Interaction among the twelve-residue segment of antifreeze protein type I, or its mutants, water and a hexagonal ice crystal

References

• Li , B. and Sun , D-W. 2001 . Novel methods for rapid freezing and thawing of foods – a review . J. Food Eng. , 54 : 175
   Web of Science ®Google Scholar
• Fletcher , G.L. , Goddard , S.V. and Wu , Y. 1999 . Antifreeze proteins and their genes: From basic research to business opportunity . Chem. Tech. , 30 ( 6 ) : 17
   Google Scholar
• Amir , G. , Rubinsky , B. , Basheer , S.Y. , Horowitz , L. , Jonathan , L. , Feinberg , M.S. , Smolinsky , A.K. and Lavee , L. 2005 . Improved viability and reduced apoptosis in sub-zero 21-hour preservation of transplanted rat hearts using anti-freeze proteins . J. Heart Lung Transplant. , 24 : 1915
   PubMed Web of Science ®Google Scholar
• Yang , D.S.C. 1988 . Crystal structure of an antifreeze polypeptide and its mechanistic implications . Nature , 333 : 232 M. Sax, A. Chakrabatty, and C.L. Hew
   PubMed Web of Science ®Google Scholar
• Knight , C.A. , Cheng , C.C. and DeVries , A.L. 1991 . Adsorption of alpha-helical antifreeze peptides on specific ice crystal surface planes . Biophys. J. , 59 : 409
   PubMed Web of Science ®Google Scholar
• Yeh , Y. and Feeney , R.E. 1996 . Antifreeze proteins: Structures and mechanisms of function . Chem. Rev. , 96 : 601
   PubMed Web of Science ®Google Scholar
• Chao , H. 1997 . A diminished role for hydrogen bonds in antifreeze protein binding to ice . Biochemistry , 36 : 14652 M.E. Houston Jr., R.S. Hodges, C.M. Kay, B.D. Sykes, M.C. Loewen, P.L. Davies, and F.D. Sönnichsen
   PubMed Web of Science ®Google Scholar
• Zhang , W. and Laursen , R.A. 1998 . Structure–function relationships in a type I antifreeze polypeptide . J. Biol. Chem. , 273 : 34806
   PubMed Web of Science ®Google Scholar
• Haymet , A.D.G. , Ward , L.G. and Harding , M.M. 1999 . Winter flounder ‘antifreeze’ proteins: Synthesis and ice growth inhibition of analogues that probe the relative importance of hydrophobic and hydrogen-bonding interactions . J. Am. Chem. Soc. , 121 : 941
   Web of Science ®Google Scholar
• Loewen , M.C. 1999 . Alternative roles for putative ice-binding residues in type I antifreeze protein . Biochemistry , 38 : 4743 H. Chao, M.E. Houston, J. Baardsnes, R. Hodges, C.M. Kay, B.D. Sykes, F.D. Sönningen, and P.L. Davies
   PubMed Web of Science ®Google Scholar
• Jorov , A. , Zhorov , B.S. and Yang , D.S.C. 2004 . Theoretical study of interaction of winter flounder antifreeze protein with ice . Protein Sci. , 13 : 1537
   Web of Science ®Google Scholar
• Cheng , A. and Merz , M. 1997 . Ice-binding mechanism of winter flounder antifreeze proteins . Biophys. J. , 73 : 2851
   PubMed Web of Science ®Google Scholar
• Dalal , P. 2001 . Hydrogen bond analysis of type 1 antifreeze protein in water and the ice/water interface . PhysChemComm , 7 : 1 J. Krickelbein, A.D.G. Haymet, F.D. Sönnichsen, and J. Madura
   Google Scholar
• Wierzbicki , A. 2007 . Antifreeze proteins at the ice/water interface: Three calculated discriminating properties for orientation of type I proteins . Biophys. J. , 93 : 1442 P. Dala, T.E. Cheatham III, J.E. Knickelbein, A.D.J. Haymet, and J.D. Madura
   PubMed Web of Science ®Google Scholar
