Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-Ã crystallographic resolution Export

@article{citeulike:1460908, abstract = {10.1073/pnas.0701204104 Here we report a normal-mode-based protocol for modeling anisotropic thermal motions of proteins in x-ray crystallographic refinement. The foundation for this protocol is a recently developed elastic normal mode analysis that produces much more accurate eigenvectors without the tip effect. The effectiveness of the procedure is demonstrated on the refinement of a 3.42-\~{A}… structure of formiminotransferase cyclodeaminase, a 0.5-MDa homooctameric enzyme. Using an order of magnitude fewer adjustable thermal parameters than the conventional isotropic refinement, this protocol resulted in a decrease of the values of and and improvements of the density map. Several poorly resolved regions in the original isotropically refined structure became clearer so that missing side chains were fitted easily and mistraced backbone was corrected. Moreover, the distribution of anisotropic thermal ellipsoids revealed functionally important structure flexibility. This normal-mode-based refinement is an effective way of describing anisotropic thermal motions in x-ray structures and is particularly attractive for the refinement of very large and flexible supramolecular complexes at moderate resolutions.}, author = {Poon, Billy K. and Chen, Xiaorui and Lu, Mingyang and Vyas, Nand K. and Quiocho, Florante A. and Wang, Qinghua and Ma, Jianpeng}, citeulike-article-id = {1460908}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0701204104}, citeulike-linkout-1 = {http://www.pnas.org/content/104/19/7869.abstract}, citeulike-linkout-2 = {http://www.pnas.org/content/104/19/7869.full.pdf}, citeulike-linkout-3 = {http://www.pnas.org/cgi/content/abstract/104/19/7869}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/17470791}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=17470791}, day = {8}, doi = {10.1073/pnas.0701204104}, journal = {Proceedings of the National Academy of Sciences}, keywords = {reading}, month = {May}, number = {19}, pages = {7869--7874}, posted-at = {2009-11-04 23:08:10}, priority = {2}, title = {Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-\~{A}… crystallographic resolution}, url = {http://dx.doi.org/10.1073/pnas.0701204104}, volume = {104}, year = {2007} }

TY - JOUR ID - citeulike:1460908 L3 - citeulike-article-id:1460908 N2 - 10.1073/pnas.0701204104 Here we report a normal-mode-based protocol for modeling anisotropic thermal motions of proteins in x-ray crystallographic refinement. The foundation for this protocol is a recently developed elastic normal mode analysis that produces much more accurate eigenvectors without the tip effect. The effectiveness of the procedure is demonstrated on the refinement of a 3.42-Å structure of formiminotransferase cyclodeaminase, a 0.5-MDa homooctameric enzyme. Using an order of magnitude fewer adjustable thermal parameters than the conventional isotropic refinement, this protocol resulted in a decrease of the values of and and improvements of the density map. Several poorly resolved regions in the original isotropically refined structure became clearer so that missing side chains were fitted easily and mistraced backbone was corrected. Moreover, the distribution of anisotropic thermal ellipsoids revealed functionally important structure flexibility. This normal-mode-based refinement is an effective way of describing anisotropic thermal motions in x-ray structures and is particularly attractive for the refinement of very large and flexible supramolecular complexes at moderate resolutions. IS - 19 JF - Proceedings of the National Academy of Sciences EP - 7874 TI - Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-Å crystallographic resolution VL - 104 SP - 7869 KW - reading AU - Poon, Billy AU - Chen, Xiaorui AU - Lu, Mingyang AU - Vyas, Nand AU - Quiocho, Florante AU - Wang, Qinghua AU - Ma, Jianpeng PY - 2007/05/08/ UR - http://dx.doi.org/10.1073/pnas.0701204104 ER -