scholarly journals Hydrogen bonding of nitroxide spin labels in membrane proteins

2014 ◽  
Vol 16 (30) ◽  
pp. 15910-15916 ◽  
Author(s):  
P. Gast ◽  
R. T. L. Herbonnet ◽  
J. Klare ◽  
A. Nalepa ◽  
C. Rickert ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Membrane Proteins ◽  
Continuous Wave ◽  
Epr Spectra ◽  
Spin Labels ◽  
Nitroxide Spin Labels

On the basis of experiments at 275 GHz, we reconsider the dependence of the continuous-wave EPR spectra of nitroxide spin-labeled protein sites in sensory- and bacteriorhodopsin on the micro-environment.

Comparing continuous wave progressive saturation EPR and time domain saturation recovery EPR over the entire motional range of nitroxide spin labels

2004 ◽  
Vol 169 (1) ◽  
pp. 129-163 ◽  
Author(s):  
Robert D. Nielsen ◽  
Stephane Canaan ◽  
James A. Gladden ◽  
Michael H. Gelb ◽  
Colin Mailer ◽  
...  
Keyword(s):  
Time Domain ◽  
Continuous Wave ◽  
Saturation Recovery ◽  
Spin Labels ◽  
Nitroxide Spin Labels

scholarly journals Reconciling Membrane Protein Simulations with Experimental DEER Spectroscopy Data

2020 ◽  
Author(s):  
Shriyaa Mittal ◽  
Diwakar Shukla
Keyword(s):  
Membrane Proteins ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
Covalent Modification ◽  
Mitigation Strategies ◽  
Residue Pair ◽  
Spin Labels ◽  
Distance Distributions ◽  
Nitroxide Spin Labels ◽  
Double Electron Electron Resonance

AbstractSpectroscopy experiments are crucial to study membrane proteins for which traditional structure determination methods still prove challenging. Double electron-electron resonance (DEER) spectroscopy experiments provide protein residue-pair distance distributions that are indicative of their conformational heterogeneity. Atomistic molecular dynamics (MD) simulations are another tool that have proved vital to study the structural dynamics of membrane proteins such as to identify inward-open, occluded, and outward-open conformations of transporter membrane proteins, among other partially open or closed states of the protein. Yet, studies have reported that there is no direct consensus between distributional data from DEER experiments and MD simulations, which has challenged validation of structures obtained from long-timescale simulations and using simulations to design experiments. Current coping strategies for comparisons rely on heuristics, such as mapping nearest matching peaks between two ensembles or biased simulations. Here we examine the differences in residue-pair distance distributions arising due to choice of membrane around the protein and covalent modification of a pair of residues to nitroxide spin labels in DEER experiments. Through comparing MD simulations of two proteins, PepTSo and LeuT - both of which have been characterized using DEER experiments previously - we show that the proteins’ dynamics are similar despite the choice of the detergent micelle as a membrane mimetic in DEER experiments. On the other hand, covalently modified residues show slight local differences in their dynamics and a huge divergence when the spin labels’ anointed oxygen atom pair distances are measured rather than protein backbone distances. Given the computational expense associated with pairwise MTSSL labeled MD simulations, we examine the use of biased simulations to explore the conformational dynamics of the spin labels only to reveal that such simulations alter the underlying protein dynamics. Our study identifies the main cause for the mismatch between DEER experiments and MD simulations and will accelerate developing potential mitigation strategies to improve simulation observables match with DEER spectroscopy experiments.

scholarly journals DEER and RIDME Measurements of the Nitroxide-Spin Labelled Copper-Bound Amine Oxidase Homodimer from Arthrobacter Globiformis

2021 ◽  
Author(s):  
Hannah Russell ◽  
Rachel Stewart ◽  
Christopher Prior ◽  
Vasily S. Oganesyan ◽  
Thembaninkosi G. Gaule ◽  
...  
Keyword(s):  
Dipolar Coupling ◽  
Amine Oxidase ◽  
Spin Labels ◽  
Arthrobacter Globiformis ◽  
Copper Amine Oxidase ◽  
Dipole Interactions ◽  
Nitroxide Spin Labels ◽  
Double Electron Electron Resonance ◽  
Dipolar Modulation ◽  
Paramagnetic Centres

AbstractIn the study of biological structures, pulse dipolar spectroscopy (PDS) is used to elucidate spin–spin distances at nanometre-scale by measuring dipole–dipole interactions between paramagnetic centres. The PDS methods of Double Electron Electron Resonance (DEER) and Relaxation Induced Dipolar Modulation Enhancement (RIDME) are employed, and their results compared, for the measurement of the dipolar coupling between nitroxide spin labels and copper-II (Cu(II)) paramagnetic centres within the copper amine oxidase from Arthrobacter globiformis (AGAO). The distance distribution results obtained indicate that two distinct distances can be measured, with the longer of these at c.a. 5 nm. Conditions for optimising the RIDME experiment such that it may outperform DEER for these long distances are discussed. Modelling methods are used to show that the distances obtained after data analysis are consistent with the structure of AGAO.

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