Paramagnetic Label Research Articles

Temperature-Dependent Rotation of Protonated Methyl Groups in Otherwise Deuterated Proteins Modulates DEER Distance Distributions

AbstractTemperature-dependent DEER effects are observed as a function of methyl rotation by either leucine- or nitroxide-specific protonated methyl groups in an otherwise deuterated background. Both species induce a site-specific enhancement in the apparent Tm relaxation of the paramagnetic nitroxide label. The presence of a single protonated methyl group in close proximity (4–10 Å) to only one of the two nitroxide rotamer ensembles in AviTagged immunoglobulin-binding B domain of protein A results in a selective and substantial decrease in Tm, manifested by differential decay of the peak intensities in the bimodal P(r) distance distribution as a function of the total dipolar evolution time, temperature, or both. The temperature-dependent differential decay of the individual distance components was globally analyzed by fitting the DEER dipolar time traces to a three-site jump model that is defined by the activation energy of leucine- or nitroxide-specific methyl rotation. Temperature-assisted Tm filtering will capture the DEER structural analysis of biomolecular systems heterogenic conformations, including complexes involving multimeric proteins.

Structural Flexibility of Tau in Its Interaction with Microtubules as Viewed by Site-Directed Spin Labeling EPR Spectroscopy.

Tau is a microtubule-associated protein that belongs to the Intrinsically Disordered Proteins (IDPs) family. IDPs or Intrinsically Disordered Regions (IDRs) play key roles in protein interaction networks and their dysfunctions are often related to severe diseases. Defined by their lack of stable secondary and tertiary structures in physiological conditions while being functional, these proteins use their inherent structural flexibility to adapt to and interact with various binding partners. Knowledges on the structural dynamics of IDPs and their different conformers are crucial to finely decipher fundamental biological processes controlled by mechanisms such as conformational adaptations or switches, induced fit, or conformational selection events. Different mechanisms of binding have been proposed: among them, the so-called folding-upon-binding in which the IDP adopts a certain conformation upon interacting with a partner protein, or the formation of a "fuzzy" complex in which the IDP partly keeps its dynamical character at the surface of its partner. The dynamical nature and physicochemical properties of unbound as well as bound IDPs make this class of proteins particularly difficult to characterize by classical bio-structural techniques and require specific approaches for the fine description of their inherent dynamics.Among other techniques, Site-Directed Spin Labeling combined with Electron Paramagnetic Resonance (SDSL-EPR) spectroscopy has gained much interest in this last decade for the study of IDPs. SDSL-EPR consists in grafting a paramagnetic label (mainly a nitroxide radical) at selected site(s) of the macromolecule under interest followed by its observation using and/or combining different EPR strategies. These nitroxide spin labels detected by continuous wave (cw) EPR spectroscopy are used as perfect reporters or "spy spins" of their local environment, being able to reveal structural transitions, folding/unfolding events, etc. Another approach is based on the measurement of inter-label distance distributions in the 1.5-8.0nm range using pulsed dipolar EPR experiments, such as Double Electron-Electron Resonance (DEER) spectroscopy. The technique is then particularly well suited to study the behavior of Tau in its interaction with its physiological partner: microtubules (MTs). In this chapter we provide a detailed experimental protocol for the labeling of Tau protein and its EPR study while interacting with preformed (Paclitaxel-stabilized) MTs, or using Tau as MT inducer. We show how the choice of nitroxide label can be crucial to obtain functional information on Tau/tubulin complexes.

Dilute Bicelles for Glycosyltransferase Studies, Novel Bicelles with Phosphatidylinositol.

Solution-state NMR can be used to study protein–lipid interactions, in particular, the effect that proteins have on lipids. One drawback is that only small assemblies can be studied, and therefore, fast-tumbling bicelles are commonly used. Bicelles contain a lipid bilayer that is solubilized by detergents. A complication is that they are only stable at high concentrations, exceeding the CMC of the detergent. This issue has previously been addressed by introducing a detergent (Cyclosfos-6) with a substantially lower CMC. Here, we developed a set of bicelles using this detergent for studies of membrane-associated mycobacterial proteins, for example, PimA, a key enzyme for bacterial growth. To mimic the lipid composition of mycobacterial membranes, PI, PG, and PC lipids were used. Diffusion NMR was used to characterize the bicelles, and spin relaxation was used to measure the dynamic properties of the lipids. The results suggest that bicelles are formed, although they are smaller than “conventional” bicelles. Moreover, we studied the effect of MTSL-labeled PimA on bicelles containing PI and PC. The paramagnetic label was shown to have a shallow location in the bicelle, affecting the glycerol backbone of the lipids. We foresee that these bicelles will be useful for detailed studies of protein–lipid interactions.

