Skip to main content
SpringerLink
Log in

Simulating the Dynamics of Macromolecules

  • Chapter
Molecular Dynamics

Part of the book series: Topics in Molecular and Structural Biology ((TMSB))

Abstract

Equilibria in biological systems are governed by their tendency to move towards states of lower free energy. The equilibrium constant K for a chemical reaction at constant temperature and pressure is related to the change in free energy by the equation

$$\Delta G = - RT\ln \;K$$
((1.1))

where G is the Gibbs free energy, R is the gas constant and T is the absolute temperature. The change in G may be related to the changes in the internal energy E, pressure P, volume V and entropy S by the equation

$$\Delta G = \Delta E + P\Delta V - T\Delta S$$
((1.2))

In a well-ordered system at modest temperatures ΔE may dominate this equation and the stable conformation of a molecular system may be calculated by minimizing the internal energy E. This energy is the sum of potential and kinetic energies and, as the latter depends only on temperature, the problem reduces to the minimization of the potential energy. This is discussed in the section entitled Other methods employed in molecular simulations.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Aqvist, J., van Gunsteren, W. F., Leijonmarck, M. and Tapia, O. (1985). A molecular dynamics study of the C-terminal fragment of the L7/L12 ribosomal protein: secondary structure motion in a 150 ps trajectory. J. Mol. Biol., 183, 461–477

    Article  CAS  PubMed  Google Scholar 

  • Arseniev, S. A., Kondakov, V. I., Maiorov, V. N. and Brystrov, V. F. (1984). FEBS Lett., 165, 57–62

    Article  Google Scholar 

  • Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A. and Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. J. Chem. Phys., 81, 3684–3690

    Article  CAS  Google Scholar 

  • Beveridge, D. L. and DiCapua, F. M. (1989). Free energy via molecular simulation: a primer. In van Gunsteren, W. F. and Weiner, P. K. (Eds.), Computer Simulation of Biomolecular Systems. Theoretical and Experimental Applications. Escom, Leiden, pp. 1–27

    Google Scholar 

  • Braun, W., Wider, G., Lee, K. M. and Wuthrich, K. (1983). Conformation of glucagon in a lipid-water interphase by 1H nuclear magnetic resonance. J. Mol. Biol., 169, 921–948

    Article  CAS  PubMed  Google Scholar 

  • Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. and Karplus, M. (1983). CHARMM: a program for macromolecular energy minimization, and dynamics calculation. J. Comput. Chem., 4, 187–217

    Article  CAS  Google Scholar 

  • Brünger, A. T. (1988). Crystallographic refinement by simulated annealing: application to a 2.8 Å resolution structure of aspartate aminotransferase. J. Mol. Biol., 203, 803–816

    Article  PubMed  Google Scholar 

  • Brünger, A. T., Brooks III, C. L. and Karplus, M. (1985). Active site dynamics of ribonuclease. Proc. Natl. Acad. Sci. USA, 82, 8458–8462

    Article  PubMed Central  PubMed  Google Scholar 

  • Burt, S. K., Mackay, D. and Hagler, A. T. (1989). Theoretical aspects of drug design: molecular mechanics and molecular dynamics. In Penn, T. J. (Ed.), Computer-Aided Drug Design. Methods and Applications. Dekker, New York, pp. 55–91

    Google Scholar 

  • Clore, G. M., Gronenborn, A. M., Brünger, A. T. and Karplus, M. (1985). Solution conformation of a heptadecapeptide comprising the DNA binding helix F of the cyclic AMP receptor protein of Escherichia coli. J. Mol. Biol., 186, 435–455

    Article  CAS  PubMed  Google Scholar 

  • Fincham, D. and Heyes, D. M. (1985). Recent advances in molecular dynamics computer simulation. Adv. Chem. Phys., 63, 493–575

    CAS  Google Scholar 

  • Fujinaga, M., Gros, P. and van Gunsteren, W. F. (1989). Testing the method of crystallo-graphic refinement using molecular dynamics. J. Appl. Crystallogr., 22, 1–8

    Article  CAS  Google Scholar 

  • van Gunsteren, W. F. (1989). Methods for calculation of free energies and binding constants: successes and problems. In van Gunsteren, W. F. and Weiner, P. K. (Eds.), Computer Simulation of Biomolecular Systems. Theoretical and Experimental Applications. Escom, Leiden, pp. 27–59

    Google Scholar 

  • van Gunsteren, W. F. and Berendsen, H. J. C. (1977). Algorithms for macromolecular dynamics and constraint dynamics. Mol. Phys., 34, 1311–1327

    Article  Google Scholar 

  • van Gunsteren, W. F. and Berendsen, H. J. C. (1987). GROMOS87. Groningen Molecular Simulation (GROMOS) Library Manual. BIOMOS, Nijenborgh 16, Groningen, pp. 1–229

    Google Scholar 

  • van Gunsteren, W. F., Berendsen, H. J. C., Hermans, J., Hol, W. G. J. and Postma, J. P. M. (1983). Computer simulation of the dynamics of hydrated protein crystals and its comparison with X-ray data. Proc. Natl. Acad. Sci. USA, 80, 4315–4319

