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Molecular & Cellular Proteomics 5:1212-1223, 2006.
© 2006 by The American Society for Biochemistry and Molecular Biology, Inc.

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Research

Local Flexibility in Molecular Function Paradigm^*

Jag Bhalla, Geoffrey B. Storchan, Caitlin M. MacCarthy, Vladimir N. Uversky and Olga Tcherkasskaya^,¶

From Biochemistry and Molecular & Cellular Biology, Georgetown University School of Medicine, Washington, D. C. 20007 and Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202

It is generally accepted that the functional activity of biological macromolecules requires tightly packed three-dimensional structures. Recent theoretical and experimental evidence indicates, however, the importance of molecular flexibility for the proper functioning of some proteins. We examined high resolution structures of proteins in various functional categories with respect to the secondary structure assessment. The latter was considered as a characteristic of the inherent flexibility of a polypeptide chain. We found that the proteins in functionally competent conformational states might be comprised of 20–70% flexible residues. For instance, proteins involved in gene regulation, e.g. transcription factors, are on average largely disordered molecules with over 60% of amino acids residing in "coiled" configurations. In contrast, oxygen transporters constitute a class of relatively rigid molecules with only 30% of residues being locally flexible. Phylogenic comparison of a large number of protein families with respect to the propagation of secondary structure illuminates the growing role of the local flexibility in organisms of greater complexity. Furthermore the local flexibility in protein molecules appears to be dependent on the molecular confinement and is essentially larger in extracellular proteins.

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