NMR Methods for Characterizing the Basic Side Chains of Proteins

Electrostatic Interactions, Hydrogen Bonds, and Conformational Dynamics

Dan Nguyen, Chuanying Chen, Bernard Pettitt, Junji Iwahara

Research output: Contribution to journalArticle

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)
JournalMethods in Enzymology
DOIs
StateAccepted/In press - Jan 1 2018

Fingerprint

Coulomb interactions
Static Electricity
Hydrogen
Hydrogen bonds
Nuclear magnetic resonance
Lysine
Molecular Dynamics Simulation
Proteins
Arginine
Molecular dynamics
Magnetic Resonance Spectroscopy
Nuclear magnetic resonance spectroscopy
Ions
Computer simulation

Keywords

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

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

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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.",
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AU - Iwahara, Junji

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