Z. Burton

发表

Aminoacyl-tRNA synthetase evolution and sectoring of the genetic code

Daewoo Pak, Yunsoo Kim, Z. Burton, 2018, Transcription.

RNA polymerase II flexibility during translocation from normal mode analysis

Michael Feig, Zachary F Burton, M. Feig, 2010, Proteins.

A Region within the RAP74 Subunit of Human Transcription Factor IIF Is Critical for Initiation but Dispensable for Complex Assembly

Z. Burton, Delin Ren, L. Lei, 1999, Molecular and Cellular Biology.

A key role for the alpha 1 helix of human RAP74 in the initiation and elongation of RNA chains.

Y. Nedialkov, Z. Burton, J. Funk, 2002, The Journal of biological chemistry.

Proteins that bind to RNA polymerase II are required for accurate initiation of transcription at the adenovirus 2 major late promoter.

J. Greenblatt, L. Ortolan, Z. Burton, 1986, The EMBO journal.

The Activity of COOH-terminal Domain Phosphatase Is Regulated by a Docking Site on RNA Polymerase II and by the General Transcription Factors IIF and IIB (*)

Z. Burton, B. Wang, M. Dahmus, 1995, The Journal of Biological Chemistry.

RNA Polymerase II-associated Protein (RAP) 74 Binds Transcription Factor (TF) IIB and Blocks TFIIB-RAP30 Binding (*)

S. Fang, Z. Burton, 1996, The Journal of Biological Chemistry.

Functions of the N- and C-Terminal Domains of Human RAP74 in Transcriptional Initiation, Elongation, and Recycling of RNA Polymerase II

Z. Burton, Delin Ren, L. Lei, 1998, Molecular and Cellular Biology.

II Elongation , and Recycling of RNA Polymerase Human RAP 74 in Transcriptional Initiation , Functions of the Nand C-Terminal Domains of

Z. Burton, Delin Ren, L. Lei, 1998 .

A model for genesis of transcription systems

J. Geiger, K. Opron, Z. Burton, 2016, Transcription.

A tRNA- and Anticodon-Centric View of the Evolution of Aminoacyl-tRNA Synthetases, tRNAomes, and the Genetic Code

K. Opron, Yunsoo Kim, Z. Burton, 2019, Life.

Chaos, Order and Systematics in Evolution of the Genetic Code

Z. Burton, L. Lei, 2020 .

Functional Domains of Human RAP74 Including a Masked Polymerase Binding Domain (*)

Z. Burton, B. Wang, Bo Qing Wang, 1995, The Journal of Biological Chemistry.

Efficient production of recombinant human transcription factor IIE.

A. Dvir, Z. Burton, L. Shukla, 2004, Protein expression and purification.

A cDNA encoding RAP74, a general initiation factor for transcription by RNA polymerase II

Joyce Li, J. Greenblatt, S. Fang, 1992, Nature.

Functional analysis of Drosophila factor 5 (TFIIF), a general transcription factor.

D. Price, Z. Burton, B. Wang, 1994, The Journal of biological chemistry.

RAP30/74: a general initiation factor that binds to RNA polymerase II

J. Greenblatt, L. Ortolan, M. Sopta, 1988, Molecular and cellular biology.

Stringent response in Escherichia coli induces expression of heat shock proteins.

A. Grossman, R. Burgess, C. Gross, 1985, Journal of molecular biology.

RNA Polymerases and Transcription

M. Kashlev, M. Kireeva, Z. Burton, 2018 .

“Superwobbling” and tRNA-34 Wobble and tRNA-37 Anticodon Loop Modifications in Evolution and Devolution of the Genetic Code

Z. Burton, L. Lei, 2022, Life.

Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details

R. Cukier, M. Feig, K. Opron, 2014, Nucleic acids research.

Translocation and fidelity of Escherichia coli RNA polymerase

Y. Nedialkov, Z. Burton, 2013, Transcription.

RNA polymerase stalls in a post-translocated register and can hyper-translocate

E. Nudler, Y. Nedialkov, Z. Burton, 2012, Transcription.

Production of human RAP30 and RAP74 in bacterial cells.

