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-β folds, using tools from graph theory. As a control, an exhaustive set of β-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.
Original language | English (US) |
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Pages (from-to) | 409-417 |
Number of pages | 9 |
Journal | Protein Science |
Volume | 11 |
Issue number | 2 |
DOIs | |
State | Published - 2002 |
Keywords
- Folding rules
- Hierarchy
- Protein domains
- Protein evolution
- Protein folding
- Protein topology
ASJC Scopus subject areas
- Biochemistry
- Molecular Biology