Structural determination of spin label immobilization and orientation

A Monte Carlo minimization approach

Ken Sale, Cecília Sár, Kim A. Sharp, K. Hideg, Peter G. Fajer

Research output: Contribution to journalArticle

46 Citations (Scopus)

Abstract

Electron paramagnetic resonance (EPR) is often used in the study of the orientation and dynamics of proteins. However, there are two major obstacles in the interpretation of EPR signals: (a) most spin labels are not fully immobilized by the protein, hence it is difficult to distinguish the mobility of the label with respect to the protein from the reorientation of the protein itself; (b) even in cases where the label is fully immobilized its orientation with respect to the protein is not known, which prevents interpretation of probe reorientation in terms of protein reorientation. We have developed a computational strategy for determining whether or not a spin label is immobilized and, if immobilized, predicting its conformation within the protein. The method uses a Monte Carlo minimization algorithm to search the conformational space of labels within known atomic level structures of proteins. To validate the method a series of spin labels of varying size and geometry were docked to sites on the myosin head catalytic and regulatory domains. The predicted immobilization and conformation compared well with the experimentally determined mobility and orientation of the label. Thus, probes can now be targeted to report on various modes of molecular dynamics: immobilized probes to report on protein backbone and domain dynamics or floppy probes to report on the extent of steric restriction experienced by the side chain.

Original languageEnglish
Pages (from-to)104-112
Number of pages9
JournalJournal of Magnetic Resonance
Volume156
Issue number1
DOIs
Publication statusPublished - 2002

Fingerprint

Spin Labels
immobilization
Immobilization
proteins
optimization
Labels
Proteins
Electron Spin Resonance Spectroscopy
retraining
probes
Immobilized Proteins
Paramagnetic resonance
Conformations
Protein Conformation
electron paramagnetic resonance
Molecular Dynamics Simulation
Myosins
myosins
Catalytic Domain
Molecular dynamics

Keywords

  • Electron paramagnetic resonance
  • Electron spin resonance
  • Monte Carlo
  • Spectroscopy
  • Spin labels

ASJC Scopus subject areas

  • Molecular Biology
  • Physical and Theoretical Chemistry
  • Spectroscopy
  • Radiology Nuclear Medicine and imaging
  • Condensed Matter Physics

Cite this

Structural determination of spin label immobilization and orientation : A Monte Carlo minimization approach. / Sale, Ken; Sár, Cecília; Sharp, Kim A.; Hideg, K.; Fajer, Peter G.

In: Journal of Magnetic Resonance, Vol. 156, No. 1, 2002, p. 104-112.

Research output: Contribution to journalArticle

Sale, Ken ; Sár, Cecília ; Sharp, Kim A. ; Hideg, K. ; Fajer, Peter G. / Structural determination of spin label immobilization and orientation : A Monte Carlo minimization approach. In: Journal of Magnetic Resonance. 2002 ; Vol. 156, No. 1. pp. 104-112.
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