My research in biophysics focuses on the kinetics of proteins and the aggregation processes leading to amyloid structures, a structure associated with numerous degenerative diseases such as Alzheimer’s and Parkinson’s.
As with materials, I am actively involved in the development of new approaches with the goal of following the kinetics of these molecules over long times, combining these techniques with more traditional methods such as molecular dynamics.
Here are a few of the projects currently underway in my group:
I have made a few notable contributions to protein folding and flexibility, in large part through methodological developments.
Applying ART to folding of small peptides, we demonstrated that misfolded beta-hairpins can reorder into their native states by first forming an incorrectly aligned conformation that corrects itself through reptation moves, a question that was of high importance 10 years ago.
Folding the full-length 60-residue protein A from a random structure using ART, an unbiased approach, we showed that folding can take place through numerous pathways. We also showed that, although of high energy, various ordered structures seem to exist for the given sequence. In particular, at higher energy, the sequence, starting from random coil, can also adopt an almost protein G-like conformation, in agreement with experimental results that show that it is possible to pass from one conformation to the other with very few mutations (St-Pierre et al, 2008).
Over the last few years, we have developed ART-based methods to sample more targeted motion. One of the application concerned large loops (up to 20 residues) where we showed that our approach was very competitive compared with other approaches for sampling of conformations (St-Pierre and NM, 2012). We also developed a multiscale ART approach (holographic ART) to characterize the apo to holo pathways of EF-hand proteins (Dupuis and NM, 2012).
Selected work on the topic
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).
Abstract: 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).
Abstract: 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).
Abstract: 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).
Abstract: 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).
Abstract: 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).
Abstract: 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).
Abstract: 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).
Abstract: 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.
I started working on amyloid peptides and proteins about 10 years ago, in collaboration with Derreumaux. We were among the first computational groups to look at these systems. We were the first to identify the beta-barrel self-assembly for amyloid peptides in equilibrium with the standard cross beta-sheet motif (Wei, NM, Derreumaux, Biophys. J 2004).
Focusing on the simulation of unbiased assembly and structural organisation, we could identify assembly mechanisms for small peptides but also for full size proteins such as beta-amyloid and amylin (for example, Laghaei et al, 2010; Côté et al, 2011). To produce these results, but also assess their validity, we have used a variety of methods and forcefields, either developed in-house (ART, OPEP) or standard (MD, REMD, CHARMM, GROMOS, etc.).
This regular comparison between various techniques and descriptions has clearly strengthened some of our predictions and conclusions. Nevertheless, since our primary consideration is always the quality of sampling, we have focused our work on reliable but simple forcefields, allowing us to perform longer simulations and reach equilibrium even with relatively large systems (60 to 120 residues) (see, for example, Laghaei et al, 2011; Nasica-Labouze et al., 2012).
For example, OPEP simulations of dimers of polyglutamine have led us to predict the existence of an double-helix anti-parallel beta-sheet nanotube, starting from random configurations, a structure that has yet to be confirmed experimentally (Laghaei and NM, 2010).
Selected work on the topic
V. Binette, S. Côté, N. Mousseau, Free energy Landscape of the Amino-terminal Fragment of Huntingtin in Aqueous Solution, Biophysical Journal (2016).
S. Côté, V. Binette, E. S. Salnikov, B. Bechinger, N. Mousseau, Probing the Huntingtin 1-17 Membrane Anchor on a Phospholipid Bilayer by Using All-Atom Simulations, Biophysical Journal 108, 1187-1198 (2015).
Abstract: Mislocalization and aggregation of the huntingtin protein are related to Huntington?s disease. Its first exon?more specifically the first 17 amino acids (Htt17)?is crucial for the physiological and pathological functions of huntingtin. It regulates huntingtin?s activity through posttranslational modifications and serves as an anchor to membrane-containing organelles of the cell. Recently, structure and orientation of the Htt17 membrane anchor were determined using a combined solution and solid-state NMR approach. This prompted us to refine this model by investigating the dynamics and thermodynamics of this membrane anchor on a POPC bilayer using all-atom, explicit solvent molecular dynamics and Hamiltonian replica exchange. Our simulations are combined with various experimental measurements to generate a high-resolution atomistic model for the huntingtin Htt17 membrane anchor on a POPC bilayer. More precisely, we observe that the single α-helix structure is more stable in the phospholipid membrane than the NMR model obtained in the presence of dodecylphosphocholine detergent micelles. The resulting Htt17 monomer has its hydrophobic plane oriented parallel to the bilayer surface. Our results further unveil the key residues interacting with the membrane in terms of hydrogen bonds, salt-bridges, and nonpolar contributions. We also observe that Htt17 equilibrates at a well-defined insertion depth and that it perturbs the physical properties?order parameter, thickness, and area per lipid?of the bilayer in a manner that could favor its dimerization. Overall, our observations reinforce and refine the NMR measurements on the Htt17 membrane anchor segment of huntingtin that is of fundamental importance to its biological functions.
