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Does secondary structure determine tertiary structure in proteins?
Author(s) -
Gong Haipeng,
Rose George D.
Publication year - 2005
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20622
Subject(s) - protein tertiary structure , dihedral angle , superfamily , sequence (biology) , protein secondary structure , protein structure , computational biology , protein structure prediction , structural alignment , sequence alignment , protein sequencing , crystallography , chemistry , bioinformatics , peptide sequence , biology , genetics , biochemistry , molecule , gene , hydrogen bond , organic chemistry
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° × 60° 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. Proteins 2005. © 2005 Wiley‐Liss, Inc.