Mixed-SAM surfaces monitoring CTX-protein, part II: Analysis using molecular dynamics simulations

IEEE Transactions on Nanobioscience

Volumn 9, Issue 4, 2010, Pages 297-306

  Hung, Shih Wei ^a   Hsiao, Pai Yi ^a   Chieng, Ching Chang ^a  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

Author keywords

Binding energy; cardiotoxin protein; hydrophobicity; molecular dynamics simulation; self assembled monolayer; solvent accessible area

Indexed keywords

ALKANETHIOLS; ATOMIC FORCE MICROSCOPES; CARDIOTOXIN PROTEIN; COBRA CARDIOTOXINS; CONTACT AREAS; DIFFERENT SOLVENTS; LINEARLY PROPORTIONAL; MAXIMUM VALUES; MIXING RATIOS; MOLECULAR DYNAMICS SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; PHYSICAL MECHANISM; PROTEIN ADSORPTION; SAMS; WATER MOLECULE;

ADSORPTION; DEWATERING; DYNAMICS; ELECTRON ENERGY LEVELS; HYDROPHOBICITY; IODINE; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MOLECULES; NUCLEAR ENERGY; ORGANIC POLYMERS; POTENTIAL ENERGY; PROTEINS; SELF ASSEMBLED MONOLAYERS; SOLVENTS;

BINDING ENERGY;

COBROTOXIN; THIOL DERIVATIVE; WATER;

ADSORPTION; ARTICLE; CHEMICAL PHENOMENA; CHEMISTRY; HUMAN; MOLECULAR DYNAMICS; PLIABILITY; SURFACE PROPERTY;

ADSORPTION; COBRA CARDIOTOXIN PROTEINS; HUMANS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MOLECULAR DYNAMICS SIMULATION; PLIABILITY; SULFHYDRYL COMPOUNDS; SURFACE PROPERTIES; WATER;

EID: 79251550145     PISSN: 15361241     EISSN: None     Source Type: Journal    
DOI: 10.1109/TNB.2010.2070517     Document Type: Article

References (47)

