Rapid model building of alpha-helices in electron-density maps

Acta Crystallogr D Biol Crystallogr. 2010 Mar;66(Pt 3):268-75. doi: 10.1107/S0907444910000314. Epub 2010 Feb 12.

Abstract

A method for the identification of alpha-helices in electron-density maps at low resolution followed by interpretation at moderate to high resolution is presented. Rapid identification is achieved at low resolution, where alpha-helices appear as tubes of density. The positioning and direction of the alpha-helices is obtained at moderate to high resolution, where the positions of side chains can be seen. The method was tested on a set of 42 experimental electron-density maps at resolutions ranging from 1.5 to 3.8 A. An average of 63% of the alpha-helical residues in these proteins were built and an average of 76% of the residues built matched helical residues in the refined models of the proteins. The overall average r.m.s.d. between main-chain atoms in the modeled alpha-helices and the nearest atom with the same name in the refined models of the proteins was 1.3 A.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Crystallography, X-Ray / methods*
  • Electrons*
  • Models, Molecular
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Proteins / analysis*
  • Proteins / chemistry
  • Time Factors

Substances

  • Proteins