Dynamic structures of globular proteins with respect to correlative movements of residues calculated in the normal mode analysis

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Abstract

Dynamic structures of globular proteins are studied on the basis of correlative movements of residues around their native conformations, which are computed by means of the normal mode analysis. To describe the dynamic structures of a protein, the core regions moving with strong positive or negative correlations to other regions of the polypeptide chain are detected from the correlation maps of the movements of residues. Such core regions are different, according to the definition, from the regions defined from a geometrical point of view, such as secondary structures, domains, modules, and so on. The core regions are actually detected for four proteins, myoglobin, Bence-Jones protein, flavodoxin, and hen egg-white lysozyme, with different folding types from each other. The results show that some of them coincide with the secondary structures, domains, or modules, but others do not. Then, the dynamic structure of each protein is discussed in terms of the dynamic cores detected, as compared with the secondary structures, domains, and modules.

Original languageEnglish
Pages (from-to)589-607
Number of pages19
JournalJournal of Protein Chemistry
Volume8
Issue number5
DOIs
Publication statusPublished - 1989 Oct 1

Keywords

  • Bence-Jones protein
  • flavodoxin
  • hen egg-white lysozyme
  • myoglobin
  • normal mode analysis of proteins
  • protein conformation
  • protein dynamics

ASJC Scopus subject areas

  • Biochemistry

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