Improved amino acid flexibility parameters

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

Research output: Contribution to journalArticle

110 Citations (Scopus)

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
Externally publishedYes

Fingerprint

Amino Acids
Proteins
Factor X
X ray crystallography
X Ray Crystallography
Quality Control
Quality control
3'-(1-butylphosphoryl)adenosine
Crystal structure
X-Rays
X rays
Molecules

Keywords

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

ASJC Scopus subject areas

  • Biochemistry

Cite this

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

Improved amino acid flexibility parameters. / Smith, David K.; Radivojac, Predrag; Obradovic, Zoran; Dunker, A.; Zhu, Guang.

In: Protein Science, Vol. 12, No. 5, 01.05.2003, p. 1060-1072.

Research output: Contribution to journalArticle

Smith, DK, Radivojac, P, Obradovic, Z, Dunker, A & Zhu, G 2003, 'Improved amino acid flexibility parameters', Protein Science, vol. 12, no. 5, pp. 1060-1072. https://doi.org/10.1110/ps.0236203
Smith DK, Radivojac P, Obradovic Z, Dunker A, Zhu G. Improved amino acid flexibility parameters. Protein Science. 2003 May 1;12(5):1060-1072. https://doi.org/10.1110/ps.0236203
Smith, David K. ; Radivojac, Predrag ; Obradovic, Zoran ; Dunker, A. ; Zhu, Guang. / Improved amino acid flexibility parameters. In: Protein Science. 2003 ; Vol. 12, No. 5. pp. 1060-1072.
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