Nanotechnologie : conception à l'échelle atomique par Stéphane Redon. Dynamique moléculaire interactive, entretien avec Serge Crouzy, propos recueillis par Dominique Chouchan.

National audienceL'exploration et la manipulation de l'infiniment petit passeront sans doute par la conception assistée par ordinateur : le prototypage virtuel d'objets nanoscopiques concerne un grand nombre d'applications industrielles, pharmacologiques..

Cd2+- or Hg2+-binding proteins can replace the Cu+-chaperone Atx1 in delivering Cu+ to the secretory pathway in yeast

AbstractCopper delivery to Ccc2 – the Golgi Cu+-ATPase – was investigated in vivo, replacing the Cu+-chaperone Atx1 by various structural homologues in an atx1-Δ yeast strain. Various proteins, displaying the same ferredoxin-like fold and (M/L)(T/S)CXXC metal-binding motif as Atx1 and known as Cu+-, Cd2+- or Hg2+-binding proteins were able to replace Atx1. Therefore, regardless of their original function, these proteins could all bind copper and transfer it to Ccc2, suggesting that Ccc2 is opportunistic and can interact with many different proteins to gain Cu+. The possible role of electrostatic potential surfaces in the docking of Ccc2 with these Atx1-homologues is discussed

Tyrosine metabolism: identification of a key residue in the acquisition of prephenate aminotransferase activity by 1β aspartate aminotransferase

International audienceAlternative routes for the post-chorismate branch of the biosynthetic pathway leading to tyrosine exist, the 4-hydroxyphenylpyruvate or the arogenate route. The arogenate route involves the transamination of prephenate into arogenate. In a previous study, we found that, depending on the microorganisms possessing the arogenate route, three different aminotransferases evolved to perform prephenate transamination, that is, 1β aspartate aminotransferase (1β AAT), N-succinyl-l,l-diaminopimelate aminotransferase, and branched-chain aminotransferase. The present work aimed at identifying molecular determinant(s) of 1β AAT prephenate aminotransferase (PAT) activity. To that purpose, we conducted X-ray crystal structure analysis of two PAT competent 1β AAT from Arabidopsis thaliana and Rhizobium meliloti and one PAT incompetent 1β AAT from R. meliloti. This structural analysis supported by site-directed mutagenesis, modeling, and molecular dynamics simulations allowed us to identify a molecular determinant of PAT activity in the flexible N-terminal loop of 1β AAT. Our data reveal that a Lys/Arg/Gln residue in position 12 in the sequence (numbering according to Thermus thermophilus 1β AAT), present only in PAT competent enzymes, could interact with the 4-hydroxyl group of the prephenate substrate, and thus may have a central role in the acquisition of PAT activity by 1β AAT

Extracellular Blockade of K+ Channels by Tea: Results from Molecular Dynamics Simulations of the Kcsa Channel

TEA is a classical blocker of K+ channels. From mutagenesis studies, it has been shown that external blockade by TEA is strongly dependent upon the presence of aromatic residue at Shaker position 449 which is located near the extracellular entrance to the pore (Heginbotham, L., and R. MacKinnon. 1992. Neuron. 8:483–491). The data suggest that TEA interacts simultaneously with the aromatic residues of the four monomers. The determination of the 3-D structure of the KcsA channel using X-ray crystallography (Doyle, D.A., J.M. Cabral, R.A. Pfuetzner, A. Kuo, J.M. Gulbis, S.L. Cohen, B.T. Chait, and R. MacKinnon. 1998. Science. 280:69–77) has raised some issues that remain currently unresolved concerning the interpretation of these observations. In particular, the center of the Tyr82 side chains in KcsA (corresponding to position 449 in Shaker) forms a square of 11.8-Å side, a distance which is too large to allow simultaneous interactions of a TEA molecule with the four aromatic side chains. In this paper, the external blockade by TEA is explored by molecular dynamics simulations of an atomic model of KcsA in an explicit phospholipid bilayer with aqueous salt solution. It is observed, in qualitative accord with the experimental results, that TEA is stable when bound to the external side of the wild-type KcsA channel (with Tyr82), but is unstable when bound to a mutant channel in which the tyrosine residue has been substituted by a threonine. The free energy profile of TEA relative to the pore is calculated using umbrella sampling simulations to characterize quantitatively the extracellular blockade. It is found, in remarkable agreement with the experiment, that the TEA is more stably bound by 2.3 kcal/mol to the channel with four tyrosine residues. In the case of the wild-type KcsA channel, TEA (which has the shape of a flattened oblate spheroid) acts as an ideal plug blocking the pore. In contrast, it is considerably more off-centered and tilted in the case of the mutant channel. The enhanced stability conferred by the tyrosine residues does not arise from Π–cation interactions, but appears to be due to differences in the hydration structure of the TEA. Finally, it is shown that the experimentally observed voltage dependence of TEA block, which is traditionally interpreted in terms of the physical position of the TEA along the axis of the pore, must arise indirectly via coupling with the ions in the pore

