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Recursive domains in proteins

¹ Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
² Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA

Reprint requests to: George D. Rose, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205; e-mail: rose{at}grserv.med.jhmi.edu; fax: (410) 614-3971.

The domain is a fundamental unit of protein structure. Numerous studies have analyzed folding patterns in protein domains of known structure to gain insight into the underlying protein folding process. Are such patterns a haphazard assortment or are they similar to sentences in a language, which can be generated by an underlying grammar? Specifically, can a small number of intuitively sensible rules generate a large class of folds, including feasible new folds? In this paper, we explore the extent to which four simple rules can generate the known all-ß folds, using tools from graph theory. As a control, an exhaustive set of ß-sandwiches was tested and found to be largely incompatible with such a grammar. The existence of a protein grammar has potential implications for both the mechanism of folding and the evolution of domains.

Keywords: Protein evolution; protein domains; protein folding; protein topology; folding rules; hierarchy

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