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List of works by John A. Tainer

2-aminopyridines as highly selective inducible nitric oxide synthase inhibitors. Differential binding modes dependent on nitrogen substitution.

scientific article

2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update

scientific article published on 18 August 2017

A Role for Acidic Residues in Di-leucine Motif-based Targeting to the Endocytic Pathway ⬇️

scientific article published on August 25, 1995

A SIM-ultaneous role for SUMO and ubiquitin

scientific article

A charged performance by gp17 in viral packaging

scientific article published on 01 December 2008

A computational framework for proteome-wide pursuit and prediction of metalloproteins using ICP-MS and MS/MS data

scientific article

A mutation in the FHA domain of Coprinus cinereus Nbs1 Leads to Spo11-independent meiotic recombination and chromosome segregation

scientific article

A nanomachine for making ends meet: MRN is a flexing scaffold for the repair of DNA double-strand breaks.

scientific article

A new structural framework for integrating replication protein A into DNA processing machinery.

scientific article

A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA

scientific article

A structural model for regulation of NHEJ by DNA-PKcs autophosphorylation

scientific article

A structure-specific nucleic acid-binding domain conserved among DNA repair proteins

scientific article

ABC ATPase signature helices in Rad50 link nucleotide state to Mre11 interface for DNA repair.

scientific article

ALS mutants of human superoxide dismutase form fibrous aggregates via framework destabilization

scientific article

ATM regulates Mre11-dependent DNA end-degradation and microhomology-mediated end joining

scientific article

ATP induces conformational changes in the carboxyl-terminal region of ClC-5

scientific article

ATP-driven Rad50 conformations regulate DNA tethering, end resection, and ATM checkpoint signaling

scientific article published on 3 March 2014

ATP-driven Rad50 conformations regulate DNA tethering, end resection, and ATM checkpoint signaling.

scientific article published on April 2016

ATP-stimulated, DNA-mediated redox signaling by XPD, a DNA repair and transcription helicase

scientific article published on 22 September 2011

Abasic site recognition by two apurinic/apyrimidinic endonuclease families in DNA base excision repair: the 3' ends justify the means

scientific article (publication date: 30 August 2000)

Accurate SAXS profile computation and its assessment by contrast variation experiments

scientific article published on August 2013

Accurate assessment of mass, models and resolution by small-angle scattering

scientific article published on April 2013

Achieving fidelity in homologous recombination despite extreme complexity: informed decisions by molecular profiling

scientific article

Active and alkylated human AGT structures: a novel zinc site, inhibitor and extrahelical base binding

scientific article

Active and inhibited human catalase structures: ligand and NADPH binding and catalytic mechanism

scientific article

Aggregation propensities of superoxide dismutase G93 hotspot mutants mirror ALS clinical phenotypes

scientific article

Alkyltransferase-like protein (Atl1) distinguishes alkylated guanines for DNA repair using cation-  interactions

scientific article

Alkyltransferase-like proteins: molecular switches between DNA repair pathways

scientific article

All stressed out without ATM kinase

scientific article published on 5 April 2011

Altering the antigenicity of proteins ⬇️

scientific article published on April 15, 1992

Amino acid substitution at the dimeric interface of human manganese superoxide dismutase

scientific article

Amyotrophic lateral sclerosis

scientific article published on 01 January 2010

Amyotrophic lateral sclerosis and structural defects in Cu,Zn superoxide dismutase

scientific article

An AAA+ ATPase Clamshell Targets Transposition

scientific article

An Intrinsically Disordered APLF Links Ku, DNA-PKcs, and XRCC4-DNA Ligase IV in an Extended Flexible Non-homologous End Joining Complex

scientific article

An atypical BRCT-BRCT interaction with the XRCC1 scaffold protein compacts human DNA Ligase IIIα within a flexible DNA repair complex

scientific article published on 16 December 2020

Anacardic acid inhibits the catalytic activity of matrix metalloproteinase-2 and matrix metalloproteinase-9

scientific article

Anchored plasticity opens doors for selective inhibitor design in nitric oxide synthase

scientific article

Antibody remodeling: a general solution to the design of a metal-coordination site in an antibody binding pocket

scientific article

Archaeal flagellar ATPase motor shows ATP-dependent hexameric assembly and activity stimulation by specific lipid binding.

scientific article published on July 2011

Archaeal genome guardians give insights into eukaryotic DNA replication and damage response proteins.

scientific article published on 20 February 2014

Atl1 Regulates Choice between Global Genome and Transcription-Coupled Repair of O6-Alkylguanines

scientific article

Atomic and residue hydrophilicity in the context of folded protein structures

scientific article published on 01 December 1995

Atomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III

scientific article published on October 16, 1992

Author Correction: Pro-metastatic collagen lysyl hydroxylase dimer assemblies stabilized by Fe2+-binding.

