Molecular dynamics simulations of a protein on hydrophobic and hydrophilic surfaces

Biophysical Journal

Volumn 71, Issue 6, 1996, Pages 2933-2941

  Tobias, Douglas J ^a,b   Mar, Wen ^a   Blasie, J Kent ^a   Klein, Michael L ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME C; MEMBRANE PROTEIN;

ALPHA HELIX; ARTICLE; COVALENT BOND; HYDROPHILICITY; HYDROPHOBICITY; MOLECULAR DYNAMICS; PROTEIN ASSEMBLY; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SURFACE PROPERTY;

EID: 0029769798     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(96)79497-3     Document Type: Article

References (29)

1. Aleby, S., and E. von Sydow. 1960. The crystal structure of methyl stearate. Acta Crystallogr. 13:487-492.
2. Allen, M. P., and D. J. Tildesley. 1989. Computer Simulation of Liquids. Oxford University Press, New York.
3. Amador, S. M., J. M. Pachence, R. Fischetti, J. P. McCauley, Jr., A. B. Smith III, and J. K. Blasie. 1993. Use of self-assembled monolayers to covalently tether protein monolayers to the surface of solid substrates. Langmuir. 9:812-817.
4. Bain, C. D., E. B. Troughten, Y.-T. Tao, J. Evall, G. M. Whitesides, and R. G. Nuzzo. 1989. Formation of monolayer films by the spontaneous assembly of organic thiols from solution onto gold. J. Am. Chem. Soc. 111:321-335.
5. Blasie, J. K., M. Erecinska, M., S. Samuels, and J. S. Leigh. 1978. The structure of a cytochrome c oxidase-lipid model membrane. Biochim. Biophys. Acta. 501:33-52.
6. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4:187-217.
7. Buckner, J. K., and W. L. Jorgensen. 1989. Energetics and hydration of the constituent ion pairs of tetramethylammonium chloride. J. Phys. Chem. 111:2507-2516.
8. Chupa, J. A., J. P. McCauley, Jr., R. M. Strongin, A. B. Smith III, J. K. Blasie, L. J. Peticolas, and J. C. Bean. 1994. Vectorially oriented membrane protein monolayers: profile structures via x-ray interferometry/holography. Biophys. J. 67:336-348.
9. Ciccotti, G., and J.-P. Ryckaert. 1986. Molecular dynamics simulation of rigid molecules. Comp. Phys. Rep. 4:347-392.
10. Delamarche, E., H. Biebuyck, B. Michel, G. Sundarababu, H. Sigrist, H. Wolf, and H. Ringsdorf. 1995. STM analysis of cytochrome c immobilized on self-assembled monolayers on gold. In Procedures in Scanning Probe Microscopies. R. Colton et al., editors. John Wiley & Son, Chichester, UK.
11. Hautman, J., J. P. Bareman, W. Mar, and M. L. Klein. 1991. Molecular dynamics investigation of self-assembled monolayers. J. Chem. Soc. Faraday Trans. 87:2031-2037.
12. Hautman, J., and M. L. Klein. 1991. Microscopic wetting phenomena. Phys. Rev. Lett. 13:1763-1766.
13. Hautman, J., and M. L. Klein. 1992. An Ewald summation method for planar surfaces and interfaces. Mol. Phys. 75:379-395.
14. Jorgensen, W. L. 1986. Intermolecular potential functions and Monte Carlo simulations for liquid sulfur compounds. J. Phys. Chem. 90:6379-6388.
15. Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
16. Louie, G. V., and G. D. Brayer. 1990. High-resolution refinement of yeast iso-1-cytochrome c and comparison with other eukaryotic cytochromes c. J. Mol. Biol. 214:527-555.
17. 3 molecules using an all-atoms model. Langmuir. 10:188-196.
18. Martyna, G. J., M. L. Klein, and M. Tuckerman. 1992. Nosé-Hoover chains: the canonical ensemble via continuous dynamics. J. Chem. Phys. 97:2635-2643.
19. Pachence, J. M., S. Amador, G. Maniara, J. Vanderkooi, P. L. Dutton, and J. K. Blasie. 1990. Orientation and lateral mobility of cytochrome c on the surface of ultrathin lipid multilayer films. Biophys. J. 58:379-389.
20. Pachence, J. M., and J. K. Blasie. 1987. The location of cytochrome c on the surface of ultrathin lipid multilayer films using x-ray diffraction. Biophys. J. 52:735-747.
21. Pachence, J. M., and J. K. Blasie. 1991. Structural investigation of the covalent and electrostatic binding of yeast cytochrome c to the surface of various ultrathin lipid multilayers using x-ray diffraction. Biophys. J. 59:894-900.
22. Pachence, J. M., R. F. Fischetti, and J. K. Blasie. 1989. Location of the heme-Fe atoms within the profile structure of a monolayer of cytochrome c bound to the surface of an ultrathin lipid multilayer film. Biophys. J. 327-337.
23. 2+-ATPase from sarcoplasmic reticulum. Biophys. J. 70:2131-2143.
24. Reiher, W. E. 1985. Theoretical Studies of Hydrogen Bonding. Ph.D. dissertation, Harvard University, Cambridge, MA.
25. Ryckaert, J.-P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Phys. 23: 327-341.
26. Wang, J., C. J. A. Wallace, I. Clark-Lewis, and M. Caffrey. 1994. Structure characterization of membrane bound and surface adsorbed protein. J. Mol. Biol. 237:1-4.
27. Wasserman, S. R., H. Biebuyck, and G. M. Whitesides. 1989. Monolayers of 11-trichlorosilylundecyl thioacetate: a system that promotes adhesion between silicon dioxide and evaporated gold. J. Mater. Res. 4:886-892.
28. Wong, C. F., C. Zheng, J. Shen, J. A. McCammon, and P. G. Wolynes. 1993. Cytochrome c: a molecular proving ground for computer simulations. J. Phys. Chem. 97:3100-3110.
29. Xu, S., R. F. Fischetti, J. K. Blasie, L. J. Peticolas, and J. C. Bean. 1993. Profile and in-plane structures of self-assembled monolayers on Ge/Si multilayer substrates by high-resolution x-ray diffraction employing x-ray interferometry/holography. J. Phys. Chem. 97:1961-1969.