Hiro Tsuruta

Full-length archaeal Rad51 structure and mutants: Mechanisms for RAD51 assembly and control by BRCA2

To clarify RAD51 interactions controlling homologous recombination, we report here the crystal structure of the full‐length RAD51 homolog from Pyrococcus furiosus. The structure reveals how RAD51 proteins assemble into inactive heptameric rings and active DNA‐bound filaments matching three‐dimensional electron microscopy reconstructions. A polymerization motif (RAD51‐PM) tethers individual subunits together to form assemblies. Subunit interactions support an allosteric ‘switch’ promoting ATPase activity and DNA binding roles for the N‐terminal domain helix–hairpin–helix (HhH) motif. Structural and mutational results characterize RAD51 interactions with the breast cancer susceptibility protein BRCA2 in higher eukaryotes. A designed P.furiosus RAD51 mutant binds BRC repeats and forms BRCA2‐dependent nuclear foci in human cells in response to γ‐irradiation‐induced DNA damage, similar to human RAD51. These results show that BRCA2 repeats mimic the RAD51‐PM and imply analogous RAD51 interactions with RAD52 and RAD54. Both BRCA2 and RAD54 may act as antagonists and chaperones for RAD51 filament assembly by coupling RAD51 interface exchanges with DNA binding. Together, these structural and mutational results support an interface exchange hypothesis for coordinated protein interactions in homologous recombination.

Integration of small angle X-ray scattering data into structural modeling of proteins and their assemblies

A major challenge in structural biology is to determine the configuration of domains and proteins in multidomain proteins and assemblies, respectively. All available data should be considered to maximize the accuracy and precision of these models. Small-angle X-ray scattering (SAXS) efficiently provides low-resolution experimental data about the shapes of proteins and their assemblies. Thus, we integrated SAXS profiles into our software for modeling proteins and their assemblies by satisfaction of spatial restraints. Specifically, we modeled the quaternary structures of multidomain proteins with structurally defined rigid domains as well as quaternary structures of binary complexes of structurally defined rigid proteins. In addition to SAXS profiles and the component structures, we used stereochemical restraints and an atomic distance-dependent statistical potential. The scoring function is optimized by a biased Monte Carlo protocol, including quasi-Newton and simulated annealing schemes. The final prediction corresponds to the best scoring solution in the largest cluster of many independently calculated solutions. To quantify how well the quaternary structures are determined based on their SAXS profiles, we used a benchmark of 12 simulated examples as well as an experimental SAXS profile of the homotetramer D-xylose isomerase. Optimization of the SAXS-dependent scoring function generally results in accurate models if sufficiently precise approximations for the constituent rigid bodies are available; otherwise, the best scoring models can have significant errors. Thus, SAXS profiles can play a useful role in the structural characterization of proteins and assemblies if they are combined with additional data and used judiciously. Our integration of a SAXS profile into modeling by satisfaction of spatial restraints will facilitate further integration of different kinds of data for structure determination of proteins and their assemblies.

Biological small-angle X-ray scattering facility at the Stanford Synchrotron Radiation Laboratory

Beamline 4-2 at the Stanford Synchrotron Radiation Laboratory is a small-angle X-ray scattering/diffraction facility dedicated to structural studies on mostly noncrystalline biological systems. The instrument consists of a pinhole camera, which covers the magnitude of the scattering vector Q in the range 0.004–1.3 A−1 [Q = (4π/λ)sin θ, where θ and λ are one half of the scattering angle and the X-ray wavelength, respectively], and a Bonse–Hart geometry ultra-small-angle X-ray scattering setup for the Q range an order of magnitude smaller. The pinhole camera allows quick automated distance and detector selection among any combination of five distances and three position-sensitive detectors. The double-crystal monochromator can have either Si 111 crystals or a pair of synthetic multilayer diffractive elements for higher flux applications. We have adopted a suite of software originally developed for macromolecular crystallography for integrated beamline control as well as static and slow time-resolved small-angle scattering data collection. This article outlines recent technological developments and specialized instrumentation for conducting noncrystalline scattering experiments in structural biology at improved time and spatial resolutions.

