List of works by James M. Berger

A Meier-Gorlin syndrome mutation in a conserved C-terminal helix of Orc6 impedes origin recognition complex formation

scientific article published on 08 October 2013

A Primase-Induced Conformational Switch Controls the Stability of the Bacterial Replisome

scientific article published on 19 May 2020

A complex suite of loci and elements in eukaryotic type II topoisomerases determine selective sensitivity to distinct poisoning agents

scientific article published on 01 September 2019

A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP6 in mRNA export

scientific article

A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function ⬇️

scientific article published on July 31, 2010

A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions

scientific article published on 26 September 2015

A microfluidic device for kinetic optimization of protein crystallization and in situ structure determination.

scientific article

A naturally chimeric type IIA topoisomerase in Aquifex aeolicus highlights an evolutionary path for the emergence of functional paralogs ⬇️

scientific article published on November 12, 2010

A new class of disordered elements controls DNA replication through initiator self-assembly

scientific article published on 27 September 2019

A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases

scientific article

A robust and scalable microfluidic metering method that allows protein crystal growth by free interface diffusion

scientific article

A structural framework for replication origin opening by AAA+ initiation factors.

scientific article published on 21 December 2012

AAA+ ATPases in the initiation of DNA replication

scientific article published on 01 May 2008

ATP binding controls distinct structural transitions of Escherichia coli DNA gyrase in complex with DNA.

scientific article published on 8 April 2012

ATP-dependent conformational dynamics underlie the functional asymmetry of the replicative helicase from a minimalist eukaryote

scientific article

Activation of the DExD/H-box protein Dbp5 by the nuclear-pore protein Gle1 and its coactivator InsP6 is required for mRNA export

scientific article

All tangled up: how cells direct, manage and exploit topoisomerase function

scientific article

An Atypical AAA+ ATPase Assembly Controls Efficient Transposition through DNA Remodeling and Transposase Recruitment

scientific article published on August 2015

Ancient Origin of cGAS-STING Reveals Mechanism of Universal 2',3' cGAMP Signaling

scientific article

Asf1-like structure of the conserved Yaf9 YEATS domain and role in H2A.Z deposition and acetylation

scientific article

Binding Mechanism of Metal⋅NTP Substrates and Stringent-Response Alarmones to Bacterial DnaG-Type Primases

scientific article

Bypassing fluoroquinolone resistance with quinazolinediones: studies of drug-gyrase-DNA complexes having implications for drug design

scientific article

Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array

scientific article

Cdc45 (cell division cycle protein 45) guards the gate of the Eukaryote Replisome helicase stabilizing leading strand engagement.

scientific article

Cell Cycle-Dependent Control and Roles of DNA Topoisomerase II

scientific article published on 30 October 2019

Computational Redesign of the SHV-1 β-Lactamase/β-Lactamase Inhibitor Protein Interface

scientific article

Conformational control and DNA-binding mechanism of the metazoan origin recognition complex

article published in the Proceedings of the National Academy of Sciences of the United States of America

Control of topoisomerase II activity and chemotherapeutic inhibition by TCA cycle metabolites

scientific article published in 2022

Crosstalk between primase subunits can act to regulate primer synthesis in trans.

scientific article published in November 2005

Crystal structure and stability of gyrase-fluoroquinolone cleaved complexes from Mycobacterium tuberculosis.

scientific article published on 20 January 2016

Crystal structure of the DNA gyrase GyrA N-terminal domain fromMycobacterium tuberculosis

scientific article

Crystal structure of the eukaryotic origin recognition complex

scientific article

DNA binding polarity, dimerization, and ATPase ring remodeling in the CMG helicase of the eukaryotic replisome.

scientific article

DNA recognition by a σ(54) transcriptional activator from Aquifex aeolicus

scientific article

DNA replication: making two forks from one prereplication complex

scientific article published on December 2010

DNA stretching by bacterial initiators promotes replication origin opening

scientific article

Direct control of type IIA topoisomerase activity by a chromosomally encoded regulatory protein

scientific article

Distinct regions of the Escherichia coli ParC C-terminal domain are required for substrate discrimination by topoisomerase IV.

scientific article published on 15 July 2013

Dynamic coupling between conformations and nucleotide states in DNA gyrase

scientific article published on 16 April 2018

Emerging roles for plant topoisomerase VI.

scientific article

Escherichia coli condensin MukB stimulates topoisomerase IV activity by a direct physical interaction.

