Protein modeling

G. Náray-Szabó, A. Perczel, A. Láng, D. K. Menyhárd

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

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 of molecular motions, structures, and interactions are discussed. Protein in relation to its surroundings is especially important, so protein hydration, ligand binding, and protein-protein interactions receive special attention. The case study of podocin provides an example for the successful application of molecular dynamics to a complex issue. At last, computer modeling of enzyme mechanisms is discussed. It is demonstrated 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 a large number of up-to-date bibliographic references helps the reader to get informed on further details.

Original languageEnglish
Title of host publicationHandbook of Computational Chemistry
PublisherSpringer International Publishing
Pages1589-1626
Number of pages38
ISBN (Electronic)9783319272825
ISBN (Print)9783319272818
DOIs
Publication statusPublished - Jan 1 2017

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ASJC Scopus subject areas

  • Chemistry(all)
  • Computer Science(all)
  • Engineering(all)
  • Mathematics(all)
  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Náray-Szabó, G., Perczel, A., Láng, A., & Menyhárd, D. K. (2017). Protein modeling. In Handbook of Computational Chemistry (pp. 1589-1626). Springer International Publishing. https://doi.org/10.1007/978-3-319-27282-5_30