Comment on mr-2022-8

Double electron-electron resonance (DEER) spectroscopy measures the distribution of distances between two electron spins in the nanometer range, often on doubly spin-labeled proteins, via the modulation of a refocused spin echo by the dipolar interaction between the spins. DEER is commonly conducted under conditions where the polarization of the spins is small. Here, we examine the DEER signal under conditions of high spin polarization, thermally obtainable at low temperatures and high magnetic fields, and show that the signal acquires a polarization-dependent out-of-phase component, both for the intra- and the inter-molecular contribution. For the latter, this corresponds to a phase shift of the spin echo that is linear in the pump pulse position. We derive a compact analytical form of this phase shift and show experimental measurements using monoradical and biradical nitroxides at several fields and temperatures. The effect highlights a novel aspect of the fundamental spin physics underlying DEER spectroscopy.

Double electron-electron resonance (DEER) spectroscopy measures distance distributions between spin labels in proteins, yielding important structural and energetic information about conformational landscapes. Analysis of an experimental DEER signal in terms of a distance distribution is a nontrivial task due to the ill-posed nature of the underlying mathematical inversion problem. This work introduces a Bayesian probabilistic inference approach to analyze DEER data, using a multi-Gauss mixture model for the distance distribution. The method uses Markov chain Monte Carlo (MCMC) sampling to determine a posterior probability distribution over model parameter space. This distribution contains all the information available from the data, including a full quantification of the uncertainty about the parameters. The corresponding uncertainty about the distance distribution is captured via an ensemble of posterior predictive distributions. Several synthetic examples illustrate the method. An experimental example shows the importance of model checking and comparison using residual analysis and Bayes factors. Overall, the Bayesian approach allows for more robust inference about protein conformations from DEER spectroscopy.

Prediction and Selection of Spin Label Rotamers for High-Resolution Insight into Protein Structures by DEER Spectroscopy

Modular assembly of bio-inspired supramolecular polymers is a powerful technique to develop new soft nanomaterials, and protein folding is a versatile basis for preparing such materials. Previous work demonstrated a significant difference in the physical properties of closely related supramolecular polymers composed of building blocks in which identical coiled-coil-forming peptides are cross-linked by one of two subtly different organic linkers (one flexible and the other rigid). Herein, we investigate the molecular basis for this observation by isolating a single subunit of the supramolecular polymer chain and probing its structure and conformational flexibility by double electron–electron resonance (DEER) spectroscopy. Experimental spin–spin distance distributions for two different labeling sites coupled with molecular dynamics simulations provide insights into how the linker structure impacts chain dynamics in the coiled-coil supramolecular polymer.

Double electron-electron resonance (DEER) combined with site-directed spin labeling can provide distance distributions between selected protein residues to investigate protein structure and conformational heterogeneity. The utilization of the full quantitative information contained in DEER data requires effective protein and spin label modeling methods. Here, we review the application of DEER data to protein modeling. First, we discuss the significance of spin label modeling for accurate extraction of protein structural information and review the most popular label modeling methods. Next, we review several important aspects of protein modeling with DEER, including site selection, how DEER restraints are applied, common artifacts, and the unique potential of DEER data for modeling structural ensembles and conformational landscapes. Finally, we discuss common applications of protein modeling with DEER data and provide an outlook.

Optimal Tikhonov regularization for DEER spectroscopy

Spectroscopy 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 been proven to be 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 the 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 the nearest matching peaks between two ensembles or biased simulations. Here we examine the differences in residue-pair distance distributions arising due to the choice of membranes 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 oxygen atom pair distances between spin labeled residues 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 the development of potential mitigation strategies to improve the match.