scientific article

Evybactin is a DNA gyrase inhibitor that selectively kills Mycobacterium tuberculosis

scientific article published on 22 August 2022

FASTDXL: a generalized screen to trap disulfide-stabilized complexes for use in structural studies

scientific article

Fluoroquinolone interactions with Mycobacterium tuberculosis gyrase: Enhancing drug activity against wild-type and resistant gyrase

scientific article published on 20 January 2016

Fluoroquinolone-gyrase-DNA complexes: two modes of drug binding

scientific article

Formation of MacroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA

scientific article

Function and Structure of a Prokaryotic Formylglycine-generating Enzyme

scientific article

Holoenzyme assembly and ATP-mediated conformational dynamics of topoisomerase VI

scientific article

How do type II topoisomerases use ATP hydrolysis to simplify DNA topology beyond equilibrium? Investigating the relaxation reaction of nonsupercoiling type II topoisomerases

scientific article

Hyperthermophilic Aquifex aeolicus initiates primer synthesis on a limited set of trinucleotides comprised of cytosines and guanines

scientific article published on 6 August 2008

IOTA: integration optimization, triage and analysis tool for the processing of XFEL diffraction images

scientific article

Identification of a DNA primase template tracking site redefines the geometry of primer synthesis

scientific article

Identification, function and structure of the mycobacterial sulfotransferase that initiates sulfolipid-1 biosynthesis

scientific journal article

Interdomain Communication of the Chd1 Chromatin Remodeler across the DNA Gyres of the Nucleosome

scientific article published on 10 January 2017

Lethal synergy involving bicyclomycin: an approach for reviving old antibiotics

scientific article

Ligand-induced and small-molecule control of substrate loading in a hexameric helicase

scientific article

Loading strategies of ring-shaped nucleic acid translocases and helicases

scientific article published on 18 December 2013

Macro-to-Micro Structural Proteomics: Native Source Proteins for High-Throughput Crystallization

scientific article

Mechanism for the Regulated Control of Bacterial Transcription Termination by a Universal Adaptor Protein

scholarly article by Michael R Lawson published in September 2018

Mechanism of Action of Mycobacterium tuberculosis Gyrase Inhibitors: A Novel Class of Gyrase Poisons

scientific article published on 17 May 2018

Mechanisms and regulation of DNA replication initiation in eukaryotes

scientific article published on 17 January 2017

Mechanisms for Defining Supercoiling Set Point of DNA Gyrase Orthologs: II. THE SHAPE OF THE GyrA SUBUNIT C-TERMINAL DOMAIN (CTD) IS NOT A SOLE DETERMINANT FOR CONTROLLING SUPERCOILING EFFICIENCY

scientific article

Mechanisms for defining supercoiling set point of DNA gyrase orthologs: I. A nonconserved acidic C-terminal tail modulates Escherichia coli gyrase activity

scientific article

Mechanisms for initiating cellular DNA replication

scientific article

Mechanisms for initiating cellular DNA replication

scientific article published on 16 February 2017

Modulated control of DNA supercoiling balance by the DNA-wrapping domain of bacterial gyrase

scientific article published on 01 February 2020

Molecular Basis for ATP-Hydrolysis-Driven DNA Translocation by the CMG Helicase of the Eukaryotic Replisome

scientific article published on 01 September 2019

Molecular basis for G protein control of the prokaryotic ATP sulfurylase

scientific article published in January 2006

Molecular determinants of origin discrimination by Orc1 initiators in archaea

scientific article

Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor

scientific article

Nanoscale protein assemblies from a circular permutant of the tobacco mosaic virus

scientific article

Narrowing substrate specificity in a directly evolved enzyme: the A293D mutant of aspartate aminotransferase

scientific article published in October 2004

Nucleotide and Partner-Protein Control of Bacterial Replicative Helicase Structure and Function

scientific article

Nucleotide-dependent conformational changes in the DnaA-like core of the origin recognition complex.

scientific article published on 9 July 2006

Origin remodeling and opening in bacteria rely on distinct assembly states of the DnaA initiator

scientific article

Physical Basis for the Loading of a Bacterial Replicative Helicase onto DNA

scientific article published on 20 February 2019

Recognition of DNA Supercoil Geometry by Mycobacterium tuberculosis Gyrase.

