Article-Journal

Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling
The formation of an amide bond is an essential step in the synthesis of materials and drugs, and in the assembly of amino acids to form …
Rolf David , Iñaki Tuñón , Damien Laage
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Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling
Understanding the Interactions of Ubiquitin-Specific Protease 7 with Its Substrates through Molecular Dynamics Simulations: Insights into the Role of Its C-Terminal Domains in Substrate Recognition
In this work, we investigated the role of the C-terminal loop (CTL) motif in ubiquitin-specific protease 7 (USP7), a deubiquitinase …
Jose Luis Velázquez , J. Caballero , J. Alzate-Morales , J. Javier Ruiz-Pernía , Iñaki Tuñón
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Understanding the Interactions of Ubiquitin-Specific Protease 7 with Its Substrates through Molecular Dynamics Simulations: Insights into the Role of Its C-Terminal Domains in Substrate Recognition
Activation and friction in enzymatic loop opening and closing dynamics
Protein loop dynamics have recently been recognized as central to enzymatic activity, specificity and stability. However, the factors …
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Activation and friction in enzymatic loop opening and closing dynamics
Electrostatics as a Guiding Principle in Understanding and Designing Enzymes
We provide in this work a technical perspective about enzyme design encounters various challenges associated with the application of …
J. Javier Ruiz-Pernía , K. Swiderek , J. Bertran , V. Moliner , Iñaki Tuñón
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Electrostatics as a Guiding Principle in Understanding and Designing Enzymes
Elucidation of the active form and reaction mechanism in human asparaginase type III using multiscale simulations
L-asparaginases catalyze the asparagine hydrolysis to aspartate. These enzymes play an important role in the treatment of acute …
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Elucidation of the active form and reaction mechanism in human asparaginase type III using multiscale simulations
Conformational Changes and ATP Hydrolysis in Zika Helicase: The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations
We computationally study the Zika NS3 helicase, a biological motor, using ATP hydrolysis energy for nucleic acid remodeling. Through …
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Conformational Changes and ATP Hydrolysis in Zika Helicase: The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations
Insights into the Enhancement of the Poly(ethylene terephthalate) Degradation by FAST-PETase from Computational Modeling
In this work, we investigated the enzymatic biodegradation of polyethylene terephthalate (PET), the most abundant polyester plastic …
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Insights into the Enhancement of the Poly(ethylene terephthalate) Degradation by FAST-PETase from Computational Modeling
Insights into the Structural and Energetic Descriptions of Ubiquitin Specific Protease 7 (USP7) Catalytic Mechanisms by Hybrid QM/MM Simulations
In this work, we conducted the first computational study of the USP7 reaction mechanism with the substrate Ubiquitin-Rhodamine 110-G …
Jose Luis Velázquez , J. Caballero , J. Alzate-Morales , J. Javier Ruiz-Pernía , Iñaki Tuñón
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Insights into the Structural and Energetic Descriptions of Ubiquitin Specific Protease 7 (USP7) Catalytic Mechanisms by Hybrid QM/MM Simulations
Unveiling the Mechanistic Singularities of Caspases: A Computational Analysis of the Reaction Mechanism in Human Caspase-1
Caspases are cysteine proteases in charge of breaking a peptide bond next to an aspartate residue. Caspases constitute an important …
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Electrostatic Embedding of Machine Learning Potentials
This work presents a variant of an electrostatic embedding scheme that allows the embedding of arbitrary machine learned potentials …
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Electrostatic Embedding of Machine Learning Potentials