scientific article published on 10 July 2018

Base excision repair enzyme family portrait: integrating the structure and chemistry of an entire DNA repair pathway.

scientific article published on December 1997

Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA.

scientific article

Bending Forks and Wagging Dogs--It's about the DNA 3' Tail.

scientific article published on June 2015

Biochemical characterization and crystal structure of a Dim1 family associated protein: Dim2

scientific article

Biochemical purification and crystallographic characterization of the fiber-forming protein pilin from Neisseria gonorrhoeae.

scientific article published in February 1990

Bridging the solution divide: comprehensive structural analyses of dynamic RNA, DNA, and protein assemblies by small-angle X-ray scattering

scientific article

Cancer, cadmium and genome integrity

scientific article published on 01 July 2003

Catalytic and structural effects of amino acid substitution at histidine 30 in human manganese superoxide dismutase: insertion of valine C gamma into the substrate access channel

scientific article (publication date: 18 March 2003)

Cell-free expression of functional receptor tyrosine kinases

scientific article published on 14 August 2015

Characterization of Y122F R2 of Escherichia coli Ribonucleotide Reductase by Time-Resolved Physical Biochemical Methods and X-ray Crystallography, ⬇️

scientific article published on April 28, 1998

Characterization of a Y-Family DNA Polymerase eta from the Eukaryotic Thermophile Alvinella pompejana.

scientific article

Characterization of the electrophile binding site and substrate binding mode of the 26-kDa glutathione S-transferase from Schistosoma japonicum

scientific article (publication date: April 2003)

Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law.

scientific article

Charge Transport Communication through DNA by Protein Fe-S Clusters: How Far Is Not Too Far?

scientific article published on 11 January 2019

Charging of Proteins in Native Mass Spectrometry

scientific article published on 12 October 2016

Chemical screening by time-resolved X-ray scattering to discover allosteric probes

scientific article published in 2024

Chemistry of antibody binding to a protein

scientific article published on 01 March 1987

Cloning, expression, and characterization of a nitric oxide synthase protein from Deinococcus radiodurans

scientific article

Coiled coils unspring protein origami.

scientific article published in November 2017

Combining H/D exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil-DNA glycosylase.

scientific article

Comparison of the catalytic parameters and reaction specificities of a phage and an archaeal flap endonuclease

scientific article

Comprehensive macromolecular conformations mapped by quantitative SAXS analyses

scientific article published on June 2013

Computational, pulse-radiolytic, and structural investigations of lysine-136 and its role in the electrostatic triad of human C u,Z n superoxide dismutase ⬇️

scientific article published on September 1, 1997

Consensus chemistry and beta-turn conformation of the active core of the insect kinin neuropeptide family

scientific article published on 01 February 1997

Consequences of the loss of O-linked glycosylation of meningococcal type IV pilin on piliation and pilus-mediated adhesion

scientific article published on 01 February 1998

Conserved Structural Chemistry for Incision Activity in Structurally Non-homologous Apurinic/Apyrimidinic Endonuclease APE1 and Endonuclease IV DNA Repair Enzymes

scientific article

Contribution of human manganese superoxide dismutase tyrosine 34 to structure and catalysis ⬇️

scientific article

Coprinus cinereus rad50 mutants reveal an essential structural role for Rad50 in axial element and synaptonemal complex formation, homolog pairing and meiotic recombination

scientific article published on 20 October 2008

Corrigendum: Phosphate steering by Flap Endonuclease 1 promotes 5′-flap specificity and incision to prevent genome instability.

scientific article

Cracking tyrosine phosphatases

scientific article published in Nature

Crystal Structure of Y34F Mutant Human Mitochondrial Manganese Superoxide Dismutase and the Functional Role of Tyrosine 34, ⬇️

scientific article published on April 7, 1998

Crystal Structure of the First Eubacterial Mre11 Nuclease Reveals Novel Features that May Discriminate Substrates During DNA Repair

scientific article

Crystal and Solution Structures of a Prokaryotic M16B Peptidase: an Open and Shut Case

scientific article

Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis

scientific article

Crystal structure and mutational analysis of the Saccharomyces cerevisiae cell cycle regulatory protein Cks1: implications for domain swapping, anion binding and protein interactions

scientific article

Crystal structure and mutational analysis of the human CDK2 kinase complex with cell cycle-regulatory protein CksHs1

scientific article

Crystal structure and novel recognition motif of rho ADP-ribosylating C3 exoenzyme from Clostridium botulinum: structural insights for recognition specificity and catalysis

scientific article

Crystal structure of human uracil-DNA glycosylase in complex with a protein inhibitor: protein mimicry of DNA

scientific article

Crystal structures of a schistosomal drug and vaccine target: glutathione S-transferase from Schistosoma japonica and its complex with the leading antischistosomal drug praziquantel

scientific article

Crystallization and crystallographic characterization of the iron-sulfur-containing DNA-repair enzyme endonuclease III from Escherichia coli.

