Je m’intéresse aux biomolécules depuis le début des années 2000. Outre les protéines amyloïdes, j’ai également produit des résultats notables en ce qui concerne le repliement et la flexibilité des protéines en m’appuyant sur des développements méthodologiques réalisés, en bonne partie, dans mon groupe. Ainsi, en appliquant ART nouveau au repliement de petits peptides, nous avons pu démontrer que le repliement des épingles bêta pouvait s’accomplir en deux étapes : tout d’abord, un pincement rapide, générant un alignement décalé, suivi d’une correction par des mécanismes de reptation, une question importante, il y a 10 ans (Wei et al., Proteins 2004).
Étudiant le repliement \emphab initio de la protéine A, une protéine de 60 acides aminés, nous avons montré que le repliement pouvait se dérouler en suivant plusieurs chemins différents dont certains menaient à des structures ordonnées métastables qui reflétaient l’existence de séquences proches mais à l’état natif différent (St-Pierre et al., J. Chem. Phys. 2008).
Au cours des dernières années, mon groupe s’est également intéressé au développement de méthodes multiéchelles permettant d’échantillonner l’évolution complexe des protéines. Nous avons ainsi développé une approche très efficace et très compétitive pour l’échantillonnage de grandes boucles flexibles (St-Pierre et Mousseau, Proteins 2012) ainsi qu’une version multiéchelle de ART (ART holographique), qui nous a permis de caractériser, pour la première fois, le passage de la structure apo à holo de la calmoduline (Dupuis et Mousseau, J. Chem. Phys. 2012).
Quelques-uns de mes travaux sur le sujet
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L. Dupuis, N. Mousseau, Holographic multiscale method used with non-biased atomistic forcefields for simulation of large transformations in protein, Journal of Physics: Conference Series 341, 012015 (2012).Résumé : We present a multiscale approach for simulating protein flexibility. The originality of our method is its ability to perform dynamic multiscaling based on continuous revaluation of overlapping areas. The holographic multiscale method overcomes the limitations of motions determined by predefined and fixed high-level descriptions and allows the reproduction of residue-specific impact on large scale motion. The method is tested with two different non-biased all atom implicit solvent forcefields. These show stretched proteins A and G, with maintained secondary structure, folding back near native states in a small number of transition events, demonstrating the advantages of this multiscale approach. -
J. - F. St-Pierre, A. Bunker, T. Róg, M. Karttunen, N. Mousseau, Molecular Dynamics Simulations of the Bacterial ABC Transporter SAV1866 in the Closed Form, The Journal of Physical Chemistry B 116, 2934-2942 (2012).Résumé : The ATP binding cassette (ABC) transporter family of proteins contains members involved in ATP-mediated import or export of ligands at the cell membrane. For the case of exporters, the translocation mechanism involves a large-scale conformational change that involves a clothespin-like motion from an inward-facing open state, able to bind ligands and adenosine triphosphate (ATP), to an outward-facing closed state. Our work focuses on SAV1866, a bacterial member of the ABC transporter family for which the structure is known for the closed state. To evaluate the ability of this protein to undergo conformational changes at physiological temperature, we first performed conventional molecular dynamics (MD) on the cocrystallized adenosine diphosphate (ADP)-bound structure and on a nucleotide-free structure. With this assessment of SAV1866?s stability, conformational changes were induced by steered molecular dynamics (SMD), in which the nucleotide binding domains (NBD) were pushed apart, simulating the ATP hydrolysis energy expenditure. We found that the transmembrane domain is not easily perturbed by large-scale motions of the NBDs. -
J. - F. St-Pierre, N. Mousseau, Large loop conformation sampling using the activation relaxation technique, ART-nouveau method, Proteins: Structure, Function, and Bioinformatics 80, 1883-1894 (2012).Résumé : We present an adaptation of the ART-nouveau energy surface sampling method to the problem of loop structure prediction. This method, previously used to study protein folding pathways and peptide aggregation, is well suited to the problem of sampling the conformation space of large loops by targeting probable folding pathways instead of sampling exhaustively that space. The number of sampled conformations needed by ART nouveau to find the global energy minimum for a loop was found to scale linearly with the sequence length of the loop for loops between 8 and about 20 amino acids. Considering the linear scaling dependence of the computation cost on the loop sequence length for sampling new conformations, we estimate the total computational cost of sampling larger loops to scale quadratically compared to the exponential scaling of exhaustive search methods. Proteins 2012; © 2012 Wiley Periodicals, Inc. -
