Characterization of the residual structure in the unfolded state of the ?131? fragment of staphylococcal nuclease Export

@article{citeulike:850845, abstract = {The determination of the conformational preferences in unfolded states of proteins constitutes an important challenge in structural biology. We use inter-residue distances estimated from site-directed spin-labeling NMR experimental measurements as ensemble-averaged restraints in all-atom molecular dynamics simulations to characterise the residual structure of the ?131? fragment of staphylococcal nuclease under physiological conditions. Our findings indicate that ?131? under these conditions shows a tendency to form transiently hydrophobic clusters similar to those present in the native state of wild-type staphylococcal nuclease. Only rarely, however, all these interactions are simultaneously realized to generate conformations with an overall native topology. Proteins 2006. {\copyright} 2006 Wiley-Liss, Inc.}, address = {Department of Chemistry, University of Cambridge, Cambridge, United Kingdom; Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia}, author = {Francis, Christopher J. and Lindorff-Larsen, Kresten and Best, Robert B. and Vendruscolo, Michele}, citeulike-article-id = {850845}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/prot.21077}, citeulike-linkout-1 = {http://www3.interscience.wiley.com/cgi-bin/abstract/112728848/ABSTRACT}, doi = {10.1002/prot.21077}, journal = {Proteins: Structure, Function, and Bioinformatics}, keywords = {denatured-state, ensemble, high-t-md}, number = {1}, pages = {145--152}, posted-at = {2006-09-20 09:08:03}, priority = {0}, title = {Characterization of the residual structure in the unfolded state of the ?131? fragment of staphylococcal nuclease}, url = {http://dx.doi.org/10.1002/prot.21077}, volume = {65}, year = {2006} }

TY - JOUR ID - citeulike:850845 L3 - citeulike-article-id:850845 N2 - The determination of the conformational preferences in unfolded states of proteins constitutes an important challenge in structural biology. We use inter-residue distances estimated from site-directed spin-labeling NMR experimental measurements as ensemble-averaged restraints in all-atom molecular dynamics simulations to characterise the residual structure of the ?131? fragment of staphylococcal nuclease under physiological conditions. Our findings indicate that ?131? under these conditions shows a tendency to form transiently hydrophobic clusters similar to those present in the native state of wild-type staphylococcal nuclease. Only rarely, however, all these interactions are simultaneously realized to generate conformations with an overall native topology. Proteins 2006. © 2006 Wiley-Liss, Inc. IS - 1 JF - Proteins: Structure, Function, and Bioinformatics AD - Department of Chemistry, University of Cambridge, Cambridge, United Kingdom; Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia EP - 152 TI - Characterization of the residual structure in the unfolded state of the ?131? fragment of staphylococcal nuclease VL - 65 SP - 145 KW - denatured-state KW - ensemble KW - high-t-md AU - Francis, Christopher AU - Lindorff-Larsen, Kresten AU - Best, Robert AU - Vendruscolo, Michele PY - 2006/// UR - http://dx.doi.org/10.1002/prot.21077 ER -