The origin of the electrostatic perturbation in acetoacetate decarboxylase

Acetoacetate decarboxylase (AADase) has long been cited as the prototypical example of the marked shifts in the pKa values of ionizable groups that can occur in an enzyme active site. In 1966, it was hypothesized that in AADase the origin of the large pKa perturbation (-4.5 log units) observed in the nucleophilic Lys 115 results from the proximity of Lys 116, marking the first proposal of microenvironment effects in enzymology. The electrostatic perturbation hypothesis has been demonstrated in a number of enzymes, but never for the enzyme that inspired its conception, owing to the lack of a three-dimensional structure. Here we present the X-ray crystal structures of AADase and of the enamine adduct with the substrate analogue 2,4-pentanedione. Surprisingly, the shift of the pKa of Lys 115 is not due to the proximity of Lys 116, the side chain of which is oriented away from the active site. Instead, Lys 116 participates in the structural anchoring of Lys 115 in a long, hydrophobic funnel provided by the novel fold of the enzyme. Thus, AADase perturbs the pKa of the nucleophile by means of a desolvation effect by placement of the side chain into the protein core while enforcing the proximity of polar residues, which facilitate decarboxylation through electrostatic and steric effects.

Small Angle X-ray Scattering as a Complementary Tool for High- throughput Structural Studies

Structural crystallography and nuclear magnetic resonance (NMR) spectroscopy are the predominant techniques for understanding the biological world on a molecular level. Crystallography is constrained by the ability to form a crystal that diffracts well and NMR is constrained to smaller proteins. Although powerful techniques, they leave many soluble, purified structurally uncharacterized protein samples. Small angle X-ray scattering (SAXS) is a solution technique that provides data on the size and multiple conformations of a sample, and can be used to reconstruct a low-resolution molecular envelope of a macromolecule. In this study, SAXS has been used in a high-throughput manner on a subset of 28 proteins, where structural information is available from crystallographic and/or NMR techniques. These crystallographic and NMR structures were used to validate the accuracy of molecular envelopes reconstructed from SAXS data on a statistical level, to compare and highlight complementary structural information that SAXS provides, and to leverage biological information derived by crystallographers and spectroscopists from their structures. All the ab initio molecular envelopes calculated from the SAXS data agree well with the available structural information. SAXS is a powerful albeit low-resolution technique that can provide additional structural information in a high-throughput and complementary manner to improve the functional interpretation of high-resolution structures.

An integrated high-throughput data acquisition system for biological solution X-ray scattering studies.

A fully automated high-throughput solution X-ray scattering data collection system has been developed for protein structure studies at beamline 4-2 of the Stanford Synchrotron Radiation Lightsource. It is composed of a thin-wall quartz capillary cell, a syringe needle assembly on an XYZ positioning arm for sample delivery, a water-cooled sample rack and a computer-controlled fluid dispenser. It is controlled by a specifically developed software component built into the standard beamline control program Blu-Ice/DCS. The integrated system is intuitive and very simple to use, and enables experimenters to customize data collection strategy in a timely fashion in concert with an automated data processing program. The system also allows spectrophotometric determination of protein concentration for each sample aliquot in the beam via an in situ UV absorption spectrometer. A single set of solution scattering measurements requires a 20-30 µl sample aliquot and takes typically 3.5 min, including an extensive capillary cleaning cycle. Over 98.5% of measurements are valid and free from artefacts commonly caused by air-bubble contamination. The sample changer, which is compact and light, facilitates effortless switching with other sample-handling devices required for other types of non-crystalline X-ray scattering experiments.

Direct structural evidence for a concerted allosteric transition in Escherichia coli aspartate transcarbamoylase

Regulation of protein function, often achieved by allosteric mechanisms, is central to normal physiology and cellular processes. Although numerous models have been proposed to account for the cooperative binding of ligands to allosteric proteins and enzymes, direct structural support has been lacking. Here, we used a combination of X-ray crystallography and small angle X-ray scattering in solution to provide direct structural evidence that the binding of ligand to just one of the six active sites of Escherichia coli aspartate transcarbamoylase induces a concerted structural transition from the T to the R state.

Tetrameric assembly of full-sequence protein zero myelin glycoprotein by synchrotron x-ray scattering.

