Choreographing an enzyme's dance

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Enzyme structure and dynamics affect hydrogen tunneling: The impact of a remote side chain (I553) in soybean lipoxygenase-1

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Extremely Large Isotope Effects in the Soybean Lipoxygenase-Linoleic Acid Reaction

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Thermal-activated protein mobility and its correlation with catalysis in thermophilic alcohol dehydrogenase

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Enzymatic Transition State Theory and Transition State Analogue Design

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Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations

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Transient Non-native Hydrogen Bonds Promote Activation of a Signaling Protein

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Enzyme Dynamics During Catalysis Measured by NMR Spectroscopy

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Four generations of transition-state analogues for human purine nucleoside phosphorylase

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Modeling temperature dependent kinetic isotope effects for hydrogen transfer in a series of soybean lipoxygenase mutants: The effect of anharmonicity upon transfer distance

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Transition Path Sampling Simulations of Biological Systems

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Structure and Dynamics of Pin1 During Catalysis by NMR

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Atomically detailed simulation of the recovery stroke in myosin by Milestoning

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Free Energy and Kinetics of Conformational Transitions from Voronoi Tessellated Milestoning with Restraining Potentials

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Protein structural transitions and their functional role

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Segmented Transition Pathway of the Signaling Protein Nitrogen Regulatory Protein C

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Visualizing transient dark states by NMR spectroscopy

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Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions

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Conserved conformational dynamics determine enzyme activity

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Optimization of Conformational Dynamics in an Epistatic Evolutionary Trajectory

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Evolutionary Aspects of Enzyme Dynamics

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Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity

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Transported Substrate Determines Exchange Rate in the Multidrug Resistance Transporter EmrE

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Protein motions and dynamic effects in enzyme catalysis

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Cell Metabolism - Cell Homeostasis and Stress Response

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Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations

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Coupled Motions Direct Electrons along Human Microsomal P450 Chains

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Computational Protein Engineering: Bridging the Gap between Rational Design and Laboratory Evolution

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Viewing Protein Fitness Landscapes Through a Next-Gen Lens

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Structural Mimicry of A-Loop Tyrosine Phosphorylation by a Pathogenic FGF Receptor 3 Mutation

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Low-Frequency Protein Motions Coupled to Catalytic Sites

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Is Buffer a Good Proxy for a Crowded Cell-Like Environment? A Comparative NMR Study of Calmodulin Side-Chain Dynamics in Buffer and E. coli Lysate

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Heavy enzymes — experimental and computational insights in enzyme dynamics

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Amino Acid Networks in a (β/α)8 Barrel Enzyme Change during Catalytic Turnover

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Perspective: pre-chemistry conformational changes in DNA polymerase mechanisms

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Mechanisms of Intramolecular Communication in a Hyperthermophilic Acylaminoacyl Peptidase: A Molecular Dynamics Investigation

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A “Diels‐Alderase” at Last

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Long-Range Interactions in the Alpha Subunit of Tryptophan Synthase Help to Coordinate Ligand Binding, Catalysis, and Substrate Channeling

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Inaccurate secondary structure predictions often indicate protein fold switching

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Paths of long-range communication in the E2 enzymes of family 3: a molecular dynamics investigation

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Activation and friction in enzymatic loop opening and closing dynamics

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Prechemistry barriers and checkpoints do not contribute to fidelity and catalysis as long as they are not rate limiting

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Kinetic and spectroscopic probes of motions and catalysis in the cytochrome P450 reductase family of enzymes

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danceroom Spectroscopy: At the Frontiers of Physics, Performance, Interactive Art and Technology

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Intrazelluläre NMR‐ und EPR‐Spektroskopie von biologischen Makromolekülen

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Fast gap-free enumeration of conformations and sequences for protein design

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Enzyme dynamics and catalysis in the mechanism of DNA polymerase

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Branch site bulge conformations in domain 6 determine functional sugar puckers in group II intron splicing

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Structure, Dynamics, and Fidelity of RNA-Dependent RNA Polymerases

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Thermodynamic framework for identifying free energy inventories of enzyme catalytic cycles

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Improved energy bound accuracy enhances the efficiency of continuous protein design

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Allosteric Activation of the Par-6 PDZ via a Partial Unfolding Transition

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Coupled motions during dynamics reveal a tunnel toward the active site regulated by the N-terminal α-helix in an acylaminoacyl peptidase

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Factors affecting enzyme activity and design

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Capture and Quality Control Mechanisms for Adenosine-5′-triphosphate Binding

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Modeling the Interaction of Dodecylphosphocholine Micelles with the Anticoccidial Peptide PW2 Guided by NMR Data

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Analyzing Biomolecular Ensembles

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De novo design of triosephosphate isomerases using generative language modelsPreprint

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A Unique and Simple Approach to Improve Sensitivity in 15N-NMR Relaxation Measurements for NH3+ Groups: Application to a Protein-DNA Complex

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Modeling methods for studying post-translational and transcriptional modifying enzymes

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Metabolic Optimization by Enzyme-Enzyme and Enzyme-Cytoskeleton Associations

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Exploring the Dynamics of Shikimate Kinase through Molecular Mechanics

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Exploring the Dynamics of Holo-Shikimate Kinase through Molecular Mechanics

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Atomistic Insights Into the Regulatory Mechanisms Mediated by Post- Translational Modifications: Molecular Dynamics Investigations

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Structure and modification

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Single-molecule studies of disulfide bond reduction pathways used by human thioredoxin

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Molecular Dynamics, Quantum Mechanics, and Combined Quantum Mechanics/Molecular Mechanics Methods for Drug Discovery and Development

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NMR Investigations on Ruggedness of Native State Energy Landscape in Folded Proteins

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Loop opening and closing dynamics in enzymes: activated or friction-limited? The case of protein tyrosine phosphatasesPreprint

Zinovjev, K., Guénon, P., Ramos‐Guzmán, C. A., Ruiz‐Pernía, J. J., Laage, D., & Tuñón, I. (2023) · ChemRxiv · doi:10.26434/chemrxiv-2023-m8v8x · Cited by 1 · see citing works

Structure-function relationships in a glycosyltransferase, a phosphatase and an oxidoreductase

Gonçalves, S. A. (2012) · Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)

Uma transição assimétrica entre estados simétricos: o alosterismo da Glucosamina 6-fosfato Desaminase

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Computational Insights Into Enzyme Catalysis

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The maximum penalty criterion for ridge regression: application to the calibration of the force constant in elastic network modelsPreprint

Bastolla, U., & Dehouck, Y. (2015) · arXiv (Cornell University) · doi:10.48550/arxiv.1512.08294

Understanding the role of conformational dynamics in human Alkbh5

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Language of Uzbek national dance art movements

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Modelagem molecular de receptores nucleares

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Protein Function | Allostery in Proteins: Canonical Models and New Insights

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Promiscuous Enzymes

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Enzyme Evolution

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Books and reviews

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Insights into the Substrate Uptake Mechanism of Mycobacterium Tuberculosis Ribose 5-Phosphate Isomerase and Perspectives on Drug Development

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Promoting Vibrations and the Function of Enzymes. Emerging Theoretical and Experimental Convergence

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Isotopic Probes of Biological Catalysis

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Coupled motions in enzyme catalysis

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A 21st century revisionist's view at a turning point in enzymology

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Atomistic description of the relationship between protein dynamics and catalysis with transition path sampling

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