scientific article published in September 1992

Crystallization and preliminary crystallographic study of human CksHs1: a cell cycle regulatory protein

scientific article published on 01 January 1995

Crystallographic characterization of recombinant human CuZn superoxide dismutase

scientific article published on 01 December 1986

Crystallographic structure reveals phosphorylated pilin from Neisseria: phosphoserine sites modify type IV pilus surface chemistry and fibre morphology

scientific article

Crystallographic structures of Discosoma red fluorescent protein with immature and mature chromophores: linking peptide bond trans-cis isomerization and acylimine formation in chromophore maturation.

scientific article published in July 2005

DNA Double-Strand Break Repair Pathway Choice Is Directed by Distinct MRE11 Nuclease Activities

scientific article

DNA Repair and Global Sumoylation Are Regulated by Distinct Ubc9 Noncovalent Complexes

scientific article

DNA apurinic-apyrimidinic site binding and excision by endonuclease IV

scientific article

DNA binding and nucleotide flipping by the human DNA repair protein AGT.

scientific article

DNA binding, nucleotide flipping, and the helix-turn-helix motif in base repair by O6-alkylguanine-DNA alkyltransferase and its implications for cancer chemotherapy

scientific article

DNA charge transport as a first step in coordinating the detection of lesions by repair proteins

scientific article published on 23 January 2012

DNA conformations in mismatch repair probed in solution by X-ray scattering from gold nanocrystals.

scientific article published on 07 October 2013

DNA damage recognition and repair pathway coordination revealed by the structural biochemistry of DNA repair enzymes.

scientific article

DNA mismatch repair: the hands of a genome guardian.

scientific article

DNA repair mechanisms for the recognition and removal of damaged DNA bases.

scientific article

DNA repair proteins.

scientific article published on February 1995

DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination [corrected]

scientific article

Dancing with the elephants: envisioning the structural biology of DNA repair pathways

scientific article published on 01 August 2000

Defining Antibody-Antigen Recognition: Towards Engineered Antibodies and Epitopes ⬇️

scientific article published on January 1, 1991

Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor

scientific article published on 2 November 2016

Defining the role of arginine 96 in green fluorescent protein fluorophore biosynthesis

scientific article published in December 2005

Design of a monomeric human glutathione transferase GSTP1, a structurally stable but catalytically inactive protein.

scientific article published in October 2002

Designing and defining dynamic protein cage nanoassemblies in solution

scientific article

Developing advanced X-ray scattering methods combined with crystallography and computation

scientific article (publication date: March 2013)

Developing master keys to brain pathology, cancer and aging from the structural biology of proteins controlling reactive oxygen species and DNA repair.

scientific article published on 15 December 2006

Differential arrangements of conserved building blocks among homologs of the Rad50/Mre11 DNA repair protein complex

scientific article published in June 2004

Dissection of DNA double-strand-break repair using novel single-molecule forceps ⬇️

scientific article published on 21 May 2018

Dynamic structures in DNA damage responses & cancer.

scientific article published on March 2015

Electrostatic orientation of the electron-transfer complex between plastocyanin and cytochrome c ⬇️

scientific article published on July 15, 1991

Emerging critical roles of Fe-S clusters in DNA replication and repair

scientific article

Envisioning how the prototypic molecular machine TFIIH functions in transcription initiation and DNA repair

scientific article published on 17 September 2020

Envisioning new targets and new approaches for molecular-based cancer therapeutics

Envisioning the dynamics and flexibility of Mre11-Rad50-Nbs1 complex to decipher its roles in DNA replication and repair

scientific article

Enzyme motifs in antibodies

scientific article published in Nature

Erratum to “ALS Mutants of Human Superoxide Dismutase form Fibrous Aggregates via Framework Destabilization” [J. Mol. Biol. 332 (2003) 601–615]

scholarly article published in Journal of Molecular Biology

Eukaryotic Class II Cyclobutane Pyrimidine Dimer Photolyase Structure Reveals Basis for Improved Ultraviolet Tolerance in Plants

scientific article

Evolution and mechanism from structures of an ADP-ribosylating toxin and NAD complex

scientific article

Excision of cytosine and thymine from DNA by mutants of human uracil-DNA glycosylase

scientific article

Exploring the repeat protein universe through computational protein design

scientific article published on 16 December 2015

FlaF Is a β-Sandwich Protein that Anchors the Archaellum in the Archaeal Cell Envelope by Binding the S-Layer Protein.

