Characterization of a Biomimetic Mesophase Composed of Nonionic Surfactants and an Aqueous Solvent

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 (d_b) of the phase was obtained from small angle scattering (SAXS/SANS) as well as from FFEM, which yielded complementary d_b values. These d_b values were neither affected by the nature of the cosurfactant nor by the addition of membrane proteins. These findings illustrate that a biomimetic surfactant sponge phase can be created in the presence of several common membrane protein-solubilizing detergents, thus making it a versatile medium for membrane protein studies.

SAXS study of the PIR domain from the Grb14 molecular adaptor: a natively unfolded protein with a transient structure primer?

Grb14 belongs to the Grb7 family of adapters and was identified as a negative regulator of insulin signal transduction. Between the PH (pleckstrin homology) and SH2 (Src homology 2) domains is a new binding domain implicated in the interaction with receptor tyrosine kinases called PIR (phosphorylated insulin receptor interaction region). Both PIR and SH2 domains interact with the insulin receptor, but their relative role varies considering the member of the Grb7 family and the tyrosine kinase receptor. In the case of Grb14, PIR is the main binding domain and is sufficient to inhibit the insulin receptor kinase activity. We have proposed, on the basis of NMR measurements, that PIR lacks ordered structure and presents a high flexibility, although remaining fully active. To complement this first study, we have used small-angle x-ray scattering in solution together with a modeling approach representing the PIR domain as a chain of pseudo residues. Circular dichroism experiments were also performed in the presence of variable amounts of trifluoroethanol. These observations, together with an ensemble of sequence analyses and previous NMR results, all support the view of PIR as essentially unstructured but with a potentially structured short stretch encompassing residues 399-407. This stretch, which may be only structured transiently in the isolated molecule, could play a major role in Grb14 PIR binding to a biological partner by undergoing a structural transition.

Overexpression, refolding, and purification of the histidine-tagged outer membrane efflux protein OprM of Pseudomonas aeruginosa

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.

Structural effects of monovalent anions on polymorphic lysozyme crystals

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.

Grb2 promotes reinitiation of meiosis in Xenopus oocytes

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.

GRB2 links signaling to actin assembly by enhancing interaction of neural Wiskott-Aldrich syndrome protein (N-WASp) with actin-related protein (ARP2/3) complex

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.

High resolution x-ray analysis of two mutants of a curaremimetic snake toxin

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.

1.7 A x-ray structure of space-grown collagenase crystals

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.

Signalling to actin: the Cdc42-N-WASP-Arp2/3 connection

The molecular link between the signalling pathway regulating the formation of filopodia and the initiation of local actin polymerization has been elucidated: N-WASP, a close homologue of WASP, which is the product of the gene responsible for the Wiskott-Aldrich syndrome, mediates a direct connection between the small G-protein Cdc42 and the Arp2/3 complex.

Mosaic spread characterization of microgravity-grown tetragonal lysozyme single crystals

Mosaic spread values for crystals grown in microgravity were measured using synchrotron radiation. Full width at half maximum (FWHM) values for diffraction line profiles in the range 10-20" (arc seconds, 1" = 1 degrees /3600) were observed. These values are similar to those measured for crystals grown on earth using the gel-acupuncture method. The crystals analysed are composed of from two to five domains producing peaks having widths from 5 to 15". The distribution of these domains is neither homogeneous (with domains of lower quality concentrated in the centre of the crystal) nor isotropic (producing peaks whose width changes depending on the observation direction). Methodological aspects are also discussed, with special consideration of the effects of mosaic spread on the data-collection procedures for high-resolution (low-intensity) reflections.

