A novel parameterization scheme for energy equations and its use to calculate the structure of protein molecules
dc.contributor.author | Snow, Mark E. | en_US |
dc.date.accessioned | 2006-04-28T17:02:13Z | |
dc.date.available | 2006-04-28T17:02:13Z | |
dc.date.issued | 1993-02 | en_US |
dc.identifier.citation | Snow, Mark E. (1993)."A novel parameterization scheme for energy equations and its use to calculate the structure of protein molecules." Proteins: Structure, Function, and Genetics 15(2): 183-190. <http://hdl.handle.net/2027.42/38519> | en_US |
dc.identifier.issn | 0887-3585 | en_US |
dc.identifier.issn | 1097-0134 | en_US |
dc.identifier.uri | https://hdl.handle.net/2027.42/38519 | |
dc.identifier.uri | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db=pubmed&list_uids=8441753&dopt=citation | en_US |
dc.description.abstract | A novel scheme for the parameterization of a type of “potential energy” function for protein molecules is introduced. The function is parameterized based on the known conformations of previously determined protein structures and their sequence similarity to a molecule whose conformation is to be calculated. Once parameterized, minima of the potential energy function can be located using a version of simulated annealing which has been previously shown to locate global and near-global minima with the given functional form. As a test problem, the potential was parameterized based on the known structures of the rubredoxins from Desulfovibrio vulgaris, Desulfovibrio desulfuricans, and Clostridium pasteurianum, which vary from 45 to 54 amino acids in length, and the sequence alignments of these molecules with the rubredoxin sequence from Desulfovibrio gigas . Since the Desulfovibrio gigas rubredeoxin conformation has also been determined, it is possible to check the accuracy of the results. Ten simulated-annealing runs from random starting conformations were performed. Seven of the 10 resultant conformations have an all-C Α rms deviation from the crystallographically determined conformation of less than 1.7 Å. For five of the structures, the rms deviation is less than 0.8 Å. Four of the structures have conformations which are virtually identical to each other except for the position of the carboxy-terminal residue. This is also the conformation which is achieved if the determined crystal structure is minimized with the same potential. The all-C Α rms difference between the crystal and minimized crystal structures is 0.6 Å. It is further observed that the “energies” of the structures according to the potential function exhibit a strong correlation with rms deviation from the native structure. The conformations of the individual model structures and the computational aspects of the modeling procedure are discussed. © 1993 Wiley-Liss, Inc. | en_US |
dc.format.extent | 702349 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 | A novel parameterization scheme for energy equations and its use to calculate the structure of protein molecules | en_US |
dc.type | Article | en_US |
dc.rights.robots | IndexNoFollow | en_US |
dc.subject.hlbsecondlevel | Molecular, Cellular and Developmental Biology | en_US |
dc.subject.hlbtoplevel | Health Sciences | en_US |
dc.description.peerreviewed | Peer Reviewed | en_US |
dc.contributor.affiliationum | University of Michigan Information Technology Division, Scientific Computation Group, Ann Arbor, Michigan 48103-4943 ; Scientific Computation Group, University of Michigan Information Technology Division, 535 West William Street, Ann Arbor, MI 48103-4943 | en_US |
dc.identifier.pmid | 8441753 | en_US |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/38519/1/340150208_ftp.pdf | en_US |
dc.identifier.doi | http://dx.doi.org/10.1002/prot.340150208 | en_US |
dc.identifier.source | Proteins: Structure, Function, and Genetics | 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.