Solvation influences flap collapse in HIV-1 protease
dc.contributor.author | Meagher, Kristin L. | en_US |
dc.contributor.author | Carlson, Heather A. | en_US |
dc.date.accessioned | 2006-04-19T14:02:12Z | |
dc.date.available | 2006-04-19T14:02:12Z | |
dc.date.issued | 2005-01-01 | en_US |
dc.identifier.citation | Meagher, Kristin L.; Carlson, Heather A. (2005)."Solvation influences flap collapse in HIV-1 protease." Proteins: Structure, Function, and Bioinformatics 58(1): 119-125. <http://hdl.handle.net/2027.42/34978> | en_US |
dc.identifier.issn | 0887-3585 | en_US |
dc.identifier.issn | 1097-0134 | en_US |
dc.identifier.uri | https://hdl.handle.net/2027.42/34978 | |
dc.identifier.uri | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db=pubmed&list_uids=15521062&dopt=citation | en_US |
dc.description.abstract | HIV-1 protease (HIVp) is an important target for the development of therapies to treat AIDS and is one of the classic examples of structure-based drug design. The flap region of HIVp is known to be highly flexible and undergoes a large conformational change upon binding a ligand. Accurately modeling the inherent flexibility of the HIVp system is critical for developing new methods for structure-based drug design. We report several 3-ns molecular dynamics simulations investigating the role of solvation in HIVp flap rearrangement. Using an unliganded crystal structure of HIVp, other groups have observed flap reorganization on the nanosecond timescale. We have also observed rapid, initial flap movement, but we propose that it may be caused by system setup. The initial solvation of the system creates vacuum regions around the protein that may encourage large conformational deformities. By reducing the vacuum space created by the solvation routine, the observed flap collapse is attenuated. Also, a more thorough equilibration procedure preserves a more stable protein conformation over the course of the simulation. Proteins 2005. © 2004 Wiley-Liss, Inc. | en_US |
dc.format.extent | 877950 bytes | |
dc.format.extent | 3118 bytes | |
dc.format.mimetype | application/pdf | |
dc.format.mimetype | text/plain | |
dc.language.iso | en_US | |
dc.publisher | Wiley Subscription Services, Inc., A Wiley Company | en_US |
dc.subject.other | Chemistry | en_US |
dc.subject.other | Biochemistry and Biotechnology | en_US |
dc.title | Solvation influences flap collapse in HIV-1 protease | en_US |
dc.type | Article | en_US |
dc.rights.robots | IndexNoFollow | en_US |
dc.subject.hlbtoplevel | Health Sciences | en_US |
dc.description.peerreviewed | Peer Reviewed | en_US |
dc.contributor.affiliationum | Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan | en_US |
dc.contributor.affiliationum | Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan ; Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church St., Ann Arbor, MI 48109-1065 | en_US |
dc.identifier.pmid | 15521062 | en_US |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/34978/1/20274_ftp.pdf | en_US |
dc.identifier.doi | http://dx.doi.org/10.1002/prot.20274 | en_US |
dc.identifier.source | Proteins: Structure, Function, and Bioinformatics | en_US |
dc.owningcollname | Interdisciplinary and Peer-Reviewed |
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