Monitoring Complex Formation by Relaxation‐Induced Pulse Electron Paramagnetic Resonance Distance Measurements

@article{Giannoulis2017MonitoringCF,
  title={Monitoring Complex Formation by Relaxation‐Induced Pulse Electron Paramagnetic Resonance Distance Measurements},
  author={Angeliki Giannoulis and Maria Oranges and Bela E. Bode},
  journal={Chemphyschem},
  year={2017},
  volume={18},
  pages={2318 - 2321}
}
Abstract Biomolecular complexes are often multimers fueling the demand for methods that allow unraveling their composition and geometric arrangement. Pulse electron paramagnetic resonance (EPR) spectroscopy is increasingly applied for retrieving geometric information on the nanometer scale. The emerging RIDME (relaxation‐induced dipolar modulation enhancement) technique offers improved sensitivity in distance experiments involving metal centers (e.g. on metalloproteins or proteins labelled with… 

Figures from this paper

Sub‐Micromolar Pulse Dipolar EPR Spectroscopy Reveals Increasing CuII‐labelling of Double‐Histidine Motifs with Lower Temperature
TLDR
The feasibility of exploiting the double‐histidine motif for EPR applications even at sub‐μm protein concentrations in orthogonally labelled CuII–nitroxide systems using a commercial Q‐band EPR instrument is shown.
Pulse EPR distance measurements to study multimers and multimerisation
ABSTRACT Pulse dipolar electron paramagnetic resonance (PD-EPR) has become a powerful tool for structural biology determining distances on the nanometre scale. Recent advances in hardware,
Pulsed Dipolar EPR Spectroscopy and Metal Ions: Methodology and Biological Applications.
TLDR
The key achievements and the remaining challenges of PDS on metal ions are summarized and critically discussed and applications are highlighted to give an idea about what kind of questions from structural biology can be answered by PDS-based distance measurements involving metal centers.
A Low-Spin CoII/Nitroxide Complex for Distance Measurements at Q-Band Frequencies
Pulse dipolar electron paramagnetic resonance spectroscopy (PDS) is continuously furthering the understanding of chemical and biological assemblies through distance measurements in the nanometer
Localization of metal ions in biomolecules by means of pulsed dipolar EPR spectroscopy.
TLDR
A complementary method is highlighted in which paramagnetic metal ions are localized by means of trilateration using a combination of site-directed spin labeling and pulsed dipolar electron paramagnetic resonance spectroscopy.
Nitroxide-nitroxide and nitroxide-metal distance measurements in transition metal complexes with two or three paramagnetic centres give access to thermodynamic and kinetic stabilities.
TLDR
P pulse EPR (electron paramagnetic resonance) spectroscopy is used to determine the stabilities of nanoscopic assemblies formed between one or two nitroxide spin-labelled tridentate 2,2':6',2''-terpyridine (tpy) ligands and divalent metal ions (FeII, ZnII, CoII and CuII).
Nanomolar Pulse Dipolar EPR Spectroscopy in Proteins; the CuII- CuII and Nitroxide-Nitroxide Cases
TLDR
CuII-CuII and nitroxide-nitroxide PDS measurements at protein concentrations below previous examples reaching 500 and 100 nM are demonstrated, demonstrating the general feasibility of sub-μM P DS measurements at short to intermediate distances.
Pulse Dipolar EPR Reveals Double-Histidine Motif CuII–NTA Spin-Labeling Robustness against Competitor Ions
TLDR
Results demonstrate double-histidine motif spin labeling using CuII-nitrilotriacetic acid (CuII–NTA) is robust against the competitor ligand ZnII-NTA at >1000-fold molar excess, and high nM binding affinity is surprisingly retained under acidic and basic conditions even though room temperature affinity shows a stronger pH dependence.
DEER and RIDME Measurements of the Nitroxide-Spin Labelled Copper-Bound Amine Oxidase Homodimer from Arthrobacter Globiformis
TLDR
Modelling methods are used to show that the distances obtained after data analysis are consistent with the structure of AGAO, and conditions for optimising the RIDME experiment such that it may outperform DEER for these long distances are discussed.
Intermolecular background decay in RIDME experiments.
TLDR
An analytical calculation of the RIDME background decay in the simple case of two types of randomly distributed spin centers each with total spin S = 1/2 is presented and the obtained equations allow the explaination of the key trends in R IDME experiments on frozen chelated metal ion solutions, and singly spin-labeled proteins.
...
...

References

SHOWING 1-10 OF 36 REFERENCES
Mapping the Structure of Metalloproteins with RIDME.
Gd3+ complexes as potential spin labels for high field pulsed EPR distance measurements.
TLDR
Pulse electron−electron double resonance distance measurements between two high spin Gd3+ ions in a novel bis-Gd 3+ complex involving two pyridine-based gadolinium tetracarboxylate systems linked by a rigid aryl−alkyne unit found the experimental distance was 2.02 ± 0.02 nm.
Comparison of PELDOR and RIDME for Distance Measurements between Nitroxides and Low-Spin Fe(III) Ions.
TLDR
Two methods, pulsed electron-electron double resonance (PELDOR) and relaxation-induced dipolar modulation enhancement (RIDME) are compared on the heme-containing and spin-labeled cytochrome P450cam and it turned out that RIDME appears to be better suited for distance measurements involving metal ions like low-spin Fe(3+) than PELDOR.
Carr-Purcell Pulsed Electron Double Resonance with Shaped Inversion Pulses.
TLDR
A pulse sequence, based on a Carr-Purcell decoupling scheme on the observer spin, where each π-pulse is accompanied by a shaped sech/tanh inversion pulse applied to the second spin, increases the upper limit and accuracy of distances that can be determined in membrane protein complexes.
RIDME Spectroscopy with Gd(III) Centers.
The relaxation induced dipolar modulation enhancement (RIDME) technique is applied at W-band microwave frequencies around 94 GHz to a pair of Gd(III) complexes that are connected by a rodlike spacer,
RIDME distance measurements using Gd(iii) tags with a narrow central transition.
TLDR
Comparisons of the most popular technique, Double Electron-Electron Resonance (DEER or PELDOR), with the dead-time free 5-pulse Relaxation-Induced Dipolar Modulation Enhancement (RIDME) method for Gd(iii)-Gd(ii) distance measurements at W-band, found the sensitivity of RIDME was found to be significantly better than DEER.
Versatile Trityl Spin Labels for Nanometer Distance Measurements on Biomolecules In Vitro and within Cells.
TLDR
The synthesis of a versatile collection of trityl spin labels is described, which show similar labeling efficiencies and better signal-to-noise ratios (SNR) as compared to the popular methanethiosulfonate spin label (MTSSL) and enabled a successful in-cell measurement.
DEER Sensitivity between Iron Centers and Nitroxides in Heme-Containing Proteins Improves Dramatically Using Broadband, High-Field EPR
TLDR
The feasibility of making sensitive nanometer distance measurements between Fe(III) heme centers and nitroxide spin labels in proteins using the double electron–electron resonance (DEER) pulsed EPR technique at 94 GHz is demonstrated.
Counting the monomers in nanometer-sized oligomers by pulsed electron-electron double resonance.
TLDR
This method is a valuable tool to determine the number of constituting spin-bearing monomers in biologically relevant homo- and heterooligomers and how their oligomerization state and geometric arrangement changes during function.
...
...