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We have investigated the physical and biomimetic properties of a sponge (L3) phase composed of pentaethylene glycol monododecyl ether (C12E5), a nonionic surfactant, an aqueous solvent, and a cosurfactant. The following cosurfactants, commonly used for solubilizing membrane proteins, were incorporated: n-octyl-β-d-glucopyranoside (β-OG), n-dodecyl-β-d-maltopyranoside (DDM), 4-cyclohexyl-1-butyl-β-d-maltoside (CYMAL-4), and 5-cyclohexyl-1-pentyl-β-d-maltoside (CYMAL-5). Partial phase diagrams of these systems were created. The L3 phase was characterized using crossed polarizers, diffusion of a fluorescent probe by fluorescence recovery after pattern photobleaching (FRAPP), and freeze fracture electron microscopy (FFEM). By varying the hydration of the phase, we were able to tune the distance between adjacent bilayers. The characteristic distance (db) of the phase was obtained from small angle scattering (SAXS/SANS) as well as from FFEM, which yielded complementary db values. These db values were neither af...

International audience; Tripartite efflux pumps are among the main actors responsible for antibiotics resistance in Gram-negative bacteria. In the last two decades, structural studies gave crucial information about the assembly interfaces and the mechanistic motions. Thus rigidifying the assembly seems to be an interesting way to hamper the drug efflux. In this context, xenon is a suitable probe for checking whether small ligands could act as conformational lockers by targeting hydrophobic cavities. Here we focus on OprN, the outer membrane channel of the MexEF efflux pump from Pseudomonas aeruginosa. After exposing OprN crystals to xenon gas pressure, 14 binding sites were observed using X-ray crystallography. These binding sites were unambiguously characterized in hydrophobic cavities of OprN. The major site is observed in the sensitive iris-like region gating the channel at the periplasmic side, built by the three key-residues Leu 405, Asp 109, and Arg 412. This arrangement defines along the tunnel axis a strong hydrophobic/polar gradient able to enhance the passive efflux mechanism of OprN. The other xenon atoms reveal strategic hydrophobic regions of the channel scaffold to target, with the aim to freeze the dynamic movements responsible of the open/ close conformational equilibrium in OprN.

Complexes of OprM and MexA, two proteins of the MexA–MexB–OprM multidrug efflux pump from Pseudomonas aeruginosa, an opportunistic Gram-negative bacterium, were reconstituted into proteoliposomes by detergent removal. Stacks of protein layers with a constant height of 21nm, separated by lipid bilayers, were obtained at stoichiometry of 1:1 (w/w). Using cryo-electron microscopy and tomography, we showed that these protein layers were composed of MexA–OprM complexes self-assembled into regular arrays. Image processing of extracted sub-tomograms depicted the architecture of the bipartite complex sandwiched between two lipid bilayers, representing an environment close to that of the native whole pump (i.e. anchored between outer and inner membranes of P. aeruginosa). The MexA–OprM complex appeared as a cylindrical structure in which we were able to identify the OprM molecule and the MexA moiety. MexA molecules have a cylindrical shape prolonging the periplasmic helices of OprM, and widening near the lipid bilayer. The flared part is likely composed of two MexA domains adjacent to the lipid bilayer, although their precise organization was not reachable mainly due to their flexibility. Moreover, the intermembrane distance of 21nm indicated that the height of the bipartite complex is larger than that of the tripartite AcrA–AcrB–TolC built-up model in which TolC and AcrB are docked into contact. We proposed a model of MexA–OprM taking into account features of previous models based on AcrA–AcrB–TolC and our structural results providing clues to a possible mechanism of tripartite system assembly.

Heptosides are found in important bacterial glycolipids such as lipopolysaccharide (LPS), the biosynthesis of which is targeted for the development of novel antibacterial agents. This work describes the synthesis of a fluorinated analogue of ADP-L-glycero-beta-D-manno-heptopyranose, the donor substrate of the heptosyl transferase WaaC, which catalyzes the incorporation of this carbohydrate into LPS. Synthetically, the key step for the preparation of ADP-2F-heptose is the simultaneous and stereoselective installation of both the fluorine atom at C-2 and the phosphoryl group at C-1 through a selectfluor-mediated (selectfluor=1-chloromethyl-4-fluorodiazoniabicyclo[2.2.2]octane bis(triflate)) electrophilic addition/nucleophilic substitution involving a heptosylglycal. Therefore, we detail in this article 1) the stereoselective preparation of the key intermediates heptosylglycals, 2) the development of a new fluorophosphorylation procedure allowing an excellent beta-gluco stereoselectivity with "all-equatorial" glycals, 3) the synthesis of the target ADP-2F-heptose, and 4) some comments on the contacts observed between the fluorine atom of the final molecule and the protein in the crystallographic structure of heptosyltransferase WaaC.

MexA, a periplasmic component of OprM-MexA-MexB tripartite multidrug efflux pump from Pseudomonas aeruginosa, is natively anchored via its fatty acid in the bacteria inner membrane protruding into the periplasm. We used supported lipid bilayer (SLB) to attach the protein to a single leaflet mimicking its perisplamic orientation. For that purpose, we studied the solubilization of DOPC lipid bilayer supported on silica surface with beta-octyl glucoside (betaOG). First we showed that SLBs resist to betaOG concentrations that usually solubilize liposomes. Native form of MexA was directly inserted in the outer leaflet at (betaOG concentrations in a range of 20-25 mM). Second, observations by cryo-electron microscopy (cryoEM) revealed a dense protein layer attached to the surface corresponding to a 13-nm layer of MexA proteins. Analysis of protein densities allows proposing a schematic organization of native MexA inserted in lipid membrane. This structural organization provides further insights with respect to the partially solved structure of the soluble form.

