Electron Paramagnetic Resonance (EPR) Biodosimetry with Human Teeth: A Crucial Technique for Acute and Chronic Exposure Assessment.

ABSTRACT: Radiation exposure is a primary concern in emergency response scenarios and long-term health assessments. Accurate quantification of radiation doses is critical for informed decision-making and patient care. This paper reviews the dose reconstruction technique using both X- and Q-bands, with tooth enamel as a reliable dosimeter. Tooth enamel, due to its exceptional resistance to alteration over time, offers a unique opportunity for assessing both acute and chronic radiation exposures. This review delves into the principles underlying enamel dosimetry, the mechanism of radiation interactions, and dose retention in tooth enamel. We explore state-of-the-art analytical methods, such as electron paramagnetic resonance (EPR) spectroscopy, that accurately estimate low and high doses in acute and chronic exposure. Furthermore, we discuss the applicability of tooth enamel dosimetry in various scenarios, ranging from historical radiological incidents to recent nuclear events or radiological incidents. The ability to reconstruct radiation doses from dental enamel provides a valuable tool for epidemiological studies, validating the assessment of health risks associated with chronic exposures and aiding in the early detection and management of acute radiation incidents. This paper underscores the significance of tooth enamel as an essential medium for radiation dose reconstruction and its broader implications for enhancing radiation protection, emergency response, and public health preparedness. Incorporating enamel EPR dosimetry into standard protocols has the potential to transform the field of radiation assessment, ensuring more accurate and timely evaluations of radiation exposure and its associated risks.

A Low-Cost, Tabletop LOD-EPR System for Nondestructive Quantification of Iron Oxide Nanoparticles in Tissues.

Iron oxide nanoparticles (IONPs) have wide utility in applications from drug delivery to the rewarming of cryopreserved tissues. Due to the complex behavior of IONPs (e.g., uneven particle distribution and aggregation), further developments and clinical translation can be accelerated by having access to a noninvasive method for tissue IONP quantification. Currently, there is no low-cost method to nondestructively track IONPs in tissues across a wide range of concentrations. This work describes the performance of a low-cost, tabletop, longitudinally detected electron paramagnetic resonance (LOD-EPR) system to address this issue in the field of cryopreservation, which utilizes IONPs for rewarming of rat kidneys. A low-cost LOD-EPR system is realized via simultaneous transmit and receive using MHz continuous-wave transverse excitation with kHz modulation, which is longitudinally detected at the modulation frequency to provide both geometric and frequency isolation. The accuracy of LOD-EPR for IONP quantification is compared with NMR relaxometry. Solution measurements show excellent linearity (R2 > 0.99) versus Fe concentration for both measurements on EMG308 (a commercial nanoparticle), silica-coated EMG308, and PEG-coated EMG308 in water. The LOD-EPR signal intensity and NMR longitudinal relaxation rate constant (R1) of water are affected by particle coating, solution viscosity, and particle aggregation. R1 remains linear but with a reduced slope when in cryoprotective agent (CPA) solution, whereas the LOD-EPR signal is relatively insensitive to this. R1 does not correlate well with Fe concentration in rat kidney sections (R2 = 0.3487), while LOD-EPR does (R2 = 0.8276), with a linear regression closely matching that observed in solution and CPA.

Assessment of blood-brain barrier leakage and brain oxygenation in Connexin-32 knockout mice with systemic neuroinflammation using pulse electron paramagnetic resonance imaging techniques.

