Paper Info
Title
Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models.
Abstract
Motivation: A common practice in X-ray crystallographic structure refinement has been to model atomic displacements or thermal fluctuations as isotropic motions. Recent high-resolution data reveal, however, significant departures from isotropy, described by anisotropic displacement parameters (ADPs) modeled for individual atoms. Yet, ADPs are currently reported for a limited set of structures, only. Results: We present a comparative analysis of the experimentally reported ADPs and those theoretically predicted by the anisotropic network model (ANM) for a representative set of structures. The relative sizes of fluctuations along different directions are shown to agree well between experiments and theory, while the cross-correlations between the (x-, y- and z-) components of the fluctuations show considerable deviations. Secondary structure elements and protein cores exhibit more robust anisotropic characteristics compared to disordered or flexible regions. The deviations between experimental and theoretical data are comparable to those between sets of experimental ADPs reported for the same protein in different crystal forms. These results draw attention to the effects of crystal form and refinement procedure on experimental ADPs and highlight the potential utility of ANM calculations for consolidating experimental data or assessing ADPs in the absence of experimental data.
Year
DOI
Venue
2007
10.1093/bioinformatics/btm186
BIOINFORMATICS
Keywords
DocType
Volume
limit set,network model,amino acid,cross correlation,comparative analysis,x ray crystallography,high resolution,protein structure,secondary structure
Conference
23
Issue
ISSN
Citations 
13
1367-4803
5
PageRank 
References 
Authors
0.65
5
4
Name
Order
Citations
PageRank
Eran Eyal111711.44
Chakra Chennubhotla28912.70
Lee-Wei Yang39612.89
Ivet Bahar436139.41