The decameric structure of bovine pancreatic trypsin inhibitor (BPTI) crystallized from thiocyanate at 2.7 A resolution

The structure of a monoclinic form of bovine pancreatic trypsin inhibitor (BPTI) crystallized from a thiocyanate solution has been determined and refined at 2.7 A resolution. The space group is P21 with a = 71.56, b = 73.83, c = 64.47 A, beta = 93.9 degrees and Z = 20. The ten independent molecules were located by a multi-body molecular-replacement search as developed in the AMoRe program, starting from a single monomer model (PDB code: 6PTI). The molecular arrangement of the subunits is a decamer resulting from the combination of two orthogonal fivefold and twofold non-crystallographic axes. This builds a globular micelle-like particle which minimizes hydrophobic interactions with the solvent. The refinement was conducted with non-crystallographic symmetry constraints up to a final residual of R = 0.20 (Rfree= 0.26). The root-mean-square deviations from ideal geometry were 0.015 A and 1.6 degrees on bond distances and bond angles, respectively. Several sites for thiocyanate ions were analyzed.

1.2 A refinement of the Kunitz-type domain from the alpha3 chain of human type VI collagen

The recombinant Kunitz-type domain (C5) of human collagen alpha3(VI) chain was previously described at 1.6 A resolution at room temperature. By changing the crystallization conditions and using synchrotron radiation, we are able to record diffraction data to 1.2 A resolution for crystals of the same space group at 291 K. The protein-water-ion model has been refined anisotropically against these new data using the program SHELXL93; the results converged to an R factor of 15.0%, with all data between 7 and 1.2 A. The final electron-density map reveals a clear chain tracing with a few disordered residues and five residues out of 58 that present alternate conformations. The Cys14-Cys38 bond presents the less frequently observed left-hand conformation (chi1 = -60 degrees). The solvent molecules and a phosphate ion are well ordered with an average B of 38 A2. The high-resolution structure reveals the N and C termini which were missing from the 1.6 A structure.

Characterization of the interaction between bovine pancreatic trypsin inhibitor and thiocyanate by NMR

The interaction between Bovine Pancreatic Trypsin Inhibitor and thiocyanate was studied using NMR spectroscopy following several experimental approaches. The chemical shift variations of the BPTI protons in the absence and in the presence of increasing thiocyanate concentrations (up to 0.2 M) were significant (> 0.05 ppm) for 30 protein protons belonging to 20 residues. The largest deviation, 0.2 ppm, was observed for the amide backbone proton of Arg42 in the absence of thiocyanate and in the presence of 40 molar equivalents of thiocyanate. The influence of the presence of thiocyanate on the electrostatic potential surrounding the protein was demonstrated by NOESY spectra selective at the water frequency: the presence of SCN- favours acid catalysed exchange and disfavours base catalysis. However, a specific effect of thiocyanate was pointed out since the comparison of the chemical shifts in the presence of 40 molar equivalents of KSCN and KCl, respectively, showed much more as well as larger deviations compared to measurements in the absence of salt. A dissociation constant, KD, for a 1/1 complex between BPTI and thiocyanate was calculated from chemical shifts measurements: KD = 89 +/- 8 mM. A second value, KD = 99 +/- 10 mM, was extracted from SC15N relaxation time measurements.

No salting-in of lysozyme chloride observed at low ionic strength over a large range of pH

Solubility of lysozyme chloride was determined in the absence of added salt and in the presence of 0.05-1.2 M NaCl, starting from isoionic lysozyme, which was then brought to pH values from 9 to 3 by addition of HCl. The main observation is the absence of a salting-in region whatever the pH studied. This is explained by a predominant electrostatic screening of the positively charged protein and/or by adsorption of chloride ions by the protein. The solubility increases with the protein net charge at low ionic strength, but the reverse is observed at high ionic strength. The solubility of lysozyme chloride seems to become independent of ionic strength at pH approximately 9.5, which is interpreted as a shift of the isoionic pH (10.8) to an isoelectric pH due to chloride binding. The crystallization at very low ionic strength, where lysozyme crystallizes at supersaturation values as low as 1.1, amplifies the effect of pH on protein solubility. Understanding the effect of the net charge and of ionic strength on protein-protein interactions is valuable not only for protein crystal growth but more generally also for the formation of protein-protein or protein-ligand complexes.

Solubility diagram of the Rhodobacter sphaeroides reaction center as a function of PEG concentration

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.

