The contribution of modern EPR to structural biology

Abstract

Electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin labelling is applicable to biomolecules and their complexes irrespective of system size and in a broad range of environments. Neither short-range nor long-range order is required to obtain structural restraints on accessibility of sites to water or oxygen, on secondary structure, and on distances between sites. Many of the experiments characterize a static ensemble obtained by shock-freezing. Compared with characterizing the dynamic ensemble at ambient temperature, analysis is simplified and information loss due to overlapping timescales of measurement and system dynamics is avoided. The necessity for labelling leads to sparse restraint sets that require integration with data from other methodologies for building models. The double electron-electron resonance experiment provides distance distributions in the nanometre range that carry information not only on the mean conformation but also on the width of the native ensemble. The distribution widths are often inconsistent with Anfinsen's concept that a sequence encodes a single native conformation defined at atomic resolution under physiological conditions.

Nickel and GTP Modulate Helicobacter pylori UreG Structural Flexibility

“…SDSL-EPR spectroscopy is a non-destructive technique that provides details on protein structure and flexibility over a wide-range of temperatures and timescales [35][36][37][38]. Proteins can be studied in their native environment, that is in membranes, in cellular extract and also inside cells [39].…”

Light‐Induced Pulsed EPR Dipolar Spectroscopy on a Paradigmatic Hemeprotein

“…[1][2][3] PDS groups a series of pulse EPR techniques that allow the measurement, via the dipolar electron-electron coupling between two paramagnetic species, of distances and distance distributions. [1][2][3] PDS groups a series of pulse EPR techniques that allow the measurement, via the dipolar electron-electron coupling between two paramagnetic species, of distances and distance distributions.…”

“…Electron paramagnetic resonance (EPR) pulsed dipolar spectroscopy (PDS) is an important biophysical technique for studying complex biological assemblies. [1][2][3] PDS groups a series of pulse EPR techniques that allow the measurement, via the dipolar electron-electron coupling between two paramagnetic species, of distances and distance distributions. Structural information in the range between 1.6 and 8 nm is obtained with high precision and reliability, while the limit of 16 nm is reached under full deuteration of the sample and solvent.…”

Combining Experimental Data and Computational Methods for the Non-Computer Specialist

“…The observable measure is a time-domain signal that is then converted into a distance distribution. To incorporate the restraint into a computational method, it is usually necessary to incorporate the distribution, which is related to the experimental uncertainty [ 110 ]. For DEER, there is not a clear consensus of the type of distribution that should be used [ 110 ].…”

“…To incorporate the restraint into a computational method, it is usually necessary to incorporate the distribution, which is related to the experimental uncertainty [ 110 ]. For DEER, there is not a clear consensus of the type of distribution that should be used [ 110 ]. Nevertheless, DEER data have been implemented in several protocols such as ensemble-biased metadynamics (EBMetaD) [ 111 , 112 ].…”