{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,11,19]],"date-time":"2024-11-19T16:32:53Z","timestamp":1732033973212},"reference-count":28,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2011,10,13]],"date-time":"2011-10-13T00:00:00Z","timestamp":1318464000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1002178","type":"journal-article","created":{"date-parts":[[2011,10,13]],"date-time":"2011-10-13T17:00:47Z","timestamp":1318525247000},"page":"e1002178","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":31,"title":["Large-Scale Conformational Changes of Trypanosoma cruzi Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation"],"prefix":"10.1371","volume":"7","author":[{"given":"C\u00e9sar Augusto F.","family":"de Oliveira","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Barry J.","family":"Grant","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michelle","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J. Andrew","family":"McCammon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2011,10,13]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"1469","DOI":"10.1016\/S0140-6736(03)14694-6","article-title":"The trypanosomiases.","volume":"362","author":"MP Barrett","year":"2003","journal-title":"Lancet"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"423","DOI":"10.2174\/092986710790226101","article-title":"Chagas Disease: Progress and New Perspectives.","volume":"17","author":"F Sanchez-Sancho","year":"2010","journal-title":"Curr Med Chem"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"890","DOI":"10.1038\/78651","article-title":"A B-cell mitogen from a pathogenic trypanosome is a eukaryotic proline racemase.","volume":"6","author":"B Reina-San-Martin","year":"2000","journal-title":"Nat Med"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"8513","DOI":"10.1021\/ja900716y","article-title":"Catalyzing Racemizations in the Absence of a Cofactor: The Reaction Mechanism in Proline Racemase.","volume":"131","author":"A Rubinstein","year":"2009","journal-title":"J Am Chem Soc"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1111\/j.1462-5822.2004.00397.x","article-title":"L-proline is essential for the intracellular differentiation of Trypanosoma cruzi.","volume":"6","author":"R Tonelli","year":"2004","journal-title":"Cell Microbiol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1111\/j.1365-2958.2005.04808.x","article-title":"Trypanosoma cruzi proline racemases are involved in parasite differentiation and infectivity.","volume":"58","author":"N Chamond","year":"2005","journal-title":"Mol Microbiol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1590\/S0074-02762009000900039","article-title":"Proline racemases: insights into Trypanosoma cruzi peptides containing D-proline.","volume":"104","author":"N Coatnoan","year":"2009","journal-title":"Mem Inst Oswaldo Cruz"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1016\/S0169-4758(99)01591-4","article-title":"Lymphocyte polyclonal activation: a pitfall for vaccine design against infectious agents.","volume":"16","author":"B Reina-San-Martin","year":"2000","journal-title":"Parasitol Today"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1705","DOI":"10.1073\/pnas.0509010103","article-title":"Crystal structure, catalytic mechanism, and mitogenic properties of Trypanosoma cruzi proline racemase.","volume":"103","author":"A Buschiazzo","year":"2006","journal-title":"Proc Natl Acad Sci Usa"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"964","DOI":"10.1038\/nature06522","article-title":"Dynamic personalities of proteins.","volume":"450","author":"K Henzler-Wildman","year":"2007","journal-title":"Nature"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"22695","DOI":"10.1021\/jp062845o","article-title":"On the application of accelerated molecular dynamics to liquid water simulations.","volume":"110","author":"CAF de Oliveira","year":"2006","journal-title":"J Phys Chem B"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"175105","DOI":"10.1063\/1.2794763","article-title":"Estimating kinetic rates from accelerated molecular dynamics simulations: Alanine dipeptide in explicit solvent as a case study.","volume":"127","author":"CAF de Oliveira","year":"2007","journal-title":"J Chem Phys"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1516","DOI":"10.1021\/ct800160q","article-title":"Coupling accelerated molecular dynamics methods with thermodynamic integration simulations.","volume":"4","author":"CAF de Oliveira","year":"2008","journal-title":"J Chem Theory Comput"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"e1000325","DOI":"10.1371\/journal.pcbi.1000325","article-title":"Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics.","volume":"5","author":"BJ Grant","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"155102","DOI":"10.1063\/1.2789432","article-title":"Sampling of slow diffusive conformational transitions with accelerated molecular dynamics.","volume":"127","author":"D Hamelberg","year":"2007","journal-title":"J Chem Phys"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"11919","DOI":"10.1063\/1.1755656","article-title":"Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules.","volume":"120","author":"D Hamelberg","year":"2004","journal-title":"J Chem Phys"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1021\/ct9005294","article-title":"Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics.","volume":"6","author":"SL Williams","year":"2010","journal-title":"J Chem Theory Comput"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"2695","DOI":"10.1093\/bioinformatics\/btl461","article-title":"Bio3d: an R package for the comparative analysis of protein structures.","volume":"22","author":"BJ Grant","year":"2006","journal-title":"Bioinformatics"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"7664","DOI":"10.1073\/pnas.0510426103","article-title":"Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations.","volume":"103","author":"WJ Zheng","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/1097-0134(20001001)41:1<1::AID-PROT10>3.0.CO;2-P","article-title":"Building-block approach for determining low-frequency normal modes of macromolecules.","volume":"41","author":"F Tama","year":"2000","journal-title":"Proteins"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1093\/bioinformatics\/btp036","article-title":"Fragment-based identification of druggable \u2018hot spots\u2019 of proteins using Fourier domain correlation techniques.","volume":"25","author":"R Brenke","year":"2009","journal-title":"Bioinformatics"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1668","DOI":"10.1002\/jcc.20290","article-title":"The Amber biomolecular simulation programs.","volume":"26","author":"DA Case","year":"2005","journal-title":"J Comput Chem"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1002\/prot.21123","article-title":"Comparison of multiple Amber force fields and development of improved protein backbone parameters.","volume":"65","author":"V Hornak","year":"2006","journal-title":"Proteins"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"10915","DOI":"10.1073\/pnas.89.22.10915","article-title":"Amino acid substitution matrices from protein blocks.","volume":"89","author":"S Henikoff","year":"1992","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1016\/0022-2836(87)90038-6","article-title":"Interior and surface of monomeric proteins.","volume":"196","author":"S Miller","year":"1987","journal-title":"J Mol Biol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1006\/jmbi.1998.1653","article-title":"Structural determinants in the sequences of immunoglobulin variable domain.","volume":"278","author":"C Chothia","year":"1998","journal-title":"J Mol Biol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1002\/prot.340110408","article-title":"Information-theoretical entropy as a measure of sequence variability.","volume":"11","author":"PS Shehkin","year":"1991","journal-title":"Proteins"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1002\/j.1538-7305.1948.tb01338.x","article-title":"The mathematical theory of communication.","volume":"27","author":"CE Shannon","year":"1948","journal-title":"The Bell system Technical Journal"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002178","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,19]],"date-time":"2018-10-19T14:53:36Z","timestamp":1539960816000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002178"}},"subtitle":[],"editor":[{"given":"Vijay S.","family":"Pande","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2011,10,13]]},"references-count":28,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2011,10,13]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1002178","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,10,13]]}}}