Protein Modeling

Proteins play a crucial role in biological processes, therefore, understanding their structure and function is very important. In this chapter we give an overview on computer models of proteins. First we treat both major experimental structure determination methods, X-ray diffraction and NMR spectroscopy. In subsequent sections computer modeling techniques as well as their application to the construction of explicit models are discussed. An overview on molecular mechanics and structure prediction is followed by an overview of molecular graphics methods of structure representation. Protein electrostatics and the concept of the solvent-accessible surface are treated in detail. We devote a special section to dynamics, where time scales, structures, and interactions are discussed. Protein interactions are especially important, so protein hydration, ligand binding, and protein–protein interactions receive special attention. Finally, computer modeling of enzyme mechanisms is discussed. We try to demonstrate that protein representation by computers arrived to a very high degree of sophistication and reliability; therefore, even lots of experimental studies make use of such models. A list with 80 up-to-date bibliographic references helps the reader to get informed on further details.