Structural Dynamics of Calmodulin using Bifunctional Spin Labels and Double Electron-Electron Resonance

The Na+-translocating nicotinamide adenine dinucleotide (NADH):quinine oxidoreductase (Na+–NQR) is a component of respiratory chain of various bacteria and it generates a redox-driven transmembrane electrochemical Na+ potential. It contains four different flavin prosthetic groups, including two flavin mononucleotide (FMN) residues covalently bound to the subunits NqrB and NqrC. Na+–NQR from Vibrio harveyi was poised at different redox potentials to prepare two samples, containing either both FMNNqrB and FMNNqrC or only FMNNqrB in a paramagnetic state. These two samples were comparatively studied using pulse electron paramagnetic resonance (EPR), electron-nuclear double resonance (ENDOR), and electron-electron double resonance (ELDOR) spectroscopy. The echo-detected EPR spectra and electron spin relaxation properties were very similar for flavin radicals in both samples. The splitting of the outer peaks in the proton ENDOR spectra, assigned to the C(8α) methyl protons, allows to identify both radicals as anionic flavosemiquinones. The mean interspin distance of 20.7 A between these radicals was determined by pulse ELDOR experiment, which allows to estimate the edge-to-edge distance (re) between these flavin centers as: 11.7 A < re < 20.7 A. The direct electron transfer between FMNNqrB and FMNNqrC during the physiological turnover of the Na+–NQR complex is suggested.

Analytical distance distributions in systems of spherical symmetry with applications to double electron–electron resonance

We present high field DEER (double electron-electron resonance) distance measurements using Gd(3+) (S = 7/2) spin labels for probing peptides' conformations in solution. The motivation for using Gd(3+) spin labels as an alternative for the standard nitroxide spin labels is the sensitivity improvement they offer because of their very intense EPR signal at high magnetic fields. Gd(3+) was coordinated by dipicolinic acid derivative (4MMDPA) tags that were covalently attached to two cysteine thiol groups. Cysteines were introduced in positions 15 and 27 of the peptide melittin and then two types of spin labeled melittins were prepared, one labeled with two nitroxide spin labels and the other with two 4MMDPA-Gd(3+) labels. Both types were subjected to W-band (95 GHz, 3.5 T) DEER measurements. For the Gd(3+) labeled peptide we explored the effect of the solution molar ratio of Gd(3+) and the labeled peptide, the temperature, and the maximum dipolar evolution time T on the DEER modulation depth. We found that the optimization of the [Gd(3+)]/[Tag] ratio is crucial because excess Gd(3+) masked the DEER effect and too little Gd(3+) resulted in the formation of Gd(3+)-tag(2) complexes, generating peptide dimers. In addition, we observed that the DEER modulation depth is sensitive to spectral diffusion processes even at Gd(3+) concentrations as low as 0.2 mM and therefore experimental conditions should be chosen to minimize it as it decreases the DEER effect. Finally, the distance between the two Gd(3+) ions, 3.4 nm, was found to be longer by 1.2 nm than the distance between the two nitroxides. The origin and implications of this difference are discussed.

SummaryProton-coupled oligopeptide transporters belong to the major facilitator superfamily (MFS) of membrane transporters. Recent crystal structures suggest the MFS fold facilitates transport through rearrangement of their two six-helix bundles around a central ligand binding site; how this is achieved, however, is poorly understood. Using modeling, molecular dynamics, crystallography, functional assays, and site-directed spin labeling combined with double electron-electron resonance (DEER) spectroscopy, we present a detailed study of the transport dynamics of two bacterial oligopeptide transporters, PepTSo and PepTSt. Our results identify several salt bridges that stabilize outward-facing conformations and we show that, for all the current structures of MFS transporters, the first two helices of each of the four inverted-topology repeat units form half of either the periplasmic or cytoplasmic gate and that these function cooperatively in a scissor-like motion to control access to the peptide binding site during transport.

High-yield production in E. coli and characterization of full-length functional p13II protein from human T-cell leukemia virus type 1

