Project description:It has been over two decades since paramagnetic NMR started to form part of the essential techniques for structural analysis of proteins under physiological conditions. Paramagnetic NMR has significantly expanded our understanding of the inherent flexibility of proteins, in particular, those that are formed by combinations of two or more domains. Here, we present a brief overview of techniques to characterize conformational ensembles of such multi-domain proteins using paramagnetic NMR restraints produced through anisotropic metals, with a focus on the basics of anisotropic paramagnetic effects, the general procedures of conformational ensemble reconstruction, and some representative reweighting approaches.
Project description:Residual dipolar couplings (RDCs) are widely used as orientation-dependent NMR restraints to improve the resolution of the NMR conformational ensemble of biomacromolecules and define the relative orientation of multidomain proteins and protein complexes. However, the interpretation of RDCs is complicated by the intrinsic degeneracy of analytical solutions and protein dynamics that lead to ill-defined orientations of the structural domains (ghost orientations). Here, we illustrate how restraints from paramagnetic relaxation enhancement (PRE) experiments lift the orientational ambiguity of multidomain membrane proteins solubilized in detergent micelles. We tested this approach on monomeric phospholamban (PLN), a 52-residue membrane protein, which is composed of two helical domains connected by a flexible loop. We show that the combination of classical solution NMR restraints (NOEs and dihedral angles) with RDC and PRE constraints resolves topological ambiguities, improving the convergence of the PLN structural ensemble and giving the depth of insertion of the protein within the micelle. The combination of RDCs with PREs will be necessary for improving the accuracy and precision of membrane protein conformational ensembles, where three-dimensional structures are dictated by interactions with the membrane-mimicking environment rather than compact tertiary folds common in globular proteins.
Project description:Quaternary distance restraints are essential to define the three-dimensional structures of protein assemblies. These distances often fall within a range of 10-18 Å, which challenges the high and low measurement limits of conventional nuclear magnetic resonance (NMR) and double electron-electron resonance electron spin resonance spectroscopies. Here, we report the use of 19F paramagnetic relaxation enhancement (PRE) NMR in combination with 19F/paramagnetic labeling to equivalent sites in different subunits of a protein complex in micelles to determine intersubunit distances. The feasibility of this strategy was evaluated on a pentameric ligand-gated ion channel, for which we found excellent agreement of the 19F PRE NMR results with previous structural information. The study suggests that 19F PRE NMR is a viable tool in extracting distance restraints to define quaternary structures.
Project description:High-quality solid-state (17)O (I=5/2) NMR spectra can be successfully obtained for paramagnetic coordination compounds in which oxygen atoms are directly bonded to the paramagnetic metal centers. For complexes containing V(III) (S=1), Cu(II) (S=1/2), and Mn(III) (S=2) metal centers, the (17)O isotropic paramagnetic shifts were found to span a range of more than 10,000 ppm. In several cases, high-resolution (17)O NMR spectra were recorded under very fast magic-angle spinning (MAS) conditions at 21.1 T. Quantum-chemical computations using density functional theory (DFT) qualitatively reproduced the experimental (17)O hyperfine shift tensors.
Project description: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.
Project description:The excellent results of dispersion-corrected density functional theory (DFT-D) calculations for static systems have been well established over the past decade. The introduction of dynamics into DFT-D calculations is a target, especially for the field of molecular NMR crystallography. Four (13) C ss-NMR calibration compounds are investigated by single-crystal X-ray diffraction, molecular dynamics and DFT-D calculations. The crystal structure of 3-methylglutaric acid is reported. The rotator phases of adamantane and hexamethylbenzene at room temperature are successfully reproduced in the molecular dynamics simulations. The calculated (13) C chemical shifts of these compounds are in excellent agreement with experiment, with a root-mean-square deviation of 2.0 ppm. It is confirmed that a combination of classical molecular dynamics and DFT-D chemical shift calculation improves the accuracy of calculated chemical shifts.
