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1 Biochemistry Department, The University of Hong Kong, Pok Fu Lam, Hong Kong
2 Center for Information Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA
3 School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, USA
4 Biochemistry Department, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
Reprint requests to: David K. Smith, Biochemistry Department, The University of Hong Kong, 21 Sassoon Road, Pok Fu Lam, Hong Kong; e-mail: dsmith{at}hkusua.hku.hk; fax: (852) 28551254.
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.
Keywords: B-factor; atomic displacement parameter; Gumbel distribution; extreme value distribution; flexibility
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