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Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)

Extracting Dynamics Information from Multiple Structures

Meaningful dynamics information can be extracted from multiple experimental structures of the same, or closely related, proteins or RNAs. The covariance matrix of atom positions is decomposable into its principal components, and in this way it is possible to rank order the changes in the set of structures, and to determine what the most significant changes are. Usually only a few principal components dominate the motions of the structures, and these usually relate to the functional dynamics. This dynamics information provides strong evidence for the plasticity of protein and RNA structures, and also suggests that these structures almost always have a highly limited repertoire of motions. In some cases, such as HIV protease the dominant motions are opening and closing over the active site. For myoglobin the changes are much smaller, reflecting in part the small changes in sequence, but nonetheless they show characteristic details that depend on the species. Sets of structures can also be used to derive the effective microscopic forces that are forcing a given conformational transition.

This research n supported by NIH R01GM072014.

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Robert L. Jernigan
Jie Liu
Kannan Sankar
Kejue Jia
Michael T. Zimmermann

Room 115, Office and Lab Building
Baker Center for Bioinformatics and Biological Statistics
Department of Biochemistry, Biophysics and Molecular Biology
Iowa State University
Ames, IA 50011-3020
Ph: (515) 294-3833
Fax: (412) 294-3841
jernigan@iastate.edu