International audience; Peptide ligands that disrupt MAPK pathways are of great interest for a better understanding of these signalling cascades and represent therefore an attractive target to control cell degenerative processes. In that context, selective disruption of the upstream Grb2/Sos complex in the Ras/MAPK cascade has focused extensive work. The Sos PPII decapeptide, which interacts with the Grb2-SH3 domains, has been modified in various positions and the best inhibitors designed so far are either dimeric ligands or peptoid analogues of the VPPPVPPRRR sequence. We report the synthesis of new Grb2 ligands in which the key Val5 residue has been replaced by a cis C(beta)-substituted proline. Both fluorescence and ITC assays have been employed to measure the affinity of these substituted peptides for a recombinant Grb2 protein. Whereas proline in position 5 completely abolished the binding potency, a cis C(beta)-methyl-L-proline restored the affinity. Other cis C(beta)-proline substituents led to a complete loss of binding potency. Combining the best modifications: a cis C(beta)-methylproline 5, N-acetylation, C-carboxamide and dimerization yielded a 560-fold affinity enhancement compared to the wild-type VPPPVPPRRR sequence. This study shows that C(beta)-substituted prolines may constitute a new alternative for PPII ligands, combining entropy and enthalpy beneficial effects.

Mimetic functional membranes on solid support are now emerging for the development of membrane biosensor or for the study of membrane-mediated processes and should have an important impact on biodiagnostics. We established a method to reconstitute a membrane protein into a lipid membrane in a selective orientation on a solid support. Membrane protein OprM, a component of OprM-MexA-MexB multidrug efflux pump, solubilized in detergent was immobilized via its extracellular domain on aminosilane-modified silica surface. The oriented protein was reconstituted into a lipid membrane by detergent removal. The membrane protein reconstitution process carried out on silica nanoparticles and on planar silica surfaces was followed by cryo-electron microscopy (cryo-EM) and quartz crystal microbalance with dissipation monitoring (QCM-D) respectively. The selective protein orientation on aminosilane-modified silica surface was assessed by cryo-EM and was compared to the nonspecific protein deposition on silica surface. Finally, the binding of MexA, a periplasmic component of the tripartite efflux complex, was monitored with QCM-D on the oriented OprM protein monolayer. The large adsorbed mass gave a direct evidence of the high affinity of MexA with the periplasmic helical part of OprM.

OprM and OprN belong to the outer membrane factor family of multidrug efflux proteins from Pseudomonas aeruginosa, a bacterium responsible of nosocomial infections. We report here the two-dimensional (2D) crystallization of OprN and OprM into lipid bilayers and the determination of their 2D projected structure by cryo-electron crystallography, at 1 and 1.4 nm, respectively. Both proteins present a dense ring of protein density, of approximately 7 nm diameter. An additional thin peripheral ring is resolved in OprN structure. Both proteins are assembled as trimers. The results presented here indicate a high structural homology between OprN (and OprM) and TolC, a multidrug efflux protein from Escherichia coli.

In vitro studies of membrane proteins are of interest only if their structure and function are significantly preserved. One approach is to insert them into the lipid bilayers of highly viscous cubic phases rendering the insertion and manipulation of proteins difficult. Less viscous lipid sponge phases are sometimes used, but their relatively narrow domain of existence can be easily disrupted by protein insertion. We present here a sponge phase consisting of nonionic surfactant bilayers. Its extended domain of existence and its low viscosity allow easy insertion and manipulation of membrane proteins. We show for the first time, to our knowledge, that transmembrane proteins, such as bacteriorhodopsin, sarcoplasmic reticulum Ca2+ATPase (SERCA1a), and its associated enzymes, are fully active in a surfactant phase.

Understanding direct salt effects on protein crystal polymorphism is addressed by comparing different crystal forms (triclinic, monoclinic, tetragonal and orthorhombic) for hen, turkey, bob white quail and human lysozymes. Four new structures of hen egg-white lysozyme are reported: crystals grown in the presence of NapTS diffracted to 1.85 A, of NaI to 1.6 A, of NaNO(3) to 1.45 A and of KSCN to 1.63 A. These new structures are compared with previously published structures in order to draw a mapping of the surface of different lysozymes interacting with monovalent anions, such as nitrate, chloride, iodide, bromide and thiocyanate. An analysis of the structural sites of these anions in the various lysozyme structures is presented. This study shows common anion sites whatever the crystal form and the chemical nature of anions, while others seem specific to a given geometry and a particular charge environment induced by the crystal packing.

The adaptor protein Grb2 plays a central role in cell proliferation and/or cell cycle progression. In this study, we investigate the role of Grb2 in signalling pathways involved in meiotic reinitiation. For that purpose, Xenopus Grb2 cRNA and its mutated forms or human Grb2 protein was microinjected into immature Xenopus oocytes. Reinitiation of meiosis was seen in unstimulated oocytes. Induction of the meiosis was time dependent and Ras dependent, and the presence in Grb2 of SH2 and SH3 domains was required. Several tyrosine phosphorylated proteins were solely detected in oocytes responsive to Grb2 injection. Our results are in favour of an unusual recruitment and initiation of the Grb2 transduction cascade independent of a receptor tyrosine kinase (RTK) stimulation.

A previous mutational analysis of erabutoxin a (Ea), a curaremimetic toxin from sea snake venom, showed that the substitutions S8G and S8T caused, respectively, 176-fold and 780-fold affinity decreases for the nicotinic acetylcholine receptor (AchR). In view of the fact that the side-chain of Ser8 is buried in the wild-type toxin, we wondered whether these affinity changes reflect a direct binding contribution of S8 to the receptor and/or conformational changes that could have occurred in Ea as a result of the introduced mutations. To approach this question, we solved X-ray structures of the two mutants S8G and S8T at high resolution (0.18 nm and 0.17 nm, with R factors of 18.0% and 17.9%, respectively). The data show that none of the mutations significantly modified the toxin structure. Even within the site where the toxin binds to the receptor the backbone conformation remained unchanged. Therefore, the low affinities of the mutants S8T and S8G cannot be explained by a large conformational change of the toxin structure. Although we cannot exclude the possibility that undetectable structural changes have occurred in the toxin mutants, our data support the view that, although buried between loop I and II, S8 is part of the functional epitope of the toxin.

