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List of works by Daniel Herschlag

2'-Fluoro substituents can mimic native 2'-hydroxyls within structured RNA ⬇️

scientific article published on August 26, 2011

A repulsive field: advances in the electrostatics of the ion atmosphere

scientific article published on 08 December 2008

Additions and Corrections: Decreasing Reactivity with Increasing Nucleophile Basicity. The Effect of Solvation on β nuc for Phosphoryl Transfer to Amines ⬇️

scientific article published on 01 September 1986

Alkaline phosphatase mono- and diesterase reactions: comparative transition state analysis

scientific article

Arginine Coordination in Enzymatic Phosphoryl Transfer: Evaluation of the Effect of Arg166 Mutations in Escherichia coli Alkaline Phosphatase † ‡

scientific article

Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray-derived conformational ensembles

scientific article published on 21 December 2020

Biological phosphoryl-transfer reactions: understanding mechanism and catalysis

scientific article

Blind tests of RNA-protein binding affinity prediction

scientific article published on 08 April 2019

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters

scientific article

Comparative Enzymology in the Alkaline Phosphatase Superfamily to Determine the Catalytic Role of an Active-Site Metal Ion

scientific article

Correction to Uncovering the Determinants of a Highly Perturbed Tyrosine p Ka in the Active Site of Ketosteroid Isomerase

scientific article published on 27 March 2018

Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble

scientific article

Decreasing reactivity with increasing nucleophile basicity. The effect of solvation on .beta.nuc for phosphoryl transfer to amines ⬇️

scientific article published on 01 February 1986

Direct Demonstration of the Catalytic Role of Binding Interactions in an Enzymatic Reaction ⬇️

scientific article published on July 14, 1998

Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding

scientific article

Dissecting eukaryotic translation and its control by ribosome density mapping

scientific article

Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole

scientific article

Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system

scientific article published on 28 October 2008

Do conformational biases of simple helical junctions influence RNA folding stability and specificity?

scientific article published on 22 October 2009

Electrostatics of Nucleic Acid Folding under Conformational Constraint ⬇️

scientific article published on February 27, 2012

Enhancement of RNA/Ligand Association Kinetics via an Electrostatic Anchor

scientific article published on 03 June 2019

Evaluating the Catalytic Contribution from the Oxyanion Hole in Ketosteroid Isomerase

scientific article

Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory

scientific article

Evaluation of the Catalytic Contribution from a Positioned General Base in Ketosteroid Isomerase

scientific article

Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets

scientific article

Exploring the folding landscape of a structured RNA

scientific article

Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast

scientific article

Fluorescence Polarization Anisotropy to Measure RNA Dynamics

scientific article published on January 1, 2009

Functional identification of catalytic metal ion binding sites within RNA.

scientific article

Fundamental challenges in mechanistic enzymology: progress toward understanding the rate enhancements of enzymes

scientific article

Gold nanocrystal labels provide a sequence-to-3D structure map in SAXS reconstructions.

scientific article

Ground State Destabilization from a Positioned General Base in the Ketosteroid Isomerase Active Site ⬇️

scientific article published on January 30, 2013

Ground state destabilization by anionic nucleophiles contributes to the activity of phosphoryl transfer enzymes

scientific article

High-resolution analysis of Zn(2+) coordination in the alkaline phosphatase superfamily by EXAFS and x-ray crystallography

scientific article

How to measure and evaluate binding affinities

scientific article published on 06 August 2020

Hydrogen Bond Coupling in the Ketosteroid Isomerase Active Site

scientific article

Hydrogen Bonds: Simple after All?

scientific article published on 16 May 2018

Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome ⬇️

scientific article published on October 18, 2010

Implications of molecular heterogeneity for the cooperativity of biological macromolecules ⬇️

scientific article published on May 15, 2011

Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics

scientific article published on 16 July 2018

Instrumentation and experimental procedures for robust collection of X-ray diffraction data from protein crystals across physiological temperatures

scientific article published on 05 November 2020

Isotope-Edited FTIR of Alkaline Phosphatase Resolves Paradoxical Ligand Binding Properties and Suggests a Role for Ground-State Destabilization ⬇️

scientific article published on July 13, 2011

Mapping the transition state for ATP hydrolysis: implications for enzymatic catalysis ⬇️

scientific article published on 01 November 1995

Metal Ion-Based RNA Cleavage as a Structural Probe

scientific article published on November 17, 2009

Methods of Site-Specific Labeling of RNA with Fluorescent Dyes

scientific article published on November 17, 2009

Multiple native states reveal persistent ruggedness of an RNA folding landscape

scientific article

Probing Nucleic Acid–Ion Interactions with Buffer Exchange-Atomic Emission Spectroscopy

scientific article published on January 1, 2009

Protein Enhancement of Hammerhead Ribozyme Catalysis ⬇️

scientific article published on October 1, 1993

Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids

scientific article

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site

scientific article

Removal of Covalent Heterogeneity Reveals Simple Folding Behavior for P4-P6 RNA ⬇️

scientific article published on April 8, 2011

Revealing enzyme functional architecture via high-throughput microfluidic enzyme kinetics

scientific article published on 01 July 2021

Riboswitch conformations revealed by small-angle X-ray scattering

scientific article

Role of SRP RNA in the GTPase Cycles of Ffh and FtsY ⬇️

scientific article published on December 18, 2001

Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering

scientific article

Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation

scientific article published on 02 August 2019

Single Molecule Analysis Research Tool (SMART): an integrated approach for analyzing single molecule data

scientific article (publication date: 2012)

Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data

scientific article

Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein

scientific article published on 27 July 2018

Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae

scientific article published on 13 October 2006

Structure–Function Analysis from the Outside In: Long-Range Tertiary Contacts in RNA Exhibit Distinct Catalytic Roles ⬇️

scientific article published on September 19, 2011

Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance

scientific article published in 2008

Testing Geometrical Discrimination within an Enzyme Active Site: Constrained Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole

scientific article

The individual and the team in collaborative science

scientific article published on 01 July 2020

The ligand-free state of the TPP riboswitch: a partially folded RNA structure

scientific article

Tungstate as a Transition State Analog for Catalysis by Alkaline Phosphatase

scientific article

Understanding nucleic acid-ion interactions

scientific article

Use of Phosphorothioates to Identify Sites of Metal-Ion Binding in RNA

scientific article published on November 17, 2009

Use of anion-aromatic interactions to position the general base in the ketosteroid isomerase active site

scientific article

Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch

scientific article

uPIC-M: Efficient and Scalable Preparation of Clonal Single Mutant Libraries for High-Throughput Protein Biochemistry

scientific article published on 02 November 2021

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