Protein Engineering, Vol. 16, No. 3, 161-167,
March 2003
© 2003 Oxford University Press
Discrete structure of van der Waals domains in globular proteins
Department of Structural Biology, The Weizmann Institute of Science, P.O.B. 26, Rehovot 76100, IsraelPresent address: Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street M-105, Cambridge, MA 02138, USA, E-mail: inberez{at}fas.harvard.edu
Most globular proteins are divisible by domains, distinct substructures of the globule. The notion of hierarchy of the domains was introduced earlier via van der Waals energy profiles that allow one to subdivide the proteins into domains (subdomains). The question remains open as to what is the possible structural connection of the energy profiles. The recent discovery of the loop-n-lock elements in the globular proteins suggests such a structural connection. A direct comparison of the segmentation by van der Waals energy criteria with the maps of the locked loops of nearly standard size reveals a striking correlation: domains in general appear to consist of one to several such loops. In addition, it was demonstrated that a variety of subdivisions of the same protein into domains is just a regrouping of the loop-n-lock elements.
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