Elastic and quasi-elastic light scattering experiments have been performed on previous deionized lysozyme to follow the concentration dependence of the macroion correlation at very low ionic strength. Nernst-Hartley protein-ion coupled diffusion coefficients have been measured over a range of pH. The analysis of experimental data has been derived within the primitive model of colloidal systems and using the hypernetted chain integral equation. In the absence of added salt, unusual behaviors are obtained for the scattered intensity and the mutual diffusion coefficient which are due to the strong, weakly screened, Coulombic coupling, to the local electroneutrality condition and to the low charge and size asymmetry between proteins and counterions. At high salinity, the electrostatic repulsion vanishes and the pair protein potential reduces to a short-range attraction which is responsible for a phase separation at finite concentration.

The quality of a macromolecular crystal can be probed by combining maximum resolution of diffraction data, Bragg reflection profiles and X-ray topographs. Concerning maximum resolution, critical parameters are the overall rms displacement of atoms, which includes both dynamic and static disorder components, and the dynamic range of integrated intensities that can be achieved for given sample and experimental conditions. Bragg reflection profiles and topographs recorded with a quasi-plane wave of X-rays give a wealth of information on the domain structure and macroscopic disorder.

In order to quantify the effect of polyethylene glycol 4000 (PEG) on the solubility of an integral membrane protein, we have crystallized the photochemical reaction center from Rhodobacter sphaeroides Y by batch method on a large range of PEG. The measurement of the solubility diagram display a semi-logarithmic dependence of solubility versus PEG concentration. Comparison of our results with previously published ones [Odahara, T., Ataka, M. and Katsura, M. (1994) Acta Cryst. D50, 639–642] suggests a notable effect of additional 1,2,3-heptane-triol and/or temperature on photochemical reaction center solubility.

For several years lipidic cubic (Q) mesophases have been used to crystallize membrane proteins. Because they have the rheology of a thick paste, working with Q-phases remain a challenge. We will present a new fluid L3 phase in which transmembrane proteins such as Bacteriodopsin, SERCA1a, and Cytochrome oxidase maintain their activity. Macroscopically a L3 phase can be viewed as a sponge made of a surfactant whereas the holes in the sponge are filled with solvent. Topologically it consists of a single bilayer surrounded on either side by a solvent forming a continuous network of channels. It is comparable to a molten cubic phase, but it possesses water-like viscosity. Locally, it is similar to a lamellar phase but it is isotropic and optically transparent and thus suitable for spectroscopic studies. The L3 phases presented here were characterized by polarized light microscopy, diffusion of a fluorescent probe by fluorescence recovery after pattern photobleaching (FRAPP) and freeze fracture electron microscopy (FFEM).Tuning the distance between adjacent bilayers from 3 to 40 nm is an asset for the study of interactions between proteins. This is obtained by varying the water content of the phase. Characteristic distances (db) of the phase were obtained from small angle scattering spectra (SAXS/SANS) as well as from FFEM, which yielded similar db values: the L3 phase preserves its structure when a transmembrane protein is incorporated into the bilayers, when the non-ionic co-surfactant is replaced by another one and when the temperature varies from 6°C to 30°C. These findings illustrate that a biomimetic surfactant sponge phase can be obtained in the presence of detergents widely used to solubilize membrane proteins and thus make it a versatile medium for membrane protein studies.

In a previous work, solubility diagrams of lysozyme and its ability to crystallize in the presence of various ions were established. Inorganic as well as organic anions showed strong effects on lysozyme solubility following the reverse order of the Hofmeister series [Ries-Kautt and Ducruix, J. Biol. Chem. 264 (1989) 745]. In the present paper, we used small angle X-ray scattering (SAXS) to characterize the influence of various salts on the protein-protein interactions of undersaturated lysozyme solutions at constant pH (4.5) and temperature (18°C). The results show that lysozyme in a low ionic strength buffer presents repulsive protein-protein interactions. Addition of increasing concentrations of salts gradually leads from repulsive to attractive interactions demonstrating the ability of a given protein to change its interactive behavior with additives. While cations (Li + , Na + , K + , NH + 4 , Cs + ) all showed similar effects, large differences were observed between anions in their efficiency to modify the interaction potentials. The order of the anions (SCN − , paratoluene sulfonate, NO − 3 , Cl − , H 2 PO − 4 ) was found to be the same as that observed for their effectiveness in reducing lysozyme solubility and inducing crystallization.

We report here the purification and the crystallization of the modular protein Grb2. The protein was expressed as a fusion with glutathione-S-transferase and purified by affinity chromatography on glutathione agarose. It was apparent from reverse phase chromatography that the purified protein was conformationally unstable. Instability was overcome by the addition of 100 mM arginine to the buffers. Because Grb2 appeared to be extremely sensitive to oxidation, crystallization experiments were performed with a dialysis button technique involving daily addition of fresh DTT to the reservoirs. The presence of 8 to 14% glycerol was necessary to obtain monocrystals. These results are discussed in relation with the modular nature of Grb2.

The effects of various anions on decreasing the solubility of acidic Hypoderma lineatum collagenase at pH 7.2 and 18 degrees C were qualitatively defined by replacing the crystallizing agent of known crystallization conditions by various ammonium salts. The solubility curves measured in the presence of the sulfate, phosphate, citrate, and chloride ammonium salts gave the following ranking of anions: HPO4(2-)/H2PO4- > SO4(2-) > citrate 3-/citrate2- >> Cl-. This order is in agreement with the Hofmeister series. In a previous study on the solubility at pH 4.5 of lysozyme, a basic protein, the effectiveness of anions in decreasing the solubility was found to be in the reverse order. This suggests that the effectiveness of anions in the crystallization of proteins is dependent on the net charge of the protein, i.e., depending on whether a basic protein is crystallized at acidic pH or an acidic protein at basic pH.

