title: Does secondary structure determine tertiary structure in proteins?
abstract: Is highly approximate knowledge of a protein's backbone structure sufficient to successfully identify its family, superfamily, and tertiary fold? To explore this question, backbone dihedral angles were extracted from the known three-dimensional structure of 2,439 proteins and mapped into 36 labeled, 60 degrees x 60 degrees bins, called mesostates. Using this coarse-grained mapping, protein conformation can be approximated by a linear sequence of mesostates. These linear strings can then be aligned and assessed by conventional sequence-comparison methods. We report that the mesostate sequence is sufficient to recognize a protein's family, superfamily, and fold with good fidelity.
authors.affiliation: Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218-2608, USA.
authors.forename: Haipeng
authors.initials: H
authors.lastname: Gong
authors.forename: George D
authors.initials: GD
authors.lastname: Rose
mesh_terms: D000465:Algorithms; D015394:Molecular Structure; D009010:Monte Carlo Method; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000145:classification; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein
chemical_list: D011506:Proteins