Improved amino acid flexibility parameters

David K. Smith, Predrag Radivojac, Zoran Obradovic, A. Keith Dunker, Guang Zhu

Research output: Contribution to journalArticle

118 Scopus citations

Abstract

Protein molecules exhibit varying degrees of flexibility throughout their three-dimensional structures, with some segments showing little mobility while others may be so disordered as to be unresolvable by techniques such as X-ray crystallography. Atomic displacement parameters, or B-factors, from X-ray crystallographic studies give an experimentally determined indication of the degree of mobility in a protein structure. To provide better estimators of amino acid flexibility, we have examined B-factors from a large set of high-resolution crystal structures. Because of the differences among structures, it is necessary to normalize the B-factors. However, many proteins have segments of unusually high mobility, which must be accounted for before normalization can be performed. Accordingly, a median-based method from quality control studies was used to identify outliers. After removal of outliers from, and normalization of, each protein chain, the B-factors were collected for each amino acid in the set. It was found that the distribution of normalized B-factors followed a Gumbel, or extreme value distribution, and the location parameter, or mode, of this distribution was used as an estimator of flexibility for the amino acid. These new parameters have a higher correlation with experimentally determined B-factors than parameters from earlier methods.

Original languageEnglish (US)
Pages (from-to)1060-1072
Number of pages13
JournalProtein Science
Volume12
Issue number5
DOIs
StatePublished - May 1 2003

Keywords

  • Atomic displacement parameter
  • B-factor
  • Extreme value distribution
  • Flexibility
  • Gumbel distribution

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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    Smith, D. K., Radivojac, P., Obradovic, Z., Dunker, A. K., & Zhu, G. (2003). Improved amino acid flexibility parameters. Protein Science, 12(5), 1060-1072. https://doi.org/10.1110/ps.0236203