1. J. J. Gray, "The interaction of proteins with solid surfaces," Curr. Opin. Struct. Biol., vol. 14, pp. 110-115, 2004.
2. D. J. Tobias, W. Mar, J. K. Blasie, and M. L. Klein, "Molecular dynamics simulations of a protein on hydrophobic and hydrophilic surfaces," Biophys. J., vol. 71, pp. 2933-2941, 1996.
3. C. E. Nordgren, D. J. Tobias, M. L. Klein, and J. K. Blasie, "Molecular dynamics simulations of a hydrated protein vectorially oriented on polar and nonpolar soft surfaces," Biophys. J., vol. 83, pp. 2906-2917, 2002.
4. J. Zhou, J. Zheng, and S. Jiang, "Molecular simulation studies of the orientation and conformation of cytochrome c adsorbed on self-assembled monolayers," J. Phys. Chem. B, vol. 108, pp. 17418-17424, 2004.
5. J. C. Hower, Y. He, M. T. Bernards, and S. Jiang, "Understanding the nonfouling mechanism of surfaces through molecular simulations of sugar-based self-assembled monolayers," J. Chem. Phys., vol. 125, P. 214704, 2006.
6. J. Zheng, L. Li, S. Chen, and S. Jiang, "Molecular simulation study of water interactions with oligo (ethylene glycol)-terminated alkanethiol self-assembled monolayers," Langmuir, vol. 20, pp. 8931-8938, 2004.
7. J. Zheng, L. Li, H.-K. Tsao, Y.-J. Sheng, S. Chen, and S. Jiang, "Strong repulsive forces between protein and oligo (ethylene glycol) self-assembled monolayers: A molecular simulation study," Biophys. J., vol. 89, pp. 158-166, 2005.
8. M. Agashe, V. Raut, S. J. Stuart, and R. A. Latour, "Molecular simulation to characterize the adsorption behavior of a fibrinogen γ-chain fragment," Langmuir, vol. 21, pp. 1103-1117, 2005.
9. M. J. Dufton and R. C. Hider, "Structure and pharmacology of elapid cytotoxins," Pharmacol. Ther., vol. 36, pp. 1-40, 1988.
10. M. Dauplais, J. M. Neumann, S. Pinkasfeld, A. Menez, and C. Roumestand, "An NMR study of the interaction of cardiotoxin γ from Naja nigricollis with perdeuterated dodecylphosphocholine micelles," Eur. J. Biochem., vol. 230, pp. 213-220, 1995.
11. S.-C. Sue, H. C. Jarrell, J.-R. Brisson, and W.-G. Wu, "Dynamic characterization of the water binding loop in the p-type cardiotoxin: Implication for the role of the bound water molecule," Biochemistry, vol. 40, pp. 12782-12794, 2001.
12. F. Forouhar, W.-N. Huang, J.-H. Liu, K.-Y. Chien, W.-G. Wu, and C.-D. Hsiao, "Structural basis of membrane-induced cardiotoxin A3 oligomerization," J. Biol. Chem., vol. 278, pp. 21980-21988, 2003.
13. W.-N. Huang, S.-C. Sue, D.-S. Wang, P.-L. Wu, and W.-G. Wu, "Peripheral binding mode and penetration depth of cobra cardiotoxin on phospholipid membranes as studied by a combined FTIR and computer simulation approach," Biochemistry, vol. 42, pp. 7457-7466, 2003.
14. S.-W. Hung, J.-K. Hwang, F. Tseng, J.-M. Chang, C.-C. Chen, and C.-C. Chieng, "Molecular dynamics simulation of the enhancement of cobra cardiotoxin and E6 protein binding on mixed self-assembled monolayer molecules," Nanotechnology, vol. 17, pp. S8-S13, 2006.
15. J. Ramstein and R. Lavery, "Energetic coupling between DNA bending and base pair opening," Proc. Nat. Acad. Sci. USA, vol. 85, pp. 7231-7235, 1988.
16. D. Chandler, "Interfaces and the driving force of hydrophobic assembly," Nature, vol. 437, pp. 640-647, 2005.
17. E. Ostuni, R. G. Chapman, M. N. Liang, G. Meluleni, G. Pier, D. E. Ingber, and G. M. Whitesides, "Self-assembled monolayers that resist the adsorption of proteins and the adhesion of bacterial and mammalian cells," Langmuir, vol. 17, pp. 6336-6343, 2001.
18. L. D. Schuler and W. F. van Gunsteren, "On the choice of dihedral angle potential energy functions for n-alkanes," Mol. Simul., vol. 25, pp. 301-319, 2000.
19. J. Hautman and M. L. Klein, "Simulation of a monolayer of alkyl thiol chains," J. Chem. Phys., vol. 91, pp. 4994-5001, 1989.
20. J. J.-P. Ryckaert and A. Bellemans, "Molecular dynamics of liquid alkanes," Faraday Discuss. Chem. Soc., vol. 66, pp. 95-106, 1978.
21. K. J. Tupper and D. W. Brenner, "Compression-induced structural transition in a self-assembled monolayer," Langmuir, vol. 10, pp. 2335-2338, 1994.
22. H. J. C. Berendsen, J. R. Grigera, and T. P. Straatsma, "The missing term in effective pair potentials," J. Phys. Chem., vol. 91, pp. 6269-6271, 1987.
23. R. K. Smith, P. A. Lewis, and P. S. Weiss, "Patterning self-assembled monolayers," Progress Surf. Sci., vol. 75, pp. 1-68, 2004.
24. C. D. Bain and G. M. Whitesides, "Formation of monolayers by the coadsorption of thiols on gold: Variation in the length of the alkyl chain," J. Amer. Chem. Soc., vol. 111, pp. 7164-7175, 1989.