X-ray fluorescence used to characterize the salt content of proteins

The quantitative measurement of the salt content in solid protein samples was performed using X-ray fluorescence. Linear calibration curves were obtained for chloride, calcium and sulfur using sulfur and chloride as internal standards in the range 1-10 protein molar equivalents. The detection limit was approximately 0.02 molar equivalents for chloride and less than 0.01 molar equivalents for calcium. X-ray fluorescence thus provides a non-destructive sensitive method of testing the efficiency of different purification methods. Commercial hen egg white lysozyme samples contain from 15 to 46 molar equivalents of chloride, whereas the calcium content remains less than 0.2 equivalents. Deionization on ion-exchange resins is a very efficient tool for removing ionic species since deionized lysozyme samples contain less than 0.34 molar equivalents of chloride. Extensive dialysis against water only partially removes chloride ions, the residual chloride content corresponding to the number of counter-ions necessary to ensure the electroneutrality of lysozyme when dissolved in water.

Purification, stabilization, and crystallization of a modular protein: Grb2

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.

1.8 Å Structure of Hypoderma lineatum Collagenase: a Member of the Serine Proteinase Family

Collagenase from the fly larvae Hypoderma lineatum cleaves triple-helical collagen in a single region. It was crystallized at neutral pH in the absence of inhibitor and 1.8 A data were collected using synchrotron radiation and a Mark II prototype detector. The structure was solved by combining multiple isomorphous replacement methods and rotation translation function in real space. Refinement between 7 and 1.8 A using the program X-PLOR led to a final R factor of 16.9%. The overall fold is similar to that of other trypsin-like enzymes but the structure differs mainly by the presence of a beta-sheet at position 31-44. The two embedded molecules of the asymmetric unit are related by a pseudo twofold axis. The beta-sheet 31-44 of one molecule is involved in hydrogen bonds with binding-pocket residues of the other molecule. It thus completely prevents access to the active site. The specificity of this enzyme probably results from the position of Phe192 and Tyr99 at the entrance of the active site.

Lysozyme solubility in H2O and D2O solutions as a function of sodium chloride concentration

Some spectroscopic methods require solubilization or crystallization of proteins in heavy water because of the large difference in neutron scattering properties between protons and deuterons. In order to quantify the impact of slightly different physical properties of D2O and H2O, lysozyme solubility curves have been measured for these solvents, using 0.2 to 3.0 M sodium chloride in 0.050 M sodium acetate buffer (pH 4.5) at 291 K. After four months of crystallization, solubility data were measured within 9% error and showed that the lysozyme solubility in H2O is 1.3 times that in D2O.

Relative effectiveness of various anions on the solubility of acidic Hypoderma lineatum collagenase at pH 7.2

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 Grb2 adaptor

Grb2 is an 'adaptor' protein made of one SH2 and two SH3 domains. The SH3 domains bind to prolinerich motifs in the C-terminal part of the ras exchange factor Sos. Binding of the Grb2 SH2 domain to phosphotyrosine motifs on receptors, or other adaptor proteins such as Shc, recruits this Grb2/Sos complex at the plasma membrane where Sos stimulates nucleotide exchange on ras, then ras activates raf and leads to MAP kinase activation. The structure of Grb2, the precise motifs recognised by its SH2 and SH3 domains, the way Grb2 performs its function, a possible regulation of its association with Sos, and its ability to complex with other proteins in vivo, are discussed.

The Perfection of Protein Crystals Probed by Direct Recording of Bragg Reflection Profiles with a Quasi-Planar X-ray Wave

Profiles of Bragg reflections from earth-grown crystals of lysozyme from hen egg-white and collagenase from Hypoderma lineatum were directly recorded with a quasi-planar X-ray wave. One crystal of each protein was chosen for a detailed investigation. Each sample is shown to consist of only a few (three and two, respectively) highly ordered domains, misoriented with respect to each other by a few arc s. The smallest rocking widths were observed for the large domain of the collagenase sample (FWHM corrected for instrumental broadening: 0.0016 degrees for a strong reflection at 3 A resolution). With appropriate improvements, this method might become a quantitative tool for characterizing the perfection of crystals from biological macromolecules.