C. Eugène, R. Laghaei, N. Mousseau, Early oligomerization stages for the non-amyloid component of alpha-synuclein amyloid, J. Chem. Phys. 141, 135103 (2014).
S. Côté, G. Wei, N. Mousseau, Atomistic mechanisms of huntingtin N-terminal fragment insertion on a phospholipid bilayer revealed by molecular dynamics simulations, Proteins: Structure, Function, and Bioinformatics 82, 1409-1427 (2014).
Abstract: The huntingtin protein is characterized by a segment of consecutive glutamines (QN) that is responsible for its fibrillation. As with other amyloid proteins, misfolding of huntingtin is related to Huntington's disease through pathways that can involve interactions with phospholipid membranes. Experimental results suggest that the N-terminal 17-amino-acid sequence (httNT) positioned just before the QN region is important for the binding of huntingtin to membranes. Through all-atom explicit solvent molecular dynamics simulations, we unveil the structure and dynamics of the httNTQN fragment on a phospholipid membrane at the atomic level. We observe that the insertion dynamics of this peptide can be described by four main steps—approach, reorganization, anchoring, and insertion—that are very diverse at the atomic level. On the membrane, the httNT peptide forms a stable α-helix essentially parallel to the membrane with its nonpolar side-chains—mainly Leu-4, Leu-7, Phe-11 and Leu-14—positioned in the hydrophobic core of the membrane. Salt-bridges involving Glu-5, Glu-12, Lys-6, and Lys-15, as well as hydrogen bonds involving Thr-3 and Ser-13 with the phospholipids also stabilize the structure and orientation of the httNT peptide. These observations do not significantly change upon adding the QN region whose role is rather to provide, through its hydrogen bonds with the phospholipids' head group, a stable scaffold facilitating the partitioning of the httNT region in the membrane. Moreover, by staying accessible to the solvent, the amyloidogenic QN region could also play a key role for the oligomerization of httNTQN on phospholipid membranes. Proteins 2014; 82:1409–1427. © 2014 Wiley Periodicals, Inc.
S. Côté, G. Wei, N. Mousseau, All-Atom Stability and Oligomerization Simulations of Polyglutamine Nanotubes with and without the 17-Amino-Acid N-Terminal Fragment of the Huntingtin Protein, The Journal of Physical Chemistry B 116, 12168-12179 (2012).
Abstract: Several neurodegenerative diseases are associated with the polyglutamine (polyQ) repeat disorder in which a segment of consecutive glutamines in the native protein is produced with too many glutamines. Huntington?s disease, for example, is related to the misfolding of the Huntingtin protein which occurs when the polyQ segment has more than approximately 36 glutamines. Experimentally, it is known that the polyQ segment alone aggregates into ?-rich conformations such as amyloid fibrils. Its aggregation is modulated by the number of glutamine residues as well as by the surrounding amino acid sequences such as the 17-amino-acid N-terminal fragment of Huntingtin which increases the aggregation rate. Little structural information is available, however, regarding the first steps of aggregation and the atomistic mechanisms of oligomerization are yet to be described. Following previous coarse-grained replica-exchange molecular dynamics simulations that show the spontaneous formation of a nanotube consisting of two intertwined antiparallel strands (Laghaei, R.; Mousseau, N. J. Chem. Phys.2010, 132, 165102), we study this configuration and some extensions of it using all-atom explicit solvent MD simulations. We compare two different lengths for the polyQ segment, 40 and 30 glutamines, and we investigate the impact of the Huntingtin N-terminal residues (httNT). Our results show that the dimeric nanotubes can provide a building block for the formation of longer nanotubes (hexamers and octamers). These longer nanotubes are characterized by large ?-sheet propensities and a small solvent exposure of the main-chain atoms. Moreover, the oligomerization between two nanotubes occurs through the formation of protein/protein H-bonds and can result in an elongation of the water-filled core. Our results also show that the httNT enhances the structural stability of the ?-rich seeds, suggesting a new mechanism by which it can increase the aggregation rate of the amyloidogenic polyQ sequence.
