Chapter

Statistical Mechanics, Protein Structure, and Protein Substrate Interactions

Volume 325 of the series NATO ASI Series pp 165-191

Moil: A Molecular Dynamics Program with Emphasis on Conformational Searches and Reaction Path Calculations

  • Ron ElberAffiliated withDept. of Physical Chemistry, The Fritz Haber Research Center and the Institute of Life Sciences, The Hebrew Univ. of Jerusalem
  • , Adrian RoitbergAffiliated withDept. of Chemistry, University of Illinois at Chicago
  • , Carlos SimmerlingAffiliated withDept. of Chemistry, University of Illinois at Chicago
  • , Robert GoldsteinAffiliated withDept. of Chemistry, University of Illinois at Chicago
  • , Gennady VerkhivkerAffiliated withDept. of Chemistry, University of Illinois at Chicago
  • , Haiying LiAffiliated withDept. of Chemistry, University of Illinois at Chicago
  • , Alex UlitskyAffiliated withDept. of Chemistry, University of Illinois at Chicago

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Abstract

The field of computational biology has expanded considerably in the last few years. Insight to the dynamics of biomolecules, the design of new drugs and the interactions that lead to stability of macromolecules has been obtained. Crucial in bringing these changes was the introduction of “user friendly” computer programs so that the number of potential users expanded considerably. It is now possible to visualize complex molecules and to study their structure and thermodynamics properties. The strength of this approach and what makes it so attractive is the possibility of studying the behavior of a variety of molecules using essentially the same set of tools. Constructing a large number of molecules was made possible by the use of a data base of molecular pieces: Different molecules are described using common fragments. For example, all proteins are constructed from the same monomers — amino acids. Another example of repeating fragments is found in the base-pairs of DNA. The fragment solution is chemically intuitive, however, it is approximate. In general the intramolecular interactions in an amino acid are influenced by its neighborhood. For example the charge distribution is determined not only by the identity of the amino acid (as is usually assumed) but also by the solvent, the nearby amino acids and the specific conformation of the fragment. Nevertheless, this approximate approach has a number of successes that are documented in the literature1 and therefore not covered in this manuscript.