Lanthanide complexes with polyaminopolycarboxylates as prospective NMR/MRI diagnostic probes: peculiarities of molecular structure, dynamics and paramagnetic properties.

The paramagnetic lanthanide complexes with polyaminopolycarboxylate (PAPC) ligands attract considerable attention from the standpoint of potential applications thereof as relaxation agents used in medical magnetic resonance imaging (MRI) and in luminescent materials, as well as owing to promising use thereof as paramagnetic labels for studying the properties of biopolymers since they exhibit thermodynamic stability, good solubility in aqueous media and moderate toxicity. For the last decades, the NMR methods have been used to determine the physical and chemical properties of paramagnetic Ln compounds. The studies concerning paramagnetic NMR lanthanide-induced shifts (LISs) in dissolved Ln complexes, as well as the analysis of band shape as a function of temperature make it possible to obtain valuable information on the structure, intra- and intermolecular dynamics and paramagnetic properties thereof. This review is devoted solely to the following features: firstly, the processes of intramolecular dynamics of lanthanide complexes with polyamino-polycarboxylate ligands such as DOTA, EDTA and DTPA and their derivatives studied by NMR; secondly, the LISs of lanthanide complexes with EDTA, DOTA, DTPA and some of their derivatives depending on temperature and pH. Moreover, in this review, for the first time, the dependence of the activation energy of molecular dynamics in complexes with polydentate ligands on the atomic number of the lanthanide cation is analyzed and a monotonic change in energy is detected, which is due to the effect of lanthanide contraction. It should be noted that this phenomenon is quite general and may also appear in the future in many other series of lanthanide complexes with both other multidentate ligands and with bidentate and monodentate ligands. In the future, it is possible to predict the dependence of the properties of certain lanthanide complexes on the ionic radius of the lanthanide cation based on the approaches presented in the review. In this review, we have also presented the dynamic NMR as the main research method widely used to analyze the processes of molecular dynamics, and the structural studies based on the NMR relaxation spectroscopy and LIS analysis.

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.

Paramagnetic spin labeling of a bacterial DnaB helicase for solid-state NMR

Labeling of biomolecules with a paramagnetic probe for nuclear magnetic resonance (NMR) spectroscopy enables determining long-range distance restraints, which are otherwise not accessible by classically used dipolar coupling-based NMR approaches. Distance restraints derived from paramagnetic relaxation enhancements (PREs) can facilitate the structure determination of large proteins and protein complexes. We herein present the site-directed labeling of the large oligomeric bacterial DnaB helicase from Helicobacter pylori with cysteine-reactive maleimide tags carrying either a nitroxide radical or a lanthanide ion. The success of the labeling reaction was followed by quantitative continuous-wave electron paramagnetic resonance (EPR) experiments performed on the nitroxide-labeled protein. PREs were extracted site-specifically from 2D and 3D solid-state NMR spectra. A good agreement with predicted PRE values, derived by computational modeling of nitroxide and Gd3+ tags in the low-resolution DnaB crystal structure, was found. Comparison of experimental PREs and model-predicted spin label-nucleus distances indicated that the size of the “blind sphere” around the paramagnetic center, in which NMR resonances are not detected, is slightly larger for Gd3+ (∼14 Å) than for nitroxide (∼11 Å) in 13C-detected 2D spectra of DnaB. We also present Gd3+-Gd3+ dipolar electron–electron resonance EPR experiments on DnaB supporting the conclusion that DnaB was present as a hexameric assembly.