The C-terminal Kunitz-type domain from the alpha 3 chain of human type VI collagen (C5), a single 58 amino acid residue chain with three disulfide bridges, was cloned, expressed and crystallized in a monoclonic form, space group P2(1), with a = 25.7 A, b = 38.2 A, c = 28.8 A and beta = 109 degrees. The structure was resolved by molecular replacement, using Alzheimer's protein precursor inhibitor and bovine pancreatic trypsin inhibitor three-dimensional structures as search models. The molecule with one sulfate ion and 43 associated water molecules was refined by XPLOR to an R-factor of 18.9% at 1.6 A. The molecule was not degraded by trypsin and did not inhibit trypsin or tested serine proteases. As opposed to the other Kunitz family members, C5 demonstrates left-handed chirality of the Cys14-Cys38 disulfide bond. Inversion of the Thr13 carbonyl and bulky side-chains at the interface with trypsin in a model of the C5-trypsin complex may explain the lack of inhibition of trypsin.

Multidrug resistance has become a serious concern in the treatment of bacterial infections. A prominent role is ascribed to the active efflux of xenobiotics out of the bacteria by a tripartite protein machinery. The mechanism of drug extrusion is rather well understood, thanks to the X-ray structures obtained for the Escherichia coli TolC/AcrA/AcrB model system and the related Pseudomonas aeruginosa OprM/MexA/MexB. However, many questions remain unresolved, in particular the stoichiometry of the efflux pump assembly. On the basis of blue native polyacrylamide gel electrophoresis (BN-PAGE) (Wittig et al., Nat. Protoc. 2006, 1, 418-428), we analyzed the binding stoichiometry of both palmitylated and non-palmitylated MexA with the cognate partner OprM trimer at different ratios and detergent conditions. We found that β-octyl glucopyranoside (β-OG) detergent was not suitable for this technique. Then we proved that MexA has to be palmitylated in order to stabilized the complex formation with OprM. Finally, we provided evidence for a two by two (2, 4, 6, or upper) binding of palmitylated MexA per trimer of OprM.

The C-terminal Kunitz-type domain from the alpha3 chain of human type VI collagen (C5), a single amino-acid residue chain with three disulfide bridges, was refined at 0.9 A resolution in a monoclinic form, space group P2(1) with one molecule per asymmetric unit, using data collected at cryogenic temperature (110 K). The average protein factor decreases from 21 A(2) at room temperature (RT) to 12 A(2) at cryotemperature (100 K, CT). The spatially close N- and C-termini remain highly disordered. The different structural motifs of C5 were analyzed in terms of rigid-body displacement (TLS analyses) and show dominant libration motion for the secondary structure.

The fluorescence recovery after pattern photobleaching (FRAPP) method was used to study the diffusion of membrane proteins, peptides, and lipids embedded into the bilayers of a biomimetic sponge phase.Lateral diffusion of membrane proteins is a useful tool for investigating the function, and association of these biopolymers. FRAPP results can also provide further information regarding their mobility, i.e. Brownian, accelerated versus slowed down, as well as their location: transmsmbrane, membrane or in between the bilayers of a sponge phase (L3).Using this L3 phase for membrane protein studies offers several advantages; the distance between unsupported bilayers is easily tunable; the phase is non-viscous and thus easy to handle; it is isotropic and therefore amenable to optical studies as well as for crystallization assays. In order to ascertain whether the phase is biologically relevant it was tested with several transmembrane proteins which retain their activity inside the phase.To illustrate our approach we will present the interaction between transmembrane proteins from a Pseudomonas aeruginosa efflux pump; MexA-MexB-OprM. By measuring their lateral diffusion we were able to deduce the mode of interaction, the size of the protein complex and its potential stoichiometry. Chiefly, we will illustrate that MexA is embedded in the bilayer; that MexA and OprM do not interact laterally but form a complex if they are inserted in opposite bilayers and that the population of bound proteins is at its maximum for bilayers separated by a distance of ∼ 200 A, which is the expected periplasmic thickness for gram negative bacteria.

International audience; We report the first crystal structure of a 1:2 hormone.receptor complex that involves prolactin (PRL) as the ligand, at 3.8-A resolution. Stable ternary complexes were obtained by generating affinity-matured PRL variants harboring an N-terminal tail from ovine placental lactogen, a closely related PRL receptor (PRLR) ligand. This structure allows one to draw up an exhaustive inventory of the residues involved at the PRL.PRLR site 2 interface, consistent with all previously reported site-directed mutagenesis data. We propose, with this description, an interaction model involving three structural components of PRL site 2 ("three-pin plug"): the conserved glycine 129 of helix alpha3, the hydrogen bond network involving surrounding residues (glycine cavity), and the N terminus. The model provides a molecular basis for the properties of the different PRL analogs designed to date, including PRLR antagonists. Finally, comparison of our 1:2 PRL.PRLR(2) structure with those of free PRL and its 1:1 complex indicates that the structure of PRL undergoes significant changes when binding the first, but not the second receptor. This suggests that the second PRLR moiety adapts to the 1:1 complex rather than the opposite. In conclusion, this structure will be a useful guiding tool for further investigations of the molecular mechanisms involved in PRLR dimerization and activation, as well as for the optimization of PRLR antagonists, an emerging class of compounds with high therapeutic potential against breast and prostate cancer.

The regularity of salts in affecting lysozyme solubility (and other proteins having a basic pI) at pH 4.5 according to the lyotropic series has been completed by solubility curve measurements. The measurement of lysozyme/NaSCN solubility shows very small difference with lysozyme/KSCN solubility, confirming the slight influence of the nature of the cation. The solubility of lysozyme nitrate inserts between the values of lysozyme chloride and thiocyanate. Some organic salts have been tested as new crystallizing agents and the solubility curve of lysozyme in the presence of sodium para-toluenesulfonate has been determined. The solubility and the crystal form of lysozyme is affected differently by temperature changes (18 and 40°C), depending on the nature of the crystallizing agent.

