Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: description of the folding pathway. Export

@article{citeulike:3020668, abstract = {Residual structure in the denatured state of a protein may contain clues about the early events in folding. We have simulated by molecular dynamics the denatured state of barnase, which has been studied by NMR spectroscopy. An ensemble of 10(4) structures was generated after 2 ns of unfolding and following for a further 2 ns. The ensemble was heterogeneous, but there was nonrandom, residual structure with persistent interactions. Helical structure in the C-terminal portion of helix alpha1 (residues 13-17) and in helix alpha2 as well as a turn and nonnative hydrophobic clustering between beta3 and beta4 were observed, consistent with NMR data. In addition, there were tertiary contacts between residues in alpha1 and the C-terminal portion of the beta-sheet. The simulated structures allow the rudimentary NMR data to be fleshed out. The consistency between simulation and experiment inspires confidence in the methods. A description of the folding pathway of barnase from the denatured to the native state can be constructed by combining the simulation with experimental data from phi value analysis and NMR.}, address = {Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195-7610, USA.}, author = {Bond, C. J. and Wong, K. B. and Clarke, J. and Fersht, A. R. and Daggett, V.}, citeulike-article-id = {3020668}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/9391038}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=9391038}, day = {9}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, keywords = {folding-nucleus, high-t-md, protein-folding}, month = {December}, number = {25}, pages = {13409--13413}, posted-at = {2008-07-19 08:27:28}, priority = {3}, title = {Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: description of the folding pathway.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/9391038}, volume = {94}, year = {1997} }

TY - JOUR ID - citeulike:3020668 L3 - citeulike-article-id:3020668 N2 - Residual structure in the denatured state of a protein may contain clues about the early events in folding. We have simulated by molecular dynamics the denatured state of barnase, which has been studied by NMR spectroscopy. An ensemble of 10(4) structures was generated after 2 ns of unfolding and following for a further 2 ns. The ensemble was heterogeneous, but there was nonrandom, residual structure with persistent interactions. Helical structure in the C-terminal portion of helix alpha1 (residues 13-17) and in helix alpha2 as well as a turn and nonnative hydrophobic clustering between beta3 and beta4 were observed, consistent with NMR data. In addition, there were tertiary contacts between residues in alpha1 and the C-terminal portion of the beta-sheet. The simulated structures allow the rudimentary NMR data to be fleshed out. The consistency between simulation and experiment inspires confidence in the methods. A description of the folding pathway of barnase from the denatured to the native state can be constructed by combining the simulation with experimental data from phi value analysis and NMR. IS - 25 JF - Proceedings of the National Academy of Sciences of the United States of America SN - 0027-8424 AD - Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195-7610, USA. EP - 13413 TI - Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: description of the folding pathway. VL - 94 SP - 13409 KW - folding-nucleus KW - high-t-md KW - protein-folding AU - Bond, CJ AU - Wong, KB AU - Clarke, J AU - Fersht, AR AU - Daggett, V PY - 1997/12/09/ UR - http://view.ncbi.nlm.nih.gov/pubmed/9391038 ER -