Analysis of nitroxide spin label motion in a protein–protein complex using multiple frequency EPR spectroscopy

White, Gaye F.; Ottignon, L; Georgiou, Theoni K.; Kleanthous, Colin; Moore, Geoffrey R.; Thomson, Andrew J.; Oganesyan, Vasily S.

doi:10.1016/j.jmr.2006.12.009

Cited by 23 publications

(28 citation statements)

References 41 publications

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“…The director's distribution bandwidth of $15 0 is in agreement with the fit obtained using the traditional Brownian dynamics simulation model as implemented in EPRSSP_DYN EPR simulation program [7]. Principle values of g and A tensors, namely, A xx ¼ 5:9 G, A yy ¼ 5:9 G, A zz ¼ 31:7 G and g xx ¼ 2:0088, g yy ¼ 2:0061, g zz ¼ 2:0027 for the spin probe dissolved in 5CB LC were taken from the literature [9,23].…”

Section: Prl 102 013005 (2009) P H Y S I C a L R E V I E W L E T T Esupporting

confidence: 78%

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Electron Paramagnetic Resonance Spectra Simulation Directly from Molecular Dynamics Trajectories of a Liquid Crystal with a Doped Paramagnetic Spin Probe

et al. 2009

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'Electron paramagnetic resonance spectra simulation directly from molecular dynamics trajectories of a liquid crystal with a doped paramagnetic spin probe.', Physical review letters., 102 (1). 013005. Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details.

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Section: Prl 102 013005 (2009) P H Y S I C a L R E V I E W L E T T Esupporting

confidence: 78%

“…EPR of spin probes has been used to test structural properties and molecular mobility of numerous complex molecular systems such as proteins and protein-protein complexes, DNA or RNA, polymers, lipids, nanostructures, monolayers at oil-water interfaces, and also liquid crystals (LC) [2][3][4][5][6][7][8][9][10].…”

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confidence: 99%

Electron Paramagnetic Resonance Spectra Simulation Directly from Molecular Dynamics Trajectories of a Liquid Crystal with a Doped Paramagnetic Spin Probe

et al. 2009

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“…(1) is D IS ¼ (l 0 /4p)l B g S c I , where l 0 is the magnetic permeability of vacuum, l B is the Bohr magneton, c I is the nuclear spin gyromagnetic ratio, and g S is the electron spin g factor. For the MTSL label g S ¼ 2.0058, 45 which leads to D IS ¼ 4.9764 Â 10 À22 m 3 s À1 for dipolar interaction between the MTSL and 1 H N . Normally, the PRE experiments target the quantity R pmag 2 ; we shall refer to it as the PRE rate.…”

Section: Overviewmentioning

confidence: 99%

Paramagnetic relaxation enhancements in unfolded proteins: Theory and application to drkN SH3 domain

et al. 2009

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Site-directed spin labeling in combination with paramagnetic relaxation enhancement (PRE) measurements is one of the most promising techniques for studying unfolded proteins. Since the pioneering work of Gillespie and Shortle (J Mol Biol 1997;268:158), PRE data from unfolded proteins have been interpreted using the theory that was originally developed for rotational spin relaxation. At the same time, it can be readily recognized that the relative motion of the paramagnetic tag attached to the peptide chain and the reporter spin such as 1 H N is best described as a translation. With this notion in mind, we developed a number of models for the PRE effect in unfolded proteins: (i) mutual diffusion of the two tethered spheres, (ii) mutual diffusion of the two tethered spheres subject to a harmonic potential, (iii) mutual diffusion of the two tethered spheres subject to a simulated mean-force potential (Smoluchowski equation); (iv) explicit-atom molecular dynamics simulation. The new models were used to predict the dependences of the PRE rates on the 1 H N residue number and static magnetic field strength; the results are appreciably different from the Gillespie-Shortle model. At the same time, the Gillespie-Shortle approach is expected to be generally adequate if the goal is to reconstruct the distance distributions between 1 H N spins and the paramagnetic center (provided that the characteristic correlation time is known with a reasonable accuracy). The theory has been tested by measuring the PRE rates in three spin-labeled mutants of the drkN SH3 domain in 2M guanidinium chloride. Two modifications introduced into the measurement scheme-using a reference compound to calibrate the signals from the two samples (oxidized and reduced) and using peak volumes instead of intensities to determine the PRE rates-lead to a substantial improvement in the quality of data. The PRE data from the denatured drkN SH3 are mostly consistent with the model of moderately expanded random-coil protein, although part of the data point toward a more compact structure (local hydrophobic cluster). At the same time, the radius of gyration reported by Choy et al. (J Mol Biol 2002;316:101) suggests that the protein is highly expanded. This seemingly contradictory evidence can be reconciled if one assumes that denatured drkN SH3 forms a conformational ensemble that is dominated by extended conformations, yet also contains compact (collapsed) species. Such behavior is apparently more complex than predicted by the model of a random-coil protein in good solvent/poor solvent.Additional Supporting Information may be found in the online version of this article.Abbreviations: drkN SH3, N-terminal SH3 domain of the Drosophila adapter protein drk; EDTA, ethylenediaminetetraacetic acid; ESR, electron spin resonance; FRET, fluorescence resonance energy transfer; MTSL, methanethiosulfonate spin label; NOE, nuclear Overhauser effect; NAG, N-acetyl-glycine.

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“…Once the averaged potential surface is defined, the nitroxide can be approximated by a single particle exposed to a mean force, resulting from this potential. This approach, which is based on the numerical solution of Langevin equation, has been successfully used by Steinhoff and Hubbell for the simulation of X-band EPR spectra of a spin labelled poly-leucine a-helix trimer [15] and by White et al to monitor changes in colicin protein complex [16].…”

Section: Introductionmentioning

confidence: 99%

Analysis of nitroxide spin label motion in a protein–protein complex using multiple frequency EPR spectroscopy

Cited by 23 publications

References 41 publications

Electron Paramagnetic Resonance Spectra Simulation Directly from Molecular Dynamics Trajectories of a Liquid Crystal with a Doped Paramagnetic Spin Probe

Electron Paramagnetic Resonance Spectra Simulation Directly from Molecular Dynamics Trajectories of a Liquid Crystal with a Doped Paramagnetic Spin Probe

Paramagnetic relaxation enhancements in unfolded proteins: Theory and application to drkN SH3 domain

A novel approach to the simulation of nitroxide spin label EPR spectra from a single truncated dynamical trajectory

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