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EJB Reviews pp 63-77 | Cite as

On the interpretation of biochemical data by molecular dynamics computer simulation

  • Wilfred F. van Gunsteren
  • Alan E. Mark
Part of the EJB Reviews book series (EJB REVIEWS, volume 1992)

Abstract

The continuous advance of experimental techniques is steadily increasing our knowledge of biochemical systems and processes. A detailed picture of many biomolecular processes is emerging due to the possibility of measuring atomic properties of biological macromolecules, such as proteins. X-ray diffraction has provided a three-dimensional picture of biomolecular assemblies of ever increasing size, ranging from small proteins to a complete macromolecular reaction centre. Other experimental techniques, like nuclear magnetic resonance (NMR) and other spectroscopic methods, yield less complete information at the atomic level. However, the development of multi-dimensional NMR has made it possible to determine the spatial structure of small proteins, albeit at low resolution. The advantage of spectroscopic measuring techniques over X-ray diffraction methods is that the former can be used to obtain information on the dynamics of specific atoms or groups of atoms in the biomolecule, while the latter only yield an indication of the mobility of atoms, not of the time scale of their motion. The other major step forward is the advent of the possibility to change the amino acid composition of a protein at will. Instead of studying the proteins with which nature has provided us, we may now make specific mutations and study their effect on protein properties.

Keywords

Force Field Root Mean Square Deviation Total Potential Energy Combination Rule Free Energy Calculation 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Federation of European Biochemical Societies 1993

Authors and Affiliations

  • Wilfred F. van Gunsteren
    • 1
  • Alan E. Mark
    • 1
  1. 1.Department of Physical ChemistrySwiss Federal Institute of Technology ZürichZürichSwitzerland

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