PURPOSE: The determination of blood-brain barrier (BBB) integrity and partial pressure of oxygen (pO2) in the brain is of substantial interest in several neurological applications. This study aimed to assess the feasibility of using trityl OX071-based pulse electron paramagnetic resonance imaging (pEPRI) to provide a quantitative estimate of BBB integrity and pO2 maps in mouse brains as a function of neuroinflammatory disease progression. METHODS: Five Connexin-32 (Cx32)-knockout (KO) mice were injected with lipopolysaccharide to induce neuroinflammation for imaging. Three wild-type mice were also used to optimize the imaging procedure and as control animals. An additional seven Cx32-KO mice were used to establish the BBB leakage of trityl using the colorimetric assay. All pEPRI experiments were performed using a preclinical instrument, JIVA-25 (25 mT/720 MHz), at times t = 0, 4, and 6 h following lipopolysaccharide injection. Two pEPRI imaging techniques were used: (a) single-point imaging for obtaining spatial maps to outline the brain and calculate BBB leakage using the signal amplitude, and (b) inversion-recovery electron spin echo for obtaining pO2 maps. RESULTS: A statistically significant change in BBB leakage was found using pEPRI with the progression of inflammation in Cx32 KO animals. However, the change in pO2 values with the progression of inflammation for these animals was not statistically significant. CONCLUSIONS: For the first time, we show the ability of pEPRI to provide pO2 maps in mouse brains noninvasively, along with a quantitative assessment of BBB leakage. We expect this study to open new queries from the field to explore the pathology of many neurological diseases and provide a path to new treatments.

Improvement of neutron sensitivity for lithium formate EPR dosemeters: a Monte Carlo analysis.

This work presents the computational analysis of the sensitivity improvements that could be achieved in lithium formate monohydrate (LFM) electron paramagnetic resonance (EPR) dosemeters exposed to neutron beams. Monte Carlo (MC) simulations were performed on LFM pellets exposed to neutron beams with different energy spectra at various depths inside a water phantom. Various computations were carried out by considering different enrichments of 6Li inside the LFM matrix as well as addition of different amounts of gadolinium oxide inside the pellet blend. The energy released per unit mass was calculated with the aim of predicting the increase in dose achievable by the addition of sensitizers inside the pellets. As expected, a larger amount of 6Li induces an increase of energy released because of the charged secondary particles (i.e. 3H ions and α-particles) produced after neutron capture. For small depths in water phantom and low-energy neutron spectra the dose increase due to 6Li enrichment is high (more than three orders of magnitude with respect to the case of with 7Li). In case of epithermal neutron beams the energy released in 6Li-enriched LFM compound is smaller but larger than in the case of fast neutron beams. On the other hand, the computational analysis evidenced that gadolinium is less effective than 6Li in improving neutron sensitivity of the LFM pellets. Discussion based on the features of MC transport code is provided. This result suggests that 6Li enrichment of LFM dosemeters would be more effective for neutron sensitivity improvement and these EPR dosemeters could be tested for dosimetric applications in Neutron Capture Therapy.

Synthesis, characterization, in vitro, in silico and in vivo investigations and biological assessment of Knoevenagel condensate ß-diketone Schiff base transition metal complexes.

A novel Schiff base ligand was synthesized by the Knoevenagel condensation of ß-diketone (obtained from substituted Curcumin and Cuminaldehyde) and 4-amino antipyrine. Metal complexes were made from this Schiff base by reacting with metal salts such as Cu(II), Ni(II), Ru(III), VO(IV), and Ce(IV). Physicochemical approaches such as UV-Vis, FT-IR, NMR, EPR, and Mass spectroscopy were used to determine the geometry of the complexes. The thermodynamic stability and biological accessibility of the complexes were investigated using density functional theory (DFT) calculations at the B3LYP/6-31G(d) level. A molecular docking analysis was also performed on 1BNA receptor. Both the Schiff base ligand and metal complexes interacted well to this protein receptor. All metal complexes have a significant potential to bind to CT DNA via the intercalation mechanism. All the in vivo and in vitro screening studies showed that the complexes exhibit higher activities than the free Schiff base.Communicated by Ramaswamy H. Sarma.

In Vivo Partial Oxygen Pressure Assessment in Subcutaneous and Intraperitoneal Sites Using Imaging of Solid Oxygen Probe.

