Stéphanie Finet

The C-terminal Domain of the Measles Virus Nucleoprotein Is Intrinsically Disordered and Folds upon Binding to the C-terminal Moiety of the Phosphoprotein

The nucleoprotein of measles virus consists of an N-terminal moiety, NCORE, resistant to proteolysis and a C-terminal moiety, NTAIL, hypersensitive to proteolysis and not visible as a distinct domain by electron microscopy. We report the bacterial expression, purification, and characterization of measles virus NTAIL. Using nuclear magnetic resonance, circular dichroism, gel filtration, dynamic light scattering, and small angle x-ray scattering, we show that NTAIL is not structured in solution. Its sequence and spectroscopic and hydrodynamic properties indicate that NTAIL belongs to the premolten globule subfamily within the class of intrinsically disordered proteins. The same epitopes are exposed in NTAIL and within the nucleoprotein, which rules out dramatic conformational changes in the isolated NTAILdomain compared with the full-length nucleoprotein. Most unstructured proteins undergo some degree of folding upon binding to their partners, a process termed “induced folding.” We show that NTAILis able to bind its physiological partner, the phosphoprotein, and that it undergoes such an unstructured-to-structured transition upon binding to the C-terminal moiety of the phosphoprotein. The presence of flexible regions at the surface of the viral nucleocapsid would enable plastic interactions with several partners, whereas the gain of structure arising from induced folding would lead to modulation of these interactions. These results contribute to the study of the emerging field of natively unfolded proteins.

Absence of equilibrium cluster phase in concentrated lysozyme solutions.

In colloidal systems, the interplay between the short range attraction and long-range repulsion can lead to a low density associated state consisting of clusters of individual particles. Recently, such an equilibrium cluster phase was also reported for concentrated solutions of lysozyme at low ionic strength and close to the physiological pH. Stradner et al. [(2004) Equilibrium cluster formation in concentrated protein solutions and colloids. Nature 432:492–495] found that the position of the low-angle interference peak in small-angle x-ray and neutron scattering (SAXS and SANS) patterns from lysozyme solutions was essentially independent of the protein concentration and attributed these unexpected results to the presence of equilibrium clusters. This work prompted a series of experimental and theoretical investigations, but also revealed some inconsistencies. We have repeated these experiments following the protein preparation protocols of Stradner et al. using several batches of lysozyme and exploring a broad range of concentrations, temperature and other conditions. Our measurements were done in multiple experimental sessions at three different high-resolution SAXS and SANS instruments. The low-ionic-strength lysozyme solutions displayed a clear shift in peak positions with concentration, incompatible with the presence of the cluster phase but consistent with the system of repulsively interacting individual lysozyme molecules. Within the decoupling approximation, the experimental data can be fitted using an effective interparticle interaction potential involving short-range attraction and long-range repulsion.

The intrinsically disordered C-terminal domain of the measles virus nucleoprotein interacts with the C-terminal domain of the phosphoprotein via two distinct sites and remains predominantly unfolded.

Measles virus is a negative‐sense, single‐stranded RNA virus within theMononegavirales order,which includes several human pathogens, including rabies, Ebola, Nipah, and Hendra viruses. Themeasles virus nucleoprotein consists of a structured N‐terminal domain, and of an intrinsically disordered C‐terminal domain, NTAIL (aa 401–525), which undergoes induced folding in the presence of the C‐terminal domain (XD, aa 459–507) of the viral phosphoprotein. With in NTAIL, an α‐helical molecular recognition element (α‐MoRE, aa 488–499) involved in binding to P and in induced folding was identified and then observed in the crystal structure of XD. Using small‐angle X‐ray scattering, we have derived a low‐resolution structural model of the complex between XD and NTAIL, which shows that most of NTAIL remains disordered in the complex despite P‐induced folding within the α‐MoRE. The model consists of an extended shape accommodating the multiple conformations adopted by the disordered N‐terminal region of NTAIL, and of a bulky globular region, corresponding to XD and to the C terminus of NTAIL (aa 486–525). Using surface plasmon resonance, circular dichroism, fluorescence spectroscopy, and heteronuclear magnetic resonance, we show that NTAIL has an additional site (aa 517–525) involved in binding to XD but not in the unstructured‐to‐structured transition. This work provides evidence that intrinsically disordered domains can establish complex interactions with their partners, and can contact them through multiple sites that do not all necessarily gain regular secondary structure.

Structural Basis of Cellulosome Efficiency Explored by Small Angle X-ray Scattering

Cellulose, the main structural component of plant cell walls, is the most abundant carbohydrate polymer in nature. To break down plant cell walls, anaerobic microorganisms have evolved a large extracellular enzyme complex termed cellulosome. This megadalton catalytic machinery organizes an enzymatic assembly, tenaciously bound to a scaffolding protein via specialized intermodular “cohesin-dockerin” interactions that serve to enhance synergistic activity among the different catalytic subunits. Here, we report the solution structure properties of cellulosome-like assemblies analyzed by small angle x-ray scattering and molecular dynamics. The atomic models, generated by our strategy for the free chimeric scaffoldin and for binary and ternary complexes, reveal the existence of various conformations due to intrinsic structural flexibility with no, or only coincidental, inter-cohesin interactions. These results provide primary evidence concerning the mechanisms by which these protein assemblies attain their remarkable synergy. The data suggest that the motional freedom of the scaffoldin allows precise positioning of the complexed enzymes according to the topography of the substrate, whereas short-scale motions permitted by residual flexibility of the enzyme linkers allow “fine-tuning” of individual catalytic domains.

