QUATERNARY STRUCTURE OF PEA PHYTOCHROME I DIMER STUDIED WITH SMALL-ANGLE X-RAY SCATTERING and ROTARY-SHADOWING ELECTRON MICROSCOPY

Abstract— The quaternary structure of pea phytochrome type I (PI) dimer in the red-light-absorbing form was studied by small-angle X-ray scattering (SAXS) technique and rotary-shadowing electron microscopy. Structural parameters for PI 114 kDa chromopeptide dimer and its tryptically digested N-terminal 59 kDa chromopeptide monomer, such as average electron density, molecular volume and the second moment of electron density distribution, were determined in terms of SAXS using the contrast variation method. Furthermore, by means of model simulation for the scattering profiles of the chromopeptides, most plausible structural models for both peptides were constructed. The distance between the chromophoric domains was estimated to be about 70 A in the resultant model for 114 kDa chromopeptide dimer. Furthermore, the model was consistent with the electron-micrographic images of both the intact PI dimer and the PI 114 kDa chromopeptide dimer, so that the N-terminal 7 kDa fragment did not significantly contribute the low-resolution images of the dimer.     

A protocol for searching the most probable phase‐retrieved maps in coherent X‐ray diffraction imaging by exploiting the relationship between convergence of the retrieved phase and success of calculation

Coherent X‐ray diffraction imaging (CXDI) is a technique for visualizing the structures of non‐crystalline particles with size in the submicrometer to micrometer range in material sciences and biology. In the structural analysis of CXDI, the electron density map of a specimen particle projected along the direction of the incident X‐rays can be reconstructed only from the diffraction pattern by using phase‐retrieval (PR) algorithms. However, in practice, the reconstruction, relying entirely on the computational procedure, sometimes fails because diffraction patterns miss the data in small‐angle regions owing to the beam stop and saturation of the detector pixels, and are modified by Poisson noise in X‐ray detection. To date, X‐ray free‐electron lasers have allowed us to collect a large number of diffraction patterns within a short period of time. Therefore, the reconstruction of correct electron density maps is the bottleneck for efficiently conducting structure analyses of non‐crystalline particles. To automatically address the correctness of retrieved electron density maps, a data analysis protocol to extract the most probable electron density maps from a set of maps retrieved from 1000 different random seeds for a single diffraction pattern is proposed. Through monitoring the variations of the phase values during PR calculations, the tendency for the PR calculations to succeed when the retrieved phase sets converged on a certain value was found. On the other hand, if the phase set was in persistent variation, the PR calculation tended to fail to yield the correct electron density map. To quantify this tendency, here a figure of merit for the variation of the phase values during PR calculation is introduced. In addition, a PR protocol to evaluate the similarity between a map of the highest figure of merit and other independently reconstructed maps is proposed. The protocol is implemented and practically examined in the structure analyses for diffraction patterns from aggregates of gold colloidal particles. Furthermore, the feasibility of the protocol in the structure analysis of organelles from biological cells is examined.     

IDATEN and G‐SITENNO: GUI‐assisted software for coherent X‐ray diffraction imaging experiments and data analyses at SACLA

Using our custom‐made diffraction apparatus KOTOBUKI‐1 and two multiport CCD detectors, cryogenic coherent X‐ray diffraction imaging experiments have been undertaken at the SPring‐8 Angstrom Compact free electron LAser (SACLA) facility. To efficiently perform experiments and data processing, two software suites with user‐friendly graphical user interfaces have been developed. The first is a program suite named IDATEN, which was developed to easily conduct four procedures during experiments: aligning KOTOBUKI‐1, loading a flash‐cooled sample into the cryogenic goniometer stage inside the vacuum chamber of KOTOBUKI‐1, adjusting the sample position with respect to the X‐ray beam using a pair of telescopes, and collecting diffraction data by raster scanning the sample with X‐ray pulses. Named G‐SITENNO, the other suite is an automated version of the original SITENNO suite, which was designed for processing diffraction data. These user‐friendly software suites are now indispensable for collecting a large number of diffraction patterns and for processing the diffraction patterns immediately after collecting data within a limited beam time.     

Classification of ab initio models of proteins restored from small‐angle X‐ray scattering

In structure analyses of proteins in solution by using small‐angle X‐ray scattering (SAXS), the molecular models are restored by using ab initio molecular modeling algorithms. There can be variation among restored models owing to the loss of phase information in the scattering profiles, averaging with regard to the orientation of proteins against the direction of the incident X‐ray beam, and also conformational fluctuations. In many cases, a representative molecular model is obtained by averaging models restored in a number of ab initio calculations, which possibly provide nonrealistic models inconsistent with the biological and structural information about the target protein. Here, a protocol for classifying predicted models by multivariate analysis to select probable and realistic models is proposed. In the protocol, each structure model is represented as a point in a hyper‐dimensional space describing the shape of the model. Principal component analysis followed by the clustering method is applied to visualize the distribution of the points in the hyper‐dimensional space. Then, the classification provides an opportunity to exclude nonrealistic models. The feasibility of the protocol was examined through the application to the SAXS profiles of four proteins.     

Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: on the correlation between crystal water sites,solvent density,and solvent dipole

The hydration structure of human lysozyme was studied with cryogenic X-ray diffraction experiment and molecular dynamics simulations. The crystal structure analysis at a resolution of 1.4 A provided 405 crystal water molecules around the enzyme. In the simulations at 300 K, the crystal structure was immersed in explicit water molecules. We examined correlations between crystal water sites and two physical quantities calculated from the 1-ns simulation trajectories: the solvent density reflecting the time-averaged distribution of water molecules, and the solvent dipole measuring the orientational ordering of water molecules around the enzyme. The local high solvent density sites were consistent with the crystal water sites, and better correlation was observed around surface residues with smaller conformational fluctuations during the simulations. Solvent dipoles around those sites exhibited coherent and persistent ordering, indicating that the hydration water molecules at the crystal water sites were highly oriented through the interactions with hydrophilic residues. Those water molecules restrained the orientational motions of adjoining water molecules and induced a solvent dipole field, which was persistent during the simulations around the enzyme. The coherent ordering was particularly prominent in and around the active site cleft of the enzyme. Because the ordering was significant up to the third to fourth solvent layer region from the enzyme surface, the coherently ordered solvent dipoles likely contributed to the molecular recognition of the enzyme in a long-distance range. The present work may provide a new approach combining computational and the experimental studies to understand protein hydration.