Retrospective analysis of 189 nonredundant strains of Pseudomonas aeruginosa sequentially recovered from the sputum samples of 46 cystic fibrosis (CF) patients over a 10-year period (1998 to 2007) revealed that 53 out of 189 (28%) samples were hypersusceptible to the β-lactam antibiotic ticarcillin (MIC ≤ 4 μg/ml) (phenotype dubbed Tic hs ). As evidenced by trans -complementation and gene inactivation experiments, the mutational upregulation of the efflux system MexXY was responsible for various degrees of resistance to aminoglycosides in a selection of 11 genotypically distinct strains (gentamicin MICs from 2 to 64 μg/ml). By demonstrating for the first time that the MexXY pump may evolve in CF strains, we found that a mutation leading to an F1018L change in the resistance-nodulation-cell division (RND) transporter MexY was able to increase pump-promoted resistance to aminoglycosides, cefepime, and fluoroquinolones twofold. The inactivation of the mexB gene (which codes for the RND transporter MexB) in the 11 selected strains showed that the Tic hs phenotype was due to a mutational or functional loss of function of MexAB-OprM, the multidrug efflux system known to contribute to the natural resistance of P. aeruginosa to β-lactams (e.g., ticarcillin and aztreonam), fluoroquinolones, tetracycline, and novobiocin. Two of the selected strains synthesized abnormally low amounts of the MexB protein, and 3 of 11 strains expressed truncated MexB ( n = 2) or MexA ( n = 1) polypeptide as a result of mutations in the corresponding genes, while 7 of 11 strains produced wild-type though nonfunctional MexAB-OprM pumps at levels similar to or even higher than that of reference strain PAO1. Overall, our data indicate that while MexXY is necessary for P. aeruginosa to adapt to the hostile environment of the CF lung, the MexAB-OprM pump is dispensable and tends to be lost or inactivated in subpopulations of P. aeruginosa .

We tested a number of salts against their ability to crystallize hen egg white lysozyme [M.M. Ries-Kautt and A.F. Ducruix, J. Biol. Chem. 264 (1989) 745] and showed that, in the case of lysozyme, the effectiveness of the ions toward crystallization is linked to the reverse order of Hofmeister series, i.e SCN − 3 > NO − 3 > Cl − > HC 6 H 5 O 2 − 7 > CH 3 COO − > H 2 PO − 4 > SO 2 − 4 . The ability of lysozyme to crystallize at very low concentration of SCN − ; is probably due to ion pairing between the anion and positively charged residues of the protein. The possibility of crystallizing basic proteins with a family of various anionic species has been studied in the present work and linked to Pearson's theory of “hard” and “soft” acid and base interactions. Although the nature of interactions between ions and proteins has not yet been measured, we demonstrate the possibility to rationalize crystallization conditions for basic proteins at acidic pH. As a consequence, it is suggested that ion pairing should be possible for acidic proteins at basic pH in the presence of appropriate cationic species. Some applications are developed.

The solubility of a protein can be defined as the concentration of the soluble protein in equilibrium with the solid phase under given conditions of pH, temperature, buffer, and/or various additives. A solubility curve represents the dependence of this saturating concentration on a single parameter, which could be the concentration of a crystallizing or precipitating agent. For accurate determinations, the solubility should be determined by both crystallization and redissolution of crystals, and it should be demonstrated that in the two methods the protein concentration converges asymptotically to the same value. In cases where fairly large amounts of protein are readily available, solubility diagram analysis provides a means of quantitatively characterizing the effect of one parameter, and hence of interpreting its influence in a meaningful way. Our analysis of lysozyme (p I = 11.1) solubility curves in presence of various salts, at pH 4.5 and 18°C, indicates that solubility is affected more by anions than by cations and that the effectiveness of the anions is in an order roughly the reverse of that of the Hofmeister series. Under these conditions, thiocyanate, a chaotropic anion at high concentration, is found to be a very effective crystallizing agent at low ( m ) concentrations. Two other monomeric proteins (erabutoxin and bovine pancreatic trypsin inhibitor) of high isoelectric point crystallized also at pH 4.5 and 18°C, confirming the much higher effectiveness of KSCN compared to NaCl. The width of the crystallization zone between the solubility curve and the curve above which only precipitation occurs also varies considerably with different anions. These observations may have useful implications in screening and optimizing crystallization conditions.

We report various experiments aimed at the resolution of the 3-dimensional structure of the photosynthetic reaction center from wild type Y Rhodobacter sphaeroides. The genes encoding the L and M polypeptides have been cloned and sequenced. They bear 2 mutations each when compared to those already sequenced in another Rb sphaeroides strain (2.4.1). In the L gene, these codon changes are silent. In the M gene, one is silent and the other one leads to a Leu- Met substitution at position 140. At the present stage of the refinement of the X-ray data (0.3 nm resolution) the structure of the Y reaction center is shown to be highly similar to that of the Rhodopseudomonas viridis reaction center. The binding of spheroidene on the M side of the Y reaction center is shown to be determined by hydrophobic interactions with neighboring amino acids and by steric factors. Preliminary results concerning the localization of the detergent (β-octylglucoside) in the unit cell are presented. This method combines low angle neutron scattering at different contrasts in H2O/D2O with X-ray crystallographic data.

Collagenolytic protease I from the fiddler crab Uca pugilator belongs to the serine proteases of the trypsin family. A graphic molecular model was built using information from sequences and X-ray structures of four homologous proteins which were superimposed to define structurally conserved regions. Protease I sequence was aligned, with sequences of the model proteins, without permitting any deletion or insertion in these regions. Elastase alpha-carbon chain was selected as a template molecule. For the structurally variable regions, fragments of the four homologous proteins which were 'closet' in sequence were selected. Intramolecular steric hindrance, that resulted from the substitution of the residues of the templates by protease I residues, was corrected by adjustment of the side-chain conformational angles. The model was then optimized by energy minimization. The primary specificity pocket in the model of collagenolytic protease I predict a substrate preference for both P1 hydrophobic and positively charged residues which is in agreement with the biochemical observations. As soybean trypsin inhibitor (STI) is known to inhibit collagenolytic protease I, a tentative model of the complex was constructed and possibilities of interaction examined.