Paramagnetic Spin Labeling of a Bacterial DnaB Helicase for Solid-State NMR

Paramagnetic Spin Labeling of a Bacterial DnaB Helicase for Solid-State NMR

Resolving distance variations by single-molecule FRET and EPR spectroscopy using rotamer libraries

Förster resonance energy transfer (FRET) and electron paramagnetic resonance (EPR) spectroscopy are complementary techniques for quantifying distances in the nanometer range. Both approaches are commonly employed for probing the conformations and conformational changes of biological macromolecules based on site-directed fluorescent or paramagnetic labeling. FRET can be applied in solution at ambient temperature and thus provides direct access to dynamics, especially if used at the single-molecule level, whereas EPR requires immobilization or work at cryogenic temperatures but provides data that can be more reliably used to extract distance distributions. However, a combined analysis of the complementary data from the two techniques has been complicated by the lack of a common modeling framework. Here, we demonstrate a systematic analysis approach based on rotamer libraries for both FRET and EPR labels to predict distance distributions between two labels from a structural model. Dynamics of the fluorophores within these distance distributions are taken into account by diffusional averaging, which improves the agreement with experiment. Benchmarking this methodology with a series of surface-exposed pairs of sites in a structured protein domain reveals that the lowest resolved distance differences can be as small as ∼0.25 nm for both techniques, with quantitative agreement between experimental and simulated transfer efficiencies within a range of ±0.045. Rotamer library analysis thus establishes a coherent way of treating experimental data from EPR and FRET and provides a basis for integrative structural modeling, including studies of conformational distributions and dynamics of biological macromolecules using both techniques.

High-performance porphyrin-like graphene quantum dots for immuno-sensing of Salmonella typhi

The extraordinary optical properties of porphyrins have inspired their applications in various fields. Herein, we introduce iron porphyrin bio-mimicked graphene quantum dots (Fe–N-GQDs) as a novel paramagnetic and fluorescent label. The Fe–N-GQD was prepared by the mechanochemical mixing of Fe, N, and C sources followed by pyrolysis at high-temperature and next, the solvothermal treatment was performed. The Fe–N sites in graphene matrix, the structural alterations during the solvothermal treatment, the optical properties, and paramagnetic behaviour were studied using FTIR, Raman and X-ray spectroscopies, and Vibrating sample magnetometer. The structural studies revealed that under solvothermal condition, Fe–N doped graphene sheets cut into ultra-small Fe–N-GQDs containing well-dispersed particles with an average diameter of about 2.5 nm. As a result of Fe–N doping, the photoluminescence quantum yield was enhanced to 86% and strong paramagnetic behaviour was observed. Due to the rich oxygen-containing groups at Fe–N-GQDs surface, it has proper sites for bio-conjugation. The bioconjugated Fe–N-GQDs serve as donors in a prominent fluorescence resonance energy transfer system, while graphene oxide acts as an acceptor. The proposed immunosensor was successfully applied for the detection of Salmonella Typhi Vi antigen in real human serum in the concentration range from 1 pg/mL to 1 μg/mL with the detection limit of 1 pg/mL.

How Effective are Retro-Inverso Peptides? Insights from MD Supported by Paramagnetic NMR Data

Early MD simulations were largely limited to observation of fast structural fluctuations in protein molecules. With recent advent of GPU computing, it became possible to model far more relevant dynamic processes: protein folding, ligand binding, allostery, etc. In our study, we use long unbiased MD simulations to model binding of the so-called retro-inverso (ri) peptide to its protein target. Retro-inverso peptides are designed from native peptides by replacing L-amino acids with D-amino acids and inverting the amino-acid sequence. They are believed to retain the binding affinity of their parent peptides, while being resistant to proteolytic degradation. We investigated the binding of retro-inverso peptide ri-Sos1 (rrrppvpppv) to N-terminal SH3 domain from adaptor protein Grb2. The peptide was initially placed in a random position inside a large simulation cell. During the course of the simulation, we observed the binding of ri-Sos1 at the canonical SH3 binding site. The resulting complex features a number of key hydrogen bonds that are similar to the ones found in the native Sos1/Grb2 N-SH3 structure. However, the pattern of these interactions has undergone some noticeable rearrangements. We argue that the concept of retro-inversion lacks any solid theoretical justification and, therefore, ri-peptides are only poor imitators of their parent peptides. To validate our findings, we conducted a number of NMR experiments. In particular, we used the peptides crrrppvpppv and rrrppvpppvc tagged with paramagnetic label MTSL to measure paramagnetic relaxation enhancements (PRE) in Grb2 N-SH3. The results were compared with the PRE rates rigorously calculated from the MD trajectories involving the two respective MTSL-tagged peptides. The 1HN,15N-HSQC-based titration data showed that ri-Sos1 is a much weaker binder than the original Sos1, thus confirming the tenuous nature of ri-peptide ligands. We acknowledge grant support from SPbU 51142660.