scientific article published on 9 April 2015

Flap endonuclease homologs in archaebacteria exist as independent proteins.

scientific article

Flap endonucleases pass 5'-flaps through a flexible arch using a disorder-thread-order mechanism to confer specificity for free 5'-ends

scientific article

Flexibility promotes fidelity.

scientific article published in May 2009

Flipping of alkylated DNA damage bridges base and nucleotide excision repair

scientific article

FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles

scientific article published on 05 May 2016

Full-length archaeal Rad51 structure and mutants: mechanisms for RAD51 assembly and control by BRCA2

scientific article

Function of the Greek key connection analysed using circular permutants of superoxide dismutase.

scientific article

Functional motifs in the (6-4) photolyase crystal structure make a comparative framework for DNA repair photolyases and clock cryptochromes

scientific article

HU multimerization shift controls nucleoid compaction

scientific article

Heparin-mediated dimerization of follistatin

scientific article published on 16 November 2020

Hexameric structures of the archaeal secretion ATPase GspE and implications for a universal secretion mechanism

scientific article

High Resolution Distance Distributions Determined by X-Ray and Neutron Scattering.

scientific article published in January 2017

High-throughput SAXS for the characterization of biomolecules in solution: a practical approach

scientific article

How substrate specificity is imposed on a histone demethylase--lessons from KDM2A

scientific article

Human ABH3 structure and key residues for oxidative demethylation to reverse DNA/RNA damage

scientific article

Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining

scientific article published on 29 June 2015

Human DNA ligase III recognizes DNA ends by dynamic switching between two DNA-bound states

scientific article

Human Flap Endonuclease Structures, DNA Double-Base Flipping, and a Unified Understanding of the FEN1 Superfamily

scientific article

Human XPG nuclease structure, assembly, and activities with insights for neurodegeneration and cancer from pathogenic mutations

scientific article published on 10 June 2020

Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits

scientific article

Human glutathione transferase A4-4 crystal structures and mutagenesis reveal the basis of high catalytic efficiency with toxic lipid peroxidation products

scientific article

Hybrid Methods Reveal Multiple Flexibly Linked DNA Polymerases within the Bacteriophage T7 Replisome.

scientific article published in January 2017

Hydrogen bonding in human manganese superoxide dismutase containing 3-fluorotyrosine.

scientific article

Identical short peptide sequences in unrelated proteins can have different conformations: a testing ground for theories of immune recognition.

scientific article published on August 1985

Identification of a coiled coil in werner syndrome protein that facilitates multimerization and promotes exonuclease processivity

scientific article

Identification of a new cryptochrome class. Structure, function, and evolution

scientific article

Identification of critical active-site residues in the multifunctional human DNA repair enzyme HAP1.

scientific article

Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source

scientific article

Improving small-angle X-ray scattering data for structural analyses of the RNA world

scientific article

Insights into FlaI Functions in Archaeal Motor Assembly and Motility from Structures, Conformations, and Genetics

scientific article

Insights into Lou Gehrig's disease from the structure and instability of the A4V mutant of human Cu,Zn superoxide dismutase

scientific article

Intact Functional Fourteen-subunit Respiratory Membrane-bound [NiFe]-Hydrogenase Complex of the Hyperthermophilic Archaeon Pyrococcus furiosus

scientific article (publication date: 23 May 2014)

Interfacial residues promote an optimal alignment of the catalytic center in human soluble guanylate cyclase: heterodimerization is required but not sufficient for activity

scientific article

Investigations of black bronchoalveolar human lavage fluid

scientific article published on 01 October 1977

Kinetic and stoichiometric characterisation of streptavidin-binding aptamers

scientific article

Kinetic mechanism of activation of the Cdk2/cyclin A complex. Key role of the C-lobe of the Cdk.

scientific article published on 16 April 2002

Kinetic studies of reduction of a 1:1 cytochrome c-flavodoxin complex by free flavin semiquinones and rubredoxin

scientific article published on 01 June 1986

Ku and DNA-dependent protein kinase dynamic conformations and assembly regulate DNA binding and the initial non-homologous end joining complex.

scientific article

LEUCINE-272-ALANINE URACIL-DNA GLYCOSYLASE BOUND TO ABASIC SITE-CONTAINING DNA

scholarly article published 6 May 1999

Learning our ABCs: Rad50 directs MRN repair functions via adenylate kinase activity from the conserved ATP binding cassette

scientific article published on 01 March 2007

Lessons learned from structural results on uracil-DNA glycosylase

scientific article (publication date: 30 August 2000)

