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Mechanism of Bacterial Transcription Initiation: RNA Polymerase - Promoter Binding, Isomerization to Initiation-Competent Open Complexes, and Initiation of RNA Synthesis

Journal of molecular biology, 2011-10, Vol.412 (5), p.754-771

2011

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Separation of preferential interaction and excluded volume effects on DNA duplex and hairpin stability

Proceedings of the National Academy of Sciences - PNAS, 2011-08, Vol.108 (31), p.12699-12704

2011

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Quantifying why urea is a protein denaturant, whereas glycine betaine is a protein stabilizer

Proceedings of the National Academy of Sciences - PNAS, 2011-10, Vol.108 (41), p.16932-16937

2011

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Hofmeister Salt Effects on Surface Tension Arise from Partitioning of Anions and Cations between Bulk Water and the Air−Water Interface

The journal of physical chemistry. B, 2007-05, Vol.111 (19), p.5411-5417

2007

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Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis

Journal of molecular biology, 2022-07, Vol.434 (13), p.167621-167621, Article 167621

2022

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Clamp Interactions with +3/+6 Duplex and Upstream-to-Downstream Allosteric Effects in Late Steps of Forming a Stable RNA Polymerase-Promoter Open Complex

Journal of molecular biology, 2023-03, Vol.435 (6), p.167990-167990, Article 167990

2023

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Thermodynamic Origin of Hofmeister Ion Effects

The journal of physical chemistry. B, 2008-08, Vol.112 (31), p.9428-9436

2008

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Experimentally determined strengths of favorable and unfavorable interactions of amide atoms involved in protein self-assembly in water

Proceedings of the National Academy of Sciences - PNAS, 2020-11, Vol.117 (44), p.27339-27345

2020

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Initial events in bacterial transcription initiation

Biomolecules, 2015-05, Vol.5 (2), p.1035-1062

2015

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Why Hofmeister effects of many salts favor protein folding but not DNA helix formation

Proceedings of the National Academy of Sciences - PNAS, 2010-04, Vol.107 (17), p.7716-7721

2010

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Partitioning of Atmospherically Relevant Ions between Bulk Water and the Water/Vapor Interface

Proceedings of the National Academy of Sciences - PNAS, 2006-09, Vol.103 (39), p.14278-14281

2006

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Temperature effects on RNA polymerase initiation kinetics reveal which open complex initiates and that bubble collapse is stepwise

Proceedings of the National Academy of Sciences - PNAS, 2021-07, Vol.118 (30)

2021

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Basis of Protein Stabilization by K Glutamate: Unfavorable Interactions with Carbon, Oxygen Groups

Biophysical journal, 2016-11, Vol.111 (9), p.1854-1865

2016

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High-throughput, fluorescent-aptamer-based measurements of steady-state transcription rates for the Mycobacterium tuberculosis RNA polymerase

Nucleic acids research, 2023-10, Vol.51 (19), p.e99-e99

2023

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Fluorescence-Detected Conformational Changes in Duplex DNA in Open Complex Formation by Escherichia coli RNA Polymerase: Upstream Wrapping and Downstream Bending Precede Clamp Opening and Insertion of the Downstream Duplex

Biochemistry (Easton), 2020-04, Vol.59 (16), p.1565-1581

2020

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Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature

Journal of computational chemistry, 2002-04, Vol.23 (6), p.600-609

2002

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Separating chemical and excluded volume interactions of polyethylene glycols with native proteins: Comparison with PEG effects on DNA helix formation

Biopolymers, 2015-09, Vol.103 (9), p.517-527

2015

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One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex

Proceedings of the National Academy of Sciences - PNAS, 2010-06, Vol.107 (23), p.10418-10423

2010

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How Glutamate Promotes Liquid-liquid Phase Separation and DNA Binding Cooperativity of E. coli SSB Protein

Journal of molecular biology, 2022-05, Vol.434 (9), p.167562-167562, Article 167562

