Sign up & Download
Sign in

Refinement of protein structures in explicit solvent

by Jens P. Linge, Mark A. Williams, C. A E M Spronk, A. M J J Bonvin, Michael Nilges
Proteins: Structure, Function and Genetics ()

Abstract

We present a CPU efficient protocol for refinement of protein structures in a thin layer of explicit solvent and energy parameters with completely revised dihedral angle terms. Our approach is suitable for protein structures determined by theoretical (e.g., homology modeling or threading) or experimental methods (e.g., NMR). In contrast to other recently proposed refinement protocols, we put a strong emphasis on consistency with widely accepted covalent parameters and computational efficiency. We illustrate the method for NMR structure calculations of three proteins: interleukin-4, ubiquitin, and crambin. We show a comparison of their structure ensembles before and after refinement in water with and without a force field energy term for the dihedral angles; crambin was also refined in DMSO. Our results demonstrate the significant improvement of structure quality by a short refinement in a thin layer of solvent. Further, they show that a dihedral angle energy term in the force field is beneficial for structure calculation and refinement. We discuss the optimal weight for the energy constant for the backbone angle omega and include an extensive discussion of meaning and relevance of the calculated validation criteria, in particular root mean square Z scores for covalent parameters such as bond lengths.

Cite this document (BETA)

Authors on Mendeley

Readership Statistics

63 Readers on Mendeley
by Discipline
 
 
 
by Academic Status
 
41% Post Doc
 
24% Ph.D. Student
 
10% Researcher (at an Academic Institution)
by Country
 
5% United States
 
3% Germany
 
2% United Kingdom

Sign up today - FREE

Mendeley saves you time finding and organizing research. Learn more

  • All your research in one place
  • Add and import papers easily
  • Access it anywhere, anytime

Start using Mendeley in seconds!

Already have an account? Sign in