Prédiction de structure d'ATPases de type P1 et simulations de dynamique moléculaire (DM) de leurs domaines de liaison des métaux

Les ATPases de type P1 sont des pompes utilisant l'énergie de l'hydrolyse de l'ATP pour transporter les ions lourds (Cu+, Zn2+, Pb2+, Cd2+) à travers la membrane cellulaire. Elles sont difficiles à purifier et cristalliser et leur structure 3D est en général inconnue. Nous nous sommes intéressés à la structure et à la dymanique de la partie membranaire de l'ATPase cadmium CadA et aux domaines de liaison du métal de l'ATPase cuivre humaine de Menkés. Similarité de séquence et analyses d'hydropathie, complétées par des expériences ont montré que les ATPases de type P1 sont constituées de 8 segments transmembranaires (TMs) au lieu de 10 pour l'ATPase calcium de structure connue. En collaboration avec les biochimistes, et en utilisant les programmes MODELLER, CHARMM, XPLOR, AMD ainsi que nos propres programmes, nous avons prédit la structure des TMs de CadA. Nous avons construit plusieurs modéles du paquet de TMs correspondant à plusieurs topologies, calculé les coordonnées atomiques avec une procédure similaire à la détermination de structure à partir d'expériences de RMN et raffiné ces coordonnées en utilisant des simulations de DM en présence de solvant implicite. Le programme AMD de DM Adaptive a été utilisé pour vérifier les modèles de manière interactive.Une autre caractéristique intéressante des ATPases de type P1 est la présence en N-ter de un à six domaine(s) de liaison des métaux (MBDS). Dans le cas de l'ATPase de Menkés, il y a 6 MBDs, chacun pouvant lier un ion Cu+. La structure de chaque MBD est connue. En utilisant des simulations de DM, nous avons étudié la dynamique de chaque MBD en presence ou absence de métal dans le but de comprendre comment le métal est transféré de la métallochaperone qui prend en charge le métal lors de son entrée dans la cellule au MBD. Ces études ont utilisé le travail récent des chercheurs de l'équipe dans le domaine de la paramétrisation des ions métalliques pour des champs de force de mécanique moléculaire. Le bon accord de nos résultats de DM sur les MBDs avec les connaissances expérimentales a montré que des modèles mécaniques sont capables de rendre compte et d'expliquer certaines propriétés de liaison et de transport des métaux dans les métalloprotéines et les ATpases, cibles pharmaceutiques bien connues.P1-type ATPases are a special kind of ATP driven pumps which transport soft heavy metals (Cu+, Zn2+, Pb2+, Cd2+) across the cell membranes. Their complete structure is, in general, unknown. We are interested in the structure and dynamics of the transmembrane part of the Cadmium ATPase (CadA) and the metal binding domains of the human Copper transporting Menkes ATPase. Sequence similarity and hydropathy analyses, completed by experiments have shown that soft metal pumps are constituted of 8 transmembrane regions (TMs), compared to 10 for SERCA, the calcium pump for which the 3D structure is known. In collaboration with the biochemists in the laboratory, and using standard programs like MODELLER, CHARMM, XPLOR, AMD together with our own programs, we have predicted the structure of the TMs of CadA. We have built several models of the TM bundle corresponding to several topologies, calculated all atom coordinates with a procedure similar to structure determination from NMR experiments and refined these coordinates using Molecular Dynamics (MD) simulations in an implicit membrane. The Adaptive MD (AMD) program has been used to interactively check the models for bad loop positioning or ''knots'' in the structure. Another interesting feature of P1-type ATPase is the presence of one to six N-terminal conserved GxTCxxC metal binding domain(s) (MBDS). In the case of the Menkes ATPase, there are 6 MBDs, each of them being able to bind Cu+. The structure of each MBD separately is known from NMR spectroscopy but the structure of the assembly is unknown. Using MD simulations, we have studied the dynamics of each MBD in the presence or absence of metal with the final goal of understanding how the metal is transferred from the metallochaperone which binds the metal when it enters the cell to the MBD and why the presence of 6 MBDs is needed for the correct functioning of the pump. These studies have used recent work of researchers in the team on the parameterization of metal ions for molecular mechanics force fields and MD studies on metallochaperones.We show that fast approximate in silico models of metal ions can help understand metal binding and transport in metalloproteins or ATPases, which are known to be major pharmaceutical targets.GRENOBLE1-BU Sciences (384212103) / SudocSudocFranceF