The purpose of this study was to assess the natural partial oxygen pressure (pO2) of subcutaneous (SC) and intraperitoneal (IP) sites in mice to determine their relative suitability as sites for placement of implants. The pO2 measurements were performed using oxygen imaging of solid probes using lithium phthalocyanine (LiPc) as the oxygen sensitive material. LiPc is a water-insoluble crystalline probe whose spin-lattice and spin-spin relaxation rates (R1 and R2) are sensitive to the local oxygen concentration. To facilitate direct in vivo oxygen imaging, we prepared a solid probe containing encapsulated LiPc crystals in polydimethylsiloxane (PDMS), an oxygen-permeable and bioinert polymer. Although LiPc-PDMS or similar probes have been used in repeated spectroscopic or average oxygen measurements using continuous wave electron paramagnetic resonance (EPR) since the late 1990s and now have advanced to clinical applications, they have not been used for pulse EPR oxygen imaging. One LiPc-PDMS probe of 2 mm diameter and 10 mm length was implanted in SC or IP sites (left or right side) in each animal. The pO2 imaging of implanted LiPc-PDMS probes was performed weekly for 6 weeks using O2M preclinical 25 mT oxygen imager, JIVA-25™, using the pulse inversion recovery electron spin echo method. At week 6, the probes were recovered, and histological examinations were performed. We report in this study, first-ever solid probe oxygen imaging of implanted devices and pO2 assessment of SC and IP sites.

THE RELATIONSHIP BETWEEN HARVEST MANAGEMENT AND CHRONIC WASTING DISEASE PREVALENCE TRENDS IN WESTERN MULE DEER (ODOCOILEUS HEMIONUS) HERDS.

We analyzed retrospective data on harvest management practices and corresponding chronic wasting disease (CWD) prevalence trends in 36 western US and Canadian mule deer (Odocoileus hemionus) management units (units). Our analyses employed logistic regression and model selection, exploiting variation in practices within and among jurisdictions to examine relationships between harvest management and apparent prevalence (the proportion of positive animals among those sampled). Despite notable differences in hunting practices among jurisdictions, our meta-analysis of combined data revealed strong evidence that the amount of harvest was related to CWD prevalence trends among adult male mule deer in the 32 units where prevalence at the start of the analysis period was ≤5%. All competitive models included the number of male deer harvested or number of hunters 1-2 yr prior as an explanatory variable, with increasing harvest leading to lower prevalence among males harvested in the following year. Competitive models also included harvest timing. Although less definitive than the number harvested, median harvest dates falling closer to breeding seasons were associated with lower prevalence in the following year. Our findings suggest harvest-when sufficient and sustained-can be an effective tool for attenuating CWD prevalence in adult male mule deer across western ranges, especially early in the course of an epidemic. Evidence of a broad relationship between the amount of harvest and subsequent changes in CWD prevalence among adult male mule deer provides an empirical basis for undertaking adaptive disease management experimentation aimed at suppressing or curtailing CWD epidemics.

S3 State Models of Nature's Water Oxidizing Complex: Analysis of Bonding and Magnetic Exchange Pathways, Assessment of Experimental Electron Paramagnetic Resonance Data, and Implications for the Water Oxidation Mechanism.

Broken symmetry density functional theory (BS-DFT) calculations on large models of Nature's water oxidizing complex (WOC) are used to investigate the electronic structure and associated magnetic interactions of this key intermediate state. The electronic origins of the ferromagnetic and antiferromagnetic couplings between neighboring Mn ions are investigated and illustrated by using corresponding orbital transformations. Protonation of the O4 and/or O6 atoms leads to large variation in the distribution of spin around the complex with associated changes in its magnetic resonance properties. Models for Sr2+ exchange and methanol addition indicate minor perturbations reflected in slightly altered spin projection coefficients for the Mn1 and Mn2 ions. These are shown to account for the observed changes observed experimentally via electron paramagnetic resonance methods and suggest a reinterpretation of the experimental findings. By comparison with experimental determinations, we show that the spin projections and resulting calculated 55Mn hyperfine couplings support the open cubane form of an oxo (O5)-hydroxo (O6) cluster in all cases with no need to invoke a closed cubane intermediate. The implications of these findings for the water oxidation mechanism are discussed.

