Four-Pulse ELDOR Theory of the Spin ½ Label Pairs Extended to Overlapping EPR Spectra and to Overlapping Pump and Observer Excitation Bands

Salikhov, K. M.; Khairuzhdinov, I. T.

doi:10.1007/s00723-014-0609-4

Cited by 28 publications

(21 citation statements)

References 21 publications

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“…Accordingly, τ 2 -dependent dipolar dephasing mechanisms related to unwanted spin flips can be excluded. One such mechanism is related to residual spin flips of unobserved spins by the observation pulses, which introduces additional dipolar evolution pathways [45]. Given the large frequency separation between pumped and observed spins, one would expect a majority of these additional evolution pathways to be negligible.…”

Section: Application To Long Distancesmentioning

confidence: 99%

Gd(III)–Gd(III) distance measurements with chirp pump pulses

Doll

Wili

et al. 2015

Journal of Magnetic Resonance

110

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The broad EPR spectrum of Gd(III) spin labels restricts the dipolar modulation depth in distance measurements between Gd(III) pairs to a few percent. To overcome this limitation, frequency-swept chirp pulses are utilized as pump pulses in the DEER experiment. Using a model system with 3.4 nm Gd-Gd distance, application of one single chirp pump pulse at Q-band frequencies leads to modulation depths beyond 10%. However, the larger modulation depth is counteracted by a reduction of the absolute echo intensity due to the pump pulse. As supported by spin dynamics simulations, this effect is primarily driven by signal loss to double-quantum coherence and specific to the Gd(III) high spin state of S = 7/2. In order to balance modulation depth and echo intensity for optimum sensitivity, a simple experimental procedure is proposed. An additional improvement by 25% in DEER sensitivity is achieved with two consecutive chirp pump pulses. These pulses pump the Gd(III) spectrum symmetrically around the observation position, therefore mutually compensating for dynamical Bloch-Siegert phase shifts at the observer spins. The improved sensitivity of the DEER data with modulation depths on the order of 20% is due to mitigation of the echo reduction effects by the consecutive pump pulses. In particular, the second pump pulse does not lead to additional signal loss if perfect inversion is assumed. Moreover, the compensation of the dynamical Bloch-Siegert phase prevents signal loss due to spatial dependence of the dynamical phase, which is caused by inhomogeneities in the driving field. The new methodology is combined with pre-polarization techniques to measure long distances up to 8.6 nm, where signal intensity and modulation depth become attenuated by long dipolar evolution windows. In addition, the influence of the zero-field splitting parameters on the echo intensity is studied with simulations. Herein, larger sensitivity is anticipated for Gd(III) complexes with zero-field splitting that is smaller than for the employed Gd-PyMTA complex.

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Section: Application To Long Distancesmentioning

confidence: 99%

Gd(III)–Gd(III) distance measurements with chirp pump pulses

Doll

Wili

et al. 2015

Journal of Magnetic Resonance

110

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“…Recent developments of the theory of the PELDOR method include the use of more accurate theoretical formulas for the analysis of the experimental results. Newly proposed aspects of a sophisticated PELDOR theory take into account the interaction between spin labels in pairs or aggregates when the EPR spectra of spins A and B overlap or coincide. In this case, corrections for theoretically calculated p b values are needed.…”

Section: Peldor Spectroscopymentioning

confidence: 99%

Review conformation, self‐aggregation, and membrane interaction of peptaibols as studied by pulsed electron double resonance spectroscopy

et al. 2016

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Pulsed EPR methods, in particular pulsed electron double resonance (PELDOR) [or double electron-electron resonance (DEER)], are very sensitive to the dipole ··· dipole interaction between electron spins in a pair of free radicals. Using PELDOR, the conformations of a number of double radical-containing biomolecules have been determined. In this review article, we focused our attention on the application of this spectroscopy to nitroxide-labeled peptaibols. This is an emerging class of naturally occurring, relatively short, linear, helical peptide molecules endowed with hydrophobic character, capability to interact with and to alter the structure of membranes, and antibiotic activity. We extracted detailed information on the secondary structures of specifically site-directed, double nitroxide-labeled peptaibols under a variety of experimental conditions, including biologically relevant environments. Moreover, we examined in-depth peptaibol clustering, related to the marked propensity of these molecules to undergo self-association in model and whole-cell membrane systems, using mainly mono-nitroxide-containing synthetic analogs. Finally, based on the PELDOR data accumulated, we proposed models of supramolecular (quaternary) structures of peptaibols and their binding modes to membranes.

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“…This case is unavoidable in homogenous labeling schemes, as in the common case of two nitroxide radical labels on one protein. A more complete expression contains additional terms, as explained in [22, 23]. For the purposes of this work, the specific forms of B ( t ) and F ( t ) are irrelevant; the analysis is only concerned with S ( t ).…”

Section: Deer and Tikhonov Regularizationmentioning

confidence: 99%

A Bayesian approach to quantifying uncertainty from experimental noise in DEER spectroscopy

Edwards

Stoll

2016

Journal of Magnetic Resonance

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Double Electron-Electron Resonance (DEER) spectroscopy is a solid-state pulse Electron Paramagnetic Resonance (EPR) experiment that measures distances between unpaired electrons, most commonly between protein-bound spin labels separated by 1.5–8 nm. From the experimental data, a distance distribution P(r) is extracted using Tikhonov regularization. The disadvantage of this method is that it does not directly provide error bars for the resulting P(r), rendering correct interpretation difficult. Here we introduce a Bayesian statistical approach that quantifies uncertainty in P(r) arising from noise and numerical regularization. This method provides credible intervals (error bars) of P(r) at each r. This allows practitioners to answer whether or not small features are significant, whether or not apparent shoulders are significant, and whether or not two distance distributions are significantly different from each other. In addition, the method quantifies uncertainty in the regularization parameter.

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Four-Pulse ELDOR Theory of the Spin ½ Label Pairs Extended to Overlapping EPR Spectra and to Overlapping Pump and Observer Excitation Bands

Cited by 28 publications

References 21 publications

Gd(III)–Gd(III) distance measurements with chirp pump pulses

Gd(III)–Gd(III) distance measurements with chirp pump pulses

Review conformation, self‐aggregation, and membrane interaction of peptaibols as studied by pulsed electron double resonance spectroscopy

A Bayesian approach to quantifying uncertainty from experimental noise in DEER spectroscopy

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