Structure of the photochemical reaction centre of a spheroidene-containing purple-bacterium,Rhodobacter sphaeroidesY, at 3 Å resolution

The crystal structure of the photochemical reaction centre from Rhodobacter sphaeroides Y, a carotenoid-containing wild-type purple bacterium, has been determined at 3 A resolution. This membrane complex consists of three subunits (281, 307 and 260 residues, respectively) and ten cofactors. It was crystallized in presence of beta-D-octylglucoside. The crystals are orthorhombic with unit-cell dimensions, a = 143.7, b = 139.8, c = 78.7 A, space group P2(1)2(1)2(1) with four molecules in the unit cell. Refinement of the structure by X-PLOR and manual reconstructions yielded an R value of 22.1% for 19630 reflections between 7 and 3 A. The secondary structure is highly homologous to those determined for Rhodopseudomonas viridis (Protein Data Bank entry 1PRC) and Rhodobacter sphaeroides R26 (Protein Data Bank entry 4RCR) reaction centres. In the latter two structures one Fe(2+) ion located between the two quinones is coordinated by four histidines and one glutamic acid. In the Rhodobacter sphaeroides Y structure, Mn(2+) occupies the same position with identical ligands and geometry. The carotenoid conformation which is a non-planar 15-15'-cis spheroidene molecule in our structure differs from the 13-14-cis 2,4-dihydroneusporene in the Rhodopseudomonas viridis structure.

Crystal structure of the mammalian Grb2 adaptor

The mammalian growth factor receptor-binding protein Grb2 is an adaptor that mediates activation of guanine nucleotide exchange on Ras. Grb2 binds to the receptor through its SH2 domain and to the carboxyl-terminal domain of Son of sevenless through its two SH3 domains. It is thus a key element in the signal transduction pathway. The crystal structure of Grb2 was determined to 3.1 angstrom resolution. The asymmetric unit is composed of an embedded dimer. The interlaced junctions between the SH2 and SH3 domains bring the two adjacent faces of the SH3 domains in van der Waals contact but leave room for the binding of proline-rich peptides.

The 1.6 A structure of Kunitz-type domain from the alpha 3 chain of human type VI collagen

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.

Crystallization of previously desalted lysozyme in the presence of sulfate ions

Lysozyme, which is known to crystallize readily in the presence of many salts, has never been crystallized by salting out with ammonium sulfate. In the present study, lysozyme was first completely desalted by treatment with strong cation- (H(+) form) and anion- (OH(-) form) exchange resins. This leads to a protein solution with only H(+) and OH(-) as counterions, corresponding to its isoionic point. Addition of 2.5-3 molar equivalents of H(2)SO(4) to isoionic lysozyme decreases the pH value to 9-8 and allows crystallization to take place. The space group was found to be P4(3)2(1)2, similar to the classical lysozyme crystals grown in the presence of NaCl at pH 4.5, with unit-cell dimensions a = b = 78.9, c = 38.5 A. Tentative explanation of the sulfate/lysozyme interaction was addressed by mass spectrometry, and shows non-covalent binding of the ions on the protein.

Three-dimensional crystal structure of recombinant erabutoxin a at 2.0 A resolution

Recombinant erabutoxin a (Ea(r)) has been crystallized by vapour diffusion in hanging drops. The crystals belong to space group P2(1)2(1)2(1) with cell dimensions a = 55.8 A, b = 53.4 A, c = 40.8 A. Diffraction data have been recorded on a FAST detector up to 2.0 A. The atomic crystal structure of Ea(r) has been determined by initial refinement of the structure of the isotoxin erabutoxin b (Eb) the crystals of which were grown under identical conditions. The R-factor was 23% at 2.0 A resolution. The secondary and tertiary structures of Ea(r) are shown to be identical with that of wild-type Eb, within the experimental error.

