Daniel Herschlag
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View article: SEISMICgraph: a web-based tool for RNA structure data visualization
SEISMICgraph: a web-based tool for RNA structure data visualization Open
In recent years, RNA has been increasingly recognized for its essential roles in biology, functioning not only as a carrier of genetic information but also as a dynamic regulator of gene expression through its interactions with other RNAs,…
View article: An Evaluation of Biomolecular Energetics Learned by AlphaFold
An Evaluation of Biomolecular Energetics Learned by AlphaFold Open
Deep learning has revolutionized protein structural prediction, with function prediction on the horizon. Because biomolecular properties emerge from atomic-level interactions and their energetics, models that learn physical principles can …
View article: Quantifying protein unfolding kinetics with a high-throughput microfluidic platform
Quantifying protein unfolding kinetics with a high-throughput microfluidic platform Open
Even after folding, proteins transiently sample unfolded or partially unfolded intermediates, and these species are often at risk of irreversible alteration ( e.g. via proteolysis, aggregation, or post-translational modification). Kinetic …
View article: Exploring the energetic and conformational properties of the sequence space connecting naturally occurring RNA tetraloop receptor motifs
Exploring the energetic and conformational properties of the sequence space connecting naturally occurring RNA tetraloop receptor motifs Open
Folded RNAs contain tertiary contact motifs whose structures and energetics are conserved across different RNAs. The transferable properties of RNA motifs simplify the RNA folding problem, but measuring energetic and conformational propert…
View article: SEISMICgraph: a web-based tool for RNA structure data visualization
SEISMICgraph: a web-based tool for RNA structure data visualization Open
In recent years, RNA has been increasingly recognized for its essential roles in biology, functioning not only as a carrier of genetic information but also as a dynamic regulator of gene expression through its interactions with other RNAs,…
View article: Exploring the energetic and conformational properties of the sequence space connecting naturally occurring RNA tetraloop receptor motifs
Exploring the energetic and conformational properties of the sequence space connecting naturally occurring RNA tetraloop receptor motifs Open
Folded RNAs contain tertiary contact motifs whose structures and energetics are conserved across different RNAs. The transferable properties of RNA motifs simplify the RNA folding problem, but measuring energetic and conformational propert…
View article: Conformational Ensembles Reveal the Origins of Serine Protease Catalysis
Conformational Ensembles Reveal the Origins of Serine Protease Catalysis Open
Enzymes exist in ensembles of states that encode the energetics underlying their catalysis. Conformational ensembles built from 1231 structures of 17 serine proteases reveal atomic-level changes across their reaction states, identify molec…
View article: Decoupling of catalysis and transition state analog binding from mutations throughout a phosphatase revealed by high-throughput enzymology
Decoupling of catalysis and transition state analog binding from mutations throughout a phosphatase revealed by high-throughput enzymology Open
Using high-throughput microfluidic enzyme kinetics (HT-MEK), we measured over 9,000 inhibition curves detailing impacts of 1,004 single-site mutations throughout the alkaline phosphatase PafA on binding affinity for two transition state an…
View article: Refinement of Multiconformer Ensemble Models from Multi-temperature X-ray Diffraction Data
Refinement of Multiconformer Ensemble Models from Multi-temperature X-ray Diffraction Data Open
Conformational ensembles underlie all protein functions. Thus, acquiring atomic-level ensemble models that accurately represent conformational heterogeneity is vital to deepen our understanding of how proteins work. Modeling ensemble infor…
View article: Dissecting the energetic architecture within an RNA tertiary structural motif via high-throughput thermodynamic measurements
Dissecting the energetic architecture within an RNA tertiary structural motif via high-throughput thermodynamic measurements Open
Structured RNAs and RNA/protein complexes perform critical cellular functions. They often contain structurally conserved tertiary contact “motifs,” whose occurrence simplifies the RNA folding landscape. Prior studies have focused on the co…
View article: Obtaining anomalous and ensemble information from protein crystals from 220 K up to physiological temperatures
Obtaining anomalous and ensemble information from protein crystals from 220 K up to physiological temperatures Open
X-ray crystallography has been invaluable in delivering structural information about proteins. Previously, an approach has been developed that allows high-quality X-ray diffraction data to be obtained from protein crystals at and above roo…