Evidence for the Supramolecular Organization of a Bacterial Outer-Membrane Protein from In Vivo Pulse Electron Paramagnetic Resonance Spectroscopy.

In the outer membrane of Gram-negative bacteria, membrane proteins are thought to be organized into domains or islands that play a role in the segregation, movement, and turnover of membrane components. However, there is presently limited information on the structure of these domains or the molecular interactions that mediate domain formation. In the present work, the Escherichia coli outer membrane vitamin B12 transporter, BtuB, was spin-labeled, and double electron-electron resonance was used to measure the distances between proteins in intact cells. These data together with Monte Carlo simulations provide evidence for the presence of specific intermolecular contacts between BtuB monomers that could drive the formation of string-like oligomers. Moreover, the EPR data provide evidence for the location of the interacting interfaces and indicate that lipopolysaccharide mediates the contacts between BtuB monomers.

Rapid Simulation of Unprocessed DEER Decay Data for Protein Fold Prediction.

Despite advances in sampling and scoring strategies, Monte Carlo modeling methods still struggle to accurately predict de novo the structures of large proteins, membrane proteins, or proteins of complex topologies. Previous approaches have addressed these shortcomings by leveraging sparse distance data gathered using site-directed spin labeling and electron paramagnetic resonance spectroscopy to improve protein structure prediction and refinement outcomes. However, existing computational implementations entail compromises between coarse-grained models of the spin label that lower the resolution and explicit models that lead to resource-intense simulations. These methods are further limited by their reliance on distance distributions, which are calculated from a primary refocused echo decay signal and contain uncertainties that may require manual refinement. Here, we addressed these challenges by developing RosettaDEER, a scoring method within the Rosetta software suite capable of simulating double electron-electron resonance spectroscopy decay traces and distance distributions between spin labels fast enough to fold proteins de novo. We demonstrate that the accuracy of resulting distance distributions match or exceed those generated by more computationally intensive methods. Moreover, decay traces generated from these distributions recapitulate intermolecular background coupling parameters even when the time window of data collection is truncated. As a result, RosettaDEER can discriminate between poorly folded and native-like models by using decay traces that cannot be accurately converted into distance distributions using regularized fitting approaches. Finally, using two challenging test cases, we demonstrate that RosettaDEER leverages these experimental data for protein fold prediction more effectively than previous methods. These benchmarking results confirm that RosettaDEER can effectively leverage sparse experimental data for a wide array of modeling applications built into the Rosetta software suite.

Assessment of the manganese cluster's oxidation state via photoactivation of photosystem II microcrystals.

Knowledge of the manganese oxidation states of the oxygen-evolving Mn4CaO5 cluster in photosystem II (PSII) is crucial toward understanding the mechanism of biological water oxidation. There is a 4 decade long debate on this topic that historically originates from the observation of a multiline electron paramagnetic resonance (EPR) signal with effective total spin of S = 1/2 in the singly oxidized S2 state of this cluster. This signal implies an overall oxidation state of either Mn(III)3Mn(IV) or Mn(III)Mn(IV)3 for the S2 state. These 2 competing assignments are commonly known as "low oxidation (LO)" and "high oxidation (HO)" models of the Mn4CaO5 cluster. Recent advanced EPR and Mn K-edge X-ray spectroscopy studies converge upon the HO model. However, doubts about these assignments have been voiced, fueled especially by studies counting the number of flash-driven electron removals required for the assembly of an active Mn4CaO5 cluster starting from Mn(II) and Mn-free PSII. This process, known as photoactivation, appeared to support the LO model since the first oxygen is reported to evolve already after 7 flashes. In this study, we improved the quantum yield and sensitivity of the photoactivation experiment by employing PSII microcrystals that retained all protein subunits after complete manganese removal and by oxygen detection via a custom built thin-layer cell connected to a membrane inlet mass spectrometer. We demonstrate that 9 flashes by a nanosecond laser are required for the production of the first oxygen, which proves that the HO model provides the correct description of the Mn4CaO5 cluster's oxidation states.

