Improved amino acid flexibility parameters

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...

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Bibliographic Details
Published in:Protein science 2003-05, Vol.12 (5), p.1060-1072
Main Authors: Smith, David K., Radivojac, Predrag, Obradovic, Zoran, Dunker, A. Keith, Zhu, Guang
Format: Article
Language:English
Subjects:
Amino Acids - chemistry
atomic displacement parameter
B‐factor
Crystallography, X-Ray
extreme value distribution
flexibility
Gumbel distribution
Models, Molecular
Pliability
Proteins - chemistry
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Summary: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.
ISSN:0961-8368
1469-896X
DOI:10.1110/ps.0236203