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The building of protein structures form α‐carbon coordinates
Author(s) -
Correa Paul E.
Publication year - 1990
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.340070408
Subject(s) - flavodoxin , side chain , crystallography , molecular dynamics , chemistry , root mean square , carbon fibers , chain (unit) , physics , computational chemistry , mathematics , algorithm , quantum mechanics , ferredoxin , biochemistry , polymer , composite number , organic chemistry , enzyme
A procedure for the construction of complete protein structures from only αcarbon coordinates is described. This involves building the backbone by sequential addition of Pro, Gly, or Ala residues. This main chain structure is then refined using molecular dynamics. Side chains are constructed by sequential addition of atoms with intermediate molecular dynamics refinement. For α lytic protease (a structure that is mostly β sheet) a backbone root mean square deviation (RMSD) of 0.19 Å and an overall RMSD of 1.24 Å from the crystallographic coordinates are attained. For troponin C (67% β‐helix), where the coordinates are available only for the α‐carbons, a backbone RMSD of 0.41 Å and an overall RMSD of 1.68 Å are attained (fits kindly provided by Dr. Michael James and Natalie Strynadka). For flavodoxin a backbone RMSD of 0.49 Å and an overall RMSD of 1.64 Å were attained.