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 can be decomposed into its principal components. Usually only a few principal components dominate the apparent motions of structures. This dynamics information provides strong evidence for the importance of domain interface motions of proteins and RNAs, and also shows that these structures usually have a limited repertoire of motions. This approach can distinguish between small differences in structures (such as myoglobin structures with very small RMSDs and small sequence differences between species) and large differences in structures (such as adenylate kinase). Overall the observed motions in the experimental structures show a close correspondence to those computed with coarse-grained elastic network models. This type of comparison is probably more meaningful than comparisons against crystallographic B-factors.

Extracting dynamics information from multiple coarse-grained structures

246th National Meeting (2013)

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