Escherichia coli phenylalanyl-tRNA synthetase is a tetrameric protein composed of two types of protomers. In order to resolve the subunit organization, neutron small-angle scattering experiments have been performed in different contrasts with all types of isotope hybrids that could be obtained by reconstituting the alpha 2 beta 2 enzyme from the protonated and deuterated forms of the alpha and beta subunits. Experiments have been also made with the isolated alpha promoter. A model for the alpha 2 beta 2 tetramer is deduced where the two alpha promoters are elongated ellipsoids (45 x 45 x 160 A3) lying side by side with an angle of about 40 degrees between their long axes and where the two beta subunits are also elongated ellipsoids (31 x 31 x 130 A3) with an angle of 30 degrees between their axes. This model was obtained by assuming that the two pairs of subunits are in contact in an orthogonal manner and by taking advantage of the measured distance between the centers of mass of the alpha 2 and beta 2 pairs (d = 23 +/- 2 A).

The injection of the Grb2 adapter in Xenopus oocytes promotes G2/M transition without stimulation from a receptor only the first day after the oocytes removal from the ovaries. This cell cycle reinitiation is Ras-dependent and requires the SH2 and SH3 domains of Grb2. The SH2 domain of Grb2 binds the tyrosine phosphorylated lipovitellin1, a homologue of the human apolipoprotein B. The N-SH3 domain of Grb2 is linked to a proline-rich sequence of the C2 domain of PLC-gamma1, PLC-gamma1 itself is linked, through its SH3 domain, to the C-terminal proline-rich region of Sos. When Grb2-PLC-gamma1-Sos is associated, PLC-gamma1 is not phosphorylated on Y783 but shows a phospholipase activity. Inhibition of lipovitellin 1 or PLC-gamma1 avoids Grb2-induced cell cycle reinitiation. Therefore, the Grb2-lipovitellin 1 association is the starting point of a novel signaling pathway, where PLC-gamma1 binds Grb2 and recruits Sos.

International audience; Competitive antagonists of the human prolactin (hPRL) receptor are a novel class of molecules of potential therapeutic interest in the context of cancer. We recently developed the pure antagonist Del1-9-G129R-hPRL by deleting the nine N-terminal residues of G129R-hPRL, a first generation partial antagonist. We determined the crystallographic structure of Del1-9-G129R-hPRL, which revealed no major change compared with wild type hPRL, indicating that its pure antagonistic properties are intrinsically due to the mutations. To decipher the molecular bases of pure antagonism, we compared the biological, physicochemical, and structural properties of numerous hPRL variants harboring N-terminal or Gly(129) mutations, alone or combined. The pure versus partial antagonistic properties of the multiple hPRL variants could not be correlated to differences in their affinities toward the hPRL receptor, especially at site 2 as determined by surface plasmon resonance. On the contrary, residual agonism of the hPRL variants was found to be inversely correlated to their thermodynamic stability, which was altered by all the Gly(129) mutations but not by those involving the N terminus. We therefore propose that residual agonism can be abolished either by further disrupting hormone site 2-receptor contacts by N-terminal deletion, as in Del1-9-G129R-hPRL, or by stabilizing hPRL and constraining its intrinsic flexibility, as in G129V-hPRL.

Competitive antagonists of the human prolactin (hPRL) receptor are a novel class of molecules of potential therapeutic interest in the context of cancer. We recently developed the pure antagonist Del1-9-G129R-hPRL by deleting the nine N-terminal residues of G129R-hPRL, a first generation partial antagonist. We determined the crystallographic structure of Del1-9-G129R-hPRL, which revealed no major change compared with wild type hPRL, indicating that its pure antagonistic properties are intrinsically due to the mutations. To decipher the molecular bases of pure antagonism, we compared the biological, physicochemical, and structural properties of numerous hPRL variants harboring N-terminal or Gly(129) mutations, alone or combined. The pure versus partial antagonistic properties of the multiple hPRL variants could not be correlated to differences in their affinities toward the hPRL receptor, especially at site 2 as determined by surface plasmon resonance. On the contrary, residual agonism of the hPRL variants was found to be inversely correlated to their thermodynamic stability, which was altered by all the Gly(129) mutations but not by those involving the N terminus. We therefore propose that residual agonism can be abolished either by further disrupting hormone site 2-receptor contacts by N-terminal deletion, as in Del1-9-G129R-hPRL, or by stabilizing hPRL and constraining its intrinsic flexibility, as in G129V-hPRL.

Human nephrocystin is a protein associated with juvenile NPH, an autosomal recessive, inherited kidney disease responsible for chronic renal failure in children. It contains an SH3 domain involved in signaling pathways controlling cell adhesion and cytoskeleton organization. The solution structure of this domain was solved by triple resonance NMR spectroscopy. Within the core, the structure is similar to those previously reported for other SH3 domains but exhibits a number of specific noncanonical features within the polyproline ligand binding site. Some of the key conserved residues are missing, and the N-Src loop exhibits an unusual twisted geometry, which results in a narrowing of the binding groove. This is induced by the replacement of a conserved Asp, Asn, or Glu residue by a Pro at one side of the N-Src loop. A systematic survey of other SH3 domains also containing a Pro at this position reveals that most of them belong to proteins involved in cell adhesion or motility. A variant of this domain, which carries a point mutation causing NPH, was also analyzed. This change, L180P, although it corresponds to a nonconserved and solvent-exposed position, causes a complete loss of the tertiary structure. Similar effects are also observed with the L180A variant. This could be a context-dependent effect resulting from an interaction between neighboring charged side-chains.

OprM and OprN belong to the outer membrane factor family proteins. These approximately 52 kDa proteins are part of the tripartite efflux pumps found in Pseudomonas aeruginosa and are responsible in part for the antibiotic resistance observed in these bacteria. Both proteins have been expressed in Escherichia coli as His-tag proteins and purified accordingly by affinity chromatography in the presence of n-octyl-beta-D-glucopyranoside detergent. OprM and OprN were crystallized using PEG 20 000/ammonium citrate and ammonium sulfate as precipitating agents, respectively. Crystals belong to space group C2, with unit-cell parameters a = 152.6, b = 87.9, c = 355.9 A, beta = 98.9 degrees and a = 151.3, b = 87.6, c = 356.5 A, beta = 98.1 degrees for OprM and OprN, respectively. Using the ESRF synchrotron-radiation source, OprM diffraction data extended to 3.4 A.

