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ReciPro: free and open-source multipurpose crystallographic software integrating a crystal model database and viewer, diffraction and microscopy simulators, and diffraction data analysis tools

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JOURNAL OF APPLIED CRYSTALLOGRAPHY 2022年第2期55卷 397-410页

作者： Seto, Yusuke Ohtsuka, Masahiro Kobe Univ Grad Sch Sci Dept Planetol Nada Ku 1-1 Rokkodai Cho Kobe Hyogo 6578501 Japan Nagoya Univ Adv Measurement Technol Ctr Inst Mat & Syst Sustainabil Chikusa Ku Furo Cho Nagoya Aichi 4648603 Japan

ReciPro is a comprehensive multipurpose crystallographic program equipped with an intuitive graphical user interface (GUI), and it is completely free and open source. This software has a built-in crystal database consisting of over 20 000 crystal models, and the visualization system can seamlessly display a specified crystal model as an attractive three-dimensional graphic. The comprehensive features are not confined to these crystal model databases and viewers. It can smoothly and quantitatively simulate not only single-crystal and/or polycrystalline (powder) diffraction patterns of X-ray, electron and neutron diffraction of a selected crystal model, based on the kinematic scattering theory, but also various electron diffraction patterns and high-resolution transmission electron microscopy (TEM) images, based on the dynamical scattering theory. The features of stereographic projection of crystal planes/axes to explore crystal orientation relationships and the semi-automatic diffraction spot indexing function for experimental diffraction patterns assist diffraction experiments and analyses. These features are linked through a user-friendly GUI, and the results can be synchronously displayed almost in real time. ReciPro will assist a wide range of crystallographers (including beginners) using X-ray, electron and neutron diffraction crystallography and TEM.

关键词： crystal structure visualization diffraction simulation diffraction data analysis transmission electron microscopy

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An Additive-Free Model for Tau Self-Assembly

An Additive-Free Model for Tau Self-Assembly

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作者： Youssra K. Al-Hilaly Karen E. Marshall Liisa Lutter Luca Biasetti Kurtis Mengham Charles R. Harrington Wei-Feng Xue Claude M. Wischik Louise C. Serpell

Tau is a natively unfolded protein that contributes to the stability of microtubules. Under pathological conditions such as Alzheimer’s disease (AD), tau protein misfolds and self-assembles to form paired helical filaments (PHFs) and straight filaments (SFs). Full-length tau protein assembles poorly and its self-assembly is enhanced with polyanions such as heparin and RNA in vitro, but a role for heparin or other polyanions in vivo remains unclear. Recently, a truncated form of tau (297–391) has been shown to self-assemble in the absence of additives which provides an alternative in vitro PHF model system. Here we describe methods to prepare in vitro PHFs and SFs from tau (297–391) named dGAE. We also discuss the range of biophysical/biochemical techniques used to monitor tau filament assembly and structure. less

关键词： Electron Microscopy (EM) Circular Dichroism Atomic Force Microscopy (AFM) TEM Immunogold Labeling SDS-PAGE Dot Blot X-ray diffraction diffraction data analysis diffraction Method Image Processing Programming Language BCA assay Lens Oryctolagus cuniculus Self-assembly Tau X-ray fibre diffraction Cross-beta Paired helical filament Thioflavin S fluorescence Tyrosine fluorescence Anti-Tau Anti-rabbit Anti-mouse

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Structure Determination of Membrane Proteins Using X-Ray Crystallography

Structure Determination of Membrane Proteins Using X-Ray Cry...

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作者： Evan Billings Karl Lundquist Claire Overly Karthik Srinivasan Nicholas Noinaj

Membrane proteins serve essential roles in all aspects of life and make up roughly one-third of all genomes from prokaryotes to eukaryotes. Their responsibilities include mediating cell signaling, nutrient import, waste export, cellular communication, trafficking, and immunity. For their critical role in many cellular processes, membrane proteins serve as targets for up to 50% of drugs currently on the market and remain primary targets in new therapeutics being developed. Despite their importance and abundance in nature, only ~1% of structures in the Protein data Bank are of transmembrane proteins. This discrepancy can be directly attributed to the biochemical properties of membrane proteins and the difficulty in producing sufficient yields for structural studies or the difficulty in growing well-ordered crystals. Here, we present methods from our work that outline our general pipeline from cloning to structure determination of membrane proteins, with a focus on using X-ray crystallography, which still yields ~90% of all structures being deposited into the Protein data Bank. less

关键词： Crystallization Structure Determination PCR X-ray Crystallography Agarose Gel Electrophoresis Restriction Enzyme Digestion DNA Sequencing SDS-PAGE Recombinant Protein Expression Snap Freeze Cell Lysis Nickel Affinity Chromatography FPLC Affinity Chromatography Fractionation Liquid Handling X-ray diffraction Molecular Replacement diffraction Method diffraction data analysis DNA Ligation Saccharomyces cerevisiae Membrane proteins Protein folding BAM complex

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Bioassay-Guided Isolation and Characterization of Metabolites from Actinobacteria

Bioassay-Guided Isolation and Characterization of Metabolite...