J. Nasica-Labouze, M. Meli, P. Derreumaux, G. Colombo, N. Mousseau, A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35, PLoS Comput Biol 7, e1002051 (2011).
Abstract: Author Summary
The formation of amyloid fibrils is associated with many neurodegenerative diseases such as Alzheimer's, Creutzfeld-Jakob, Parkinson's, the Prion disease and diabetes mellitus. In all cases, proteins misfold to form highly ordered insoluble aggregates called amyloid fibrils that deposit intra- and extracellularly and are resistant to proteases. All proteins are believed to have the instrinsic capability of forming amyloid fibrils that share common specific structural properties that have been observed by X-ray crystallography and by NMR. However, little is known about the aggregation dynamics of amyloid assemblies, and their toxicity mechanism is therefore poorly understood. It is believed that small amyloid oligomers, formed on the aggregation pathway of full amyloid fibrils, are the toxic species. A detailed atomic characterization of the oligomerization process is thus necessary to further our understanding of the amyloid oligomer's toxicity. Our approach here is to study the aggregation dynamics of a 7-residue amyloid peptide GNNQQNY through a combination of numerical techniques. Our results suggest that this amyloid sequence can form fibril-like structures and is polymorphic, which agrees with recent experimental observations. The ability to fully characterize and describe the aggregation pathway of amyloid sequences numerically is key to the development of future drugs to target amyloid oligomers.
R. Laghaei, N. Mousseau, Spontaneous formation of polyglutamine nanotubes with molecular dynamics simulations, The Journal of Chemical Physics 132, 165102 (2010).
Abstract: Expansion of polyglutamine (polyQ) beyond the pathogenic threshold (35–40 Gln) is associated with several neurodegenerative diseases including Huntington’s disease, several forms of spinocerebellar ataxias and spinobulbar muscular atrophy. To determine the structure of polyglutamine aggregates we perform replica-exchange molecular dynamics simulations coupled with the optimized potential for effective peptide forcefield. Using a range of temperatures from 250 to 700 K, we study the aggregation kinetics of the polyglutamine monomer and dimer with chain lengths from 30 to 50 residues. All monomers show a similar structural change at the same temperature from α -helical structure to random coil, without indication of any significant β -strand. For dimers, by contrast, starting from random structures, we observe spontaneous formation of antiparallel β -sheets and triangular and circular β -helical structures for polyglutamine with 40 residues in a 400 ns 50 temperature replica-exchange molecular dynamics simulation (total integrated time 20 μ s ). This ∼ 32 Å diameter structure reorganizes further into a tight antiparallel double-stranded ∼ 22 Å nanotube with 22 residues per turn close to Perutz’ model for amyloid fibers as water-filled nanotubes. This diversity of structures suggests the existence of polymorphism for polyglutamine with possibly different pathways leading to the formation of toxic oligomers and to fibrils.
A. Melquiond, G. Boucher, N. Mousseau, P. Derreumaux, Following the aggregation of amyloid-forming peptides by computer simulations, The Journal of Chemical Physics 122, 174904 (2005).
Abstract: There is experimental evidence suggesting that the toxicity of neurodegenerative diseases such as Alzheimer’s disease may result from the soluble intermediate oligomers. It is therefore important to characterize extensively the early steps of oligomer formation at atomic level. As these structures are metastable and short lived, experimental data are difficult to obtain and they must be complemented with numerical simulations. In this work, we use the activation-relaxation technique coupled with a coarse-grained energy model to study in detail the mechanisms of aggregation of four lys–phe–phe–glu (KFFE) peptides. This is the shortest peptide known to form amyloidfibrilsin vitro. Our simulations indicate that four KFFE peptides adopt a variety of oligomeric states (tetramers, trimers, and dimers) with various orientations of the chains in rapid equilibrium. This conformational distribution is consistent with all-atom molecular-dynamics simulations in explicit solvent and is sequence dependent; as seen experimentally, the lys–pro–gly–glu (KPGE) peptides adopt disordered structures in solution. Our unbiased simulations also indicate that the assembly process is much more complex than previously thought and point to intermediate structures which likely are kinetic traps for longer chains.
Quantitative biology is a very active field of research in Canada. As it is scattered around disciplines, however, it is not always easy to find who is doing what in the field.
Happily, Andrew Rutenberg at Dalhousie University has set up an uptodate list of researchers working in the field. Visit this site to discover what is happening in quantitative biology across Canada!
Quantitative Biology in Canada