Characterizing metal-binding sites in proteins with X-ray crystallography

Principles and methods used to grow and optimize crystals of protein–metallodrug adducts, to determine metal binding sites and to assign metal ligands

(2017) Irene Russo Krauss et al.   Metallomics

Optimization of overexpression of a chaperone protein of steroid C25 dehydrogenase for biochemical and biophysical characterization

(2017) Ewa Niedzialkowska et al.   PROTEIN EXPRESSION AND PURIFICATION

CheckMyMetal: a macromolecular metal-binding validation tool

(2017) Heping Zheng et al.   Acta Crystallographica Section D-Structural Biology

New leads for fragment-based design of rhenium/technetium radiopharmaceutical agents

(2017) Alice Brink et al.   IUCrJ

Metalloprotein Crystallography: More than a Structure

(2016) Sarah E. J. Bowman et al.   ACCOUNTS OF CHEMICAL RESEARCH

Oxaliplatin Binding to Human Copper Chaperone Atox1 and Protein Dimerization

(2016) Benny D. Belviso et al.   INORGANIC CHEMISTRY

X-ray Structure Analysis of Indazolium trans-[Tetrachlorobis(1H-indazole)ruthenate(III)] (KP1019) Bound to Human Serum Albumin Reveals Two Ruthenium Binding Sites and Provides Insights into the Drug Binding Mechanism

(2016) Aleksandar Bijelic et al.   JOURNAL OF MEDICINAL CHEMISTRY

Circulatory zinc transport is controlled by distinct interdomain sites on mammalian albumins

(2016) Katarzyna B. Handing et al.   Chemical Science

Re-refinement of 4g4a: room-temperature X-ray diffraction study of cisplatin and its binding to His15 of HEWL after 14 months chemical exposure in the presence of DMSO

(2016) Simon W. M. Tanley et al.   Acta Crystallographica Section F-Structural Biology Communications

Improving diffraction resolution using a new dehydration method

(2016) Qingqiu Huang et al.   Acta Crystallographica Section F-Structural Biology Communications

Re-refinement of 4xan: hen egg-white lysozyme with carboplatin in sodium bromide solution

(2016) Simon W. M. Tanley et al.   Acta Crystallographica Section F-Structural Biology Communications

Divalent Metal Ions Mg2+ and Ca2+ Have Distinct Effects on Protein Kinase A Activity and Regulation

(2015) Matthias J. Knape et al.   ACS Chemical Biology

Monitoring one-electron photo-oxidation of guanine in DNA crystals using ultrafast infrared spectroscopy

(2015) James P. Hall et al.   Nature Chemistry

Magnesium-binding architectures in RNA crystal structures: validation, binding preferences, classification and motif detection

(2015) Heping Zheng et al.   NUCLEIC ACIDS RESEARCH

Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin

(2015) Ivan Shabalin et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Structural study of the X-ray-induced enzymatic reaction of octahaem cytochromecnitrite reductase

(2015) A. A. Trofimov et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Copper Active Sites in Biology

(2014) Edward I. Solomon et al.   CHEMICAL REVIEWS

Double trouble-Buffer selection and His-tag presence may be responsible for nonreproducibility of biomedical experiments

(2014) Karolina A. Majorek et al.   PROTEIN SCIENCE

Analysis of the tryptic search space in UniProt databases

(2014) Emanuele Alpi et al.   PROTEOMICS

Optimization of crystallization conditions for biological macromolecules

(2014) Alexander McPherson et al.   Acta Crystallographica Section F-Structural Biology Communications

Structural, Functional, and Inhibition Studies of a Gcn5-relatedN-Acetyltransferase (GNAT) Superfamily Protein PA4794

(2013) Karolina A. Majorek et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server

(2013) Heping Zheng et al.   Nature Protocols

Diradical intermediate within the context of tryptophan tryptophylquinone biosynthesis

(2013) E. T. Yukl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Solubilities of metal hydroxides

(2013) Yu. F. Orlov et al.   RUSSIAN JOURNAL OF INORGANIC CHEMISTRY

Towards accurate structural characterization of metal centres in protein crystals: the structures of Ni and Cu T6bovine insulin derivatives

(2013) Christian Grundahl Frankaer et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

A universal indicator dye pH assay for crystallization solutions and other high-throughput applications

(2012) Janet Newman et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Implementing an X-ray validation pipeline for the Protein Data Bank

(2012) Swanand Gore et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

A high-pressure cryocooling method for protein crystals and biological samples with reduced background X-ray scatter

(2012) Chae Un Kim et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Protein metalation by metal-based drugs: reactions of cytotoxic gold compounds with cytochrome c and lysozyme

(2012) Chiara Gabbiani et al.   JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY

Metalloprotein active site structure determination: Synergy between X-ray absorption spectroscopy and X-ray crystallography