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作者： Ramasamy Balagurunathan Manikkam Radhakrishnan Thangavel Shanmugasundaram Venugopal Gopikrishnan Joseph Jerrine

The amounts of active ingredients present in the natural products are always fairly low. The lab-intensive and time-consuming extraction and isolation process has been the bottleneck in exploring natural products for drug development. Extraction is the first step to separate the desired natural products from the plants, marine organisms or microbial fermentation medium. Liquid–liquid extraction method is very commonly used for the extraction of bioactive compounds from Actinobacteria. The components present in the natural extract are complex and contain a variety of natural products that require further separation and purification to obtain the active compounds. The separation depends on the physical or chemical difference of the individual compounds present in the crude extract. Chromatography, especially TLC, column chromatography, and HPLC are the main methods used to obtain pure natural products from a complex mixture. However, the percentage of purity to be obtained may vary with the different chromatographic method. Once the compound isolated in pure, the structure elucidation is rather routine work. This owes to amazing development of modern spectroscopic techniques. In this chapter different chromatographic and spectroscopic methods are described for the isolation and characterization of bioactive compounds from actinobacteria. less

关键词： Column Chromatography HPLC NMR Spectroscopy Fermentation Separation And Purification Gradient Elution X-ray diffraction diffraction data analysis TLC FT–IR

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Interactive visualization of multi-data-set Rietveld analyses using Cinema: Debye-Scherrer

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JOURNAL OF APPLIED CRYSTALLOGRAPHY 2018年第3期51卷 943-951页

作者： Vogel, Sven C. Biwer, Chris M. Rogers, David H. Ahrens, James P. Hackenberg, Robert E. Onken, Drew Zhang, Jianzhong Los Alamos Natl Lab Mat Sci & Technol Div Los Alamos NM 87545 USA Los Alamos Natl Lab Comp Computat & Stat Sci Div Los Alamos NM 87545 USA Los Alamos Natl Lab Sigma Mfg Sci Div Los Alamos NM 87545 USA Wake Forest Univ Dept Phys Winston Salem NC 27109 USA

A tool named Cinema: Debye-Scherrer to visualize the results of a series of Rietveld analyses is presented. The multi-axis visualization of the high-dimensional data sets resulting from powder diffraction analyses allows identification of analysis problems, prediction of suitable starting values, identification of gaps in the experimental parameter space and acceleration of scientific insight from the experimental data. The tool is demonstrated with analysis results from 59 U-Nb alloy samples with different compositions, annealing times and annealing temperatures as well as with a high-temperature study of the crystal structure of CsPbBr3. A script to extract parameters from a series of Rietveld analyses employing the widely used GSAS Rietveld software is also described. Both software tools are available for download.

关键词： visualization diffraction data analysis automated analysis

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Against Method: Table 1-Cui Bono?

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STRUCTURE 2018年第7期26卷 919-923页

作者： Rupp, Bernhard Kk Hofkristallamt San Diego CA 92084 USA Med Univ Innsbruck Div Genet Epidemiol Schopfstr 41 A-6020 Innsbruck Tyrol Austria

The almost universally required "Table 1,'' summarizing data-collection and data-processing statistics, has in its present form outlived its usefulness in almost all publications of biomolecular crystal structure reports. Information contained in "Table 1'' is insufficient to evaluate or repeat the experiment;is redundant with information extractable from deposited diffraction data;and includes data items whose meaning is under increased scrutiny in the crystallographic community. Direct and consistent extraction and analysis of data quality metrics from preferably unmerged intensity data with graphical presentation of reciprocal space features, including impact on map and model features, should replace "Table 1.''

关键词： data collection statistics diffraction data analysis merging statistics data quality indicators reciprocal space diffraction data presentation

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Methods for Structural analysis of Amyloid Fibrils in Misfolding Diseases

Methods for Structural Analysis of Amyloid Fibrils in Misfol...

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作者： Devkee M. Vadukul Youssra K. Al-Hilaly Louise C. Serpell

Many proteins and peptides are able to self-assemble in solution in vitro and in vivo to form amyloid-like fibrils. These fibrils share common structural characteristics. In order for a fibril to be characterized as amyloid, it is expected to fit certain criteria including the composition of cross-β. Here we describe how the formation of amyloid fibrils can be characterized in vitro using a variety of methods including circular dichroism and intrinsic tyrosine/tryptophan fluoresence to follow conformational changes; Thioflavin and/or ThS assembly to monitor nucleation and growth; transmission electron microscopy to visualize fibrillar morphology and X-ray fiber diffraction to examine cross-β structure. less

关键词： Electron Microscopy (EM) Circular Dichroism Negative-stain Electron Microscopy Immunogold Labeling TEM Sonication Protein Quantitation Assay Linear Dichroism Spectroscopy Electrophoresis Western Blot diffraction data analysis SDS-PAGE Self-assembly Oligomer Protofibril Cross-β Protofilaments Thioflavin T/S fluorescence Tyrosine/tryptophan fluorescence X-ray fiber diffraction

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