High pressure-jump apparatus for kinetic studies of protein folding reactions using the small-angle synchrotron x-ray scattering technique

An apparatus suitable for pressure-jump experiments with variable pressure amplitude and a fast response time to facilitate time-resolved small-angle x-ray scattering at synchrotron facilities is described. The high pressure-jump apparatus is capable of performing bidirectional pressure jumps at a time resolution as high as 5 ms. The high pressure sample cell presented has flat diamond windows and is suited for pressures up to 0.7 GPa operating in the temperature range from −40 to 120 °C. The cell is designed for investigating biological and other soft condensed matter materials. Modifications on the window supports allow also simultaneous wide-angle x-ray scattering data to be taken. We have used the equipment to study the kinetics of protein folding reactions. The performance of the apparatus is demonstrated by presenting data on the pressure-induced un/refolding reaction of the water-soluble protein SNase WT.

Understanding salt or PEG induced attractive interactions to crystallize biological macromolecules

Phase diagrams of biological macromolecules are governed by an appropriate combination of interaction potentials in solution. Repulsive regimes favor solubility, whereas the presence of attractive potentials may induce a variety of phase transitions, including the desired macromolecular crystallization. The forces at work may be analyzed with a combination of small angle X-ray scattering and of numerical treatments. From the results obtained with a variety of model systems, the respective advantages and drawbacks of using monovalent salts or PEGs as crystallizing agents are discussed.

A pressure-jump time-resolved x-ray diffraction study of cubic-cubic transition kinetics in monoolein

In the past two decades, the geometric pathways involved in the transformations between inverse bicontinuous cubic phases in amphiphilic systems have been extensively theoretically modeled. However, little experimental data exists on the cubic-cubic transformation in pure lipid systems. We have used pressure-jump time-resolved X-ray diffraction to investigate the transition between the gyroid QGII and double-diamond QDII phases in mixtures of 1-monoolein in 30 wt % water. We find for this system that the cubic-cubic transition occurs without any detectable intermediate structures. In addition, we have determined the kinetics of the transition, in both the forward and reverse directions, as a function of pressure-jump amplitude, temperature, and water content. A recently developed model allows (at least in principle) the calculation of the activation energy for lipid phase transitions from such data. The analysis is applicable only if kinetic reproducibility is achieved, at least within one sample, and achievement of such kinetic reproducibility is shown here, by carrying out prolonged pressure-cycling. The rate of transformation shows clear and consistent trends with pressure-jump amplitude, temperature, and water content, all of which are shown to be in agreement with the effect of the shift in the position of the cubic-cubic phase boundary following a change in the thermodynamic parameters.

Abnormal Assemblies and Subunit Exchange of RB-Crystallin R120 Mutants Could Be Associated with Destabilization of the Dimeric Substructure†

Mutation of the Arg120 residue in the human alphaB-crystallin sequence has been shown to be associated with a significant ability to aggregate in cultured cells and have an increased oligomeric size coupled to a partial loss of the chaperone-like activity in vitro. In the present study, static and dynamic light scattering, small-angle X-ray scattering, and size exclusion chromatography were used to follow the temperature and pressure induced structural transitions of human alphaB-crystallin and its R120G, R120D, and R120K mutants. The wild type alphaB-crystallin was known to progressively increase in size with increasing temperature, from 43 to 60 degrees C, before aggregating after 60 degrees C. The capacity to increase in size with temperature or pressure, while remaining soluble, had disappeared with the R120G mutant and was found to be reduced for the R120K and R120D mutants. The R120K mutant, which preserves the particle charge, was the less impaired. The deficit of quaternary structure plasticity was well correlated with the decrease in chaperone-like activity previously observed. However, the mutant ability to exchange subunits, measured with a novel anion exchange chromatography assay, was found to be increased, suggesting subtle relationships between structural dynamics and function. From molecular dynamic simulations, the R120 position appeared critical to conserve proper intra- and intersubunit interactions. In silico mutagenesis followed by simulated annealing of the known small heat shock protein 3D structures suggested a destabilization of the dimeric substructure by the R120 mutations. The whole of the results demonstrated the importance of the R120 residue for structural integrity, both static and dynamic, in relation with function.

In situ X-ray measurements to probe a new solid-state polycondensation mechanism for the design of supramolecular organo-bridged silsesquioxanes.

A long-range ordered organic/inorganic material is synthesized from a bis-silane, (EtO)(3)Si-(CH(2))(3)-NHCONH-C(6)H(4)-NHCONH-(CH(2))(3)-Si(OEt)(3). This crosslinked sol-gel solid exhibits a supramolecular organization via intermolecular hydrogen bonding interactions between urea groups (-NHCONH-) and covalent siloxane bonding, triple bond Si-O-Si triple bond. Time-resolved in situ X-ray measurements (coupling small- and wide-angle X-ray scattering techniques) are performed to follow the different steps involved in the synthetic process. A new mechanism based on the crystallization of the hydrolyzed species followed by their polycondensation in solid state is proposed.

Controlling biomolecular crystallization by understanding the distinct effects of PEGs and salts on solubility.

Publisher Summary This chapter discusses the controlling of the biomolecular crystallization by understanding the distinct effects of PEGs and salts on solubility. In the biomacromolecular field, crystallization usually has been discussed in reference to the position of a “solubility curve” in a phase diagram that is an admission that crystallization is a normal thermodynamic process. This chapter shows that SAXS can be particularly useful to analyze the interactions in solution leading to crystallization. From a series of experiments performed on a variety of model systems, the chapter tries to show that the two types of additives, that both induce attractive interactions, are playing a major role: salts and neutral polymers. As a consequence, it now seems possible to better rationalize and limit the number of trials for a first screening of crystallization conditions. Finally, this chapter concludes that for the future, other potential applications would be to clarify the role of interactions in the kinetic aspects of crystallization, nucleation, and crystal growth.