Project description:When experimental protein NMR data are too sparse to apply traditional structure determination techniques, de novo protein structure prediction methods can be leveraged. Here, we describe the incorporation of NMR restraints into the protein structure prediction algorithm BCL::Fold. The method assembles discreet secondary structure elements using a Monte Carlo sampling algorithm with a consensus knowledge-based energy function. New components were introduced into the energy function to accommodate chemical shift, nuclear Overhauser effect, and residual dipolar coupling data. In particular, since side chains are not explicitly modeled during the minimization process, a knowledge based potential was created to relate experimental side chain proton-proton distances to Cβ -Cβ distances. In a benchmark test of 67 proteins of known structure with the incorporation of sparse NMR restraints, the correct topology was sampled in 65 cases, with an average best model RMSD100 of 3.4 ± 1.3 Å versus 6.0 ± 2.0 Å produced with the de novo method. Additionally, the correct topology is present in the best scoring 1% of models in 61 cases. The benchmark set includes both soluble and membrane proteins with up to 565 residues, indicating the method is robust and applicable to large and membrane proteins that are less likely to produce rich NMR datasets.
Project description:The current trend for ultra-high-field magnetic resonance imaging (MRI) technologies opens up new routes in clinical diagnostic imaging as well as in material imaging applications. MRI selectivity is further improved by using contrast agents (CAs), which enhance the image contrast and improve specificity by the paramagnetic relaxation enhancement (PRE) mechanism. Generally, the efficacy of a CA at a given magnetic field is measured by its longitudinal and transverse relaxivities r1 and r2, i.e., the longitudinal and transverse relaxation rates T1-1 and T2-1 normalized to CA concentration. However, even though basic NMR sensitivity and resolution become better in stronger fields, r1 of classic CA generally decreases, which often causes a reduction of the image contrast. In this regard, there is a growing interest in the development of new contrast agents that would be suitable to work at higher magnetic fields. One of the strategies to increase imaging contrast at high magnetic field is to inspect other paramagnetic ions than the commonly used Gd(III)-based CAs. For lanthanides, the magnetic moment can be higher than that of the isotropic Gd(III) ion. In addition, the symmetry of electronic ground state influences the PRE properties of a compound apart from diverse correlation times. In this work, PRE of water 1H has been investigated over a wide range of magnetic fields for aqueous solutions of the lanthanide containing polyoxometalates [DyIII(H2O)4GeW11O39]5- (Dy-W11), [ErIII(H2O)3GeW11O39]5- (Er-W11) and [{ErIII(H2O)(CH3COO)(P2W17O61)}2]16- (Er2-W34) over a wide range of frequencies from 20 MHz to 1.4 GHz. Their relaxivities r1 and r2 increase with increasing applied fields. These results indicate that the three chosen POM systems are potential candidates for contrast agents, especially at high magnetic fields.
Project description:BackgroundThe COVID-19 pandemic represents a so far unknown challenge for the medical community. Autopsies are important for studying this disease, but their safety was challenged at the beginning of the pandemic.ObjectivesTo determine whether COVID-19 autopsies can be performed under existing legal conditions and which safety standards are required.Materials and methodsThe autopsy procedure undertaken in five institutions in Germany, Austria, and Switzerland is detailed with respect to legal and safety standards.ResultsIn all institutions the autopsies were performed in technically feasible rooms. The personal equipment consisted of functional clothing including a disposable gown and apron, a surgical cap, eye protection, FFP‑3 masks, and two pairs of gloves. In four institutions, complete autopsies were performed; in one institution the ultrasound-guided biopsy within the postmortal imaging and biopsy program. The latter does not allow the appreciation of gross organ pathology; however, it is able to retrieve standardized biopsies for diagnostic and research purposes. Several scientific articles in highly ranked journals resulted from these autopsies and allowed deep insights into organ damage and conclusions to better understand the pathomechanisms. Viral RNA was frequently detectable in the COVID-19 deceased, but the issue of infectivity remains unresolved and it is questionable if Ct values are greater than 30.ConclusionsWith appropriate safeguards, autopsies of people who have died from COVID-19 can be performed safely and are highly relevant to medical research.