25. J. P. Folkers, P. E. Laibinis, and G. M. Whitesides, "Self-assembled monolayers of alkanethios on gold-Comparisons of monolayers containing mixtures of short-chain and long-chain constituents with CH3 and CH2OH terminal groups," Langmuir, vol. 8, pp. 1330-1341, 1992.
26. P. E. Laibinis, R. G. Nuzzo, and G. M. Whitesides, "Structure of monolayers formed by coadsorption of 2 normal-alkanethiols of different chain lengths on gold and its relation to wetting," J. Phys. Chem., vol. 96, pp. 5097-5105, 1992.
27. K. Tamada, M. Hara, H. Sasabe, and W. Knoll, "Surface phase behavior of n-alkanethiol self-assembled monolayers adsorbed on Au(111): An atomic force microscope study," Langmuir, vol. 13, pp. 1558-1566, 1997.
28. R. G. Efremov, D. E. Nolde, A. G. Konshina, N. P. Syrtcev, and A. S. Arseniev, "Peptides and proteins in membranes: What can we learn via computer simulations?," Curr. Med. Chem., vol. 11, pp. 2421-2442, 2004.
29. M. A. Lomize, A. L. Lomize, I. D. Pogozheva, and H. I. Mosberg, "OPM: Orientations of proteins in membranes database," Bioinformatics, vol. 22, pp. 623-625, 2006.
30. S. Kirkpatrick, C. D. Gelatt, and M. P. Vecchi, "Optimization by simulated annealing," Science, vol. 220, pp. 671-680, 1983.
31. H. J. C. Berendsen, J. P. M. Postma, W. F. V. Gunsteren, A. DiNola, and J. R. Haak, "Molecular dynamics with coupling to an external bath," J. Chem. Phys., vol. 81, pp. 3684-3690, 1984.
32. B. Hess, H. Bekker, H. J. C. Berendsen, and J. G. E. M. Fraaije, "LINCS: A linear constraint solver for molecular simulations," J. Comput. Chem., vol. 18, pp. 1463-1472, 1997.
33. P. J. Steinbach and B. R. Brooks, "New spherical-cutoff methods for long-range forces in macromolecular simulation," J. Comput. Chem., vol. 15, pp. 667-683, 1994.
34. W. F. V. Gunsteren and H. J. C. Berendsen, "Computer simulation of molecular dynamics: Methodology, applications, and perspectives in chemistry," Angew. Chem. Int. Ed. (English), vol. 29, pp. 992-1023, 1990.
35. D. V. D. Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. C. Berendsen, "GROMACS: Fast, flexible, and free," J. Comput. Chem., vol. 26, pp. 1701-1718, 2005.
36. W. L. DeLano, The PyMOL Molecular Graphics System. Palo Alto, CA, 2002.
37. P. Fenter, A. Eberhardt, K. S. Liang, and P. Eisenberger, "Epitaxy and chainlength dependent strain in self-assembled monolayers," J. Chem. Phys., vol. 106, pp. 1600-1608, Jan. 1997.
38. D. Eisenberg and A. D. McLachlan, "Solvation energy in protein folding and binding," Nature, vol. 319, pp. 199-203, Jan. 1986.
39. J. A. Reynolds, D. B. Gilbert, and C. Tanford, "Empirical correlation between hydrophobic free-energy and aqueous cavity surface-area," Proc. Nat. Acad. Sci. USA, vol. 71, pp. 2925-2927, 1974.
40. S. H. White and W. C. Wimley, "Peptides in lipid bilayers-Structural and thermodynamic basis for partitioning and folding," Curr. Opin. Struct. Biol., vol. 4, pp. 79-86, 1994.
41. F. Eisenhaber, P. Lijnzaad, P. Argos, C. Sander, and M. Scharf, "The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies," J. Comput. Chem., vol. 16, pp. 273-284, 1995.
42. K. L. Prime and G. M. Whitesides, "Self-assembled organic monolayers: Model systems for studying adsorption of proteins at surfaces," Science, vol. 252, pp. 1164-1167, 1991.
43. J. Kyte and R. F. Doolittle, "A simple method for displaying the hydropathic character of a protein," J. Mol. Biol., vol. 157, pp. 105-132, 1982.
44. M. D. Porter, T. B. Bright, D. L. Allara, and C. E. D. Chidsey, "Spontaneously organized molecular assemblies. 4. Structural characterization of n-alkyl thiol monolayers on gold by optical ellipsometry, infrared spectroscopy, and electrochemistry," J. Amer. Chem. Soc., vol. 109, pp. 3559-3568, 1987.
45. D. Schwendel, T. Hayashi, R. Dahint, A. Pertsin, M. Grunze, R. Steitz, and F. Schreiber, "Interaction of water with self-assembled monolayers: Neutron reflectivity measurements of the water density in the interface region," Langmuir, vol. 19, pp. 2284-2293, 2003.
46. Q. X. Zhang, J. Zheng, A. Shevade, L. Z. Zhang, S. H. Gehrke, G. S. Heffelfinger, and S. Y. Jiang, "Transport diffusion of liquid water and methanol through membranes," J. Chem. Phys., vol. 117, pp. 808-818, 2002.
47. P. E. Smith and B. M. Pettitt, "Modeling solvent in biomolecular systems," J. Phys. Chem., vol. 98, pp. 9700-9711, 1994.