Does secondary structure determine tertiary structure in proteins?
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.
Gong
Haipeng
H
Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218-2608, USA.
Rose
George D
GD
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
D011506:Proteins