L. Dupuis, N. Mousseau, Understanding the EF-hand closing pathway using non-biased interatomic potentials, The Journal of Chemical Physics 136, 035101 (2012).Résumé : The EF-hand superfamily of proteins is characterized by the presence of calcium binding helix-loop-helix structures. Many of these proteins undergo considerable motion responsible for a wide range of properties upon binding but the exact mechanism at the root of this motion is not fully understood. Here, we use an unbiased accelerated multiscale simulation scheme, coupled with two force fields — CHARMM-EEF1 and the extended OPEP — to explore in details the closing pathway, from the unbound holo state to the closed apo state, of two EF-hand proteins, the Calmodulin and Troponin C N-terminal nodules. Based on a number of closing simulations for these two sequences, we show that the EF-hand β-scaffold, identified as crucial by Grabarek for the EF-hand opening driven by calcium binding, is also important in closing the EF-hand. We also show the crucial importance of the phenylalanine situated at the end of first EF-hand helix, and identify an intermediate state modulating its behavior, providing a detailed picture of the closing mechanism for these two representatives of EF-hand proteins. -
J. - F. St-Pierre, N. Mousseau, P. Derreumaux, The complex folding pathways of protein A suggest a multiple-funnelled energy landscape, The Journal of Chemical Physics 128, 045101 (2008).Résumé : Folding proteins into their native states requires the formation of both secondary and tertiary structures. Many questions remain, however, as to whether these form into a precise order, and various pictures have been proposed that place the emphasis on the first or the second level of structure in describing folding. One of the favorite test models for studying this question is the B domain of protein A, which has been characterized by numerous experiments and simulations. Using the activation-relaxation technique coupled with a generic energy model (optimized potential for efficient peptide structure prediction), we generate more than 50 folding trajectories for this 60-residue protein. While the folding pathways to the native state are fully consistent with the funnel-like description of the free energy landscape, we find a wide range of mechanisms in which secondary and tertiary structures form in various orders. Our nonbiased simulations also reveal the presence of a significant number of non-native β and α conformations both on and off pathway, including the visit, for a non-negligible fraction of trajectories, of fully ordered structures resembling the native state of nonhomologous proteins. -
P. Derreumaux, N. Mousseau, Coarse-grained protein molecular dynamics simulations, The Journal of Chemical Physics 126, 025101 (2007).Résumé : A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solventmolecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer’s A β 16 – 22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50 ns time scale. Based on two 220 ns trajectories starting from disordered chains, we find that four A β 16 – 22 peptides can form a three-stranded β sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies. -
M. - R. Yun, N. Mousseau, P. Derreumaux, Sampling small-scale and large-scale conformational changes in proteins and molecular complexes, The Journal of Chemical Physics 126, 105101 (2007).Résumé : Sampling of small-scale and large-scale motions is important in various computational tasks, such as protein-protein docking and ligand binding. Here, we report further development and applications of the activation-relaxation technique for internal coordinate space trajectories (ARTIST). This method generates conformational moves of any complexity and size by identifying and crossing well-defined saddle points connecting energy minima. Simulations on two all-atom proteins and three protein complexes containing between 70 and 300 amino acids indicate that ARTIST opens the door to the full treatment of all degrees of freedom in dense systems such as protein-protein complexes. -
M. - R. Yun, R. Lavery, N. Mousseau, K. Zakrzewska, P. Derreumaux, ARTIST: An activated method in internal coordinate space for sampling protein energy landscapes, Proteins: Structure, Function, and Bioinformatics 63, 967-975 (2006).Résumé : We present the first applications of an activated method in internal coordinate space for sampling all-atom protein conformations, the activation–relaxation technique for internal coordinate space trajectories (ARTIST). This method differs from all previous internal coordinate-based studies aimed at folding or refining protein structures in that conformational changes result from identifying and crossing well-defined saddle points connecting energy minima. Our simulations of four model proteins containing between 4 and 47 amino acids indicate that this method is efficient for exploring conformational space in both sparsely and densely packed environments, and offers new perspectives for applications ranging from computer-aided drug design to supramolecular assembly. Proteins 2006. © 2006 Wiley-Liss, Inc.
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