yefimov S.; citation_author=Tieleman D. P.; citation_author=Alex H. D.; citation_journal_title=Phys. Chem. B; citation_year=2007; citation_volume=111; citation_pages=7812-7824;

citation_title=GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation; citation_author=Hess B.; citation_author=Kutzner C.; citation_author=van der Spoel D.; citation_author=Lindahl E.; citation_journal_title=Chem. Theory Comput.; citation_year=2008; citation_volume=4; citation_pages=435-447;

citation_title=Particle mesh Ewald: An Nlog (N) method for Ewald sums in large systems; citation_author=Darden T.; citation_author=York D.; citation_author=Pedersen J.; citation_journal_title=Chem. Phys.; citation_year=1993; citation_volume=98; citation_pages=10089-10092;

citation_title=Molecular dynamics with coupling to an external bath; citation_author=Berendsen H. J. C.; citation_author=Postma J. P. M.; citation_author=Gunsteren W. F. V.; citation_author=Dinola A.; citation_author=Haak J. R.; citation_journal_title=Chem. Phys.; citation_year=1984; citation_volume=81; citation_pages=3684-3690;

citation_title=Polymorphic transitions in single crystals: A new molecular dynamics method; citation_author=Parrinello M.; citation_author=Rahman A.; citation_journal_title=Appl. Phys.; citation_year=1981; citation_volume=52; citation_pages=7182-7190;

citation_title=Quiet high resolution computer models of plasma; citation_author=Hockney R. W.; citation_author=Goel S. P.; citation_author=Eastwood J.; citation_journal_title=J. Comput. Phys.; citation_year=1974; citation_volume=14; citation_pages=148-158;

citation_title=Structure of ice crystallized from supercooled water; citation_author=Tamsin L. M.; citation_author=Benjamin J. M.; citation_author=Andrey V. B.; citation_author=Anwar J.; citation_author=Christoph G. S.; citation_journal_title=Proc. Natl. Acad. Sci. U.S.A.; citation_year=2011; citation_volume=109; citation_pages=1041-1045;

citation_title=Interface-limit growth of heterogeneously nucleated ice in supercooled water; citation_author=Nistor R. A.; citation_author=Markland T. E.; citation_author=Berne B. J.; citation_journal_title=Phys. Chem. B; citation_year=2014; citation_volume=118; citation_pages=752-760;