Trajectory-Based Simulation of EPR Spectra: Models of Rotational Motion for Spin Labels on Proteins.

Direct time-domain simulation of continuous-wave (CW) electron paramagnetic resonance (EPR) spectra from molecular dynamics (MD) trajectories has become increasingly popular, especially for proteins labeled with nitroxide spin labels. Due to the time-consuming nature of simulating adequately long MD trajectories, two approximate methods have been developed to reduce the MD-trajectory length required for modeling EPR spectra: hindered Brownian diffusion (HBD) and hidden Markov models (HMMs). Here, we assess the accuracy of these two approximate methods relative to direct simulations from MD trajectories for three spin-labeled protein systems (a simple helical peptide, a soluble protein, and a membrane protein) and two nitroxide spin labels with differing mobilities (R1 and 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC)). We find that the HMMs generally outperform HBD. Although R1 dynamics partially resembles hindered Brownian diffusion, HMMs accommodate the multiple dynamic time scales for the transitions between rotameric states of R1 that cannot be captured accurately by a HBD model. The MD trajectories of the TOAC-labeled proteins show that its dynamics closely resembles slow multisite exchange between twist-boat and chair ring puckering states. This motion is modeled well by HMM but not by HBD. All MD-trajectory data processing, stochastic trajectory simulations, and CW EPR spectral simulations are implemented in EasySpin, a free software package for MATLAB.

Positional Distributions of the Tethered Modules in Nitric Oxide Synthase: Monte Carlo Calculations and Pulsed EPR Measurements.

The nitric oxide synthase (NOS) enzyme consists of multiple domains connected by flexible random coil tethers. In a catalytic cycle, the NOS domains move within the limits determined by the length and flexibility of the interdomain tethers and form docking complexes with each other. This process represents a key component of the electron transport from the flavin adenine dinucleotide/reduced nicotinamide adenine dinucleotide phosphate binding domain to the catalytic heme centers located in the oxygenase domain. Studying the conformational behavior of NOS is therefore imperative for a full understanding of the overall catalytic mechanism. In this work, we have investigated the equilibrium positional distributions of the NOS domains and the bound calmodulin (CaM) by using Monte Carlo calculations of the NOS conformations. As a main experimental reference, we have used the magnetic dipole interaction between a bifunctional spin label attached to T34C/S38C mutant CaM and the NOS heme centers, which was measured by pulsed electron paramagnetic resonance. In general, the calculations of the conformational distributions allow one to determine the range and statistics of positions occupied by the tethered protein domains, assess the crowding effect of the multiple domains on each other, evaluate the accessibility of various potential domain docking sites, and estimate the interaction energies required to achieve target populations of the docked states. In the particular application described here, we have established the specific mechanisms by which the bound CaM facilitates the flavin mononucleotide (FMN)/heme interdomain docking in NOS. We have also shown that the intersubunit FMN/heme domain docking and electron transfer in the homodimeric NOS protein are dictated by the existing structural makeup of the protein. Finally, from comparison of the calculated and experimental docking probabilities, the characteristic stabilization energies for the CaM/heme domain and the FMN domain/heme domain docking complexes have been estimated as -4.5kT and -10.5kT, respectively.

Assessment of the Relaxation-Enhancing Properties of a Nitroxide-Based Contrast Agent TEEPO-Glc with In Vivo Magnetic Resonance Imaging.

Magnetic resonance imaging examinations are frequently carried out using contrast agents to improve the image quality. Practically all clinically used contrast agents are based on paramagnetic metals and lack in selectivity and specificity. A group of stable organic radicals, nitroxides, has raised interest as new metal-free contrast agents for MRI. Their structures can easily be modified to incorporate different functionalities. In the present study, a stable nitroxide TEEPO (2,2,6,6-tetraethylpiperidin-1-oxyl) was linked to a glucose moiety (Glc) to construct a water-soluble, potentially tumor-targeting compound with contrast-enhancing ability. The ability was assessed with in vivo MRI experiments. The constructed TEEPO-Glc agent proved to shorten the T 1 relaxation time in tumor, while the T 1 time in healthy brain tissue remained the same. The results indicate the potential of TEEPO-Glc as a valuable addition to the growing field of metal-free contrast enhancement in MRI-based diagnostics.

