Structural origin of weakly ordered nitroxide motion in spin-labeled proteins

Protein Sci. 2009 May;18(5):893-908. doi: 10.1002/pro.96.

Abstract

A disulfide-linked nitroxide side chain (R1) used in site-directed spin labeling of proteins often exhibits an EPR spectrum characteristic of a weakly ordered z-axis anisotropic motion at topographically diverse surface sites, including those on helices, loops and edge strands of beta-sheets. To elucidate the origin of this motion, the first crystal structures of R1 that display simple z-axis anisotropic motion at solvent-exposed helical sites (131 and 151) and a loop site (82) in T4 lysozyme have been determined. Structures of 131R1 and 151R1 determined at cryogenic or ambient temperature reveal an intraresidue C(alpha)--H...S(delta) interaction that immobilizes the disulfide group, consistent with a model in which the internal motions of R1 are dominated by rotations about the two terminal bonds (Columbus, Kálai, Jeko, Hideg, and Hubbell, Biochemistry 2001;40:3828-3846). Remarkably, the 131R1 side chain populates two rotamers equally, but the EPR spectrum reflects a single dominant dynamic population, showing that the two rotamers have similar internal motion determined by the common disulfide-backbone interaction. The anisotropic motion for loop residue 82R1 is also accounted for by a common disulfide-backbone interaction, showing that the interaction does not require a specific secondary structure. If the above observations prove to be general, then significant variations in order and rate for R1 at noninteracting solvent-exposed helical and loop sites can be assigned to backbone motion because the internal motion is essentially constant.

Publication types

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

MeSH terms

  • Bacteriophage T4 / enzymology
  • Crystallography, X-Ray
  • Disulfides / chemistry
  • Electron Spin Resonance Spectroscopy
  • Models, Molecular
  • Muramidase / chemistry
  • Nitrogen Oxides / chemistry*
  • Protein Conformation
  • Protein Interaction Domains and Motifs
  • Proteins / chemistry*
  • Spin Labels*
  • Temperature
  • Viral Proteins / chemistry

Substances

  • Disulfides
  • Nitrogen Oxides
  • Proteins
  • Spin Labels
  • Viral Proteins
  • Muramidase