J. Appl. Cryst.の発刊に際して

Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.

/pdf/macromolecular-structure-determination-using-x-rays-neutrons-7udc75ny0s.pdf

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

Heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) respond to a variety of different external stimuli and activate G proteins. GPCRs share many structural features, including a bundle of seven transmembrane alpha helices connected by six loops of varying lengths. We determined the structure of rhodopsin from diffraction data extending to 2.8 angstroms resolution. The highly organized structure in the extracellular region, including a conserved disulfide bridge, forms a basis for the arrangement of the seven-helix transmembrane motif. The ground-state chromophore, 11-cis-retinal, holds the transmembrane region of the protein in the inactive conformation. Interactions of the chromophore with a cluster of key residues determine the wavelength of the maximum absorption. Changes in these interactions among rhodopsins facilitate color discrimination. Identification of a set of residues that mediate interactions between the transmembrane helices and the cytoplasmic surface, where G-protein activation occurs, also suggests a possible structural change upon photoactivation.

/pdf/crystal-structure-of-rhodopsin-a-g-protein-coupled-receptor-16y9vf8azt.pdf

Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor

phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.

/pdf/towards-automated-crystallographic-structure-refinement-with-43hriikvv9.pdf

Towards automated crystallographic structure refinement with phenix.refine

/pdf/the-ultimate-fast-fourier-transform-for-crystallography-2eg6ktdjrm.pdf

The ultimate fast Fourier transform for crystallography

The title compound, C10H10Br2O2, is a well known inhibitor of respiratory and photosynthetic processes. The methyl groups of the iso­propyl group assume approximately equal distances from the ring plane and maximum distances from the neighboring Br atom, possibly to avoid unfavourable steric interactions.

2,5-Di­bromo-6-iso­propyl-3-methyl-p-benzo­quinone

In the process of assembling a protein model, the electron density is fitted with fragments consisting of several peptide units In low‐quality regions of electron density maps, one runs into problems arising from either too many substantially different fragments, or a missing peptide bond It is then crucial to reduce the set of hypotheses by disqualifying inconsistent onesTo this end, we characterize the local shape of a main‐chain segment by angles between vectors connecting four consecutive C‐alpha atoms The local conformation is described by three quasi‐conformation angles: two flat and one dihedral angle We investigate the probability distribution of these angles and find that the conformational space of the angles is highly restricted This allows one to connect disjoint fragments more efficiently Since the procedure of matching hypotheses is computationally expensive, one needs a simple description of the quasi‐conformation angle space We present such a convenient description and compute its 

/pdf/stereochemical-rules-for-connecting-disjoint-protein-4yc0phv90v.pdf

Stereochemical rules for connecting disjoint protein fragments

In electron microscopy, the resolution of results has a softer character compared to X-ray crystallography. The core procedure involved in estimating resolution is comparing two reconstructions derived from two halves of the data. The 3D reconstruction process uses image data and the end results are real-space maps. However, intermediate calculations are performed mainly in reciprocal space, and due to the low signal-to-noise ratio of the starting images, elaborate filtering and weighting are necessary to produce the best possible results. Phase contrast imaging, which is the core of cryoEM methodology, necessitates complex CTF filtering, supplemented by additional weights resulting from correcting for motion, particle quality, etc. 3D reconstruction from multiple back projections is performed in reciprocal space, where data from multiple images are merged according to their statistical estimators (weights). The merging is enabled by the particles having finite size, and so data from local environments in reciprocal space could be statistically averaged. The particle finite size description is converted into using a particular filter, for example a Kaiser-Bessel, truncated Gaussian, or a sinc function. This is equivalent to applying a particle mask, but of a rather simple shape. what is critical

/pdf/the-conundrum-of-depositing-half-maps-for-experimental-cryo-djfpfila.pdf

The conundrum of depositing half-maps for experimental cryo-EM data

Cryo-EM structures of the TolQ membrane protein in complex with inner membrane protein partner TolR from the opportunistic pathogen Acinetobacter baumannii provide information on structure and stoichiometry.

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Zbyszek Otwinowski

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The ultimate fast Fourier transform for crystallography

2,5-Dibromo-6-isopropyl-3-methyl-p-benzoquinone

Stereochemical rules for connecting disjoint protein fragments

The conundrum of depositing half-maps for experimental cryo-EM data

Cryo-EM structures of the TolQ membrane protein in complex with inner membrane protein partner TolR from the opportunistic pathogen Acinetobacter baumannii provide information on structure and stoichiometry.

Zbyszek Otwinowski

Author Tools

Chat about Author

Papers

The ultimate fast Fourier transform for crystallography

2,5-Di­bromo-6-iso­propyl-3-methyl-p-benzo­quinone

Stereochemical rules for connecting disjoint protein fragments

The conundrum of depositing half-maps for experimental cryo-EM data

Cryo-EM structures of the TolQ membrane protein in complex with inner membrane protein partner TolR from the opportunistic pathogen Acinetobacter baumannii provide information on structure and stoichiometry.

2,5-Dibromo-6-isopropyl-3-methyl-p-benzoquinone