Correlating dynamics to conformational properties

An analysis of atomic displacement parameters (B-values) in high-resolution protein structures

S. Parthasarathy, M. R N Murthy

Research output: Contribution to journalArticle

Abstract

Atomic displacement parameters (ADPs) obtained by high resolution X-ray diffraction studies on single crystals of proteins represent the mean square displacement of atoms about their mean position. The relationship between the flexibility of the protein molecule and its conformation could be examined by a careful analysis of these ADPs. This communication presents the results of such a statistical analysis. It is shown that the ADPs are related to side chain conformations and are low for energetically favourable rotamers. Examination of the dependence of ADPs on non-planar distortions of the peptide geometry as represented by ω̄ angle reveals that the parameters depend on the direction of non-planar distortion. Those conformations with ω̄ larger than the ideal trans geometry (180°-190°) are more flexible when compared to those with ω̄ < 180° (170° -180°). The average ADP of a peptide unit depends weakly on the Ramachandran angles at the corresponding Cα atom. Thus, the flexibility of different segments of the polypeptide appears to be sensitive to the conformation of the side chains as well as the main chain.

Original languageEnglish (US)
Pages (from-to)1123-1126
Number of pages4
JournalCurrent Science
Volume78
Issue number9
StatePublished - May 10 2000
Externally publishedYes

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protein structure
peptides
crystal proteins
Peptides
X-ray diffraction
polypeptides
Proteins
statistical analysis
X-Ray Diffraction
proteins
geometry

ASJC Scopus subject areas

  • General
  • Agricultural and Biological Sciences(all)

Cite this

Correlating dynamics to conformational properties : An analysis of atomic displacement parameters (B-values) in high-resolution protein structures. / Parthasarathy, S.; Murthy, M. R N.

In: Current Science, Vol. 78, No. 9, 10.05.2000, p. 1123-1126.

Research output: Contribution to journalArticle

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