2022

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Quantifying Amide–Aromatic Interactions at Molecular and Atomic Levels: Experimentally Determined Enthalpic and Entropic Contributions to Interactions of Amide sp2O, N, C and sp3C Unified Atoms with Naphthalene sp2C Atoms in Water

Biochemistry (Easton), 2023-10, Vol.62 (19), p.2841-2853

2023

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Introductory lecture: interpreting and predicting Hofmeister salt ion and solute effects on biopolymer and model processes using the solute partitioning model

Faraday discussions, 2013, Vol.160, p.9-44

2013

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Mechanism of transcription initiation and promoter escape by E. coli RNA polymerase

Proceedings of the National Academy of Sciences - PNAS, 2017-04, Vol.114 (15), p.E3032-E3040

2017

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Protein Diffusion in the Periplasm of E. coli under Osmotic Stress

Biophysical journal, 2011-01, Vol.100 (1), p.22-31

2011

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Probing the protein-folding mechanism using denaturant and temperature effects on rate constants

Proceedings of the National Academy of Sciences - PNAS, 2013-10, Vol.110 (42), p.16784-16789

2013

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Positioning the Intracellular Salt Potassium Glutamate in the Hofmeister Series by Chemical Unfolding Studies of NTL9

Biochemistry (Easton), 2016-04, Vol.55 (15), p.2251-2259

2016

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Mechanism of Bacterial Transcription Initiation: RNA Polymerase - Promoter Binding, Isomerization to Initiation-Competent Open Complexes, and Initiation of RNA Synthesis

Separation of preferential interaction and excluded volume effects on DNA duplex and hairpin stability

Quantifying why urea is a protein denaturant, whereas glycine betaine is a protein stabilizer

Hofmeister Salt Effects on Surface Tension Arise from Partitioning of Anions and Cations between Bulk Water and the Air−Water Interface

Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis

Clamp Interactions with +3/+6 Duplex and Upstream-to-Downstream Allosteric Effects in Late Steps of Forming a Stable RNA Polymerase-Promoter Open Complex

Thermodynamic Origin of Hofmeister Ion Effects

Experimentally determined strengths of favorable and unfavorable interactions of amide atoms involved in protein self-assembly in water

Initial events in bacterial transcription initiation

Why Hofmeister effects of many salts favor protein folding but not DNA helix formation

Partitioning of Atmospherically Relevant Ions between Bulk Water and the Water/Vapor Interface

Temperature effects on RNA polymerase initiation kinetics reveal which open complex initiates and that bubble collapse is stepwise

Basis of Protein Stabilization by K Glutamate: Unfavorable Interactions with Carbon, Oxygen Groups

High-throughput, fluorescent-aptamer-based measurements of steady-state transcription rates for the Mycobacterium tuberculosis RNA polymerase

Fluorescence-Detected Conformational Changes in Duplex DNA in Open Complex Formation by Escherichia coli RNA Polymerase: Upstream Wrapping and Downstream Bending Precede Clamp Opening and Insertion of the Downstream Duplex

Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature

Separating chemical and excluded volume interactions of polyethylene glycols with native proteins: Comparison with PEG effects on DNA helix formation

One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex

How Glutamate Promotes Liquid-liquid Phase Separation and DNA Binding Cooperativity of E. coli SSB Protein

Quantifying Amide–Aromatic Interactions at Molecular and Atomic Levels: Experimentally Determined Enthalpic and Entropic Contributions to Interactions of Amide sp2O, N, C and sp3C Unified Atoms with Naphthalene sp2C Atoms in Water

Introductory lecture: interpreting and predicting Hofmeister salt ion and solute effects on biopolymer and model processes using the solute partitioning model

Mechanism of transcription initiation and promoter escape by E. coli RNA polymerase

Protein Diffusion in the Periplasm of E. coli under Osmotic Stress

Probing the protein-folding mechanism using denaturant and temperature effects on rate constants

Positioning the Intracellular Salt Potassium Glutamate in the Hofmeister Series by Chemical Unfolding Studies of NTL9

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