Spectroscopy and imaging are widely used to characterise systems structurally and functionally, and this information allows for the rational development of novel drugs and theranostics in many diverse areas of medicine. This thesis focuses on applying Electron Paramagnetic Resonance (EPR) techniques to determine the structure and function of protein molecules. A feasibility study to develop paramagnetic probes for EPR imaging is also presented.In EPR the probe is a paramagnetic centre and information is obtained by measuring interactions of this probe with its environment. In this thesis continuous wave (CW) EPR and Double Electron Electron Resonance (DEER) in conjunction with a site-directed spin labelling (SDSL) were employed to study structure and function of spin-labelled protein molecules. The techniques allow examination of molecular systems that cannot be crystallised or are too big for efficient NMR investigation. DEER provides information on distance distributions between two spin labels located on Cys-mutated residues of the protein molecule and can access longer distances in comparison with NMR. CW EPR provides information about the mobility of a single spin label which can be used to characterise protein dynamics. Structural modelling was used to combine the crystal structures and Molecular Dynamics (MD) simulations with DEER distance constraints to present a DEER-based structural model of the conformational variability of the protein molecule.Chapters 2 and 3 focus on characterising two metal ion substrate binding proteins (SBP), Zn2+-binding AdcA and Mn2+-binding PsaA, using DEER and CW EPR. The ATP-Binding Cassette (ABC) permeases, with which the SBPs are associated, are a primary importer used by bacteria to scavenge the essential first-row metal ions (e.g. iron, zinc, manganese) from a host environment. The process is essential for bacterial survival and propagation. Understanding the metal ion acquisition mechanisms by these SBPs can provide new opportunities for targeted drug development. Collectively, the CW EPR and DEER data along with crystal structures, differential scanning fluorimetry (DSF), Molecular Dynamics simulation, and smFRET microscopy, were able to determine a structural model for Zn2+-binding in the AdcA protein referred to as “trap-door” mechanism. Our data show that the “trap-door” mechanism employed by AdcA is different from the “spring-hammer” mechanism employed by PsaA.Non-Ribosomal Peptide Synthetase (NRPS) are the topic of chapter 4. NRPS’s are a family of mega enzymes that produce a diverse range of pharmaceuticals, yet how these molecular machines operate to produce such complex chemicals is very poorly understood. This project will investigate module 7 of the teicoplanin NRPS, a 200 kDa protein, which is the last step in the production of the glycopeptide antibiotics (GPA). A comprehensive structural and functional understanding of the teicoplanin NRPS machinery will provide a paradigm for this enzyme family, enabling the tailored re-engineering of the in vivo NRPS biosynthesis for the development of new antibiotics and pharmaceuticals. This thesis concentrates on a di-domain complex PCP-X from module 7 (Tcp12) of teicoplanin NRPS which contains the peptidyl carrier protein (PCP) domain and the X-domain. These two domains are joined by a long linker which is thought to be flexible. The goal is to investigate conformational dynamics of the PCP-X construct in different states. This includes the PCP domain in loaded and unloaded states, and how the PCP-X construct interacts with an OxyB (P450) protein. Using DEER data from a large number of double spin-labelled PCP-X mutants, rigid-body structural models based on the domain’s crystal structures were investigated to characterise the mobility of the PCP-X di-domain and compare it to very limited crystal structure data of the larger domain construct.Chapter 5 describes the application of the Maximum Entropy (MaxEnt) approach to 2D HYSCORE image reconstruction and its comparison with the conventionally utilised Discrete Fourier Transformation (DFT). HYSCORE is a widely used electron spin echo envelope (ESEEM) experiment used for measuring the nuclear quadrupole and hyperfine couplings. While EPR experiments are generally very sensitive, the time required for two and higher dimensional techniques are a significant limitation. The results show that the MaxEnt algorithm allows sampling of data non-uniformity, provides better sensitivity and an increase in resolution compared to DFT.Lastly, chapter 6 describes the development of PEG-based hyperbranched polymers and pPEGMA-coated gold nanoparticles as EPR imaging agents and sensors. Both nanoparticles have been shown as promising platforms that can be functionalized with targeting ligands and various imaging probes (i.e. a paramagnetic spin label) for the purpose of using multiple molecular imaging modalities for in vivo theranostics. The choice of a spin label dictates the possible application of the final agent, either for EPR imaging or EPR spectroscopy. The preliminary study assessed the sensitivity of commercially available EPR equipment and showed that nitroxides are more suitable for use as a sensor rather than an imaging probe. Future work based on the results in the thesis are discussed at the end of this chapter.

Orientation selective DEER measurements on vinculin tail at X-band frequencies reveal spin label orientations