title: Deriving correlated motions in proteins from X-ray structure refinement by using TLS parameters.
abstract: Dynamic information in proteins may provide valuable information for understanding allosteric regulation of protein complexes or long-range effects of the mutations on enzyme activity. Experimental data such as X-ray B-factors or NMR order parameters provide a convenient estimate of atomic fluctuations (or atomic auto-correlated motions) in proteins. However, it is not as straightforward to obtain atomic cross-correlated motions in proteins - one usually resorts to more sophisticated computational methods such as Molecular Dynamics, normal mode analysis or atomic network models. In this report, we show that atomic cross-correlations can be reliably obtained directly from protein structure using X-ray refinement data. We have derived an analytic form of atomic correlated motions in terms of the original TLS parameters used to refine the B-factors of X-ray structures. The correlated maps computed using this equation are well correlated with those of the method based on a mechanical model (the correlation coefficient is 0.75) for a non-homologous dataset comprising 100 structures. We have developed an approach to compute atomic cross-correlations directly from X-ray protein structure. Being in analytic form, it is fast and provides a feasible way to compute correlated motions in proteins in a high throughput way. In addition, avoiding sophisticated computational operations; it provides a quick, reliable way, especially for non-computational biologists, to obtain dynamics information directly from protein structure relevant to its function.
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 30068, Taiwan, ROC. yyl.bi97g@nctu.edu.tw
authors.forename: Yen-Yi
authors.initials: YY
authors.lastname: Liu
authors.forename: Chien-Hua
authors.initials: CH
authors.lastname: Shih
authors.forename: Jenn-Kang
authors.initials: JK
authors.lastname: Hwang
authors.forename: Chih-Chieh
authors.initials: CC
authors.lastname: Chen
mesh_terms: D015099:3-Oxoacyl-(Acyl-Carrier-Protein) Synthase / Q000737:chemistry; D018360:Crystallography, X-Ray; D050746:Dihydrodipicolinate Reductase / Q000737:chemistry; D007527:Isoenzymes / Q000737:chemistry; D008958:Models, Molecular; D016011:Normal Distribution; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D007527:Isoenzymes; D011506:Proteins; D050746:Dihydrodipicolinate Reductase; C078182:beta-ketoacyl-acyl carrier protein synthase I; D015099:3-Oxoacyl-(Acyl-Carrier-Protein) Synthase