4.5 Article

Protein-to-structure pipeline for ambienttemperature in situ crystallography at VMXi

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Ecology

Marine picocyanobacterial PhnD1 shows specificity for various phosphorus sources but likely represents a constitutive inorganic phosphate transporter

Bhumika S. S. Shah et al.

Summary: Despite low surface concentrations, phosphorus (P) availability in marine environments is crucial for biological processes. Picocyanobacteria strains possess a putative phosphorus transporter, PhnDCE, but lack the ability to degrade phosphite or utilize alternate phosphorus sources. Our study found that Synechococcus PhnD1 proteins selectively bind phosphorus compounds, with a higher affinity for phosphite. However, growth experiments showed that Synechococcus strains cannot utilize phosphite as a sole phosphorus source, suggesting that the PhnDCE transporter is a constitutively expressed, medium-affinity phosphate transporter.

ISME JOURNAL (2023)

Editorial Material Biochemical Research Methods

Protein structure predictions to atomic accuracy with AlphaFold

John Jumper et al.

NATURE METHODS (2022)

Article Biochemistry & Molecular Biology

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

Mihaly Varadi et al.

Summary: AlphaFold DB is an openly accessible database with high-accuracy protein-structure predictions, powered by DeepMind's AlphaFold v2.0. It provides programmatic access to a vast number of predicted structures and is expanding to cover more sequences.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemistry & Molecular Biology

DIALS as a toolkit

Graeme Winter et al.

Summary: The DIALS software is introduced as a toolkit for processing X-ray diffraction data, emphasizing its usage as a toolkit for data processing, with support for automated systems and command-line usage, and the ability to write new tools using the API for bespoke analysis. In addition to macromolecular X-ray crystallography, DIALS can also be applied to techniques outside of this field.

PROTEIN SCIENCE (2022)

Article Biochemical Research Methods

xia2.multiplex: a multi-crystal data-analysis pipeline

Richard J. Gildea et al.

Summary: In macromolecular crystallography, data collection from a single crystal is limited by radiation damage. Thus, merging data sets from multiple crystals is necessary. A new program called xia2.multiplex has been developed to facilitate the scaling and merging of multi-crystal data sets, including symmetry analysis and analysis of factors affecting data quality.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2022)

Article Biochemical Research Methods

Crystal structure of thermally stable homodimeric cytochrome c′-β from Thermus thermophilus

Taisuke Yoshimi et al.

Summary: This study reports the crystal structure of cytochrome c'-beta from Thermus thermophilus, which exhibits high thermal stability. Mutational analysis suggests that the increased homodimeric interface area and rigid loop structure contribute to its high thermal stability.

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS (2022)

Article Biochemical Research Methods

In situ crystal data-collection and ligand-screening system at SPring-8

Hideo Okumura et al.

Summary: In situ diffraction data collection using crystallization plates is a useful method for evaluating crystal quality without additional sample treatment. Recent advances in data collection methods have overcome the limitation of crystal rotation. In this study, a system consisting of a goniometer, a robot, and plate storage was used to obtain complete data sets. Combined with an acoustic liquid handler, this system successfully facilitated structural analysis and ligand screening for protein-ligand complex crystals.

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS (2022)

Article Biochemical Research Methods

Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals

Filip Yabukarski et al.

Summary: Cryo-cooling is widely used in protein X-ray crystallography to reduce X-ray damage, while room-temperature X-ray crystallography provides more accurate ensemble information but raises concerns about data reliability due to increased sensitivity to X-ray damage. Further research is needed to address the impact of X-ray damage on conformational heterogeneity in both cryo-cooled and room-temperature crystals.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2022)

Article Biochemical Research Methods

Probing ligand binding of endothiapepsin by 'temperature-resolved' macromolecular crystallography

Chia Ying Huang et al.

Summary: Continuous developments in cryogenic X-ray crystallography have provided us with most of our understanding of 3D protein structures. However, the use of cryogenic temperatures may result in fictitious structures, limiting our knowledge of protein dynamics. In this study, a room-temperature X-ray crystallographic method was developed to capture structural snapshots under physiological conditions, revealing surprising binding discrepancies and capturing multiple binding poses and their interactions with DMSO. This opens up new prospects for structure determination and interpretation at physiological temperatures.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2022)

Article

Embedding AI in the Protein Crystallography Workflow

Richard J. Gildea et al.

Synchrotron Radiation News (2022)

Article Biochemical Research Methods

Crystal structure of the TLDc domain of human NCOA7-AS

Mary Arnaud-Arnould et al.

Summary: The TLDc domain is associated with oxidation resistance related functions and well conserved among eukaryotes. Proteins with a TLDc domain in humans, such as NCOA7 and NCOA7-AS, play a protective role against oxidative stress and interact with subunits of the vacuolar proton pump V-ATPase to impair viral infection through the endosomal pathway. The crystal structure of the TLDc domain from NCOA7 and NCOA7-AS has been reported at 1.8 A resolution, providing insights into its function and potential therapeutic applications.

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS (2021)

Review Biophysics

Macromolecular room temperature crystallography

Marcus Fischer

Summary: This review discusses practical aspects of preparing, acquiring, and analyzing X-ray crystallography data at room temperature, aiming to demystify preconceived impracticalities that freeze progress of routine room temperature data collection at synchrotron sources. Examples are provided as conceptual and experimental templates, illustrating the diversity and utility of gaining novel insights into protein conformational landscapes. An integrative view of protein conformational dynamics offers opportunities to advance basic and biomedical research.