MDB: the Metalloprotein Database and Browser at The Scripps Research Institute

scientific article

MRE11 facilitates the removal of human topoisomerase II complexes from genomic DNA.

scientific article

MacroBac: New Technologies for Robust and Efficient Large-Scale Production of Recombinant Multiprotein Complexes

scientific article published on 15 May 2017

Manganese Superoxide Dismutase

Manganese superoxide dismutase induction during measles virus infection.

scientific article published on July 2003

Mapping interactions between the RNA chaperone FinO and its RNA targets ⬇️

scientific article

Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease SPRTN.

scientific article published on 27 October 2016

Mechanism and energetics of green fluorescent protein chromophore synthesis revealed by trapped intermediate structures

scientific article

Mechanism of DNA substrate recognition by the mammalian DNA repair enzyme, Polynucleotide Kinase.

scientific article published on 11 August 2009

Mechanism of efficient double-strand break repair by a long non-coding RNA

scientific article published on 12 October 2020

Mechanism of efficient double-strand break repair by a long non-coding RNA

scientific article published on 18 December 2020

Mechanisms of antibody binding to a protein

scientific article published on 01 March 1987

Mechanistic insights into the role of Hop2-Mnd1 in meiotic homologous DNA pairing

scientific article published on 22 October 2013

Metal-binding sites in proteins

scientific article published on August 1, 1991

Metalloantibodies

scientific article published on 01 August 1990

Metals in biology: defining metalloproteomes

scientific article

Methods for using new conceptual tools and parameters to assess RNA structure by small-angle X-ray scattering.

scientific article published in January 2014

Microbial metalloproteomes are largely uncharacterized.

scientific article

Microhomology-mediated end joining is activated in irradiated human cells due to phosphorylation-dependent formation of the XRCC1 repair complex

scientific article

ModBase, a database of annotated comparative protein structure models and associated resources.

scientific article

Modeling macromolecular motions by x-ray-scattering-constrained molecular dynamics

scientific article published on May 2015

Molecular biology: DNA repair without flipping out.

scientific article

Molecular mimicry of SUMO promotes DNA repair

scientific article

Molecular recognition in DNA-binding proteins and enzymes.

scientific article published on August 1993

Mre11 ATLD17/18 mutation retains Tel1/ATM activity but blocks DNA double-strand break repair

scientific article

Mre11 Dimers Coordinate DNA End Bridging and Nuclease Processing in Double-Strand-Break Repair

scientific article

Mre11-Rad50-Nbs1 conformations and the control of sensing, signaling, and effector responses at DNA double-strand breaks

scientific article

Mre11-Rad50-Nbs1 is a keystone complex connecting DNA repair machinery, double-strand break signaling, and the chromatin template.

scientific article published on August 2007

MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily

scientific article

N-terminal domain swapping and metal ion binding in nitric oxide synthase dimerization.

scientific article

Nbs1 Flexibly Tethers Ctp1 and Mre11-Rad50 to Coordinate DNA Double-Strand Break Processing and Repair

scientific article

Neutralizing mutations of carboxylates that bind metal 2 in T5 flap endonuclease result in an enzyme that still requires two metal ions

scientific article

New aspects of chemotaxis. Specific target-cell attraction by lipid and lipoprotein fractions of Escherichia coli chemotactic factor ⬇️

scientific article published on November 1, 1975

Newly discovered archaebacterial flap endonucleases show a structure-specific mechanism for DNA substrate binding and catalysis resembling human flap endonuclease-1.

scientific article

Nickel Superoxide Dismutase Structure and Mechanism†

scientific article (publication date: June 2004)

Nitric-oxide Synthase Forms N-NO-pterin and S-NO-Cys: IMPLICATIONS FOR ACTIVITY, ALLOSTERY, AND REGULATION

scientific article

Non-chemokinetic neutrophil attractants derived from arachidonic acid

scientific article published on 01 October 1983

Noncoding RNA joins Ku and DNA-PKcs for DNA-break resistance in breast cancer

scientific article published on June 2016

Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure

scientific article

Nse1 RING-like domain supports functions of the Smc5-Smc6 holocomplex in genome stability.

scientific article published on 30 July 2008

P53 conformational switching for selectivity may reveal a general solution for specific DNA binding.

scientific article

Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues

scientific article published on 3 March 2016

Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability

scientific article

Predicting molecular interactions and inducible complementarity: fragment docking of Fab-peptide complexes.

scientific article published in September 1994

Pro-metastatic collagen lysyl hydroxylase dimer assemblies stabilized by Fe2+-binding.

scientific article

Probing DNA by 2-OG-dependent dioxygenase.