Molecular Dynamics Simulations of the Transmembrane Domain of the Oncogenic ErbB2 Receptor Dimer in a DMPC Bilayer

International audienceMolecular dynamics simulations of an atomic model of the transmembrane domain of the oncogenic ErbB2 receptor dimer embedded in an explicit dimyristoylphosphatidylcholine (DMPC) bilayer were performed for more than 4 ns. The oncogenic Glu mutation in the membrane spanning segment plays a major role in tyrosine kinase activity and receptor dimerization, and is thought to be partly responsible for the structure of the transmembrane domain of the active receptor. MD results show that the interactions between the two transmembrane helices are characteristic of a left-handed packing as previously demonstrated from in vacuo simulations. Moreover, MD results reveal the absence of persistent hydrogen bonds between the Glu side chains in a membrane environment, which raise the question of the ability for Glu alone to stabilize the TM domain of the ErbB2 receptor. Interestingly the formation of the alpha-pi motif in the two ErbB2 transmembrane helices confirms the concept of intrinsic sequence-induced conformational flexibility. From a careful analysis of our MD results, we suggest that the left-handed helix-helix packing could be the key to correctly orient the intracellular domain of the activated receptor dimer. The prediction of such interactions from computer simulations represents a new step towards the understanding of signaling mechanisms

Dynamics and Stability of the Metal Binding Domains of the Menkes ATPase and Their Interaction with Metallochaperone HAH1

Human copper-ATPases ATP7A and ATP7B are essential for intracellular copper homeostasis. The main roles of the Menkes protein, ATP7A, are the delivery of copper to the secretory pathway and the export of excess copper from the enterocytes. The N-terminal domain of membrane protein ATP7A consists of six repetitive sequences of 60–70 amino acids (Mnk1–Mnk6) that fold into individual metal binding domains (MBDs) and bind a single copper ion in the reduced Cu^I form via two cysteine residues. The structure of each individual MBD is known from nuclear magnetic resonance experiments. Here, we were interested in the stability and dynamics of each isolated MBD in their apo and holo forms and their interactions with the soluble metallochaperone HAH1 that delivers copper to ATP7A. Using molecular dynamics simulations of the MBDs under different conditions, we show that some MBDs (Mnk1 and Mnk5) present large root-mean-square deviations from initial structures or large root-mean-square fluctuations, and great care has to be taken in setting up the simulations. We propose that the first MBD, Mnk1, probably important in the transfer of copper between the metallochaperone and ATPase, could be stabilized by interactions with other MBDs, including a domain located in the loop between Mnk1 and Mnk2. An important result of this work is the apparent direct correlation between the difference in the fluctuations of the metal binding site loop in its apo and holo forms and the measured affinity of the MBD for copper. This difference decreases from Mnk1 to Mnk6, Mnk4, and Mnk2 in this order. The study of the exposure to the solvent of the metal and the residues of the metal binding loop of the MBDs also shows different behavior for each MBD. In particular, copper in serine-rich domain Mnk3 and largely fluctuating domain Mnk5 appears to be more solvent-exposed than in the other MBDs. In the second part of this work, we investigated the importance of electrostatics in the MBD–chaperone interactions using different docking programs. Mnk1 and Mnk4 present a large electrostatic dipole moment and large stabilizing interaction energies with HAH1. Finally, we propose a model structure of ATP7A from Mnk6 (E561) to P1413 based on the crystal structure of LpCopA and docking simulations

Etude structurale des aptamères peptidiques anti-Fur et de leur interaction avec leur cible

