A Molecular Dynamics Method for Calculating Molecular Volume Changes Appropriate for Biomolecular Simulation

Biophysical Journal

Volumn 85, Issue 5, 2003, Pages 2801-2807

  DeVane, Russell ^a   Ridley, Christina ^a   Larsen, Randy W ^a   Space, Brian ^a   Moore, Preston B ^b   Chan, Sunney I ^c  

^a UNIVERSITY OF SOUTH FLORIDA   (United States)

^b UNIVERSITY OF THE SCIENCES   (United States)

^c ACADEMIA SINICA   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANALYTIC METHOD; ARTICLE; BIOMOLECULAR ELECTRONICS; CALCULATION; MEASUREMENT; MOLECULAR DYNAMICS; SAMPLING; SIMULATION; SOLVATION; TECHNIQUE; THERMODYNAMICS;

EID: 0242290884     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)74703-1     Document Type: Article

References (26)

1. Ahlborn, H., X. Ji, B. Space, and P. B. Moore. 1999. A combined instantaneous normal mode and time correlation function description of the infrared vibrational spectrum of water. J. Chem. Phys. 111:10622-10632.
2. 2O): a combined time correlation function and instantaneous normal mode analysis. J. Chem. Phys. 112:8083.
3. Allen, M. P., and D. J. Tildesley. 1989. Computer Simulation of Liquids. Clarendon Press, Oxford, UK.
4. Chen, P., C. Lin, H. Jan, and S. I. Chan. 2001. Effects of turn residues in directing the formation of the β-sheet and in the stability of the β-sheet. Prot. Sci. 10:1794-1800.
5. Dadarlat, V. M., and C. B. Post. 2001. Insights into protein compressibility from molecular dynamics simulations. J. Chem. Phys. B. 105:715-724.
6. Foygel, K., S. Spector, S. Chatterjee, and P. C. Kahn. 1995. Volume changes of the molten globule transition of horse heart ferricytochrome c: a thermodynamic cycle. Prot. Sci. 4:1426-1429.
7. Friedberg, R., and J. E. Cameron. 1970. Test of the Monte Carlo method: fast simulation of a small Ising lattice. J. Chem. Phys. 52:6049-6058.
8. Hansen, K. C., R. S. Rock, R. W. Larsen, and S. I. Chan. 2000. A method for photo-initiating protein folding in a non-denaturing environment. J. Am. Chem. Soc. 122:11567-11568.
9. Hansson, T., C. Oostenbrink, and W. F. van Gunsteren. 2002. Molecular dynamics simulations. Curr. Op. Struct. Biol. 12:190-196.
10. Herzberg, G. 1946. Infrared and Raman Spectra of Polyatomic Molecules. D. Van Nostrand Company, Inc., New York, NY.
11. Imai, T., Y. Harano, A. Kovalenko, and F. Hirata. 2001. Theoretical study for volume changes associated with the helix coil transition of peptides. Biopolymers. 59:512-519.
12. Jacucci, G., and A. Rahman. 1984. Comparing the efficiency of metropolis Monte Carlo and molecular dynamics methods for configuration space sampling. Nuovo Cimento. D4:341-356.
13. Larsen, R. W., and T. Langley. 1999. Volume changes associated with CO photolysis from fully reduced bovine heart Cyt-aa3. J. Am. Chem. Soc. 121:4495-4499.
14. Larsen, R. W., J. Osborne, T. Langley, and R. B. Gennis. 1998. Volume changes associated with CO photodissociation from fully reduced cytochrome. J. Am. Chem. Soc. 120:8887-8888.
15. Lockwood, L. M., and P. J. Rossky. 1999. Evaluation of functional group contributions to excess volumetric properties of solvated molecules. J. Phys. Chem. B. 103:1982-1990.
16. Lockwood, L. M., P. J. Rossky, and R. M. Levy. 2000. Functional group contributions to partial molar compressibilities of alcohols in water. J. Phys. Chem. B. 104:4210-4217.
17. Martyna, G. J., M. E. Tuckerman, D. J. Tobias, and M. L. Klein. 1996. Explicit reversible integrators for extended systems dynamics. Mol. Phys. 87:1117.
18. Matubayasi, N., and R. M. Levy. 2000. Thermodynamics of the hydration shell. 2. Excess volume and compressibility of a hydrophobic solute. J. Phys. Chem. B. 104:4210-4217.
19. Moore, P. B., Q. Zhong, T. Husslein, and M. L. Klein. 1998. Simulation of the HIV-1 VPU transmembrane domain as a pentameric bundle. FEBS Lett. 431:143-148.
20. Moore, P. B., C. F. Lopez, and M. L. Klein. 2001. Dynamical properties of a dimiristoylphosphatidylcholine fully hydrated bilayer from a multi-nanosecond molecular dynamics simulation. Biophys. J. 81:2484-2494.
21. Moore, P., H. Ahlborn, and B. Space. 2002. A combined time correlation function and instantaneous normal mode investigation of liquid state vibrational spectroscopy. In Liquid Dynamics Experiment, Simulation and Theory. M. D. Fayer., and John T. Fourkas, editors. ACS Symposium Series, New York.
22. Sigfridsson, E. 1998. A comparison of methods for deriving atomic charges from the electrostatic potential and its moments. J. Comp. Chem. 19:377-395.
23. Tarek, M., K. Tu, M. L. Klein, and D. J. Tobias. 1999. Molecular dynamics simulations of supported phospholipid/alkanethiol bilayers on a gold(111) surface. Biophys. J. 77:964-972.
24. Tuckerman, M. E., and G. J. Martyna. 2000. Understanding modern molecular dynamics: techniques and applications. J. Phys. Chem. B. 104:159-178.
25. van Eldik, R. 1989. Activation and reaction volumes in solution II. Chem. Rev. 89:549.
26. Zhong, Q., P. B. Moore, and M. L. Klein. 1998. Molecular dynamics study of the LS3 voltage-gated ion channel. FEBS Lett. 427: 267-274.