scientific article published on December 2013

Probing the active site of human manganese superoxide dismutase: the role of glutamine 143

scientific article

Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications.

scientific article

Protein metal-binding sites

scientific article published on August 1, 1992

Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase

scientific article

Purification and characterization of Thermotoga maritima endonuclease IV, a thermostable apurinic/apyrimidinic endonuclease and 3'-repair diesterase.

scientific article

Purification and crystallization of a schistosomal glutathione S-transferase.

scientific article

Purification, crystallization and space group determination of DNA repair enzyme exonuclease III from E. coli

scientific article published on 01 January 1993

RNA Modifications: Reversal Mechanisms And Cancer

article

RNF4 interacts with both SUMO and nucleosomes to promote the DNA damage response

scientific article

RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment

scientific article

Rad50/SMC proteins and ABC transporters: unifying concepts from high-resolution structures.

scientific article

Rational design and expression of a heparin-targeted human superoxide dismutase

scientific article published on 01 January 1993

Recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loading.

scientific article

Repair complexes of FEN1 endonuclease, DNA, and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability

scientific article

Repair of O4-alkylthymine by O6-alkylguanine-DNA alkyltransferases

scientific article

Repair of O6-G-alkyl-O6-G interstrand cross-links by human O6-alkylguanine-DNA alkyltransferase.

scientific article published on 20 September 2008

Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB.

scientific article

Robust Production, Crystallization, Structure Determination, and Analysis of [Fe-S] Proteins: Uncovering Control of Electron Shuttling and Gating in the Respiratory Metabolism of Molybdopterin Guanine Dinucleotide Enzymes.

scientific article published on 19 December 2017

Role of tryptophan 161 in catalysis by human manganese superoxide dismutase

scientific article published on 01 September 1999

SUMO-targeted ubiquitin ligase, Rad60, and Nse2 SUMO ligase suppress spontaneous Top1-mediated DNA damage and genome instability

scientific article

SUMO-targeted ubiquitin ligases in genome stability.

scientific article

Screening a peptidyl database for potential ligands to proteins with side-chain flexibility

scientific article published on 01 October 1998

Sculpting of DNA at Abasic Sites by DNA Glycosylase Homolog Mag2

scientific article

Selective small molecule PARG inhibitor causes replication fork stalling and cancer cell death

scientific article published on 11 December 2019

Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1.

scientific article published on 23 February 2017

Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy

scientific article published on 4 January 2018

Small angle X-ray scattering-assisted protein structure prediction in CASP13 and emergence of solution structure differences

scientific article published on 16 October 2019

Software for the high-throughput collection of SAXS data using an enhanced Blu-Ice/DCS control system

scientific article

Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on PCNA

scientific article

Solution structure of RNase P RNA.

scientific article

Structural Basis of Guanine Nucleotide Exchange Mediated by the T-Cell Essential Vav1

scientific article

Structural Basis ofO6-Alkylguanine Recognition by a Bacterial Alkyltransferase-like DNA Repair Protein

scientific article

Structural Characterization of Zinc-deficient Human Superoxide Dismutase and Implications for ALS

scientific article

Structural Tuning of the Fluorescent Protein iLOV for Improved Photostability

scientific article

Structural analysis of flexible proteins in solution by small angle X-ray scattering combined with crystallography

scientific article published on 27 October 2006

Structural and functional analysis of Mre11-3.

scientific article published on 26 March 2004

Structural and functional characterization of the PNKP-XRCC4-LigIV DNA repair complex

scientific article

Structural basis for endothelial nitric oxide synthase binding to calmodulin

scientific article (publication date: 17 February 2003)

Structural basis for isozyme-specific regulation of electron transfer in nitric-oxide synthase.

scientific article

Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii

scientific article

Structural basis for recognition of 5′-phosphotyrosine adducts by Tdp2

scientific article

Structural basis for the removal and exclusion of uracil from DNA

article published in 1996

Structural biochemistry and interaction architecture of the DNA double-strand break repair Mre11 nuclease and Rad50-ATPase

scientific article

Structural biochemistry of a type 2 RNase H: RNA primer recognition and removal during DNA replication

scientific article

Structural biology of Rad50 ATPase: ATP-driven conformational control in DNA double-strand break repair and the ABC-ATPase superfamily

scientific article published in June 2000

Structural chemistry of a green fluorescent protein Zn biosensor

scientific article

Structural control of nonnative ligand binding in engineered mutants of phosphoenolpyruvate carboxykinase

scientific article published on 15 November 2018

Structural dynamics and single-stranded DNA binding activity of the three N-terminal domains of the large subunit of replication protein A from small angle X-ray scattering

scientific article

Structural dynamics in DNA damage signaling and repair

scientific article

Structural evidence for an enolate intermediate in GFP fluorophore biosynthesis.

