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

Pour une démocratie socio-environnementale : cadre pour une plate-forme participative « transition écologique »

Contribution publiée in Penser une démocratie alimentaire Volume II – Proposition Lascaux entre ressources naturelles et besoins fondamentaux, F. Collart Dutilleul et T. Bréger (dir), Inida, San José, 2014, pp. 87-111.International audienceL’anthropocène triomphant actuel, avec ses forçages environnementaux et sociaux, est à l’origine de l’accélération des dégradations des milieux de vie sur Terre et de l’accentuation des tensions sociales et géopolitiques. Passer à un anthropocène de gestion équitable, informé et sobre vis-à-vis de toutes les ressources et dans tous les secteurs d’activité (slow anthropocene), impose une analyse préalable sur l’ensemble des activités et des rapports humains. Cette transition dite « écologique », mais en réalité à la fois sociétale et écologique, est tout sauf un ajustement technique de secteurs dits prioritaires et technocratiques. Elle est avant tout culturelle, politique et philosophique au sens propre du terme. Elle est un horizon pour des trajectoires de développement humain, pour des constructions sociales et économiques, censées redéfinir socialement richesse, bien-être, travail etc. La dénomination « transition écologique » est largement véhiculée, mais ses bases conceptuelles ne sont pas entièrement acquises ni même élaborées. Dans ce contexte, les étudiants en première année de Master BioSciences à l’Ecole Normale Supérieure (ENS) de Lyon ont préparé une première étude analytique de ce changement radical et global de société pour mieux comprendre dans quelle société ils souhaitent vivre, en donnant du sens aux activités humaines présentes et à venir. Une trentaine de dossiers sur divers secteurs d’activités et acteurs de la société ont été produits et ont servis de support à cette synthèse. Plus largement, le but est de construire un socle conceptuel et une plate-forme de travail sur lesquels les questions de fond, mais aussi opérationnelles, peuvent être posées et étudiées en permanence. Cette démarche participative est ouverte à la collectivité sur le site http://institutmichelserres.ens-lyon.fr/

MAS NMR Studies of Hierarchical Interplay in Protein Dynamics

The functionality of proteins is governed by the interplay between their structure and dynamics. Thus, understanding the mechanism and nature of protein motion is essential to understand their biological activity. Here we present and evaluate a novel method to study the basic and fundamental question concerning hierarchical protein motions. What are the dynamical modes of a protein, what is the interplay of these different modes, and how are they linked to the energy landscape of the protein? It is known that different motional modes are present simultaneously in the protein system. These motions occur at different time scales and at the same and/or different regions in the protein, while simultaneously influencing each other. All these motions can be described as thermally activated fluctuations. Nuclear spin relaxation parameters measured by nuclear magnetic resonance (NMR) are modulated primary by motions around the nuclear site. Thus, they are uniquely suited to study protein dynamics since it is possible to simultaneously gather information about different motional timescales and of different parts of the protein

Metabolomic Profiling of Body Fluids in Mouse Models Demonstrates that Nuclear Magnetic Resonance Is a Putative Diagnostic Tool for the Presence of Thyroid Hormone Receptor α1 Mutations

International audienceBackground: Resistance to thyroid hormone alpha (RTH alpha) is a rare genetic disease due to mutations in the THRA gene, which encodes thyroid hormone receptor alpha 1 (TR alpha 1). Since its first description in 2012, 46 cases of RTH alpha have been reported worldwide, corresponding to 26 different mutations of TR alpha 1. RTH alpha patients share some common symptoms with hypothyroid patients, without significant reduction in thyroid hormone level. The high variability of clinical features and the absence of reliable biochemical markers make the diagnosis of this disease difficult. Some of these mutations have been recently modeled in mice. Methods: In our study, we used four different mouse models heterozygous for frameshift mutations in the Thra gene. Two of them are very close to human mutations, while the two others have not yet been found in patients. We characterized the metabolic phenotypes of urine and plasma samples collected from these four animal models using an untargeted nuclear magnetic resonance (NMR)-based metabolomic approach. Results: Multivariate statistical analysis of the metabolomic profiles shows that biofluids of mice that carry human-like mutations can be discriminated from controls. Metabolic signatures associated with Thra mutations in urine and plasma are stable over time and clearly differ from the metabolic fingerprint of hypothyroidism in the mouse. Conclusion: Our results provide a proof-of-principle that easily accessible NMR-based metabolic fingerprints of biofluids could be used to diagnose RTH alpha in humans

Probing Protein Dynamics Using Multifield Variable Temperature NMR Relaxation and Molecular Dynamics Simulation

International audienceUnderstanding the interplay between protein function and dynamics is currently one of the fundamental challenges of physical biology. Recently, a method using variable temperature solid-state nuclear magnetic resonance relaxation measurements has been proposed for the simultaneous measurement of 12 different activation energies reporting on distinct dynamic modes in the protein GB1. Here, we extend this approach to measure relaxation at multiple magnetic field strengths, allowing us to better constrain the motional models and to simultaneously evaluate the robustness and physical basis of the method. The data reveal backbone and side-chain motions, exhibiting low- and high-energy modes with temperature coefficients around 5 and 25 kJ·mol-1. The results are compared to variable temperature molecular dynamics simulation of the crystal lattice, providing further support for the interpretation of the experimental data in terms of molecular motion

Synergic interplay of the La motif, RRM1 and the interdomain linker of LARP6 in the recognition of collagen mRNA expands the RNA binding repertoire of the La module

The La-related proteins (LARPs) form a diverse group of RNA-binding proteins characterized by the possession of a composite RNA binding unit, the La module. The La module comprises two domains, the La motif (LaM) and the RRM1, which together recognize and bind to a wide array of RNA substrates. Structural information regarding the La module is at present restricted to the prototypic La protein, which acts as an RNA chaperone binding to 3′ UUU(OH) sequences of nascent RNA polymerase III transcripts. In contrast, LARP6 is implicated in the regulation of collagen synthesis and interacts with a specific stem-loop within the 5′ UTR of the collagen mRNA. Here, we present the structure of the LaM and RRM1 of human LARP6 uncovering in both cases considerable structural variation in comparison to the equivalent domains in La and revealing an unprecedented fold for the RRM1. A mutagenic study guided by the structures revealed that RNA recognition requires synergy between the LaM and RRM1 as well as the participation of the interdomain linker, probably in realizing tandem domain configurations and dynamics required for substrate selectivity. Our study highlights a considerable complexity and plasticity in the architecture of the La module within LARPs

Toxicologie predictive: les voies du futur

National audienc

Toxicologie predictive: les voies du futur

National audienc