Similarities and Differences among Protein Dynamics Studied by Variable Temperature Nuclear Magnetic Resonance Relaxation

Understanding and describing the dynamics of proteins is one of the major challenges in biology. Here, we use multifield variable-temperature NMR longitudinal relaxation (R-1) measurements to determine the hierarchical activation energies of motions of four different proteins: two small globular proteins (GB1 and the SH3 domain of alpha-spectrin), an intrinsically disordered protein (the C-terminus of the nucleoprotein of the Sendai virus, Sendai Ntail), and an outer membrane protein (OmpG). The activation energies map the motions occurring in the side chains, in the backbone, and in the hydration shells of the proteins. We were able to identify similarities and differences in the average motions of the proteins. We find that the NMR relaxation properties of the four proteins do share similar features. The data characterizing average backbone motions are found to be very similar, the same for methyl group rotations, and similar activation energies are measured. The main observed difference occurs for the intrinsically disordered Sendai Ntail, where we observe much lower energy of activation for motions of protons associated with the protein-solvent interface as compared to the others. We also observe variability between the proteins regarding side chain N-15 relaxation of lysine residues, with a higher activation energy observed in OmpG. This hints at strong interactions with negatively charged lipids in the bilayer and provides a possible mechanistic clue for the "positive-inside" rule for helical membrane proteins. Overall, these observations refine the understanding of the similarities and differences between hierarchical dynamics in proteins

Mg2+-dependent conformational equilibria in CorA and an integrated view on transport regulation

The CorA family of proteins regulates the homeostasis of divalent metal ions in many bacteria, archaea, and eukaryotic mitochondria, making it an important target in the investigation of the mechanisms of transport and its functional regulation. Although numerous structures of open and closed channels are now available for the CorA family, the mechanism of the transport regulation remains elusive. Here, we investigated the conformational distribution and associated dynamic behaviour of the pentameric Mg2+ channel CorA at room temperature using small-angle neutron scattering (SANS) in combination with molecular dynamics (MD) simulations and solid-state nuclear magnetic resonance spectroscopy (NMR). We find that neither the Mg2+-bound closed structure nor the Mg2+-free open forms are sufficient to explain the average conformation of CorA. Our data support the presence of conformational equilibria between multiple states, and we further find a variation in the behaviour of the backbone dynamics with and without Mg2+. We propose that CorA must be in a dynamic equilibrium between different non-conducting states, both symmetric and asymmetric, regardless of bound Mg2+ but that conducting states become more populated in Mg2+-free conditions. These properties are regulated by backbone dynamics and are key to understanding the functional regulation of CorA.Peer reviewe

Rapid Proton-Detected NMR Assignment for Proteins with Fast Magic Angle Spinning

Using a set of six 1H-detected triple-resonance NMR experiments, we establish a method for sequence-specific backbone resonance assignment of magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra of 5–30 kDa proteins. The approach relies on perdeuteration, amide 2H/1H exchange, high magnetic fields, and high-spinning frequencies (ωr/2π ≥ 60 kHz) and yields high-quality NMR data, enabling the use of automated analysis. The method is validated with five examples of proteins in different condensed states, including two microcrystalline proteins, a sedimented virus capsid, and two membrane-embedded systems. In comparison to contemporary 13C/15N-based methods, this approach facilitates and accelerates the MAS NMR assignment process, shortening the spectral acquisition times and enabling the use of unsupervised state-of-the-art computational data analysis protocols originally developed for solution NMR

RMN en rotation à l’angle magique de métalloprotéines paramagnétiques

Most of our understanding of metalloproteins derives from atomic or molecular structures obtained from diffraction methods on single crystal samples. However, not all proteins are amenable for diffraction studies, and even when a highly-resolved structure is available, often the nature of the metal ion, its coordination geometry or its oxidation state are not determined. The aim of the present thesis is the investigation of structural properties of metal sites in paramagnetic metalloproteins by Magic-Angle Spinning Nuclear Magnetic Resonance (MAS NMR). MAS NMR is a powerful technique for the investigation of biological systems, and may represent a direct probe of the structure at the active site of paramagnetic metalloproteins. However, it suffers from limited sensitivity and resolution when applied to nuclei close to a paramagnetic center.In this thesis, we address these limitations by developing NMR methods based on ultra-fast (60-111 kHz) MAS rates. A “toolkit” of suitably designed pulse sequences is built for the detection and the assignment of nuclei in close proximity of a paramagnetic center. State-of-the-art computational techniques are also employed to convert the experimental data into structural restraints for obtaining atomic-resolution geometries of active sites. We benchmark this approach with the study of Fe, Cu and Co sites in two microcrystalline proteins, and we also provide preliminary data on a non-diffracting divalent metal ion transporter in lipid membranes. We anticipate that the techniques described here are an essential tool to elucidate many currently unanswered questions about structure and function of metal sites in structural biology.À ce jour, nos connaissances sur les propriétés structurales et fonctionnelles des métalloprotéines sont essentiellement basées sur des structures résolues par des méthodes de diffraction à rayons X appliquées à des échantillons monocristallins. Cependant, certaines protéines ne cristallisent pas ou cristallisent sous une forme qui n’est pas manipulable ou compatible avec des techniques des diffraction, et même si une structure à très haute résolution est disponible, la nature de l’ion métallique, sa géométrie de coordination ou son état d’oxydation restent souvent indéterminés.La Résonance Magnétique Nucléaire en rotation à l’angle magique (MAS NMR) est une technique très performante pour l’étude de systèmes biologiques et pour la caractérisation de la structure du site actif des métalloprotéines paramagnétiques, mais son application à l’analyse des noyaux proches d’un site paramagnétique est limitée à cause de la résolution et de la sensibilité faibles.L’objectif de cette thèse a été de développer des méthodes RMN basées sur des hautes fréquences de rotation (60-111 kHz MAS) pour faire face à ces problématiques. Un répertoire de séquences d’impulsion pour la détection et l’attribution des noyaux à proximité d’un centre paramagnétique est proposé, et à l’aide de méthodes de calculs de pointes, les données expérimentales acquises sont converties en contraintes structurales afin de déterminer la géométrie du site actif à l’échelle atomique. Cette approche est validée avec l’analyse de sites actifs de deux protéines microcristallines contenants différents ions paramagnétiques : Fe, Cu et Co. Ensuite, des données préliminaires sur un transporteur membranaire d’ions métalliques divalents non cristalline sont présentées.Les méthodes analytiques présentées ici constituent un ensemble d’outils indispensable pour l’élucidation de la structure et la fonction des sites métalliques de systèmes macromoléculaires biologiques