High-Spin Cobalt(II) Complex with Record-Breaking Anisotropy of the Magnetic Susceptibility According to Paramagnetic NMR Spectroscopy Data

The tetrahedral cobalt(II) complex [CoL2](HNEt3)2 (I), where L is 1,2-bis(methanesulfonamido)benzene, exhibiting the properties of a single-molecule magnet is synthesized and characterized. The electronic structure parameters of complex I are determined by paramagnetic NMR spectroscopy. They completely reproduce the results of less available methods of studying single-molecule magnets. The value of axial anisotropy of the magnetic susceptibility estimated for complex I (Δχax = 34.5 × 10–32 m3 at 20°C) is record-breaking among all transition metal complexes studied by the NMR method, which provides wide possibilities for the use of complex I as a paramagnetic label for structural biology or as a contrast agent and even a temperature sensor for medical diagnostics. The data obtained indicate the advantages of paramagnetic NMR spectroscopy as a method of investigation of the magnetic properties and electronic structures of highly anisotropic transition metal complexes, which are precursors of many functional materials.

Phosphorylation of Troponin I finely controls the positioning of Troponin for the optimal regulation of cardiac muscle contraction

Troponin is the Ca2+ molecular switch that regulates striated muscle contraction. In the heart, troponin Ca2+ sensitivity is also modulated by the PKA-dependent phosphorylation of a unique 31-residue N-terminal extension region of the Troponin I subunit (NH2-TnI). However, the detailed mechanism for the propagation of the phosphorylation signal through Tn, which results in the enhancement of the myocardial relaxation rate, is difficult to examine within whole Tn. Several models exist for how phosphorylation modulates the troponin response in cardiac cells but these are mostly built from peptide-NMR studies and molecular dynamics simulations. Here we used a paramagnetic spin labeling approach to position and track the movement of the NH2-TnI region within whole Tn. Through paramagnetic relaxation enhancement (PRE)-NMR experiments, we show that the NH2-TnI region interacts with a broad surface area on the N-domain of the Troponin C subunit. This region includes the Ca2+ regulatory Site II and the TnI switch-binding site. Phosphorylation of the NH2-TnI both weakens and shifts this region to an adjacent site on TnC. Interspin EPR distances between NH2-TnI and TnC further reveal a phosphorylation induced re-orientation of the TnC N-domain under saturating Ca2+ conditions. We propose an allosteric model where phosphorylation triggered cooperative changes in both the interaction of the NH2-TnI region with TnC, and the re-orientation of the TnC interdomain orientation, together promote the release of the TnI switch-peptide. Enhancement of the myocardial relaxation rate then occurs. Knowledge of this unique role of phosphorylation in whole Tn is important for understanding pathological processes affecting the heart.

Membrane dynamics in Leishmania amazonensis and antileishmanial activities of β-carboline derivatives

Two β-carboline compounds, 8i and 6d, demonstrated in vitro antileishmanial activity against Leishmania (L.) amazonensis promastigotes similar to that of miltefosine (MIL). Estimates of the membrane-water partition coefficient (KM/W) and the compound concentrations in the membrane (cm50) and aqueous phase (cw50) for half maximal inhibitory concentration were made. Whereas these biophysical parameters for 6d were not significantly different from those reported for MIL, 8i showed lower affinity for the parasite membrane (lower KM/W) and a lower concentration of the compound in the membrane required to inhibit the growth of the parasite (lower cm50). A 2-hour treatment of Leishmania promastigotes with the compounds 8i and 6d caused membrane rigidity in a concentration-dependent manner, as demonstrated by the electron paramagnetic resonance (EPR) technique and spin label method. This increased rigidity of the membrane was interpreted to be associated with the occurrence of cross-linking of oxidized cytoplasmic proteins to the parasite membrane skeleton. Importantly, the two β-carboline-oxazoline derivatives showed low hemolytic action, both in experiments with isolated red blood cells or with whole blood, denoting their great Leishmania/erythrocyte selectivity index. Using electron microscopy, changes in the membrane of both the amastigote and promastigote form of the parasite were confirmed, and it was demonstrated that compounds 8i and 6d decreased the number of amastigotes in infected murine macrophages. Furthermore, 8i and 6d were more toxic to the protozoa than to J774A.1 macrophages, with treated promastigotes exhibiting a decrease in cell volume, mitochondrial membrane potential depolarization, accumulation of lipid bodies, increased ROS production and changes in the cell cycle.