• Yang , C. and Sharp , K.A. 2005 . Hydrophobic tendency of polar group hydration as a major force in type I antifreeze protein recognition . Proteins: Struct. Funct. Bioinform. , 59 : 266
   PubMed Web of Science ®Google Scholar
• Haymet , A.D.G. 1998 . Valine substituted winter flounder ‘antifreeze’: Preservation of ice growth hysteresis . FEBS Lett. , 430 : 301 L.G. Ward, M.M. Harding, and C.A. Knight
   PubMed Web of Science ®Google Scholar
• Coger , R. , Rubinsky , B. and Fletcher , G. 1994 . Microscopic pattern of ice crystal growth in the presence of thermal hysteresis proteins . (Trans. Am. Soc. Mech. Eng.) J. Offshore Mech. Arotic Eng. , 116 : 173
   Google Scholar
• Nobekawa , T. , Taniguchi , H. and Hagiwara , Y. 2008 . Interaction between a twelve-residue segment of antifreeze protein type I, or its mutants, and water molecules . Mol. Simul. , 34 : 309
   Web of Science ®Google Scholar
• Gear , C.W. 1971 . Numerical Initial Value Problems in Ordinary Differential Equations , Englewood Cliffs : Prentice-Hall .
   Google Scholar
• Iwasaki , K. and Hagiwara , Y. 2004 . Inhibition of ice nucleus growth in water by alanine dipeptide . Mol. Simul. , 30 : 487
   Web of Science ®Google Scholar
• Jorgensen , W.J. 1983 . Comparison of simple potential functions for simulating liquid water . J. Chem. Phys. , 79 : 926 J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein
   Web of Science ®Google Scholar
• Matsumoto , M. , Saito , S. and Ohmine , I. 2002 . Molecular dynamics simulation of the ice nucleation and growth process leading to water freezing . Nature , 416 : 409
   PubMed Web of Science ®Google Scholar
• Nada , H. , van der Eerden , J.P. and Furukawa , Y. 2004 . A clear observation of crystal growth of ice from water in a molecular dynamics simulation with a six-site potential model of H2O . J. Crystal Growth , 266 : 297
   Web of Science ®Google Scholar
• Verlet , L. 1968 . Computer ‘experiments’ on classical fluids. II. Equilibrium correlation functions . Phys. Rev. , 165 : 201
   Web of Science ®Google Scholar
• Frenkel , D. and Smit , B. 1996 . Understanding Molecular Simulation , San Diego : Academic Press .
   Google Scholar
• Ryckart , J.P. , Ciccotti , G. and Berendsen , H.J.C. 1977 . Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes . J. Comput. Phys. , 23 : 327
   Web of Science ®Google Scholar
• Jorgensen , W.J. and Tirado-Rives , J. 1988 . The OPLS potential functions for proteins: Energy minimisations for crystals of cyclic peptides and crambin . J. Am. Chem. Soc. , 110 : 1657
   PubMed Web of Science ®Google Scholar
• Reach , A.W. 1996 . Molecular Modelling – Principles and Applications , 2nd ed. , Pearson Education Ltd .
   Google Scholar
• Nguyen , D.H. 2004 . Intermolecular interaction studies of winter flounder antifreeze protein reveal the existence of thermally accessible binding state . Biopolymers , 75 : 109 M.E. Colvin, Y. Yeh, R.E. Feeney, and W.H. Fink
   Google Scholar
• Allen , M.P. and Tildesley , D.J. 1987 . Computer Simulation of Liquid , Oxford : Oxford Science .
   Google Scholar
• Umemura , M. 2003 . Structure of water molecules in aqueous maltose and cellobiose solutions using molecular dynamics simulation. II. Dynamics . J. Mol. Struct. (Theochem) , 636 : 215 T. Nakagawa, S. Hayashi, H. Urakawa, and K. Kajiwara
   Google Scholar