scientific article

Structural implications of BER enzymes: dragons dancing--the structural biology of DNA base excision repair

scientific article published on 01 January 2001

Structural insights into NHEJ: building up an integrated picture of the dynamic DSB repair super complex, one component and interaction at a time

scientific article

Structural insights into the interaction of IL-33 with its receptors

scientific article

Structural, Functional, and Immunogenic Insights on Cu,Zn Superoxide Dismutase Pathogenic Virulence Factors from Neisseria meningitidis and Brucella abortus

scientific article

Structurally distinct ubiquitin- and sumo-modified PCNA: implications for their distinct roles in the DNA damage response

scientific article

Structure and activity of a thermostable thymine-DNA glycosylase: evidence for base twisting to remove mismatched normal DNA bases ⬇️

scientific article published on January 18, 2002

Structure and function of Escherichia coli endonuclease III.

scientific article published on July 1994

Structure and function of the double-strand break repair machinery.

scientific article published in August 2004

Structure and mechanism of copper, zinc superoxide dismutase ⬇️

scientific article published on November 17, 1983

Structure and mechanism of the RuvB Holliday junction branch migration motor

scientific article

Structure of a designed protein cage that self-assembles into a highly porous cube

scientific article

Structure of an Essential Type IV Pilus Biogenesis Protein Provides Insights into Pilus and Type II Secretion Systems

scientific article

Structure of mammalian poly(ADP-ribose) glycohydrolase reveals a flexible tyrosine clasp as a substrate-binding element

scientific article

Structure of nitric oxide synthase oxygenase dimer with pterin and substrate

scientific article

Structure of the DNA repair and replication endonuclease and exonuclease FEN-1: coupling DNA and PCNA binding to FEN-1 activity

scientific article

Structures of Tetrahydrobiopterin Binding-Site Mutants of Inducible Nitric Oxide Synthase Oxygenase Dimer and Implicated Roles of Trp457, ⬇️

scientific article published on October 30, 2001

Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair

scientific article

Substrate recognition and catalysis by flap endonucleases and related enzymes

scientific article published on April 2010

Substrate specificity of prostate-specific antigen (PSA)

scientific article published on 01 September 1998

Subunit-destabilizing mutations in Drosophila copper/zinc superoxide dismutase: neuropathology and a model of dimer dysequilibrium

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Super-resolution in solution X-ray scattering and its applications to structural systems biology.

scientific article published on 11 March 2013

Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis

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Synthesis and characterization of a recombinant myohemerythrin protein encoded by a synthetic gene ⬇️

scientific article published on March 15, 1991

Synthesis and characterization of oligonucleotides containing 2'-fluorinated thymidine glycol as inhibitors of the endonuclease III reaction

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Targeting Allostery with Avatars to Design Inhibitors Assessed by Cell Activity: Dissecting MRE11 Endo- and Exonuclease Activities

scientific article published on 22 February 2018

The ARTT motif and a unified structural understanding of substrate recognition in ADP-ribosylating bacterial toxins and eukaryotic ADP-ribosyltransferases.

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The ATPase Motor Turns for Type IV Pilus Assembly

scientific article published in November 2016

The BARD1 C-Terminal Domain Structure and Interactions with Polyadenylation Factor CstF-50.

scientific article published on 20 April 2009

The BARD1 C-terminal domain structure and interactions with polyadenylation factor CstF-50.

scientific article published on 09 October 2008

The C-terminal domain of yeast PCNA is required for physical and functional interactions with Cdc9 DNA ligase

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The D90A mutation results in a polymorphism of Cu, Zn superoxide dismutase that is prevalent in northern Sweden and Finland

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The DNA repair endonuclease XPG interacts directly and functionally with the WRN helicase defective in Werner syndrome

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The MRE11-RAD50-NBS1 Complex Conducts the Orchestration of Damage Signaling and Outcomes to Stress in DNA Replication and Repair.

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The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures

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The Rad50 hook domain regulates DNA damage signaling and tumorigenesis

scientific article published on 14 February 2014

The Rad50 zinc-hook is a structure joining Mre11 complexes in DNA recombination and repair

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The Salmonella type III secretion system virulence effector forms a new hexameric chaperone assembly for export of effector/chaperone complexes

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The Structure of the CRISPR-Associated Protein Csa3 Provides Insight into the Regulation of the CRISPR/Cas System

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The Structure of the MAP2K MEK6 Reveals an Autoinhibitory Dimer

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The case of the missing ring: radical cleavage of a carbon-carbon bond and implications for GFP chromophore biosynthesis

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The chemistry and mechanism of antibody binding to protein antigens.