Metal‐Chelated Polymer Nanodiscs for NMR Studies

AbstractParamagnetic relaxation enhancement (PRE) is commonly used to speed up spin lattice relaxation time (T1) for rapid data acquisition in NMR structural studies. Consequently, there is significant interest in novel paramagnetic labels for enhanced NMR studies on biomolecules. Herein, we report the synthesis and characterization of a modified poly(styrene‐co‐maleic acid) polymer which forms nanodiscs while showing the ability to chelate metal ions. Cu2+‐chelated nanodiscs are demonstrated to reduce the T1 of protons for both polymer and lipid‐nanodisc components. The chelated nanodiscs also decrease the proton T1 values for a water‐soluble DNA G‐quadruplex. These results suggest that polymer nanodiscs functionalized with paramagnetic tags can be used to speed‐up data acquisition from lipid bilayer samples and also to provide structural information from water‐soluble biomolecules.

Metal-Chelated Polymer Nanodiscs for NMR Studies.

Paramagnetic relaxation enhancement (PRE) is commonly used to speed up spin lattice relaxation time (T1 ) for rapid data acquisition in NMR structural studies. Consequently, there is significant interest in novel paramagnetic labels for enhanced NMR studies on biomolecules. Herein, we report the synthesis and characterization of a modified poly(styrene-co-maleic acid) polymer which forms nanodiscs while showing the ability to chelate metal ions. Cu2+ -chelated nanodiscs are demonstrated to reduce the T1 of protons for both polymer and lipid-nanodisc components. The chelated nanodiscs also decrease the proton T1 values for a water-soluble DNA G-quadruplex. These results suggest that polymer nanodiscs functionalized with paramagnetic tags can be used to speed-up data acquisition from lipid bilayer samples and also to provide structural information from water-soluble biomolecules.

Paramagnetic-iterative relaxation matrix approach: extracting PRE-restraints from NOESY spectra for 3D structure elucidation of biomolecules.

Paramagnetic relaxation enhancement (PRE) can be used to determine long-range distance restraints in biomolecules. The PREs are typically determined by analysis of intensity differences in HSQC experiments of paramagnetic and diamagnetic spin labels. However, this approach requires both isotope- and spin-labelling. Herein, we report a novel method to evaluate NOESY intensities in the presence of a paramagnetic moiety to determine PRE restraints. The advantage of our approach over HSQC-based approaches is the increased number of available signals without the need for isotope labelling. NOESY intensities affected by a paramagnetic center were evaluated during a structure calculation within the paramagnetic iterative relaxation matrix approach (P-IRMA). We applied P-IRMA to a 14-mer RNA with a known NMR solution structure, which allowed us to assess the quality of the PRE restraints. To this end, three different spin labels have been attached at different positions of the 14-mer to test the influence of flexibility on the structure calculation. Structural disturbances introduced by the spin label have been evaluated by chemical shift analysis. Furthermore, the impact of P-IRMA on the quality of the structure bundles were tested by intentionally leaving out available diamagnetic restraints. Our analyses show that P-IRMA is a powerful tool to refine RNA structures for systems that are insufficiently described by using only diamagnetic restraints.

The Hunt for the Closed Conformation of the Fruit‐Ripening Enzyme 1‐Aminocyclopropane‐1‐carboxylic Oxidase: A Combined Electron Paramagnetic Resonance and Molecular Dynamics Study

1-Aminocyclopropane-1-carboxylic oxidase (ACCO) is a non-heme iron(II)-containing enzyme involved in the biosynthesis of the phytohormone ethylene, which regulates fruit ripening and flowering in plants. The active conformation of ACCO, and in particular that of the C-terminal part, remains unclear and open and closed conformations have been proposed. In this work, a combined experimental and computational study to understand the conformation and dynamics of the C-terminal part is reported. Site-directed spin-labeling coupled to electron paramagnetic resonance (SDSL-EPR) spectroscopy was used. Mutagenesis experiments were performed to generate active enzymes bearing two paramagnetic labels (nitroxide radicals) anchored on cysteine residues, one in the main core and one in the C-terminal part. Inter-spin distance distributions were measured by pulsed EPR spectroscopy and compared with the results of molecular dynamics simulations. The results reveal the existence of a flexibility of the C-terminal part. This flexibility generates several conformations of the C-terminal part of ACCO that correspond neither to the existing crystal structures nor to the modelled structures. This highly dynamic region of ACCO raises questions on its exact function during enzymatic activity.