A toxin that recognizes muscarinic acetylcholine receptors. Preparation and characterization of crystals suitable for structural analysis

Muscarinic toxin 2 from Dendroaspis angusticeps has been crystallized by vapour diffusion, in sodium acetate using sodium thiocyanate as a precipitant. Trigonal crystals (space group P3(1)21 or P3(2)21) have been obtained. The unit cell parameters are a = b = 64.2 A and c = 37.1 A. The presence of one molecule per asymmetric unit is estimated.

Structure determination of a dimeric form of erabutoxin-b, crystallized from a thiocyanate solution

Erabutoxin-b, M(r) = 6861.1, a single 62 amino-acid chain folded by four disulfide bridges, was crystallized in a new orthorhombic form by using thiocyanate as crystallizing agent. The space group is P2(1)2(1)2(1) with a = 53.36 (4), b = 40.89 (4), c = 55.71 (5) A, V = 121533.1 A and Z = 8. X-ray diffraction data were recorded at the LURE synchrotron facility (lambda = 1.405 A). The structure was solved by molecular replacement and shows a dimeric association through an anti-parallel beta-sheet around the twofold non-crystallographic axis. The two independent molecules, one SCN- ion and 97 associated water molecules were refined by molecular dynamics and annealing techniques to R = 19.6% (10,913 Fobs, resolution 5-1.7 A). The thiocyanate ion is located at the interface of the dimer and close to the non-crystallographic twofold axis.

Structure of the detergent phase and protein-detergent interactions in crystals of the wild-type (strain Y) Rhodobacter sphaeroides photochemical reaction center

Rhodobacter sphaeroides (strain Y) reaction center (RC) crystals were grown in the presence of n-octyl beta-glucoside (beta-OG). In order to determine the structure of the detergent phase in these crystals, low-resolution neutron diffraction experiments were performed at different contrasts obtained by varying the H2O/D2O ratio in the solvent. From the contrast variation data and from the RC atomic coordinates determined by X-ray diffraction [Arnoux, B., Ducruix, A., Reiss-Husson, F., Lutz, M., Norris, J., Schiffer, M., & Chang, C. H. (1989) FEBS Lett. 258, 47-50], a model was obtained for the structure of the detergent phase in the crystal. The detergent forms a ring-shaped micelle surrounding the most hydrophobic part of the transmembrane alpha helices of the RC. Each detergent ring is connected to two next-neighbor rings by intermicellar bridges. The detergent phase is organized thus in infinite zigzag chains parallel to the b axis of the P2(1)2(1)2(1) unit cell. The main interactions between beta-OG molecules and the RC molecules are hydrophobic and are localized at the level of the transmembrane alpha helices. This interaction replaces the phospholipid-protein interaction existing in vivo in the membrane and, to some extent, also the light harvesting complex-protein interaction. Secondary hydrophilic interactions are found between a few of the charged residues of the H subunit and the hydrophilic surface of the detergent ring from a neighboring RC molecule. A comparison with a previous study on Rhodopseudomonas viridis crystals [which grow in the presence of lauryldimethylamine N-oxide (LDAO) and belong to a different space group] [Roth, M., Lewit-Bentley, A., Michel, H., Deisenhofer, J., Huber, R., & Oesterhelt, D. (1989) Nature 340, 659-661] shows a quasi identity of shape and position of the beta-OG and LDAO rings around the transmembrane alpha helices. The secondary interactions, involving in both cases the external surface of the H subunit, differ because of the different molecular packing in the two space groups. The role and structural requirements of the detergent in the crystallization process are discussed.

Preliminary X-ray analysis of crystals of fasciculin 1, a potent acetylcholinesterase inhibitor from green mamba venom

Fasciculin 1 from Dendroaspis angusticeps has been crystallized by vapour diffusion, in sodium acetate using sodium thiocyanate as precipitant. Tetragonal crystals (space group P4(1)2(1)2 or P4(3)2(1)2) diffract to 1.8 A resolution. The unit cell parameters are a = 40.4 A and c = 81.1 A. We estimated the presence of one molecule in the asymmetric unit.

Towards the understanding of the function of Rb sphaeroides Y wild type reaction center: gene cloning, protein and detergent structures in the three-dimensional crystals

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 (beta-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.

