A combined EPR and MD simulation study of a nitroxyl spin label with restricted internal mobility sensitive to protein dynamics

Abstract

EPR studies combined with fully atomistic Molecular Dynamics (MD) simulations and an MD-EPR simulation method provide evidence for intrinsic low rotameric mobility of a nitroxyl spin label, Rn, compared to the more widely employed label MTSL (R1). Both experimental and modelling results using two structurally different sites of attachment to Myoglobin show that the EPR spectra of Rn are more sensitive to the local protein environment than that of MTSL. This study reveals the potential of using the Rn spin label as a reporter of protein motions.

Prediction of EPR Spectra of Lyotropic Liquid Crystals using a Combination of Molecular Dynamics Simulations and the Model‐Free Approach

“…The GAFF parameters for 5DSA spin probe have been generated in analogy with other spin probes developed by us previously . Quantum chemical calculations of 5DSA were performed with the Gaussian 09 software package, at the B3LYP/6–311++g(d,p) level of theory and the CHELPG charge Scheme to obtain partial charges.…”

“…The GAFFp arameters for 5DSA spin probe have been generated in analogy with other spin probes developed by us previously. [51,57] Quantum chemical calculations of 5DSA were performed with the Gaussian09 [58] software package, at the B3LYP/6-311 ++g(d,p)l evel of theory and the CHELPG [59] charge Scheme to obtain partial charges. Force field parameters for the new atom types of the nitroxide moiety in 5DSA (the unsaturated carbon atoms of the nitroxide ring, the saturated carbon atoms of the nitroxide ring, the nitrogen and the oxygen) were taken from ac ombinationofg eometry optimization calculations in the gas phase and previousc alculations.…”

“…Such techniques can greatly simplify the interpretation and analysis of experimental spectra, and hence provide unambiguous conclusions about molecular order and motions. These MD‐EPR methods have been successfully applied to spin labelled proteins and thermotropic liquid crystals …”

Direct Prediction of EPR Spectra from Lipid Bilayers: Understanding Structure and Dynamics in Biological Membranes

“…At the same time some discrepancies are present between the predicted and experimental spectra, although in several instances the agreement between the prediction and experiment appears to be better than between the fitted and experimental spectra typically reported in the literature. Apart from the accuracy of the employed MD simulation model itself, the discrepancies are attributed to the limited lengths of the dynamical trajectories employed . In order to illustrate this point, we have performed a simulation of EPR spectrum of 5‐PC probe in DPPC at 308 K using a different 1.2 μs MD trajectory.…”

EPR spectroscopy and molecular dynamics modelling: a combined approach to study liquid crystals

“…This approach has paved the way for the first-time prediction of motional EPR spectra directly and completely from MD trajectories of actual molecular structures. It has been successfully applied to proteins [29,30], DNA [31], lipid bilayers [32] and also LCs [33][34][35]. A computer code developed by the author [27,28], which includes both options, namely the propagation of the trajectories along the entire sampling time and the use of truncated trajectories combined with autocorrelation function method, has been employed for the simulation of EPR spectra of LC systems reported in this review.…”