(2012) Julien J.H. Cotelesage et al.   JOURNAL OF INORGANIC BIOCHEMISTRY

X-ray absorption spectroscopy at a protein crystallography facility: the Canadian Light Source beamline 08B1-1

(2012) Julien J. H. Cotelesage et al.   JOURNAL OF SYNCHROTRON RADIATION

Calcium Ion Gradients Modulate the Zinc Affinity and Antibacterial Activity of Human Calprotectin

(2012) Megan Brunjes Brophy et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular basis for phosphospecific recognition of histone H3 tails by Survivin paralogues at inner centromeres

(2012) Ewa Niedzialkowska et al.   MOLECULAR BIOLOGY OF THE CELL

Correction: Nucleosomes Correlate with In Vivo Progression Pattern of De Novo Methylation of p16 CpG Islands in Human Gastric Carcinogenesis

(2012) Zhe-Ming Lu et al.   PLoS One

JBluIce–EPICScontrol system for macromolecular crystallography

(2011) Sergey Stepanov et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

REFMAC5 for the refinement of macromolecular crystal structures

(2011) Garib N. Murshudov et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Overview of theCCP4 suite and current developments

(2011) Martyn D. Winn et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Structure-based de novo prediction of zinc-binding sites in proteins of unknown function

(2011) Wei Zhao et al.   BIOINFORMATICS

Characterization of metalloproteins by high-throughput X-ray absorption spectroscopy

(2011) W. Shi et al.   GENOME RESEARCH

MetalDetector v2.0: predicting the geometry of metal binding sites from protein sequence

(2011) Andrea Passerini et al.   NUCLEIC ACIDS RESEARCH

Radiation damage in macromolecular crystallography: what is it and why should we care?

(2010) Elspeth F. Garman   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

XDS

(2010) Wolfgang Kabsch   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Crystallization, preliminary X-ray diffraction studies and Raman microscopy of the major haemoglobin from the sub-Antarctic fishEleginops maclovinusin the carbomonoxy form

(2010) Antonello Merlino et al.   Acta Crystallographica Section F-Structural Biology and Crystallization Communications

Structural Basis of Low-Affinity Nickel Binding to the Nickel-Responsive Transcription Factor NikR fromEscherichia coli

(2010) Christine M. Phillips et al.   BIOCHEMISTRY

The crystal structures of human S100B in the zinc- and calcium-loaded state at three pH values reveal zinc ligand swapping

(2010) Thorsten Ostendorp et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

The C6 Web Tool: A Resource for the Rational Selection of Crystallization Conditions

(2010) Janet Newman et al.   CRYSTAL GROWTH & DESIGN

Single-crystal Raman spectroscopy and X-ray crystallography at beamline X26-C of the NSLS

(2010) Deborah Stoner-Ma et al.   JOURNAL OF SYNCHROTRON RADIATION

Triggered infrared spectroscopy for investigating metalloprotein chemistry

(2010) K. A. Vincent   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

FINDSITE-metal: Integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level

(2010) Michal Brylinski et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

ESG: extended similarity group method for automated protein function prediction

(2009) Meghana Chitale et al.   BIOINFORMATICS

Structure, Properties, and Engineering of the Major Zinc Binding Site on Human Albumin

(2009) Claudia A. Blindauer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Crystal structure and molecular modeling study of N-carbamoylsarcosine amidase Ta0454 from Thermoplasma acidophilum

(2009) Hai-Bin Luo et al.   JOURNAL OF STRUCTURAL BIOLOGY

Biological X-ray absorption spectroscopy and metalloproteomics

(2009) Isabella Ascone et al.   JOURNAL OF SYNCHROTRON RADIATION

Can soaked-in scavengers protect metalloprotein active sites from reduction during data collection?

(2009) Sofia Macedo et al.   JOURNAL OF SYNCHROTRON RADIATION

Metalloproteomics, metalloproteomes, and the annotation of metalloproteins

(2009) Wolfgang Maret   Metallomics

A novel method for detection of selenomethionine incorporation in protein crystalsviaRaman microscopy

(2008) Alessandro Vergara et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Determination of Protein Structures—A Series of Fortunate Events

(2008) Maksymilian Chruszcz et al.   BIOPHYSICAL JOURNAL

Data mining of metal ion environments present in protein structures

(2008) Heping Zheng et al.   JOURNAL OF INORGANIC BIOCHEMISTRY

Structural Insight into the Mechanism of Substrate Specificity and Catalytic Activity of an HD-Domain Phosphohydrolase: The 5′-Deoxyribonucleotidase YfbR from Escherichia coli

(2008) Matthew D. Zimmerman et al.   JOURNAL OF MOLECULAR BIOLOGY

Lower limits of detection of synchrotron radiation high-energy X-ray fluorescence spectrometry and its possibility for the forensic application for discrimination of glass fragments

(2007) Toshio Nakanishi et al.   FORENSIC SCIENCE INTERNATIONAL