Potential of mean force calculation of the free energy of adsorption of Type I winter flounder antifreeze protein on ice

Journal of Crystal Growth

Volumn 312, Issue 8, 2010, Pages 1257-1261

  Battle, Keith ^a   Alan Salter, E ^a   Wesley Edmunds, R ^a   Wierzbicki, Andrzej ^a  

^a UNIVERSITY OF SOUTH ALABAMA   (United States)

Author keywords

A1. Adsorption; A1. Biocrystallization; A1. Computer simulation; B1. Biological macromolecules

Indexed keywords

A1. BIOCRYSTALLIZATION; ANTIFREEZE PROTEIN; B1. BIOLOGICAL MACROMOLECULES; BIOCRYSTALLIZATION; BIOLOGICAL MACROMOLECULE; EXPLICIT WATER; FREE ENERGY OF ADSORPTION; GASPHASE; HYDROPHOBIC RESIDUES; ICE GROWTH; METHANE ADSORPTION; METHYL GROUP; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR MECHANISM; PERIODIC BOUNDARY CONDITIONS; PLANE WAVE; POTENTIAL OF MEAN FORCE; PSEUDOPOTENTIALS; THREONINE RESIDUES; UMBRELLA SAMPLING; WILD TYPES; WINTER FLOUNDER;

ADSORPTION; AMINO ACIDS; COMPUTATIONAL METHODS; COMPUTER SIMULATION; FREE ENERGY; HYDROPHOBICITY; ICE; MACROMOLECULES; METHANE; MOLECULAR DYNAMICS; PHOSPHATASES;

PROTEINS;

EID: 77949606870     PISSN: 00220248     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jcrysgro.2009.12.038     Document Type: Article

References (29)

1. Feeney R.E., Burcham T.S., and Yeh Y. Antifreeze glycoproteins from polar fish blood. Annual Review of Biophysics and Biophysical Chemistry 15 (1986) 59-78
2. Davies P.L., and Hew C.L. Biochemistry of fish antifreeze proteins. FASEB Journal 4 (1990) 2460-2468
3. Scholander P.F., Dam L.V., Kanwisher J., Hammel T., and Gordon M.S. Supercooling and osmoregulation in arctic fish. Journal of Cellular and Comparative Physiology 49 (1957) 5-24
4. Baardsnes J., Jelokhani-Niaraki M., Kondejewski L.H., Kuiper M.J., Kay C.M., Hodges R.S., and Davies P.L. Antifreeze protein from the shorthorn sculpin: identification of the ice-binding surface. Protein Science 10 (2001) 2566-2576
5. Chao H., Houston M.E., Hodges R.S., Kay C.M., Sykes B.D., Loewen M.C., Davies P.L., and Sönnichsen F.D. A diminished role for hydrogen bonds in antifreeze protein binding to ice. Biochemistry 36 48 (1997) 14652-14660
6. Baardsnes J., Kondejewski L.H., Hodges R.S., Chao H., Kay C., and Davies P.L. New ice-binding face for Type I antifreeze protein. FEBS Letters 463 1-2 (1999) 87-91
7. Haymet A.D.J., Ward L.G., Harding M.M., and Knight C.A. Valine substituted winter flounder antifreeze-preservation of ice growth hysteresis. FEBS Letters 430 3 (1998) 301-306
8. Knight C.A., Cheng C.-H.C., and DeVries A.L. Adsorption of α-helical antifreeze peptides on specific ice crystal surface planes. Biophysical Journal 59 (1991) 409-418
9. Zhang W., and Laursen R.A. Structure-function relationships in a Type I antifreeze polypeptide-the role of threonine methyl and hydroxyl groups in antifreeze activity. Journal of Biological Chemistry 273 52 (1998) 34806-34812
10. Davies P.L., Baardsnes J., Kuiper M.J., and Walker V.K. Structure and function of antifreeze proteins. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 357 1423 (2002) 927-935
11. Sicheri F., and Yang D.S. Ice-binding structure and mechanism of an antifreeze protein from winter flounder. Nature 375 (1995) 427-431
12. Zhang W., and Laursen R.A. Artificial antifreeze polypeptides: alpha-helical peptides with KAAK motifs have antifreeze and ice crystal morphology modifying properties. FEBS Letters 455 3 (1999) 372-376
13. Wierzbicki A., Dalal P., Cheatham III T.E., Knickelbein J.E., Haymet A.D.J., and Madura J.D. Antifreeze proteins at the ice/water interface: three calculated discriminating properties for orientation of Type I proteins. Biophysical Journal 93 (2007) 1442-1451
14. Wierzbicki A., Knight C.A., Salter E.A., Henderson C.N., and Madura J.D. The role of non-polar amino acid functional groups in the surface-orientation-dependent adsorption of natural and synthetic antifreeze peptides on ice. Crystal Growth and Design 8 9 (2008) 3420-3429
15. 4 adsorption on ice and snow. Journal of Colloid and Interface Sciences 224 (2000) 104-110
16. CPMD, 3.13.2, IBM Research Division: Stuttgart, Germany, 2009.
17. D.A. Case, T.A. Darden, T.E. Cheatham III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, K.M. Merz, J. Wang, B. Pearlman, D.A. Crowley, M. Brozel, V. Tsui, H. Gohlke, J. Mongan, V. Hornak, G. Cui, P. Beroza, C. Schafmeister, C. Caldwell, J.W. Ross, P.A. Kollman, AMBER10i, San Francisco, California, 2008.
18. h for common water models calculated from direct coexistence of the solid-liquid interface. Journal of Chemical Physics 124 (2006) 144506
19. Chimera, 7, UCSF: San Francisco, CA, 2007.
20. Grossfield, A. Weighted Histogram Analysis Method (WHAM), 2008.
21. Kumar S., Rosenberg J.M., Bouzida D., Swendsen R.H., and Kollman P.A. Mutidimensional free-energy calculation using the weighted histogram analysis method. Journal of Computational Chemistry 16 11 (2004) 1339-1350
22. MathSoft Engineering & Education, I. Mathcad 2001i Professional, 2001.
23. Cerius2, 4.8.1, Accelrys, Inc.: San Diego, CA, 2003.
24. CASTEP, 4.6 Accelrys, Inc.: San Diego, CA, 2001.
25. Milman V., Winkler B., White J.A., Pickard C.J., Payne M.C., Akhmatskaya E.V., and Nobes R.H. Electronic structure, properties, and phase stability of inorganic crystals: a pseudopotential plane-wave study. International Journal of Quantum Chemistry 77 (2000) 895-910
26. Perdew J.P., Burke K., and Ernzerhof M. Physics Review Letters 77 (1996) 3865
27. Lin I.-C., Coutinho-Neto M.D., Felsenheimer C., von Lilienfeld O.A., Tavernelli I., and Rothlisberger U. Library of dispersion-corrected atom-centered potentials for generalized gradient approximation functionals: elements H, C, N, O, He, Ne, Ar, and Kr. Physical Review B 75 20 (2007) 205131-205135
28. Boys S.F., and Bernardi F. The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Molecular Physics 19 (1970) 553-566
29. Haymet A.D.J., Ward L.G., and Harding M.M. Winter flounder "antifreeze" proteins: synthesis and ice growth inhibition of analogues that probe the relative importance of hydrophobic and hydrogen-bonding interactions. Journal of the American Chemical Society 121 5 (1999) 941-948