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-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.
Smith
David K
DK
Biochemistry Department, The University of Hong Kong, Pok Fu Lam, Hong Kong. Center for Information Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA. dsmith@hkusa.hku.hk
Radivojac
Predrag
P
Obradovic
Zoran
Z
Dunker
A Keith
AK
Zhu
Guang
G
D000596:Amino Acids / Q000737:chemistry*; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D018583:Pliability; D011506:Proteins / Q000737:chemistry*
D000596:Amino Acids; D011506:Proteins