scientific article published on January 1988

The crystal structure of the human DNA repair endonuclease HAP1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites ⬇️

scientific article published on November 3, 1997

The cutting edges in DNA repair, licensing, and fidelity: DNA and RNA repair nucleases sculpt DNA to measure twice, cut once

scientific article published on 19 April 2014

The disordered C-terminal domain of human DNA glycosylase NEIL1 contributes to its stability via intramolecular interactions

scientific article published on 27 March 2013

The food of sweet and bitter fancy

scientific article published on 01 January 2000

The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures

scientific article published on November 5, 1992

The intricate structural chemistry of base excision repair machinery: implications for DNA damage recognition, removal, and repair.

scientific article published on 8 January 2007

The nucleotide-dependent interaction of FlaH and FlaI is essential for assembly and function of the archaellum motor.

scientific article published on 28 October 2015

The pilus and porin of Neisseria gonorrhoeae cooperatively induce Ca(2+) transients in infected epithelial cells

scientific article published on 01 December 2005

The reactivity of anti-peptide antibodies is a function of the atomic mobility of sites in a protein

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The structural biochemistry of the superoxide dismutases.

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The structure of human mitochondrial manganese superoxide dismutase reveals a novel tetrameric interface of two 4-helix bundles

scientific article published on October 2, 1992

The structure of nitric oxide synthase oxygenase domain and inhibitor complexes

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The structure of the periplasmic FlaG-FlaF complex and its essential role for archaellar swimming motility

scientific article published on 16 December 2019

The wonders of flap endonucleases: structure, function, mechanism and regulation.

scientific article published on January 2012

Three dimensional structure of bacterial pili.

scientific article published in January 1987

Three metal ions participate in the reaction catalyzed by T5 flap endonuclease.

scientific article published on 11 August 2008

Transcription preinitiation complex structure and dynamics provide insight into genetic diseases

scientific article published on 20 May 2019

Translocation and deletion breakpoints in cancer genomes are associated with potential non-B DNA-forming sequences

scientific article published on 15 April 2016

Transplanted LDL and mannose-6-phosphate receptor internalization signals promote high-efficiency endocytosis of the transferrin receptor ⬇️

scientific article published on November 1, 1991

Tryptophan 409 controls the activity of neuronal nitric-oxide synthase by regulating nitric oxide feedback inhibition

scientific article published on 01 September 1999

Two novel SOD1 mutations in patients with familial amyotrophic lateral sclerosis

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Type IV pilin structure and assembly: X-ray and EM analyses of Vibrio cholerae toxin-coregulated pilus and Pseudomonas aeruginosa PAK pilin

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Type IV pilus structure by cryo-electron microscopy and crystallography: implications for pilus assembly and functions

scientific article published on September 2006

Type-4 pilus-structure: outside to inside and top to bottom – aminireview ⬇️

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Ultrahigh Resolution and Full-length Pilin Structures with Insights for Filament Assembly, Pathogenic Functions, and Vaccine Potential

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Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease

scientific article published on 06 October 2020

Uncovering the secrets of protein interactions with the DNA enforcing genomic stability

scientific article published in August 2017

Understanding GFP chromophore biosynthesis: controlling backbone cyclization and modifying post-translational chemistry.

scientific article published in February 2005

Understanding GFP posttranslational chemistry: structures of designed variants that achieve backbone fragmentation, hydrolysis, and decarboxylation.

scientific article published in April 2006

Unpairing and gating: sequence-independent substrate recognition by FEN superfamily nucleases

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Unusual trigonal-planar copper configuration revealed in the atomic structure of yeast copper-zinc superoxide dismutase

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Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects

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Vibrio cholerae El Tor TcpA crystal structure and mechanism for pilus-mediated microcolony formation

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Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM

scientific article published on 20 September 2020

WRN exonuclease structure and molecular mechanism imply an editing role in DNA end processing

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What Combined Measurements From Structures and Imaging Tell Us About DNA Damage Responses.

scientific article published on 29 May 2017

X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution

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XLF regulates filament architecture of the XRCC4·ligase IV complex

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XPB and XPD helicases in TFIIH orchestrate DNA duplex opening and damage verification to coordinate repair with transcription and cell cycle via CAK kinase.

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XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations

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XRCC4 Protein Interactions with XRCC4-like Factor (XLF) Create an Extended Grooved Scaffold for DNA Ligation and Double Strand Break Repair

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XRCC4 and XLF form long helical protein filaments suitable for DNA end protection and alignment to facilitate DNA double strand break repair

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p38α MAP Kinase C-Terminal Domain Binding Pocket Characterized by Crystallographic and Computational Analyses

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γH2A binds Brc1 to maintain genome integrity during S-phase

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