Determining methyl sidechain conformations in a CS-ROSETTA model using methyl 1 H- 13 C residual dipolar couplings

J Biomol NMR. 2020 Mar;74(2-3):111-118. doi: 10.1007/s10858-019-00294-w. Epub 2020 Jan 16.

Abstract

Modelling of protein structures based on backbone chemical shifts, using programs such as CS-ROSETTA, is becoming increasingly popular, especially for systems where few restraints are available or where homologous structures are already known. While the reliability of CS-ROSETTA calculations can be improved by incorporation of some additional backbone NMR data such as those afforded by residual dipolar couplings or minimal NOE data sets involving backbone amide protons, the sidechain conformations are largely modelled by statistical energy terms. Here, we present a simple method based on methyl residual dipolar couplings that can be used to determine the rotameric state of the threefold symmetry axis of methyl groups that occupy a single rotamer, determine rotameric distributions, and identify regions of high flexibility. The method is demonstrated for methyl side chains of a deletion variant of the human chaperone DNAJB6b.

Keywords: CS-ROSETTA; Methyl NMR; Protein structure refinement; Residual dipolar couplings; Sidechain conformation.

MeSH terms

  • Computer Simulation*
  • HSP40 Heat-Shock Proteins / chemistry*
  • Humans
  • Models, Molecular*
  • Molecular Chaperones / chemistry*
  • Nerve Tissue Proteins / chemistry*
  • Nuclear Magnetic Resonance, Biomolecular*

Substances

  • DNAJB6 protein, human
  • HSP40 Heat-Shock Proteins
  • Molecular Chaperones
  • Nerve Tissue Proteins