Highly purified myelin P0 glycoprotein was solubilized to 1-8 mg/ml in 0.1% sodium dodecyl sulfate (SDS), and the solution structure of the P0 assembly was studied using synchrotron x-ray scattering. The full-length P0, which was isolated from bovine intradural roots, included both the extracellular and cytoplasmic domains of the molecule. At the higher concentrations (4, 6, and 8 mg/ml, respectively), an x-ray intensity maximum was observed at 316 A, 245 A, and 240 A Bragg spacing. Because the position of this intensity depended on P0 concentration, it is most likely due to interparticle interference. By contrast, the position of a second intensity maximum, which was at approximately 40 A Bragg spacing, was invariant with P0 concentration. This latter intensity was accounted for by monodispersed, 80 A-diameter particles that are composed of eight, approximately 30 A-diameter spheres. Chemical parameters suggest that the 80 A particles correspond to the size of a tetramer of P0 molecules. Therefore, the approximately 30 A spheres would correspond to the sizes of the extracellular and cytoplasmic domains for each of the P0 monomers. The invariance of the second intensity maximum with P0 concentration indicates that the structure of the 80 A-diameter, tetrameric particles is unaltered. According to the liquid model for interparticle interference from charged spheres, the 80 A-diameter particle has 10 negative surface charges which likely arise from negatively charged SDS molecules bound to the transmembrane domain of P0. This binding, however, apparently does not alter the tetrameric assembly of P0, suggesting that intermolecular interactions involving extracellular domains and cytoplasmic domains likely stabilize this assembly. Some of our results have been published in abstract form (Inouye, H., H. Tsuruta, D. A. Kirschner, J. Sedzik, and K. Uyemura. Abstracts of the 4th International School and Symposium on Synchrotron Radiation in Natural Science, June 15-20, 1998. Ustron-Jaszowiec, Poland. p. 31).

Solution X-Ray Scattering-Based Estimation of Electron Cryomicroscopy Imaging Parameters for Reconstruction of Virus Particles

Structure factor amplitudes and phases can be computed directly from electron cryomicroscopy images. Inherent aberrations of the electromagnetic lenses and other instrumental factors affect the structure factors, however, resulting in decreased accuracy in the determined three-dimensional reconstruction. In contrast, solution x-ray scattering provides absolute and accurate measurement of spherically averaged structure factor amplitudes of particles in solution but does not provide information on the phases. In the present study, we explore the merits of using solution x-ray scattering data to estimate the imaging parameters necessary to make corrections to the structure factor amplitudes derived from electron cryomicroscopic images of icosahedral virus particles. Using 400-kV spot-scan images of the bacteriophage P22 procapsid, we have calculated an amplitude contrast of 8.0 +/- 5.2%. The amplitude decay parameter has been estimated to be 523 +/- 188 A2 with image noise compensation and 44 +/- 66 A2 without it. These results can also be used to estimate the minimum number of virus particles needed for reconstruction at different resolutions.

A Wide-Bandpass Multilayer Monochromator for Biological Small-Angle Scattering and Fiber Diffraction Studies

Many biological applications of small-angle X-ray scattering, in particular time-resolved studies, are often limited by the flux incident on the sample due to the smaller scattering cross section of biological specimens. The wider-energy bandpass of a monochromator that consists of a pair of synthetic multilayer microstructures can, in principle, provide a flux two orders of magnitude higher than that of an Si(111) double-crystal monochromator. Two types of multilayers have been installed in the standard monochromator tank of beamline 4-2 at the Stanford Synchrotron Radiation Laboratory; the multilayer beam has been characterized for studies of small-angle X-ray scattering/diffraction from biological materials. Reflectivity and topography measurements indicate that the multilayers are quite adequate for these applications and a pair of Mo/B4C multilayers provided a 10–30 times increase in flux, compared with the flux level obtained with an Si(111) double-crystal monochromator. The increased flux level is very useful in time-resolved scattering studies as well as for recording weak scattering at higher angles. Having carried out many solution scattering and fiber diffraction experiments, we conclude that the use of multilayer does not result in significant broadening of diffraction peaks nor does it have appreciable effects on small-angle resolution. No significant increase in background is observed.