Fur (Ferric Uptake Regulator) est un régulateur transcriptionnel spécifique des bactéries qui intervient dans le contrôle de l'homéostasie du fer, ce qui en fait une cible antibactérienne intéressante. Avant mon arrivée au laboratoire, quatre inhibiteurs interagissant spécifiquement avec Fur avaient été isolés. La partie active de ces inhibiteurs consiste en des peptides de 13 acides aminés. Au cours de cette thèse, j'ai utilisé une double-approche : théorique et expérimentale pour étudier l'interaction de ces peptides avec Fur afin de comprendre le mécanisme d'inhibition. J'ai synthétisé plusieurs séquences peptidiques, montré par des tests biochimiques que certaines inhibaient Fur et déterminé les interactions importantes à l'activité inhibitrice. J'ai obtenu des modèles théoriques des complexes Fur/peptides par amarrage moléculaire, cohérents avec les résultats expérimentaux, qui ont mis en évidence une zone d'inhibition de Fur. Des criblages in silico dans cette zone ont permis de sélectionner de petites molécules, inhibitrices potentielles de Fur et donc intéressantes pour des applications thérapeutiques.Fur (Ferric Uptake Regulator) is a transcriptional regulator involved in the control of iron homeostasis. Specific to bacteria, Fur is an attractive antibacterial target. Before my arrival in the laboratory, four inhibitors interacting specifically with Fur had been isolated. The active part of these inhibitors consists of peptides of 13 amino acids. In this thesis I have used both theoretical and experimental approaches to study interactions of these peptides with Fur in order to understand the inhibition mechanism. I have synthesized several peptide sequences, shown through biochemical assays that some of them could inhibit Fur and I have identified residues important to the inhibitory activity. I ve obtained theoretical models of Fur/peptide complexes consistent with experimental results, which reveal an inhibition pocket in Fur. Small molecules have then been selected though In silico screening of this pocket, that could potentially inhibit Fur, and thus be interesting for therapeutic applications.SAVOIE-SCD - Bib.électronique (730659901) / SudocGRENOBLE1/INP-Bib.électronique (384210012) / SudocGRENOBLE2/3-Bib.électronique (384219901) / SudocSudocFranceF

Structure, dynamique moléculaire et sélectivité de métallochaperones à cuivre et à mercure

Les métallochaperones à cuivre assurent l'acheminement des ions cu(i) dans la cellule. Ainsi, les protéines de la famille d'Atx1 et de merP, une chaperone à mercure, présentent une forte homologie de séquence et le même repliement. Cette thèse vise à mettre en évidence des propriétés dynamiques et structurales responsables de la sélectivite des métallochaperones pour le cu(I) ou le hg(II). Des simulations de dynamique moléculaire des métallochaperones à cuivre, Atx1 et Har1, et de merP, dans les formes apo, et liees au cu(I) ou au hg(II), ont révélé des caractéristiques dynamiques et énergétiques communes aux trois holoprotéines natives. Des interactions entre la boucle du site de chelation et deux autres boucles, ont été identifiées et varient d'un état lié à l'autre. Il pourrait définir une éventuelle sélectivite pour les métaux. La boucle du site de chelation montre une grande structuration en présence de métal, accompagnée d'une rigidification si ce métal est le métal natif. Les expériences d'absorption x du cu(I) chélaté par atx1 ont montré que le cu(I) possède toujours une géométrie trigonale dont les ligands sont les deux cystéines du site de chélation, et un ligand endogène ou exogène. Atx1 présente donc au cu(I) une géométrie qui lui est préférentielle. Cette propriété est un déterminant de la sélectivité au cu(I) par rapport à d'autres métaux. En présence de glutathion, le complexe atx1-cu(I) forme un homodimère binucléaire associé à deux molécules de glutathion. L'implication de ce ligand exogène est proposée comme un facteur de sélectivité in vivo d'atx1 pour le cu(I), et pourrait favoriser la reconnaissance par atx1 de sa protéine cible.GRENOBLE1-BU Sciences (384212103) / SudocSudocFranceF

Short oligopeptides with three cysteine residues as models of sulphur-rich Cu( i )- and Hg( ii )-binding sites in proteins

International audienceThe essential Cu(i) and the toxic Hg(ii) ions possess similar coordination properties, and therefore, similar cysteine rich proteins participate in the control of their intracellular concentration. In this work we present the metal binding properties of linear and cyclic model peptides incorporating the three-cysteine motifs, CxCxxC or CxCxC, found in metallothioneins. Cu(i) binding to the series of peptides at physiological pH revealed to be rather complicated, with the formation of mixtures of polymetallic species. In contrast, the Hg(ii) complexes display well-defined structures with spectroscopic features characteristic for a HgS2 and HgS3 coordination mode at pH = 2.0 and 7.4, respectively. Stability data reflect a ca. 20 orders of magnitude larger affinity of the peptides for Hg(ii) (log βpH7.4HgP ≈ 41) than for Cu(i) (log βpH7.4CuP ≈ 18). The different behaviour with the two metal ions demonstrates that the use of Hg(ii) as a probe for Cu(i), coordinated by thiolate ligands in water, may not always be fully appropriate