View article: Issue Information
Issue Information Open
colleagues review the current understanding of bone tissue mineralisation and structure, providing a critical outlook on the existing biomimetic strategies of mineralising collagen for bone tissue engineering applications.Featured on the c…
View article: Data for: RNA conformational propensities determine cellular activity
Data for: RNA conformational propensities determine cellular activity Open
This is the raw data and analysis to convert to free energy values for the four assay types described in the manuscript: RNA conformational propensities determine cellular activity. The prism file includes all data and generated figures in…
View article: Dissecting the energetic architecture within an RNA tertiary structural motif via high-throughput thermodynamic measurements
Dissecting the energetic architecture within an RNA tertiary structural motif via high-throughput thermodynamic measurements Open
Structured RNAs and RNA/protein complexes perform critical cellular functions. They often contain structurally conserved tertiary contact “motifs,” whose occurrence simplifies the RNA folding landscape. Prior studies have focused on the co…
View article: RNA conformational propensities determine cellular activity
RNA conformational propensities determine cellular activity Open
Cellular processes are the product of interactions between biomolecules, which associate to form biologically active complexes 1 . These interactions are mediated by intermolecular contacts, which if disrupted, lead to alterations in cell …
View article: High-throughput enzymology reveals mutations throughout a phosphatase that decouple catalysis and transition state analog affinity
High-throughput enzymology reveals mutations throughout a phosphatase that decouple catalysis and transition state analog affinity Open
Using High-Throughput Microfluidic Enzyme Kinetics (HT-MEK), we measured over 9,000 inhibition curves detailing impacts of 1,004 single-site mutations throughout the Alkaline Phosphatase PafA on binding affinity for two transition state an…
View article: Ensemble-function relationships to dissect mechanisms of enzyme catalysis
Ensemble-function relationships to dissect mechanisms of enzyme catalysis Open
Decades of structure-function studies have established our current extensive understanding of enzymes. However, traditional structural models are snapshots of broader conformational ensembles of interchanging states. We demonstrate the nee…
View article: Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals
Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals Open
Cryo-cooling has been nearly universally adopted to mitigate X-ray damage and facilitate crystal handling in protein X-ray crystallography. However, cryo X-ray crystallographic data provide an incomplete window into the ensemble of conform…
View article: Direct Measurement of Interhelical DNA Repulsion and Attraction by Quantitative Cross-Linking
Direct Measurement of Interhelical DNA Repulsion and Attraction by Quantitative Cross-Linking Open
To better understand the forces that mediate nucleic acid compaction in biology, we developed the disulfide cross-linking approach xHEED (X-linking of Helices to measure Electrostatic Effects at Distance) to measure the distance-dependent …
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Issue Information Open
Grün and Schwalbe review current experimental approaches to study the folding processes of DNA and RNA G-quadruplexes.Folding of nucleic acids with non-canonical secondary structures is an intriguing yet enigmatic process.In particular, G-…
View article: Systematic investigation of the link between enzyme catalysis and cold adaptation
Systematic investigation of the link between enzyme catalysis and cold adaptation Open
Cold temperature is prevalent across the biosphere and slows the rates of chemical reactions. Increased catalysis has been predicted to be a dominant adaptive trait of enzymes to reduced temperature, and this expectation has informed physi…
View article: Author response: Systematic investigation of the link between enzyme catalysis and cold adaptation
Author response: Systematic investigation of the link between enzyme catalysis and cold adaptation Open
Article Figures and data Abstract Editor's evaluation Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Cold temperature is pr…
View article: A comprehensive thermodynamic model for RNA binding by the Saccharomyces cerevisiae Pumilio protein PUF4
A comprehensive thermodynamic model for RNA binding by the Saccharomyces cerevisiae Pumilio protein PUF4 Open
Genomic methods have been valuable for identifying RNA-binding proteins (RBPs) and the genes, pathways, and processes they regulate. Nevertheless, standard motif descriptions cannot be used to predict all RNA targets or test quantitative m…