C. F. Kostrub, Z. Burton, B. Wang, 1993, Protein expression and purification.

The RAP74 Subunit of Human Transcription Factor IIF Has Similar Roles in Initiation and Elongation

Z. Burton, Delin Ren, L. Lei, 1999, Molecular and Cellular Biology.

RNA polymerase structure, function, regulation, dynamics, fidelity, and roles in gene expression.

M. Kashlev, M. Kireeva, Z. Burton, 2013, Chemical reviews.

Computational Simulation Strategies for Analysis of Multisubunit RNA Polymerases

Michael Feig, Zachary F. Burton, Robert I. Cukier, 2013, Chemical reviews.

RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation.

Michael Feig, Zachary F Burton, M. Feig, 2010, Biophysical journal.

The Old and New Testaments of gene regulation

Z. Burton, 2014, Transcription.

The Old and New Testaments of gene regulation Evolution of multi-subunit RNA polymerases and co-evolution of eukaryote complexity with the RNAP II CTD

Z. Burton, 2014 .

The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation.

R. Cukier, E. Nudler, M. Kashlev, 2013, Biochimica et biophysica acta.

Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase

Benoit Coulombe, Robert I Cukier, Zachary F Burton, 2012, BMC biophysics.

Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase.

Michael Feig, Michael Hampsey, Benoit Coulombe, 2010, Biochimica et biophysica acta.

Translocation by multi-subunit RNA polymerases.

Zachary F Burton, M. Kashlev, M. Kireeva, 2010, Biochimica et biophysica acta.

Site-directed mutagenesis, purification and assay of Saccharomyces cerevisiae RNA polymerase II.

B. Coulombe, M. Kashlev, J. Archambault, 2010, Protein expression and purification.

Millisecond phase kinetic analysis of elongation catalyzed by human, yeast, and Escherichia coli RNA polymerase.

M. Kashlev, Y. Nedialkov, Chunfen Zhang, 2009, Methods.

Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II.

Michael Feig, Zachary F Burton, Chunfen Zhang, 2005, Molecular cell.

α-Amanitin Blocks Translocation by Human RNA Polymerase II*

Y. Nedialkov, Z. Burton, X. Gong, 2004, Journal of Biological Chemistry.

A Tunable Ratchet Driving Human RNA Polymerase II Translocation Adjusted by Accurately Templated Nucleoside Triphosphates Loaded at Downstream Sites and by Elongation Factors*

Zachary F Burton, Yalin Xiong, Z. Burton, 2007, Journal of Biological Chemistry.

NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases.

Michael Feig, Zachary F Burton, Chunfen Zhang, 2005, Biochemistry and cell biology = Biochimie et biologie cellulaire.

Transcription factors IIF and IIS and nucleoside triphosphate substrates as dynamic probes of the human RNA polymerase II mechanism.

Chunfen Zhang, Z. Burton, 2004, Journal of molecular biology.

Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation.

J. Strathern, M. Kashlev, Y. Nedialkov, 2008, Molecular cell.

Human RNA Polymerase II Elongation in Slow Motion: Role of the TFIIF RAP74 α1 Helix in Nucleoside Triphosphate-Driven Translocation

Zachary F. Burton, Chunfen Zhang, Chunfen Zhang, 2005, Molecular and Cellular Biology.

Interaction of RNA Polymerase II Fork Loop 2 with Downstream Non-template DNA Regulates Transcription Elongation*

B. Coulombe, M. Kashlev, M. Kireeva, 2011, The Journal of Biological Chemistry.

Alpha-amanitin blocks translocation by human RNA polymerase II.

Y. Nedialkov, Z. Burton, X. Gong, 2004, The Journal of biological chemistry.

Combinatorial Control of Human RNA Polymerase II (RNAP II) Pausing and Transcript Cleavage by Transcription Factor IIF, Hepatitis δ Antigen, and Stimulatory Factor II*

Honggao Yan, Chunfen Zhang, Z. Burton, 2003, Journal of Biological Chemistry.

NTP-driven Translocation by Human RNA Polymerase II*

Hiroshi Handa, Yuki Yamaguchi, Honggao Yan, 2003, The Journal of Biological Chemistry.

