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The building of protein structures form α-carbon coordinates

✍ Scribed by Paul E. Correa

Publisher
John Wiley and Sons
Year
1990
Tongue
English
Weight
966 KB
Volume
7
Category
Article
ISSN
0887-3585

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✦ Synopsis

Abstract

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.

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