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Biophys J, April 2000, p. 2093-2106, Vol. 78, No. 4

Proteins with Similar Architecture Exhibit Similar Large-Scale Dynamic Behavior

O. Keskin,* R. L. Jernigan,dagger and I. Bahar*dagger

 *Chemical Engineering Department and Polymer Research Center, Bogazici University, and TUBITAK Advanced Polymeric Materials Research Center, Bebek 80815, Istanbul, Turkey, and  dagger Molecular Structure Section, Laboratory of Experimental and Computational Biology, Division of Basic Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5677 USA

We have investigated the similarities and differences in the computed dynamic fluctuations exhibited by six members of a protein fold family with a coarse-grained Gaussian network model. Specifically, we consider the cofactor binding fragment of CysB; the lysine/arginine/ornithine-binding protein (LAO); the enzyme porphobilinogen deaminase (PBGD); the ribose-binding protein (RBP); the N-terminal lobe of ovotransferrin in apo-form (apo-OVOT); and the leucine/isoleucine/valine-binding protein (LIVBP). All have domains that resemble a Rossmann fold, but there are also some significant differences. Results indicate that similar global dynamic behavior is preserved for the members of a fold family, and that differences usually occur in regions only where specific function is localized. The present work is a computational demonstration that the scaffold of a protein fold may be utilized for diverse purposes. LAO requires a bound ligand before it conforms to the large-scale fluctuation behavior of the three other members of the family, CysB, PBGD, and RBP, all of which contain a substrate (cofactor) at the active site cleft. The dynamics of the ligand-free enzymes LIVBP and apo-OVOT, on the other hand, concur with that of unliganded LAO. The present results suggest that it is possible to construct structure alignments based on dynamic fluctuation behavior.

Biophys J, April 2000, p. 2093-2106, Vol. 78, No. 4
© 2000 by the Biophysical Society   0006-3495/00/04/2093/14  $2.00


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