scientific article published on 18 September 2017

Regulation of bacterial priming and daughter strand synthesis through helicase-primase interactions

scientific article

Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex

scientific article

Resveratrol: a novel type of topoisomerase II inhibitor

scientific article published on 26 October 2017

Running in Reverse: The Structural Basis for Translocation Polarity in Hexameric Helicases

scientific article

Structural Synergy and Molecular Crosstalk between Bacterial Helicase Loaders and Replication Initiators

scientific article

Structural and Biochemical Characterization of the Interaction between KPC-2 β-Lactamase and β-Lactamase Inhibitor Protein,

scientific article

Structural and computational characterization of the SHV-1 beta-lactamase-beta-lactamase inhibitor protein interface

scientific article

Structural and functional characterization of the Spo11 core complex

scientific article published on 04 January 2021

Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling

scientific article published on 9 July 2006

Structural basis for the MukB-topoisomerase IV interaction and its functional implicationsin vivo

scientific article

Structural basis for topoisomerase VI inhibition by the anti-Hsp90 drug radicicol

scientific article

Structural dissection of ATP turnover in the prototypical GHL ATPase TopoVI.

scientific article published in June 2005

Structural frameworks for considering microbial protein- and nucleic acid-dependent motor ATPases

scientific article published on 21 July 2008

Structural insights into RNA-dependent ring closure and ATPase activation by the Rho termination factor

scientific article published in November 2006

Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin

scientific article published in January 2005

Structure and Function of the Conserved Core of Histone Deposition Protein Asf1

Structure and function of the conserved core of histone deposition protein Asf1

scientific article

Structure of Human cGAS Reveals a Conserved Family of Second-Messenger Enzymes in Innate Immunity

scientific article

Structure of M11L: A myxoma virus structural homolog of the apoptosis inhibitor, Bcl-2

scientific article

Structure of a topoisomerase II–DNA–nucleotide complex reveals a new control mechanism for ATPase activity

scientific article

Structure of the ATP-binding domain of Plasmodium falciparum Hsp90

scientific article

Structure of the C-terminus of the mRNA export factor Dbp5 reveals the interaction surface for the ATPase activator Gle1

scientific article

Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading

scientific article

Structure of the topoisomerase II ATPase region and its mechanism of inhibition by the chemotherapeutic agent ICRF-187

scientific article

Structure of the topoisomerase VI-B subunit: implications for type II topoisomerase mechanism and evolution

scientific article

Structure of the yeast histone H3-ASF1 interaction: implications for chaperone mechanism, species-specific interactions, and epigenetics

scientific article

Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases

scientific article published on January 2004

Structure-guided reprogramming of human cGAS dinucleotide linkage specificity

scientific article

Synergistic Coordination of Chromatin Torsional Mechanics and Topoisomerase Activity

scientific article published on 01 October 2019

THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves

scientific article

The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold

scientific article

The Crystal Structure of the Hinge Domain of the Escherichia coli Structural Maintenance of Chromosomes Protein MukB

scientific article

The N-terminal domain of Nup159 forms a beta-propeller that functions in mRNA export by tethering the helicase Dbp5 to the nuclear pore

scientific article

The Structure of DNA-Bound Human Topoisomerase II Alpha: Conformational Mechanisms for Coordinating Inter-Subunit Interactions with DNA Cleavage

scientific article

The X-ray structure of the papillomavirus helicase in complex with its molecular matchmaker E2.

scientific article published on 02 August 2004

The ancestral role of ATP hydrolysis in type II topoisomerases: prevention of DNA double-strand breaks

scientific article

The bacterial DnaC helicase loader is a DnaB ring breaker

scientific article published on 4 April 2013

The nuts and bolts of ring-translocase structure and mechanism

scientific article published on February 2011

The role of ATP-dependent machines in regulating genome topology

scientific article published on 28 January 2016

The role of DNA bending in type IIA topoisomerase function

scientific article published on 10 April 2013

The structural basis for MCM2-7 helicase activation by GINS and Cdc45.

scientific article

The structural basis for substrate specificity in DNA topoisomerase IV.

scientific article published in August 2005

Topoisomerase VI senses and exploits both DNA crossings and bends to facilitate strand passage.

scientific article published on 29 March 2018

Trapped topoisomerase II initiates formation of de novo duplications via the nonhomologous end-joining pathway in yeast

scientific article published on 12 October 2020

Tuning the sequence specificity of a transcription terminator

scientific article published on 09 February 2019

Two surfaces on the histone chaperone Rtt106 mediate histone binding, replication, and silencing

scientific article

Viral hijacking of a replicative helicase loader and its implications for helicase loading control and phage replication

scientific article

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