    Article  PubMed Central  PubMed  Google Scholar 

  • Hagler, A. T., Maple, J. R., Thacher, T. S., Fitzgerald, G. B. and Dinur, U. (1989). Potential energy functions for organic and biomolecular systems. In van Gunsteren, W. F. and Weiner, P. K. (Eds.), Computer Simulation of Biomolecular Systems. Theoretical and Experimental Applications. Escom, Leiden, pp. 149–167

    Google Scholar 

  • Haneef, I. (1986). PhD Thesis, London

    Google Scholar 

  • Havel, T. F. and Wuthrich, K. (1985). An evaluation of the combined use of nuclear magnetic resonance and distance geometry for the determination of protein conformations in solution. J. Mol. Biol., 182, 281–294

    Article  CAS  PubMed  Google Scholar 

  • Karplus, M. and McCammon, J. A. (1981). The internal dynamics of globular proteins. CRC Crit. Rev. Biochem., 9, 293–349

    Article  CAS  PubMed  Google Scholar 

  • Karplus, M. and McCammon, J. A. (1986). The dynamics of proteins. Sci. Am., 254, April, 42–51

    Article  CAS  PubMed  Google Scholar 

  • Kuki, A. and Wolynes, P. G. (1987). Electron tunneling paths in proteins. Science, 236, 1647–1652

    Article  CAS  PubMed  Google Scholar 

  • Levitt, M. (1983). Molecular dynamics of native protein: II. Analysis and nature of motion. J. Mol. Biol., 168, 595–620

    Article  CAS  PubMed  Google Scholar 

  • Lifson, S. (1981). Potential energy functions for structural molecular biology. In NATO Advanced Study Institute/FEBS Advanced Course No. 78. Current Methods in Structural Molecular Biology. pp. 1–27

    Google Scholar 

  • Maple, J. R., Dinur, U. and Hagler, A. T. (1988). Derivation of force fields for molecular mechanics and dynamics from ab initio energy surfaces. Proc. Natl. Acad. Sci. USA, 85, 5350–5354

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • McCammon, J. A. (1984). Protein dynamics. Rep. Prog. Phys., 47, 1–46

    Article  Google Scholar 

  • Palca, J. (1986). Cooperation on new molecules. Nature, 322, 586

    Google Scholar 

  • van der Ploeg, P. (1982). PhD Thesis, Groningen

    Google Scholar 

  • Press, W. H., Flanny, B. P., Teukolskey, S. A. and Vetterling, W. T. (1988). Numerical Recipes: the Art of Scientific Computing. Cambridge University Press, Cambridge, pp. 307–330

    Google Scholar 

  • Rees, D. C. (1980). Experimental evaluation of the effective dielectric constant of proteins. J. Mol. Biol., 141, 323–326

    Article  CAS  PubMed  Google Scholar 

  • Singh, U. C., Brown, F. K., Bash, P. A. and Kollman, P. A. (1987). An approach to the application of free energy perturbation methods using molecular dynamics. J. Am. Chem. Soc., 109, 1607–1614

    Article  CAS  Google Scholar 

  • Verlet, L. (1967). Computer ‘experiments’ on the classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys. Rev., 159, 98–103

    Article  CAS  Google Scholar 

  • Wagner, G. and Wüthrich, K. (1982). Amide proton exchange and surface conformation of the basic pancreatic trypsin inhibitor in solution. Studies with two-dimensional nuclear magnetic resonance. J. Mol. Biol., 160, 343–361

    Article  CAS  PubMed  Google Scholar 

  • Warshel, A., Sussman, F. and Hwang, J.-K. (1988). Evaluation of catalytic free energies in genetically modified proteins. J. Mol. Biol., 201, 139–159

    Article  CAS  PubMed  Google Scholar 

  • Williamson, M. P., Havel, T. F. and Wuthrich, K. (1985). Solution conformation of proteinase inhibitor IIA from bull seminal plasma by 1H nuclear magnetic resonance and distance geometry. J. Mol. Biol., 182, 295–315

    Article  CAS  PubMed  Google Scholar 

  • Zheng, C., Wong, C. F., McCammon, J. A. and Wolynes, P. G. (1988). Quantum simulation of ferrocytochrome c. Nature, 334, 726–728

    Article  CAS  PubMed  Google Scholar 

Download references

Authors
  1. T. P. Flores
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. D. S. Moss
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Dept of Crystallography, Birkbeck College, London, UK

    Julia M. Goodfellow

Copyright information

© 1991 Macmillan Publishers Limited

About this chapter

Cite this chapter

Flores, T.P., Moss, D.S. (1991). Simulating the Dynamics of Macromolecules. In: Goodfellow, J.M. (eds) Molecular Dynamics. Topics in Molecular and Structural Biology. Palgrave, London. https://doi.org/10.1007/978-1-349-11044-5_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-349-11044-5_1

  • Publisher Name: Palgrave, London

  • Print ISBN: 978-1-349-11046-9

  • Online ISBN: 978-1-349-11044-5

  • eBook Packages: EngineeringEngineering (R0)

Publish with us

Policies and ethics

Search

Navigation