Direct and indirect assessment of cancer metabolism explored by MRI.

Magnetic resonance-based approaches to obtain metabolic information on cancer have been explored for decades. Electron paramagnetic resonance (EPR) has been developed to pursue metabolic profiling and successfully used to monitor several physiologic parameters such as pO2 , pH, and redox status. All these parameters are associated with pathophysiology of various diseases. Especially in oncology, cancer hypoxia has been intensively studied because of its relationship with metabolic alterations, acquiring treatment resistance, or a malignant phenotype. Thus, pO2 imaging leads to an indirect metabolic assessment in this regard. Proton electron double-resonance imaging (PEDRI) is an imaging technique to visualize EPR by using the Overhauser effect. Most biological parameters assessed in EPR can be visualized using PEDRI. However, EPR and PEDRI have not been evaluated sufficiently for clinical application due to limitations such as toxicity of the probes or high specific absorption rate. Hyperpolarized (HP) 13 C MRI is a novel imaging technique that can directly visualize the metabolic profile. Production of metabolites of the HP 13 C probe delivered to target tissue are evaluated in this modality. Unlike EPR or PEDRI, which require the injection of radical probes, 13 C MRI requires a probe that can be physiologically metabolized and efficiently hyperpolarized. Among several methods for hyperpolarizing probes, dissolution dynamic nuclear hyperpolarization is a widely used technique for in vivo imaging. Pyruvate is the most suitable probe for HP 13 C MRI because it is part of the glycolytic pathway and the high efficiency of pyruvate-to-lactate conversion is a distinguishing feature of cancer. Its clinical applicability also makes it a promising metabolic imaging modality. Here, we summarize the applications of these indirect and direct MR-based metabolic assessments focusing on pO2 and pyruvate-to-lactate conversion. The two parameters are strongly associated with each other, hence the acquired information is potentially interchangeable when evaluating treatment response to oxygen-dependent cancer therapies.

Multifaceted assessment of the APP/PS1 mouse model for Alzheimer's disease: Applying MRS, DTI, and ASL.

Transgenic animal models of Alzheimer's disease (AD) can mimic pathological and behavioral changes occurring in AD patients, and are usually viewed as the first choice for testing novel therapeutics. Validated biomarkers, particularly non-invasive ones, are urgently needed for AD diagnosis or evaluation of treatment results. However, there are few studies that systematically characterize pathological changes in AD animal models. Here, we investigated the brain of 8-month-old amyloid precursor protein/presenilin 1 (APP/PS1) transgenic and wild-type (WT) mice, employing 7.0-T magnetic resonance imaging (MRI). Magnetic resonance spectroscopy (MRS), diffusion tensor imaging (DTI), and arterial spin labeling (ASL) were obtained through micro-MRI scanning. After MRI examination in both transgenic (n = 12) and WT (n = 12) mice, immunohistochemical staining and ultrastructural analysis were subsequently performed. Cerebral blood flow (CBF) was significantly decreased in the left hippocampus, left thalamus, and right cortex of AD mice (P < 0.05). Moreover, MRS showed significantly changed NAA/Cr, Glu/Cr, and mI/Cr ratios in the hippocampus of transgenic mice. While only NAA/Cr and mI/Cr ratios varied significantly in the cortex of transgenic mice. Regarding DTI imaging, however, the values of FA, MD, DA and DR were not significantly different between transgenic and WT mice. Finally, it is worth noting that pathological damage of metabolism, CBF, and white matter was more distinct between transgenic and WT mice by pathological examination. Altogether, our results suggest that intravital imaging evaluation of 8-month-old APP/PS1 transgenic mice by MRS and ASL is an alternative tool for AD research.

In Vivo EPR Assessment of pH, pO2, Redox Status, and Concentrations of Phosphate and Glutathione in the Tumor Microenvironment.