Integrative Protein Modeling in RosettaNMR from Sparse Paramagnetic Restraints

Computational methods to predict protein structure from nuclear magnetic resonance (NMR) restraints that only require assignment of backbone signals, hold great potential to study larger proteins. Ideally, computational methods designed to work with sparse data need to add atomic detail that is missing in the experimental restraints. We introduce a comprehensive framework into the Rosetta suite that uses NMR restraints derived from paramagnetic labeling. Specifically, RosettaNMR incorporates pseudocontact shifts, residual dipolar couplings, and paramagnetic relaxation enhancements. It continues to use backbone chemical shifts and nuclear Overhauser effect distance restraints. We assess RosettaNMR for protein structure prediction by folding 28 monomeric proteins and 8 homo-oligomeric proteins. Furthermore, the general applicability of RosettaNMR is demonstrated on two protein-protein and three protein-ligand docking examples. Paramagnetic restraints generated more accurate models for 85% of the benchmark proteins and, when combined with chemical shifts, sampled high-accuracy models (≤2Å) in 50% of the cases.

Chemical Modification of 1-Aminocyclopropane Carboxylic Acid (ACC) Oxidase: Cysteine Mutational Analysis, Characterization, and Bioconjugation with a Nitroxide Spin Label.

1-Aminocyclopropane carboxylic acid oxidase (ACCO) catalyzes the last step of ethylene biosynthesis in plants. Although some sets of structures have been described, there are remaining questions on the active conformation of ACCO and in particular, on the conformation and potential flexibility of the C-terminal part of the enzyme. Several techniques based on the introduction of a probe through chemical modification of amino acid residues have been developed for determining the conformation and dynamics of proteins. Cysteine residues are recognized as convenient targets for selective chemical modification of proteins, thanks to their relatively low abundance in protein sequences and to their well-mastered chemical reactivity. ACCOs have generally 3 or 4 cysteine residues in their sequences. By a combination of approaches including directed mutagenesis, activity screening on cell extracts, biophysical and biochemical characterization of purified enzymes, we evaluated the effect of native cysteine replacement and that of insertion of cysteines on the C-terminal part in tomato ACCO. Moreover, we have chosen to use paramagnetic labels targeting cysteine residues to monitor potential conformational changes by electron paramagnetic resonance (EPR). Given the level of conservation of the cysteines in ACCO from different plants, this work provides an essential basis for the use of cysteine as probe-anchoring residues.

Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP.

Mechanistic understanding of dynamic membrane proteins such as transporters, receptors, and channels requires accurate depictions of conformational ensembles, and the manner in which they interchange as a function of environmental factors including substrates, lipids, and inhibitors. Spectroscopic techniques such as electron spin resonance (ESR) pulsed electron-electron double resonance (PELDOR), also known as double electron-electron resonance (DEER), provide a complement to atomistic structures obtained from x-ray crystallography or cryo-EM, since spectroscopic data reflect an ensemble and can be measured in more native solvents, unperturbed by a crystal lattice. However, attempts to interpret DEER data are frequently stymied by discrepancies with the structural data, which may arise due to differences in conditions, the dynamics of the protein, or the flexibility of the attached paramagnetic spin labels. Recently, molecular simulation techniques such as EBMetaD have been developed that create a conformational ensemble matching an experimental distance distribution while applying the minimal possible bias. Moreover, it has been proposed that the work required during an EBMetaD simulation to match an experimentally determined distribution could be used as a metric with which to assign conformational states to a given measurement. Here, we demonstrate the application of this concept for a sodium-coupled transport protein, BetP. Because the probe, protein, and lipid bilayer are all represented in atomic detail, the different contributions to the work, such as the extent of protein backbone movements, can be separated. This work therefore illustrates how ranking simulations based on EBMetaD can help to bridge the gap between structural and biophysical data and thereby enhance our understanding of membrane protein conformational mechanisms.