OprM and OprN belong to the outer membrane factor family of multidrug efflux proteins from Pseudomonas aeruginosa, a bacterium responsible of nosocomial infections. We report here the two-dimensional (2D) crystallization of OprN and OprM into lipid bilayers and the determination of their 2D projected structure by cryo-electron crystallography, at 1 and 1.4 nm, respectively. Both proteins present a dense ring of protein density, of approximately 7 nm diameter. An additional thin peripheral ring is resolved in OprN structure. Both proteins are assembled as trimers. The results presented here indicate a high structural homology between OprN (and OprM) and TolC, a multidrug efflux protein from Escherichia coli.

Grb14 belongs to the Grb7 family of adapter proteins and was identified as a negative regulator of insulin signal transduction. Its inhibitory effect on the insulin receptor kinase activity is controlled by a newly discovered domain called PIR. To investigate the biochemical and biophysical characteristics of this new domain, we cloned and purified recombinant PIR-SH2, PIR, and SH2 domains. The isolated PIR and PIR-SH2 domains were physiologically active and inhibited insulin-induced reinitiation of meiosis in the Xenopus oocytes system. However, NMR experiments on 15N-labelled PIR revealed that it did not present secondary structure. These results suggest that the PIR domain belongs to the growing family of intrinsically unstructured proteins.

The activation of growth factor receptors induces phosphorylation of tyrosine residues in its C-terminal part, creating binding sites for SH2 domain-containing proteins. Grb2 is a protein that recruits Sos, the exchange factor for Ras. Recruitment of Sos allows for Ras activation and subsequent signal transmission. This promotes translocation of MAP kinases into the nucleus and activation of early transcription factors. Grb2, a 25 kDa protein, is composed of one SH2 domain surrounded by two SH3 domains. The SH2 domain of Grb2 binds to class II phosphotyrosyl peptides with the consensus sequence pYXNX. Thus, Grb2 is a good example of a bifunctional adaptor protein that brings proteins into close proximity, allowing signal transduction through proteins located in different compartments. To explore the interactions between Grb2 and phosphorylated ligands, we have solved the crystal structure of complexes between the Grb2-SH2 domain and peptides corresponding to Shc-derived sequences. Two structures are described: the Grb2-SH2 domain in complex with PSpYVNVQN at 1.5 A; and the Grb2-SH2 domain in complex with mAZ*-pY-(alphaMe)pY-N-NH2 pseudo-peptide, at 2 A. Both are compared to an unliganded SH2 structure determined at 2.7 A which, interestingly enough, forms a dimer through two swapping subdomains from two symmetry-related molecules. The nanomolar affinity of the mAZ-pY-(alphaMe)pY-N-NH2 pseudo-peptide for Grb2-SH2 is related to new interactions with non- conserved residues. The design of Grb2-SH2 domain inhibitors that prevent interaction with tyrosine kinase proteins or other adaptors like Shc or IRS1 should provide a means to interrupt the Ras signaling pathway. Newly synthesized pseudo-peptides exhibit nanomolar affinities for the Grb2-SH2 domain. It will then be possible to design new inhibitors with similar affinity and simpler chemical structures.

This paper describes the overproduction and purification of the C-terminus polyhistidine-tagged outer membrane protein OprM, which is a part of the MexA-MexB-OprM active efflux system of Pseudomonas aeruginosa. Renaturation of the protein from inclusion bodies of Escherichia coli was achieved using guanidine-HCl as denaturing agent and n-octylpolyoxyethylene (C8POE) and n-octyltetraoxyethylene (C8E4) as nonionic detergents. The refolded protein was purified by ion-exchange and nickel-affinity chromatography. The final yield was 6 mg of pure histidine-tagged OprM per liter of E. coli culture. Renaturation was monitored by the effects of heating prior to SDS-PAGE, using a typical and exclusive property of outer membrane proteins. Immunoblotting revealed that the recombinant protein is addressed to the outer membrane of E. coli, after maturation by excision of its N-terminal signal sequence. Complementation of an oprM deletion mutant with the plasmid encoded histidine-tagged OprM protein restored antibiotic susceptibilities to wild-type levels, demonstrating functionality of recombinant OprM.

A plethora of membrane proteins studies have been performed on micellar systems containing detergent solubilised proteins. A major drawback of these systems is their rather poor mimicry of biological membranes. Therefore, development of new biologically relevant membrane systems is justified.We illustrate an original approach combining fluorescence recovery after fringe pattern photobleaching (FRAPP) with the use of an optically isotropic, extremely fluid phase of bilayers (the sponge phase). In this biologically relevant system, well suited for spectroscopic studies, the spacing between two adjacent bilayers and the thickness of the bilayers can be easily and very precisely tuned. So when the membranes are sufficiently separated, the only possible interactions occur between proteins embedded in the same bilayer, whereas when the membranes come together, interactions between proteins embedded in adjacent membranes may also occur.We present studies of interactions between proteins of the efflux pump of Pseudomonas aeruginosa: MexB (the rotor of the pump connecting the interior of the bacterium and the periplasm), OprM (a pipe connecting the periplasm to the outside of the bacterium) and perplasmic MexA. The mode of interaction, the size of protein complexes and their stoichiometry were determined. In particular we show that MexA and OprM interact only if they are incorporated in opposite bilayers. The population of this complex reaches its maximum when the bilayers are separated by a distance of about 200 A, which is the thickness of the Pseudomonas aeruginosa periplasm. The stoichiometry of the above complex will be presented as well as results describing Mexa-MexB and MexB-OprM associations.We will thus demonstrate the versatility of our system, which is well suited to study the associations of membrane proteins in a biologically relevant environment.

