NMR Methods for Characterizing the Basic Side Chains of Proteins: Electrostatic Interactions, Hydrogen Bonds, and Conformational Dynamics

Dan Nguyen, Chuanying Chen, B. Montgomery Pettitt, Junji Iwahara

Research output: Chapter in Book/Report/Conference proceedingChapter

8 Scopus citations

Abstract

NMR spectroscopy is a powerful tool for studying protein dynamics. Conventionally, NMR studies on protein dynamics have probed motions of protein backbone NH, side-chain aromatic, and CH3 groups. Recently, there has been remarkable progress in NMR methodologies that can characterize motions of cationic groups in protein side chains. These NMR methods allow investigations of the dynamics of positively charged lysine (Lys) and arginine (Arg) side chains and their hydrogen bonds as well as their electrostatic interactions important for protein function. Here, describing various practical aspects, we provide an overview of the NMR methods for dynamics studies of Lys and Arg side chains. Some example data on protein–DNA complexes are shown. We will also explain how molecular dynamics (MD) simulations can facilitate the interpretation of the NMR data on these basic side chains. Studies combining NMR and MD have revealed the highly dynamic nature of short-range electrostatic interactions via ion pairs, especially those involving Lys side chains.

Original languageEnglish (US)
Title of host publicationBiological NMR Part B
EditorsA. Joshua Wand
PublisherAcademic Press Inc.
Pages285-332
Number of pages48
ISBN (Print)9780128167625
DOIs
StatePublished - Jan 1 2019

Publication series

NameMethods in Enzymology
Volume615
ISSN (Print)0076-6879
ISSN (Electronic)1557-7988

Keywords

  • Arginine
  • Dynamics
  • Electrostatic interactions
  • Hydrogen bond
  • Ion pair
  • Lysine
  • NMR

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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