Albany 2013: Book of Abstracts
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.
Robert L. Jernigan
Room 115, Office and Lab Building