This protocol demonstrates the capability of low-field electron paramagnetic resonance (EPR)-based techniques in combination with functional paramagnetic probes to provide quantitative information on the chemical tumor microenvironment (TME), including pO2, pH, redox status, concentrations of interstitial inorganic phosphate (Pi), and intracellular glutathione (GSH). In particular, an application of a recently developed soluble multifunctional trityl probe provides unsurpassed opportunity for in vivo concurrent measurements of pH, pO2 and Pi in Extracellular space (HOPE probe). The measurements of three parameters using a single probe allow for their correlation analyses independent of probe distribution and time of the measurements.

A [4Fe-4S]-Fe(CO)(CN)-L-cysteine intermediate is the first organometallic precursor in [FeFe] hydrogenase H-cluster bioassembly.

Biosynthesis of the [FeFe] hydrogenase active site (the 'H-cluster') requires the interplay of multiple proteins and small molecules. Among them, the radical S-adenosylmethionine enzyme HydG, a tyrosine lyase, has been proposed to generate a complex that contains an Fe(CO)2(CN) moiety that is eventually incorporated into the H-cluster. Here we describe the characterization of an intermediate in the HydG reaction: a [4Fe-4S][(Cys)Fe(CO)(CN)] species, 'Complex A', in which a CO, a CN- and a cysteine (Cys) molecule bind to the unique 'dangler' Fe site of the auxiliary [5Fe-4S] cluster of HydG. The identification of this intermediate-the first organometallic precursor to the H-cluster-validates the previously hypothesized HydG reaction cycle and provides a basis for elucidating the biosynthetic origin of other moieties of the H-cluster.

Theory and practice of using solvent paramagnetic relaxation enhancement to characterize protein conformational dynamics.

Paramagnetic relaxation enhancement (PRE) has been established as a powerful tool in NMR for investigating protein structure and dynamics. The PRE is usually measured with a paramagnetic probe covalently attached at a specific site of an otherwise diamagnetic protein. The present work provides the numerical formulation for probing protein structure and conformational dynamics based on the solvent PRE (sPRE) measurement, using two alternative approaches. An inert paramagnetic cosolute randomly collides with the protein, and the resulting sPRE manifests the relative solvent exposure of protein nuclei. To make the back-calculated sPRE values most consistent with the observed values, the protein structure is either refined against the sPRE, or an ensemble of conformers is selected from a pre-generated library using a Monte Carlo algorithm. The ensemble structure comprises either N conformers of equal occupancy, or two conformers with different relative populations. We demonstrate the sPRE method using GB1, a structurally rigid protein, and calmodulin, a protein comprising two domains and existing in open and closed states. The sPRE can be computed with a stand-alone program for rapid evaluation, or with the invocation of a module in the latest release of the structure calculation software Xplor-NIH. As a label-free method, the sPRE measurement can be readily integrated with other biophysical techniques. The current limitations of the sPRE method are also discussed, regarding accurate measurement and theoretical calculation, model selection and suitable timescale.

Integrated Structural Biology for α-Helical Membrane Protein Structure Determination.

While great progress has been made, only 10% of the nearly 1,000 integral, α-helical, multi-span membrane protein families are represented by at least one experimentally determined structure in the PDB. Previously, we developed the algorithm BCL::MP-Fold, which samples the large conformational space of membrane proteins de novo by assembling predicted secondary structure elements guided by knowledge-based potentials. Here, we present a case study of rhodopsin fold determination by integrating sparse and/or low-resolution restraints from multiple experimental techniques including electron microscopy, electron paramagnetic resonance spectroscopy, and nuclear magnetic resonance spectroscopy. Simultaneous incorporation of orthogonal experimental restraints not only significantly improved the sampling accuracy but also allowed identification of the correct fold, which is demonstrated by a protein size-normalized transmembrane root-mean-square deviation as low as 1.2 Å. The protocol developed in this case study can be used for the determination of unknown membrane protein folds when limited experimental restraints are available.