Assay of transient state kinetics of RNA polymerase II elongation.

H. Handa, Y. Yamaguchi, Y. Nedialkov, 2003, Methods in enzymology.

Importance of codon preference for production of human RAP74 and reconstitution of the RAP30/74 complex.

Z. Burton, B. Wang, B Q Wang, 1994, Protein expression and purification.

Early Evolution of Transcription Systems and Divergence of Archaea and Bacteria

Z. Burton, L. Lei, 2021, Frontiers in Molecular Biosciences.

Energetic and structural details of the trigger-loop closing transition in RNA polymerase II.

M. Feig, A. Predeus, Z. Burton, 2013, Biophysical journal.

Hinge action versus grip in translocation by RNA polymerase

R. Cukier, Y. Nedialkov, K. Opron, 2017, Transcription.

DNA Bending and Wrapping around RNA Polymerase: a “Revolutionary” Model Describing Transcriptional Mechanisms

B. Coulombe, Z. Burton, 1999, Microbiology and Molecular Biology Reviews.

The σ enigma: Bacterial σ factors, archaeal TFB and eukaryotic TFIIB are homologs

Z. Burton, Samuel P Burton, 2014, Transcription.

Minimal Promoter Systems Reveal the Importance of Conserved Residues in the B-finger of Human Transcription Factor IIB*

N. Thompson, R. Burgess, Z. Burton, 2009, The Journal of Biological Chemistry.

Spacing requirements for simultaneous recognition of the adenovirus major late promoter TATAAAAG box and initiator element.

Y. Nedialkov, Z. Burton, Delin Ren, 2005, Archives of biochemistry and biophysics.

Structural and Functional Interactions of Transcription Factor (TF) IIA with TFIIE and TFIIF in Transcription Initiation by RNA Polymerase II*

B. Coulombe, Z. Burton, D. Forget, 2001, The Journal of Biological Chemistry.

Flexibility–rigidity index for protein–nucleic acid flexibility and fluctuation analysis

Guo-Wei Wei, Kelin Xia, Kristopher Opron, 2015, J. Comput. Chem..

10 How is fidelity maintained in nucleic acids? Two tales in DNA repair and DNA transcription from computer simulations

R. Cukier, M. Feig, S. Law, 2015, Journal of biomolecular structure & dynamics.

Checkpoints controlled by PCNA , DNA and ATP direct the timing and order of events in the clamp loading mechanism

R. Cukier, M. Feig, S. Law, 2015 .

Transcription from a heat-inducible promoter causes heat shock regulation of the sigma subunit of E. coli RNA polymerase

A. Grossman, R. Burgess, C. Gross, 1984, Cell.

RAP74 induces promoter contacts by RNA polymerase II upstream and downstream of a DNA bend centered on the TATA box.

F. Robert, J. Greenblatt, B. Coulombe, 1997, Proceedings of the National Academy of Sciences of the United States of America.

Nucleotide sequence of the rpsU-dnaG-rpoD operon from Salmonella typhimurium and a comparison of this sequence with the homologous operon of Escherichia coli.

R. Burgess, K. Watanabe, Z. Burton, 1985, Gene.

The operen that encodes the sigma subunit of RNA polymerase also encodes ribosomal protein S21 and DNA primase in E. coli K12

R. Burgess, C. Gross, Z. Burton, 1983, Cell.

Homology threading to generate RNA polymerase structures.

Yunsoo Kim, Z. Burton, K. Padmanabhan, 2018, Protein expression and purification.

Paf1p, an RNA polymerase II-associated factor in Saccharomyces cerevisiae, may have both positive and negative roles in transcription

P. Wade, A. Wolf, Z. Burton, 1996, Molecular and cellular biology.

A novel collection of accessory factors associated with yeast RNA polymerase II.

N. Thompson, R. Burgess, J. Leykam, 1996, Protein expression and purification.

Cdc73p and Paf1p are found in a novel RNA polymerase II-containing complex distinct from the Srbp-containing holoenzyme

C. Chang, P. Wade, A. Wolf, 1997, Molecular and cellular biology.

The small subunit of transcription factor IIF recruits RNA polymerase II into the preinitiation complex.

