title: Recursive domains in proteins.
abstract: 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-beta folds, using tools from graph theory. As a control, an exhaustive set of beta-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.
authors.affiliation: Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
authors.forename: Teresa
authors.initials: T
authors.lastname: Przytycka
authors.forename: Rajgopal
authors.initials: R
authors.lastname: Srinivasan
authors.forename: George D
authors.initials: GD
authors.lastname: Rose
mesh_terms: D019281:Dimerization; D007700:Kinetics; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins