Docking Peptides on Proteins: How to Open a Lock, in the Dark, with a Flexible Key

In this issue of Structure, Schindler et al. (2015b) present us with pepATTRACT, a protocol embedded in the ATTRACT docking engine for fully blind flexible peptide docking on proteins that yields high quality models of complexes

Conformational and mechanical stability of the isolated large subunit of membrane-bound [NiFe]-hydrogenase from Cupriavidus necator

Comprising at least a bipartite architecture, the large subunit of [NiFe]-hydrogenase harbors the catalytic nickel–iron site while the small subunit houses an array of electron-transferring Fe-S clusters. Recently, some [NiFe]-hydrogenase large subunits have been isolated showing an intact and redox active catalytic cofactor. In this computational study we have investigated one of these metalloproteins, namely the large subunit HoxG of the membrane-bound hydrogenase from Cupriavidus necator (CnMBH), targeting its conformational and mechanical stability using molecular modelling and long all-atom Gaussian accelerated molecular dynamics (GaMD). Our simulations predict that isolated HoxG is stable in aqueous solution and preserves a large portion of its mechanical properties, but loses rigidity in regions around the active site, in contrast to the MBH heterodimer. Inspired by biochemical data showing dimerization of the HoxG protein and IR measurements revealing an increased stability of the [NiFe] cofactor in protein preparations with higher dimer content, corresponding simulations of homodimeric forms were also undertaken. While the monomeric subunit contains several flexible regions, our data predicts a regained rigidity in homodimer models. Furthermore, we computed the electrostatic properties of models obtained by enhanced sampling with GaMD, which displays a significant amount of positive charge at the protein surface, especially in solvent-exposed former dimer interfaces. These data offer novel insights on the way the [NiFe] core is protected from de-assembly and provide hints for enzyme anchoring to surfaces, which is essential information for further investigations on these minimal enzymes

Assessing the effect of dynamics on the closed-loop protein-folding hypothesis

The closed-loop (loop-n-lock) hypothesis of protein folding suggests that loops of about 25 residues, closed through interactions between the loop ends (locks), play an important role in protein structure. Coarse-grain elastic network simulations, and examination of loop lengths in a diverse set of proteins, each supports a bias towards loops of close to 25 residues in length between residues of high stability. Previous studies have established a correlation between total contact distance (TCD), a metric of sequence distances between contacting residues (cf. contact order), and the log-folding rate of a protein. In a set of 43 proteins, we identify an improved correlation ( r 2 = 0.76), when the metric is restricted to residues contacting the locks, compared to the equivalent result when all residues are considered ( r 2 = 0.65). This provides qualified support for the hypothesis, albeit with an increased emphasis upon the importance of a much larger set of residues surrounding the locks. Evidence of a similar-sized protein core/extended nucleus (with significant overlap) was obtained from TCD calculations in which residues were successively eliminated according to their hydrophobicity and connectivity, and from molecular dynamics simulations. Our results suggest that while folding is determined by a subset of residues that can be predicted by application of the closed-loop hypothesis, the original hypothesis is too simplistic; efficient protein folding is dependent on a considerably larger subset of residues than those involved in lock formation. </jats:p

Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling

The Joint Evolutionary Trees (JET) method detects protein interfaces, the core residues involved in the folding process, and residues susceptible to site-directed mutagenesis and relevant to molecular recognition. The approach, based on the Evolutionary Trace (ET) method, introduces a novel way to treat evolutionary information. Families of homologous sequences are analyzed through a Gibbs-like sampling of distance trees to reduce effects of erroneous multiple alignment and impacts of weakly homologous sequences on distance tree construction. The sampling method makes sequence analysis more sensitive to functional and structural importance of individual residues by avoiding effects of the overrepresentation of highly homologous sequences and improves computational efficiency. A carefully designed clustering method is parametrized on the target structure to detect and extend patches on protein surfaces into predicted interaction sites. Clustering takes into account residues' physical-chemical properties as well as conservation. Large-scale application of JET requires the system to be adjustable for different datasets and to guarantee predictions even if the signal is low. Flexibility was achieved by a careful treatment of the number of retrieved sequences, the amino acid distance between sequences, and the selective thresholds for cluster identification. An iterative version of JET (iJET) that guarantees finding the most likely interface residues is proposed as the appropriate tool for large-scale predictions. Tests are carried out on the Huang database of 62 heterodimer, homodimer, and transient complexes and on 265 interfaces belonging to signal transduction proteins, enzymes, inhibitors, antibodies, antigens, and others. A specific set of proteins chosen for their special functional and structural properties illustrate JET behavior on a large variety of interactions covering proteins, ligands, DNA, and RNA. JET is compared at a large scale to ET and to Consurf, Rate4Site, siteFiNDER|3D, and SCORECONS on specific structures. A significant improvement in performance and computational efficiency is shown

Représentations gros-grain pour la modélisation des protéines : Propriétés mécaniques et interactions

HDR délivrée par l'UFR Sciences du VivantMes travaux de recherche portent sur le développement de modèles gros-grains et d'algorithmes pour l'étude des propriétés mécaniques des protéines et des interactions protéine-protéine. Sur le plan mécanique, le programme ProPHet (Probing Protein Heterogeneity) permet de sonder la rigidité protéique à l'échelle du résidu et d'étudier la réponse d'un système moléculaire soumis à une déformation anisotrope. Cette réponse mécanique peut être mise en rapport avec les propriétés structurales de la protéine concernée (notamment j'agencement de ses différents éléments de structure secondaire), mais aussi avec son fonctionnement biologique (comme l'activité enzymatique. Du point de vue des interactions protéine-protéine, l'analyse des résultats des calculs effectués avec le programme MAXDo (Macromolecular Association via Cross-Docking) sur une grille d'internautes )(WorldCommunityGrid) permet mieux comprendre la spécificité des phénomènes de reconnaissance protéiqu

Mechanical variations in proteins with large-scale motions highlight the formation of structural locks

International audienc

Fluides nanoconfinés dans des systèmes de basse symétrie : Simulations et théorie

Jury de thèse : Rapporteurs : M. L. Rosinberg et S. Hess Examinateurs : R. Tétot, G. Findenegg, R. LaveryThe thermodynamic and mechanical properties of fluids confined at a sub-microscopic scale dramatically differ from those of the bulk liquid. As far as numerical simulations are concerned, the actual studies on confined fluids mostly concern high symmetry cases where there is no simple access to the system's grand potential. This restriction drastically reduces the field of complex systems that can be theoretically studied, even though progress in microtechnologies now allow to fabricate a wide range of confining substrates bearing a nanoscopic structure. In this thesis we developped a method to compute the grand potential based on a thermodynamic scheme that can be applied to any low symmetry case. Monte Carlo simulations in the Grand Canonical ensemble of a simple fluid confined in two model systems (where the substrates either show a chemical structure or a geometrical one) were employed to make a complete investigation of the phase behavior of the fluid in these systems. In particular we identified the different morphologies the fluid can adopt, and their domain of thermodynamic stability. We also studied for the first time the effects of torsion on a confined fluid. We investigated the phase behavior of bridges morphologies (that can appear when a fluid is confined by nanostructured substrates) and their rheology when exposed to torsion.Les propriétés thermodynamiques et mécaniques des fluides confinés à l'échelle sub-microscopique diffèrent profondément de celles du liquide macroscopique. Dans le cadre de la simulation numérique, les études actuelles sur les fluides confinés concernent pour la plupart des cas de haute symétrie où le grand potentiel du système est aisément accessible. Cette limitation restreint grandement le champ des systèmes complexes étudiés théoriquement, alors même que les progrès réalisés dans le domaine des microtechnologies permettent la préparation d'une grande variété de substrats confinants présentant une structure nanométrique. Dans cette thèse nous avons donc développé une méthode de calcul du grand potentiel par intégration thermodynamique applicable aux cas de basse symétrie. Un travail de simulation de Monte Carlo dans l'ensemble Grand Canonique sur un fluide simple confiné dans deux systèmes modèles (où les substrats portent une structure chimique ou géométrique) associé à cette méthode nous a permis de réaliser une étude approfondie du comportement de phase du fluide dans ces systèmes, notamment en identifiant les différentes morphologies que le fluide peut adopter ainsi que leur domaine de stabilité thermodynamique. Nous avons aussi étudié pour la première fois les effets de la torsion sur un fluide confiné. On s'est penché tout particulièrement sur le comportement de phase des morphologies pont (que l'on voit apparaître lors du confinement par des substrats nanostructurés), et sur leur rhéologie lors de la torsion

Coarse-grain simulations on NMR conformational ensembles highlight functional residues in proteins

International audienc

Fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus?

International audienc