D. Reinberg, J. Greenblatt, M. Killeen, 1991, Proceedings of the National Academy of Sciences of the United States of America.

Structure and associated DNA-helicase activity of a general transcription initiation factor that binds to RNA polymerase II

J. Greenblatt, M. Sopta, Z. Burton, 1989, Nature.

positive and negative roles in transcription. in Saccharomyces cerevisiae, may have both Paf1p, an RNA polymerase II-associated factor

P. Wade, A. Wolf, Z. Burton, 2013 .

Wrapping of promoter DNA around the RNA polymerase II initiation complex induced by TFIIF.

F. Robert, J. Greenblatt, B. Coulombe, 1998, Molecular cell.

Factors involved in specific transcription by mammalian RNA polymerase II. RNA polymerase II-associating protein 30 is an essential component of transcription factor IIF.

D. Reinberg, J. Greenblatt, E. Maldonado, 1988, The Journal of biological chemistry.

The nudeotide sequence of the cloned rpoD gene for the RNA polymerase sigma subunit from E. coil K12

R. Burgess, C. Gross, Z. Burton, 1981 .

The nucleotide sequence of the cloned rpoD gene for the RNA polymerase sigma subunit from E coli K12.

R. Burgess, C. Gross, Z. Burton, 1981, Nucleic acids research.

RAP30/74 (transcription factor IIF) is required for promoter escape by RNA polymerase II.

C. F. Kostrub, Z. Burton, C. Chang, 1993, The Journal of biological chemistry.

Cloning of a Drosophila cDNA with sequence similarity to human transcription factor RAP74.

J. Greenblatt, D. Price, Z. Burton, 1993, Nucleic Acids Research.

tRNA evolution from the proto-tRNA minihelix world

R. Root-Bernstein, Yunsoo Kim, Z. Burton, 2016, Transcription.

A Key Role for the α1 Helix of Human RAP74 in the Initiation and Elongation of RNA Chains*

Y. Nedialkov, Z. Burton, J. Funk, 2002, The Journal of Biological Chemistry.

Evolution of the genetic code

Z. Burton, L. Lei, 2021, Transcription.

Type-II tRNAs and Evolution of Translation Systems and the Genetic Code

K. Opron, Yunsoo Kim, Z. Burton, 2018, International journal of molecular sciences.

Auto-Acetylation of Transcription Factors as a Control Mechanism in Gene Expression

A. Usheva, Z. Burton, Chu H. Choi, 2004, Cell cycle.

Rooted tRNAomes and evolution of the genetic code

Nan Du, Daewoo Pak, Yunsoo Kim, 2018, Transcription.

Ribosome Structure, Function, and Early Evolution

K. Opron, Z. Burton, 2018, International journal of molecular sciences.

The 3-Minihelix tRNA Evolution Theorem

Z. Burton, 2020, Journal of Molecular Evolution.

tRNA structure and evolution and standardization to the three nucleotide genetic code

R. Root-Bernstein, Daewoo Pak, Z. Burton, 2017, Transcription.

ELECTRON MICROSCOPY OF GLUTAMINE SYNTHETASE DNA INTERACTIONS

D. Eisenberg, B. Magasanik, M. Blumenberg, 1976 .

Evolution of Life on Earth: tRNA, Aminoacyl-tRNA Synthetases and the Genetic Code

Zachary F Burton, Z. Burton, Lei Lei, 2020, Life.

Translocation by multi-subunit RNA polymerases.

M. Kashlev, M. Kireeva, Z. Burton, 2010, Biochimica et biophysica acta.

The 3 31 Nucleotide Minihelix tRNA Evolution Theorem and the Origin of Life

Z. Burton, Lei Lei, 2023, Life.

The 3-Minihelix tRNA Evolution Theorem

Zachary F. Burton, Z. Burton, 2020, Journal of Molecular Evolution.

A procedure for rapid isolation of both groE protein and glutamine synthetase from E coli.

Z. Burton, D. Eisenberg, 1980, Archives of biochemistry and biophysics.