Iterative cluster-NMA: A tool for generating conformational transitions in proteins
dc.contributor.author | Schuyler, Adam D. | en_US |
dc.contributor.author | Jernigan, Robert L. | en_US |
dc.contributor.author | Qasba, Pradman K. | en_US |
dc.contributor.author | Ramakrishnan, Boopathy | en_US |
dc.contributor.author | Chirikjian, Gregory S. | en_US |
dc.date.accessioned | 2009-02-03T16:16:53Z | |
dc.date.available | 2010-04-14T17:40:06Z | en_US |
dc.date.issued | 2009-02-15 | en_US |
dc.identifier.citation | Schuyler, Adam D.; Jernigan, Robert L.; Qasba, Pradman K.; Ramakrishnan, Boopathy; Chirikjian, Gregory S. (2009). "Iterative cluster-NMA: A tool for generating conformational transitions in proteins." Proteins: Structure, Function, and Bioinformatics 74(3): 760-776. <http://hdl.handle.net/2027.42/61529> | en_US |
dc.identifier.issn | 0887-3585 | en_US |
dc.identifier.issn | 1097-0134 | en_US |
dc.identifier.uri | https://hdl.handle.net/2027.42/61529 | |
dc.identifier.uri | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db=pubmed&list_uids=18712827&dopt=citation | en_US |
dc.description.abstract | Computational models provide insight into the structure–function relationship in proteins. These approaches, especially those based on normal mode analysis, can identify the accessible motion space around a given equilibrium structure. The large magnitude, collective motions identified by these methods are often well aligned with the general direction of the expected conformational transitions. However, these motions cannot realistically be extrapolated beyond the local neighborhood of the starting conformation. In this article, the iterative cluster-NMA (icNMA) method is presented for traversing the energy landscape from a starting conformation to a desired goal conformation. This is accomplished by allowing the evolving geometry of the intermediate structures to define the local accessible motion space, and thus produce an appropriate displacement. Following the derivation of the icNMA method, a set of sample simulations are performed to probe the robustness of the model. A detailed analysis of Β1,4-galactosyltransferase-T1 is also given, to highlight many of the capabilities of icNMA. Remarkably, during the transition, a helix is seen to be extended by an additional turn, emphasizing a new unknown role for secondary structures to absorb slack during transitions. The transition pathway for adenylate kinase, which has been frequently studied in the literature, is also discussed. Proteins 2009. © 2008 Wiley-Liss, Inc. | en_US |
dc.format.extent | 453178 bytes | |
dc.format.extent | 3118 bytes | |
dc.format.mimetype | application/pdf | |
dc.format.mimetype | text/plain | |
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 | Iterative cluster-NMA: A tool for generating conformational transitions in proteins | en_US |
dc.type | Article | en_US |
dc.rights.robots | IndexNoFollow | en_US |
dc.subject.hlbsecondlevel | Biological Chemistry | en_US |
dc.subject.hlbtoplevel | Science | en_US |
dc.description.peerreviewed | Peer Reviewed | en_US |
dc.contributor.affiliationum | Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109 | en_US |
dc.contributor.affiliationother | L.H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, Iowa 50011 | en_US |
dc.contributor.affiliationother | Structural Glycobiology Section, CCR Nanobiology Program, Frederick, Maryland 21702 | en_US |
dc.contributor.affiliationother | Structural Glycobiology Section, CCR Nanobiology Program, Frederick, Maryland 21702 ; Basic Science Program, SAIC-Frederick, Inc., CCR, NCI-Frederick, Frederick, Maryland 21702 | en_US |
dc.contributor.affiliationother | Department of Mechanical Engineering, The Johns Hopkins University, Baltimore, Maryland 21218 ; Department of Mechanical Engineering, The Johns Hopkins University, 223 Latrobe Hall, 3400 North Charles Street, Baltimore, MD 21218 | en_US |
dc.identifier.pmid | 18712827 | en_US |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/61529/1/22200_ftp.pdf | |
dc.identifier.doi | http://dx.doi.org/10.1002/prot.22200 | en_US |
dc.identifier.source | "Proteins: Structure, Function, and Bioinformatics" | en_US |
dc.owningcollname | Interdisciplinary and Peer-Reviewed |
Files in this item
Remediation of Harmful Language
The University of Michigan Library aims to describe library materials in a way that respects the people and communities who create, use, and are represented in our collections. Report harmful or offensive language in catalog records, finding aids, or elsewhere in our collections anonymously through our metadata feedback form. More information at Remediation of Harmful Language.
Accessibility
If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.