QUARTERLY REVIEWS OF BIOPHYSICS (2021)

Article Biochemical Research Methods

What is the structural chemistry of the living organism at its temperature and pressure?

John R. Helliwell

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2020)

Article Biochemistry & Molecular Biology

X-ray-induced photoreduction of heme metal centers rapidly induces active-site perturbations in a protein-independent manner

Vera Pfanzagl et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2020)

Article Multidisciplinary Sciences

Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography

Daniel W. Kneller et al.

NATURE COMMUNICATIONS (2020)

Article Biochemical Research Methods

Strategies for sample delivery for femtosecond crystallography

Isabelle Martiel et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2019)

Article Chemistry, Multidisciplinary

Specific radiation damage is a lesser concern at room temperature

Guillaume Gotthard et al.

Article Instruments & Instrumentation

VMXi: a fully automated, fully remote, high-flux insitu macromolecular crystallography beamline

Juan Sanchez-Weatherby et al.

JOURNAL OF SYNCHROTRON RADIATION (2019)

Article Biochemistry & Molecular Biology

MolProbity: More and better reference data for improved all-atom structure validation

Christopher J. Williams et al.

PROTEIN SCIENCE (2018)

Article Biochemistry & Molecular Biology

Structural and functional insights into thermally stable cytochrome c' from a thermophile

Sotaro Fujii et al.

PROTEIN SCIENCE (2017)

Editorial Material Biochemistry & Molecular Biology

PyMOL and Inkscape Bridge the Data and the Data Visualization

Shuguang Yuan et al.

STRUCTURE (2016)

Article Biochemical Research Methods

In-vacuum long-wavelength macromolecular crystallography

Armin Wagner et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2016)

Article Chemistry, Multidisciplinary

SynchWeb: a modern interface for ISPyB

S. J. Fisher et al.

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2015)

Article Biochemical Research Methods

Fingerprinting redox and ligand states in haemprotein crystal structures using resonance Raman spectroscopy

Demet Kekilli et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2014)

Meeting Abstract Chemistry, Multidisciplinary

DIMPLE - a pipeline for the rapid generation of difference maps from protein crystals with putatively bound ligands

Marcin Wojdyr et al.

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES (2013)

Article Biochemical Research Methods

How good are my data and what is the resolution?

Philip R. Evans et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2013)

Article Biochemistry & Molecular Biology

Reshaping Antibody Diversity

Feng Wang et al.

Software Review Chemistry, Multidisciplinary

RADDOSE-3D: time- and space-resolved modelling of dose in macromolecular crystallography

Oliver B. Zeldin et al.

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2013)

Article Chemistry, Multidisciplinary

A fast, simple and robust protocol for growing crystals in the lipidic cubic phase

Margaret Aherne et al.

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2012)

Article Biochemistry & Molecular Biology

Crystal structure of the TLDc domain of oxidation resistance protein 2 from zebrafish

Mickael Blaise et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2012)

Article Biochemical Research Methods

In-plate protein crystallization, in situ ligand soaking and X-ray diffraction

Albane le Maire et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2011)

Article Biochemical Research Methods

REFMAC5 for the refinement of macromolecular crystal structures

Garib N. Murshudov et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2011)

Article Biochemical Research Methods

ISPyB: an information management system for synchrotron macromolecular crystallography

Solange Delageniere et al.

BIOINFORMATICS (2011)

Article Chemistry, Multidisciplinary

SLS Crystallization Platform at Beamline X06DA-A Fully Automated Pipeline Enabling in Situ X-ray Diffraction Screening

R. Bingel-Erlenmeyer et al.

CRYSTAL GROWTH & DESIGN (2011)

Article Biochemical Research Methods

The Phenix software for automated determination of macromolecular structures

Paul D. Adams et al.

METHODS (2011)

Article Multidisciplinary Sciences

Accessing protein conformational ensembles using room-temperature X-ray crystallography

James S. Fraser et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biochemical Research Methods

XDS

Wolfgang Kabsch

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)

Article Biochemistry & Molecular Biology

PONDR-FIT: A meta-predictor of intrinsically disordered amino acids

Bin Xue et al.

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2010)

Article Chemistry, Multidisciplinary

xia2: an expert system for macromolecular crystallography data reduction

G. Winter

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2010)

Article Biochemical Research Methods

Crystallizing membrane proteins using lipidic mesophases

Martin Caffrey et al.

NATURE PROTOCOLS (2009)

Article Biochemical Research Methods

Semi-automated microseeding of nanolitre crystallization experiments

Thomas S. Walter et al.

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS (2008)

Article Chemistry, Multidisciplinary

Phaser crystallographic software

Airlie J. McCoy et al.

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2007)

Article Instruments & Instrumentation

Cryoradiolytic reduction of crystalline heme proteins:: analysis by UV-Vis spectroscopy and X-ray crystallography

Thorsten Beitlich et al.

JOURNAL OF SYNCHROTRON RADIATION (2007)

Article Biochemical Research Methods

Protein production by auto-induction in high-density shaking cultures

FW Studier

PROTEIN EXPRESSION AND PURIFICATION (2005)

Article Biochemical Research Methods

Coot:: model-building tools for molecular graphics

P Emsley et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2004)

Article Biochemical Research Methods

ARP/wARP and molecular replacement

A Perrakis et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2001)