International audience; Proteins of the Wiskott-Aldrich Syndrome protein (WASp) family connect signaling pathways to the actin polymerization-driven cell motility. The ubiquitous homolog of WASp, N-WASp, is a multidomain protein that interacts with the Arp2/3 complex and G-actin via its C-terminal WA domain to stimulate actin polymerization. The activity of N-WASp is enhanced by the binding of effectors like Cdc42-guanosine 5'-3-O-(thio)triphosphate, phosphatidylinositol bisphosphate, or the Shigella IcsA protein. Here we show that the SH3-SH2-SH3 adaptor Grb2 is another activator of N-WASp that stimulates actin polymerization by increasing the amount of N-WASp. Arp2/3 complex. The concentration dependence of N-WASp activity, sedimentation velocity and cross-linking experiments together suggest that N-WASp is subject to self-association, and Grb2 enhances N-WASp activity by binding preferentially to its active monomeric form. Use of peptide inhibitors, mutated Grb2, and isolated SH3 domains demonstrate that the effect of Grb2 is mediated by the interaction of its C-terminal SH3 domain with the proline-rich region of N-WASp. Cdc42 and Grb2 bind simultaneously to N-WASp and enhance actin polymerization synergistically. Grb2 shortens the delay preceding the onset of Escherichia coli (IcsA) actin-based reconstituted movement. These results suggest that Grb2 may activate Arp2/3 complex-mediated actin polymerization downstream from the receptor tyrosine kinase signaling pathway.

Collagenases, divided into metallocollagenases and serine collagenases, are the only proteases that cleave the triple helix of collagen under physiological conditions. In the present work, the serine protease collagenase purified from Hypoderma lineatum larvae is studied. From crystals grown in the International Microgravity Laboratory (IML2), a data set was collected at 1.7 A using synchrotron radiation. Although the resolution is not very different, the signal-to-noise ratio and the quality of the electron density are much improved. Alternate conformations were revealed for several residues, in particular Tyr99, suggesting a gate mechanism of recognition.

The word ‘crystal’ is derived from the Greek root ‘krustallos’ meaning ‘clear ice’. Like ice, crystals are chemically well defined, and many among of them are of transparent and glittering appearance, like quartz, which was for a long time the archetype. Often they are beautiful geometrical solids with regular faces and sharp edges, which probably explains why crystallinity, even in the figurative meaning, is taken as a symbol of perfection and purity. From the physical point of view, crystals are regular three-dimensional arrays of atoms, ions, molecules, or molecular assemblies. Ideal crystals can be imagined as infinite and perfect arrays in which the building blocks (the asymmetric units) are arranged according to well-defined symmetries (forming the 230 space groups) into unit cells that are repeated in the three-dimensions by translations. Experimental crystals, however, have finite dimensions. An implicit consequence is that a macroscopic fragment from a crystal is still a crystal, because the orderly arrangement of molecules within such a fragment still extends at long distances. The practical consequence is that crystal fragments can be used as seeds (Chapter 7). In laboratory-grown crystals the periodicity is never perfect, due to different kinds of local disorders or long-range imperfections like dislocations. Also, these crystals are often of polycrystalline nature. The external forms of crystals are always manifestations of their internal structures and symmetries, even if in some cases these symmetries may be hidden at the macroscopic level, due to differential growth kinetics of the crystal faces. Periodicity in crystal architecture is also reflected in their macroscopic physical properties. The most straightforward example is given by the ability of crystals to diffract X-rays, neutrons, or electrons, the phenomenon underlying structural chemistry and biology (for introductory texts see refs 1 and 2), and the major aim of this book is to present the methods employed to produce three-dimensional crystals of biological macromolecules, but also two-dimensional crystals (Chapter 12), needed for diffraction studies. Other properties of invaluable practical applications should not be overlooked either, as is the case of optical and electronic properties which are at the basis of non-linear optics and modern electronics (for an introduction to physical properties of molecular crystals see ref. 3).

Biological macromolecules follow the same thermodynamic rules as inorganic or organic small molecules concerning supersaturation, nucleation, and crystal growth (1). Nevertheless macromolecules present particularities, because the intramolecular interactions responsible of their tertiary structure, the intermolecular interactions involved in the crystal contacts, and the interactions necessary to solubilize them in a solvent are similar. Therefore these different interactions may become competitive with each other. In addition, the biological properties of biological macromolecules may be conserved although the physico-chemical properties, such as the net charge, may change depending on the crystallization conditions (pH, ionic strength, etc.). A charged biological macromolecule requires counterions to maintain the electroneutrality of the solution; therefore it should be considered as a protein (or nucleic acid) salt with its own physico-chemical properties, depending on the nature of the counterions. To crystallize a biological macromolecule, its solution must have reached supersaturation which is the driving force for crystal growth. The understanding of the influence of the crystallization parameters on protein solubility of model proteins is necessary to guide the preparation of crystals of new proteins and their manipulation. Only the practical issues are developed in this chapter, and the reader should refer to recent reviews (2-4) for a description of the fundamental physical chemistry underlying crystallogenesis. The solubilization of a solute (e.g. a biological macromolecule) in an efficient solvent requires solvent-solute interactions, which must be similar to the solvent-solvent interactions and to the solute-solute interactions of the compound to be dissolved. All of the compounds of a protein solution (protein, water, buffer, crystallizing agents, and others) interact with each other via various, often weak, types of interactions: monopole-monopole, monopole-dipole, dipole-dipole, Van der Waals hydrophobic interactions, and hydrogen bonds. Solubility is defined as the amount of solute dissolved in a solution in equilibrium with its crystal form at a given temperature. For example, crystalline ammonium sulfate dissolves at 25°C until its concentration reaches 4.1 moles per litre of water, the excess remaining non-dissolved. More salt can be dissolved when raising the temperature, but if the temperature is brought back to 25°C, the solution becomes supersaturated, and the excess of salt crystallizes until its concentration reaches again its solubility value at 25°C (4.1 moles per litre of water).