Modeling of protease I collagenolytic enzyme from the fiddler crab Uca pugilator

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.

Low-resolution structure of the tetrameric phenylalanyl-tRNA synthetase from Escherichia coli. A neutron small-angle scattering study of hybrids composed of protonated and deuterated protomers

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).

Structure of spheroidene in the photosynthetic reaction center from Y Rhodobacter sphaeroides

The structure of the reaction center of Y Rhodobacter sphaeroides has been solved at 3 A resolution, using the atomic coordinates of the reaction center from the carotenoidless mutant R26 Rhodobacter sphaeroides. The structure has been refined by a stimulated annealing with the computer program X-PLOR, leading to a crystallographic R factor of 0.22 using reflections between 8 and 3 A. The spheroidene molecule which is bound to the Y reaction center has been fitted in the electron density map as a 15-cis isomer with a highly asymmetric structure. The cis-bond is located at proximity from ring 1 of the accessory bacteriochlorophyll on the inactive M side. The nature of the cis-bond was confirmed by resonance Raman spectra obtained from Y reaction center crystals. The structure of spheroidene in Y reaction center is compared to that proposed for 1,2-dihydroneurosporene in Rhodopseudomonas viridis reaction center crystals.

Preliminary characterization by X-ray diffraction of crystals of photochemical reaction centres from wild-type Rhodopseudomonas spheroides

Reaction centres from wild-type Rhodopseudomonas spheroides (strain Y) in a solution of octylglucoside have been crystallized with polyethylene glycol as precipitant, either by vapour diffusion or dialysis. Orthorhombic crystals (space group P2(1)2(1)2(1)) diffract to 3.5 A resolution. The unit cell parameters are a = 142.5 A, b = 141.5 A, c = 80 A; they are compatible with the presence of one reaction centre per asymmetric unit.

Purification and reversible subunit dissociation of overproduced Escherichia coli phenylalanyl-tRNA synthetase

Phenylalanyl-tRNA synthetase (EC 6.1.1.20) has been purified to homogeneity from a 100-fold overproducing Escherichia coli strain carrying a hybrid pBR322 plasmid containing the pheS-pheT locus. The purified enzyme is identical to the phenylalanyl-tRNA synthetase isolated form an haploid strain. The enzyme was found to dissociate in the presence of 0.5 M NaSCN and the alpha- and beta-subunits composing the native alpha 2 beta 2 enzyme were separated by gel filtration. Neither isolated subunit showed significant catalytic activity. A complex indistinguishable from the native enzyme with full catalytic activity is recovered upon mixing the subunits. The N- and C-terminal sequences and the amino acid composition of each subunit were determined. They are compared to the available data concerning the primary structure of the subunits, as deduced from nucleotide sequencing of the pheS-pheT operon.

Neutron scattering study of the binding of tRNAPhe to Escherichia coli phenylalanyl-tRNA synthetase

Escherichia coli phenylalanyl-tRNA synthetase has been characterized by small-angle neutron scattering. In solution (20 mM imidazole hydrochloride, pH 7.6, 10 mM 2-mercaptoethanol, and 0.1 mM ethylenediaminetetraacetic acid), this enzyme has a molecular weight of 227K +/- 20K with a radius of gyration of 48.3 +/- 0.6 A, independent of the presence of MgCl2 up to 50 mM. The change of the scattering upon adding tRNAPhe to the enzyme has been followed with 10 mM MgCl2 present in the buffer. One enzyme molecule is capable of binding two tRNAPhe molecules with affinity constants larger than 10(6) M-1. Parallel titration experiments in 73% 2H2O, close to the matching point of tRNA, show that the RG of the enzyme is not changed by the binding of one or two tRNAPhe molecules. These results are compared with quasi-electric light scattering studies [Holler, E., Wang, C. C., & Ford, N.C., Jr. (1981) Biochemistry 20, 861-867] where the addition of either MgCl2 or tRNAPhe was shown to cause dramatic changes of the apparent translational diffusion constant of phenylalanyl-tRNA synthetase.