Methyl NMR spectroscopy: Measurement of dynamics in viral RNA-directed RNA polymerases

Methods. 2018 Sep 15;148:100-114. doi: 10.1016/j.ymeth.2018.05.021. Epub 2018 May 30.

Abstract

Measurement of nuclear spin relaxation provides a powerful approach to access information about biomolecular conformational dynamics over several orders of magnitude in timescale. In several cases this knowledge in combination with spatial information from three-dimensional structures yields unique insight into protein stability and the kinetics and thermodynamics of their interactions and function. However, due to intrinsic difficulties in studying large systems using solution state nuclear magnetic resonance (NMR) approaches, until recently these measurements were limited to small-to-medium-sized systems. However, the development of a wide range of novel strategies that allow the selective isotope labeling of methyl groups in proteins have allowed the exploitation of the unique relaxation properties of this spin-system. This has in turn enabled the extension of NMR approaches to high molecular weight proteins including a variety of enzymes and their complexes. Here, we recount our experiences in obtaining assignments of the methyl resonances for two representative members of a class of RNA-directed RNA polymerases (RdRps) encoded by bacteriophages of the Cystoviridae family. We demonstrate the utility of these methyl probes, limited in number for one case and more numerous for the other, to investigate the conformational dynamics of RdRps on the fast (ps-ns) and slow (μs-ms) timescales.

Keywords: Methyl labeling; Protein dynamics; RNA-directed RNA Polymerase (RdRP); Spin-relaxation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Bacterial Proteins / analysis
  • Bacterial Proteins / chemistry
  • Methylation
  • Molecular Dynamics Simulation*
  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Protein Conformation
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • RNA Replicase / analysis*
  • RNA Replicase / chemistry*
  • RNA, Viral / analysis*
  • RNA, Viral / chemistry*

Substances

  • Bacterial Proteins
  • RNA, Viral
  • RNA Replicase