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The sigma54 RNA polymerase holoenzyme functions in enhancer-dependent transcription. The structural organization of the sigma54 subunit of bacterial RNA polymerase in solution is analyzed by synchrotron x-ray scattering. Scattering patterns are collected from the full-length protein and from a large fragment able to bind the core RNA polymerase, and their low resolution shapes are restored using two ab initio shape determination techniques. The sigma54 subunit is a highly elongated particle, and the core binding fragment can be unambiguously positioned inside the full-length protein. The boomerang-like shape of the core binding fragment is similar to that of the atomic model of a fragment of the Escherichia coli sigma70 protein, indicating that, although the sigma54 and sigma70 factors are unrelated by primary sequence, they may share some structural similarity. Potential DNA binding surfaces of sigma54 are also predicted by comparison with the sigma54 core binding fragment.

New results obtained from a two-dimensional sequence analysis of the small heat shock protein (shsp) family are described. It is confirmed that the conserved C-terminal α -crystallin domain is essentially made of β -strands, most probably two groups of β -strands separated by a large loop. A direct correspondence between the putative β -strands that have been identified in shsps and the seven β -strands of a classical immunoglobulin-like fold is proposed. The hypothesis that the shsp family could belong to the immunoglobulin superfamily (IgSF) is consistent with the ubiquitous distribution and the multifunctional properties of the crystallins that are now emerging.

alphaB-crystallin, a member of the small heat-shock protein family and a major eye lens protein, is a high molecular mass assembly and can act as a molecular chaperone. We report a synchrotron radiation x-ray solution scattering study of a truncation mutant from the human alphaB-crystallin (alphaB57-157), a dimeric protein that comprises the alpha-crystallin domain of the alphaB-crystallin and retains a significant chaperone-like activity. According to the sequence analysis (more than 23% identity), the monomeric fold of the alpha-crystallin domain should be close to that of the small heat-shock protein from Methanococcus jannaschii (MjHSP16.5). The theoretical scattering pattern computed from the crystallographic model of the dimeric MjHSP16.5 deviates significantly from the experimental scattering by the alpha-crystallin domain, pointing to different quaternary structures of the two proteins. A rigid body modeling against the solution scattering data yields a model of the alpha-crystallin domain revealing a new dimerization interface. The latter consists of a strand-turn-strand motif contributed by each of the monomers, which form a four-stranded, antiparallel, intersubunit composite beta-sheet. This model agrees with the recent spin labeling results and suggests that the alphaB-crystallin is composed by flexible building units with an extended surface area. This flexibility may be important for biological activity and for the formation of alphaB-crystallin complexes of variable sizes and compositions.

International audience; Biological macromolecules in solution interact with each other through medium-range (from a few Angstrom to a few nm) interaction potentials. These potentials control the macromolecular distribution in solution, the macromolecular phase diagram and the crystallization process. We have previously shown that small angle X-ray scattering (SAXS) is a convenient tool to characterize the resulting potential, either attractive or repulsive, and to follow the changes induced by the crystallizing agents. In the present paper SAXS and simulation methods derived from statistical mechanics are coupled to determine the best fit potentials from the comparison of experimental and theoretical intensity curves. The currently used models in the colloid field are derived from the DLVO (Derjaguin, Landau, Verwey, Overbeek) potential where three types of interactions play a major role: hard sphere and electrostatic are repulsive, van der Waals are attractive. A combination of a short-range attractive potential and a coulombic repulsive indeed correctly accounts at low ionic strength for the phase diagram as a function of pH and salt concentration. The origin of the ion specificities at high ionic strength associated with the so-called "Hofmeister series" remain, however, unclear. The whole of the data demonstrates that the colloidal approach may be applied with success to protein crystallization. (C) 1999 Elsevier Science B.V. All rights reserved.

International audience; Osmotic pressure, small-angle X-ray scattering and quasi-elastic light scattering were used to study the medium-range interaction potentials between macromolecules in solution. These potentials determine macromolecular crystallization. Calf eye lens gamma-crystallins were used as a model system with the charge, and therefore the interactions, varied with pH. The second virial coefficient was determined under the same conditions with each of the three techniques. Osmotic pressure and quasi-elastic light scattering can be used conveniently in the laboratory to rapidly test the type of interactions (either attractive or repulsive) present in the solution. The measurement is direct with osmotic pressure, whereas with quasi-elastic light scattering, the directly measured coefficient is a combination of thermodynamic and hydrodynamic terms. X-rays, which require more sophisticated equipment such as synchrotron radiation facilities, can provide more detailed information on the interparticle potentials when models are used. At low ionic strength, two potentials were found necessary to account for the temperature and pH phase diagram as a function of protein concentration. The first potential is the van der Waals attractive potential that was previously shown to account for the fluid-fluid phase separation at low temperature. The second potential is an electrostatic coulombic repulsive potential which is a function of the protein charge and thus of the pH. The interaction trail could be followed at protein concentrations as low as 10 mg ml(-1). The results as a whole are expected to be valid for all compact low molecular weight proteins at low ionic strength.

International audience; Concentrated gamma-crystallin and lysozyme solutions have been reported to undergo a fluid-fluid phase separation when cooled below a critical temperature. This behavior is under control of the weak forces acting in solution between macromolecules. We have used small angle x-ray scattering at the synchrotron radiation facility LURE (Orsay, France) to analyze the interaction potentials. A model of attractive interactions which depends upon three parameters, protein diameter, potential depth, and range, is able to account for both the x-ray structure factors measured at high temperature and for the low temperature phase separation. Although van der Waals forces could be at the origin of the attractive interaction potentials, other more specific effects also contribute to the protein phase diagrams. (C) 1996 American Institute of Physics.

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Hfq is a bacterial RNA binding protein that facilitates small RNA-mediated posttranscriptional gene regulation. In Vibrio cholerae, Hfq and four Hfq-dependent small RNAs are essential for the expression of virulence genes, but little is known about this mechanism at the molecular level. To better understand V. cholerae Hfq structure and mechanism, we characterized the protein, alongside Escherichia coli Hfq for comparison, using biochemical and biophysical techniques. The N-terminal domain (NTD) of the two proteins is highly conserved, but the C-terminal regions (CTRs) vary in both sequence and length. Small-angle X-ray scattering studies showed that both proteins adopt a star-shaped hexameric structure in which the conserved NTD adopts the expected Sm fold while the variable CTR is disordered and extends radially outwards from the folded core. Despite their structural similarity, SDS-PAGE stability assays and collision-induced dissociation mass spectrometry revealed that the V. cholerae hexamer is less stable than that of E. coli. We propose that this is due to minor differences between the intersubunit interface formed by the NTDs and the ability of the E. coli CTR to stabilize this interface. However, based on electrophoretic mobility shift assays, the divergent CTRs do appear to perform a common function with regard to RNA-binding specificity. Overall, the similarities and differences in the fundamental properties of V. cholerae and E. coli Hfq provide insight into their assembly and molecular mechanisms., Graphical Abstract Highlights ► This is the first study of V. cholerae Hfq, an RNA binding protein that regulates virulence genes. ► The NTD is homologous to E. coli Hfq, the CTR is not. ► Both V. cholerae and E. coli Hfq CTRs extend outwards from a hexameric NTD core. ► Both V. cholerae and E. coli Hfq CTRs enhance the RNA binding specificity of Hfq. ► Only the E. coli CTR stabilizes the Hfq hexamer.