Spectroscopically Orthogonal Spin Labels in Structural Biology at Physiological Temperatures

Electron paramagnetic resonance spectroscopy (EPR) is mostly used in structural biology in conjunction with pulsed dipolar spectroscopy (PDS) methods to monitor interspin distances in biomacromolecules at cryogenic temperatures both in vitro and in cells. In this context, spectroscopically orthogonal spin labels were shown to increase the information content that can be gained per sample. Here, we exploit the characteristic properties of gadolinium and nitroxide spin labels at physiological temperatures to study side chain dynamics via continuous wave (cw) EPR at X band, surface water dynamics via Overhauser dynamic nuclear polarization at X band and short-range distances via cw EPR at high fields. The presented approaches further increase the accessible information content on biomolecules tagged with orthogonal labels providing insights into molecular interactions and dynamic equilibria that are only revealed under physiological conditions.

Isolation of a novel heterodimeric PSII complex via strep-tagged PsbO

The multi-subunit membrane protein complex photosystem II (PSII) catalyzes the light-driven oxidation of water and with this the initial step of photosynthetic electron transport in plants, algae, and cyanobacteria. Its biogenesis is coordinated by a network of auxiliary proteins that facilitate the stepwise assembly of individual subunits and cofactors, forming various intermediate complexes until fully functional mature PSII is present at the end of the process. In the current study, we purified PSII complexes from a mutant line of the thermophilic cyanobacterium Thermosynechococcus vestitus BP-1 in which the extrinsic subunit PsbO, characteristic for active PSII, was fused with an N-terminal Twin-Strep-tag. Three distinct PSII complexes were separated by ion-exchange chromatography after the initial affinity purification. Two complexes differ in their oligomeric state (monomeric and dimeric) but share the typical subunit composition of mature PSII. They are characterized by the very high oxygen evolving activity of approx. 6000 μmol O₂·(mg Chl·h)^-1. Analysis of the third (heterodimeric) PSII complex revealed lower oxygen evolving activity of approx. 3000 μmol O₂·(mg Chl·h)^-1 and a manganese content of 2.7 (±0.2) per reaction center compared to 3.7 (±0.2) of fully active PSII. Mass spectrometry and time-resolved fluorescence spectroscopy further indicated that PsbO is partially replaced by Psb27 in this PSII fraction, thus implying a role of this complex in PSII repair.

Benchmark Test and Guidelines for DEER/PELDOR Experiments on Nitroxide-Labeled Biomolecules

Distance distribution information obtained by pulsed dipolar EPR spectroscopy provides an important contribution to many studies in structural biology. Increasingly, such information is used in integrative structural modeling, where it delivers unique restraints on the width of conformational ensembles. In order to ensure reliability of the structural models and of biological conclusions, we herein define quality standards for sample preparation and characterization, for measurements of distributed dipole-dipole couplings between paramagnetic labels, for conversion of the primary time-domain data into distance distributions, for interpreting these distributions, and for reporting results. These guidelines are substantiated by a multi-laboratory benchmark study and by analysis of data sets with known distance distribution ground truth. The study and the guidelines focus on proteins labeled with nitroxides and on double electron-electron resonance (DEER aka PELDOR) measurements and provide suggestions on how to proceed analogously in other cases.

In-Cell Double Electron-Electron Resonance at Nanomolar Protein Concentrations

Electron paramagnetic resonance (EPR) spectroscopy is an established technique to site-specifically monitor conformational changes of spin-labeled biomolecules. Emerging in-cell EPR approaches aiming to address spin-labeled proteins in their native environment still struggle to reach a broad applicability and to target physiologically relevant protein concentrations. Here, we present a comparative in vitro and in-cell double electron-electron resonance (DEER) study demonstrating that nanomolar protein concentrations are at reach to measure distances up to 4.5 nm between protein sites carrying commercial gadolinium spin labels.

In cell Gd3+-based site-directed spin labeling and EPR spectroscopy of eGFP

A newly synthesized Gd³⁺ chelate complex allows in cell spin labeling and detection of eGFP by EPR spectroscopy.