Insights into ion channel structure and function by ultrafast magic angle spinning NMR

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Paramagnetic Properties of a Crystalline Iron-Sulfur Protein by Magic-Angle Spinning NMR Spectroscopy

International audienceWe present the first solid-state NMR study of an iron sulfur protein. The combined use of very fast (60 kHz) magic-angle spinning and tailored radiofrequency irradiation schemes allows the detection and the assignment of most of the H-1 and C-13 resonances of the oxidized high-potential iron sulfur protein I from Ectothiorhodospira halophila (EhHiPIP I), including those in residues coordinating the Fe4S4 cluster. For these residues, contact shifts as large as 100 and 400 ppm for H-1 and C-13 resonances, respectively, were observed, which represent the most shifted solid-state NMR signals ever measured in metalloproteins. Interestingly, by targeting EhHiPIP I in a crystalline environment, we were able to capture distinct paramagnetic signatures from the two conformations present in the asymmetric unit. The magnetic properties of the system were verified by following the temperature dependence of the contact-shifted cysteine resonances

The lineage-specific, intrinsically disordered N-terminal extension of monothiol glutaredoxin 1 from trypanosomes contains a regulatory region

Abstract Glutaredoxins (Grx) are small proteins conserved throughout all the kingdoms of life that are engaged in a wide variety of biological processes and share a common thioredoxin-fold. Among them, class II Grx are redox-inactive proteins involved in iron-sulfur (FeS) metabolism. They contain a single thiol group in their active site and use low molecular mass thiols such as glutathione as ligand for binding FeS-clusters. In this study, we investigated molecular aspects of 1CGrx1 from the pathogenic parasite Trypanosoma brucei brucei, a mitochondrial class II Grx that fulfills an indispensable role in vivo. Mitochondrial 1CGrx1 from trypanosomes differs from orthologues in several features including the presence of a parasite-specific N-terminal extension (NTE) whose role has yet to be elucidated. Previously we have solved the structure of a truncated form of 1CGrx1 containing only the conserved glutaredoxin domain but lacking the NTE. Our aim here is to investigate the effect of the NTE on the conformation of the protein. We therefore solved the NMR structure of the full-length protein, which reveals subtle but significant differences with the structure of the NTE-less form. By means of different experimental approaches, the NTE proved to be intrinsically disordered and not involved in the non-redox dependent protein dimerization, as previously suggested. Interestingly, the portion comprising residues 65–76 of the NTE modulates the conformational dynamics of the glutathione-binding pocket, which may play a role in iron-sulfur cluster assembly and delivery. Furthermore, we disclosed that the class II-strictly conserved loop that precedes the active site is critical for stabilizing the protein structure. So far, this represents the first communication of a Grx containing an intrinsically disordered region that defines a new protein subgroup within class II Grx

Structural Investigation of the Active Site in a Paramagnetic Metalloprotein by Fast Magic Angle Spinning NMR

The ENC Ritchey Travel Award was established to honor William M. Ritchey, who founded the ENC in 1960. The award was established with contributions from Professor Ritchey’s former students. The amount of the annual Award is $1,000 to be used for travel to the ENC. The recipient of the 2018 ENC Ritchey Travel Award is Andrea BertarelloInternational audienc

Dynamic Nuclear Polarization Enhancement of 200 at 21.15 T Enabled by 65 kHz Magic Angle Spinning

Solid-state nuclear magnetic resonance under magic angle spinning (MAS) enhanced with dynamic nuclear polarization (DNP) is a powerful approach to characterize many important classes of materials, allowing access to previously inaccessible structural and dynamic parameters. Here, we present the first DNP MAS experiments using a 0.7 mm MAS probe, which allows us to reach spinning frequencies of 65 kHz, with microwave irradiation, at 100 K. At the highest magnetic field available for DNP today (21.1 T), we find that the polarizing agent HyTEK2 provides DNP enhancements as high as 200 at a spinning rate of 65 kHz at 100 K, and BDPA yields an enhancement of 106 under the same conditions. Fast spinning rates enable excellent DNP performance, but they also yield unprecedented 1H resolution under DNP conditions. We report well-resolved 1H-detected 1H–13C and 1H–15N correlation spectra of microcrystalline histidine·HCl·H2O