EPR Techniques to Probe Insertion and Conformation of Spin-Labeled Proteins in Lipid Bilayers

Electron paramagnetic resonance (EPR) spectroscopy of spin-labeled membrane proteins is a valuable biophysical technique to study structural details and conformational transitions of proteins close to their physiological environment, for example, in liposomes, membrane bilayers, and nanodiscs. Unlike in nuclear magnetic resonance (NMR) spectroscopy, having only one or few specific side chains labeled at a time with paramagnetic probes makes the size of the object under investigation irrelevant in terms of technique sensitivity. As a drawback, extensive site-directed mutagenesis is required in order to analyze the properties of the protein under investigation. EPR can provide detailed information on side chain dynamics of large membrane proteins or protein complexes embedded in membranes with an exquisite sensitivity for flexible regions and on water accessibility profiles across the membrane bilayer. Moreover, distances between the two spin-labeled side chains in membrane proteins can be detected with high precision at cryogenic temperatures. The application of EPR to membrane proteins still presents some challenges in terms of sample preparation, sensitivity and data interpretation, thus it is difficult to give ready-to-go methodological recipes. However, new technological developments (arbitrary waveform generators) and new spin labels spectroscopically orthogonal to nitroxides increased the range of applicability from in vitro toward in-cell EPR experiments. This chapter is an updated version of the one published in the first edition of the book and describes the state of the art in the application of nitroxide-based site-directed spin labeling EPR to membrane proteins, addressing new tools such as arbitrary waveform generators and spectroscopically orthogonal labels, such as Gd(III)-based labels. We will present challenges in sample preparation and data analysis for functional and structural membrane protein studies using site-directed spin labeling techniques and give experimental details on EPR techniques providing information on side chain dynamics and water accessibility using nitroxide probes. An updated optimal Q-band DEER setup for nitroxide probes will be described, and its extension to gadolinium-containing samples will be addressed.

DDT-related compounds as non-extractable residues in submarine sediments of the Palos Verdes Shelf, California, USA

The Palos Verdes Shelf (PVS) and the continental slope off the Palos Verdes Peninsula are highly contaminated by degradation products of the pesticide DDT (1-chloro-4-[2,2,2-trichloro-1-(4-chlorophenyl)ethyl]benzene). Sediment samples from two box cores were analyzed to obtain further information about the fate of DDT and its degradation products within the environment. After solvent extraction, an alkaline hydrolysis procedure was applied. A comprehensive screening for 26 DDT compounds revealed that DDT and its degradates contaminate not only the extractable fraction but also the fraction released by alkaline hydrolysis. A comparison of the quantitative distribution of DDT degradation products in the extractable fraction and released by alkaline hydrolysis showed a distinct difference. DDE (1-chloro-4-[2,2-dichloro-1-(4-chlorophenyl)ethenyl]benzene), DDD (1-chloro-4-[2,2-dichloro-1-(4-chlorophenyl)ethyl]benzene), DDMS (1-chloro-4-[2-chloro-1-(4-chlorophenyl)ethyl]benzene), and DDMU (1-chloro-4-[2-chloro-1-(4-chlorophenyl)ethenyl]benzene) were predominant in the sediment extracts but minor components of the hydrolyzable fraction. The most abundant compounds released by the alkaline hydrolysis were DBP (bis(4-chlorophenyl)methanone), DDNU (1-chloro-4-[1-(4-chlorophenyl)ethenyl]benzene), DDM (1-chloro-4-[(4-chlorophenyl)methyl]benzene) and the water-soluble DDA (2,2-bis(4-chlorophenyl)acetic acid). The release of DDA may point to the presence of an important degradation pathway in marine environments. Concentration levels of DDT-related compounds showed corresponding vertical profiles in both fractions, but were significantly lower in the fraction released by alkaline hydrolysis. In contrast to fluvial sediments contaminated by DDT and its degradates the alkaline hydrolysis products represented a minor portion of the total sedimentary burden in the analyzed marine sediments. These findings show the necessity of a comprehensive screening for all DDT isomers and breakdown products in the extractable and non-extractable fraction to assess the total contamination abundance and potential environmental risks.

Orthogonal spin labeling using click chemistry for in vitro and in vivo applications

Site-directed spin labeling for EPR- and NMR spectroscopy has mainly been achieved exploiting the specific reactivity of cysteines. For proteins with native cysteines or for in vivo applications, an alternative coupling strategy is required. In these cases click chemistry offers major benefits by providing a fast and highly selective, biocompatible reaction between azide and alkyne groups. Here, we establish click chemistry as a tool to target unnatural amino acids in vitro and in vivo using azide- and alkyne-functionalized spin labels. The approach is compatible with a variety of labels including reduction-sensitive nitroxides. Comparing spin labeling efficiencies from the copper-free with the strongly reducing copper(I)-catalyzed azide-alkyne click reaction, we find that the faster kinetics for the catalyzed reaction outrun reduction of the labile nitroxide spin labels and allow quantitative labeling yields within short reaction times. Inter-spin distance measurements demonstrate that the novel side chain is suitable for paramagnetic NMR- or EPR-based conformational studies of macromolecular complexes.