Darío A. Estrı́n
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View article: Fenton‐like Reactivity on Fe <sub>3</sub> O <sub>4</sub> Nanozymes Driven by Charge Transfer and Interfacial Water
Fenton‐like Reactivity on Fe <sub>3</sub> O <sub>4</sub> Nanozymes Driven by Charge Transfer and Interfacial Water Open
Magnetite (Fe 3 O 4 ) nanoparticles, widely recognized as inorganic nanozymes due to their enzyme‐like catalytic activity, are emerging as effective heterogeneous catalysts for Fenton‐like reactions, in which lattice iron activates hydroge…
View article: From QM/MM to ML/MM: A new era in multiscale modeling
From QM/MM to ML/MM: A new era in multiscale modeling Open
Hybrid machine-learning/molecular-mechanics (ML/MM) methods extend the classical QM/MM paradigm by replacing the quantum description with neural network interatomic potentials trained to reproduce accurately quantum-mechanical (QM) results…
View article: Proteins and Carbon Dioxide Struggle Against Peroxynitrite
Proteins and Carbon Dioxide Struggle Against Peroxynitrite Open
Nitrosative stress plays a key role in the etiology of several human diseases, such as atherosclerosis, inflammation, cancer, and neurological diseases. Peroxynitrite is one of the most potent biological nitrosative agents, being produced …
View article: Advancing Multiscale Molecular Modeling with Machine Learning-Derived Electrostatics
Advancing Multiscale Molecular Modeling with Machine Learning-Derived Electrostatics Open
We introduce an innovative machine learning (ML)-based framework for multiscale molecular modeling, in which the ML subsystem is treated as an electrostatic entity interacting with its molecular mechanics (MM) environment through classical…
View article: Insights into the flexibility of the domain‐linking loop in actinobacterial coproheme decarboxylase through structures and molecular dynamics simulations
Insights into the flexibility of the domain‐linking loop in actinobacterial coproheme decarboxylase through structures and molecular dynamics simulations Open
Prokaryotic heme biosynthesis in Gram‐positive bacteria follows the coproporphyrin‐dependent heme biosynthesis pathway. The last step in this pathway is catalyzed by the enzyme coproheme decarboxylase, which oxidatively transforms two prop…
View article: Advancing Multiscale Molecular Modeling with Machine Learning-Derived Electrostatics
Advancing Multiscale Molecular Modeling with Machine Learning-Derived Electrostatics Open
We introduce an innovative machine learning (ML)-based framework for multiscale molecular modeling, in which the ML subsystem is treated as an electrostatic entity interacting with its molecular mechanics (MM) environment through classical…
View article: ANI Neural Networks Meet Electrostatics: A ML/MM Implementation in Amber
ANI Neural Networks Meet Electrostatics: A ML/MM Implementation in Amber Open
We present a novel integration of the ANI neural networks into the Amber software suite, offering a sophisticated machine learning/molecular mechanics (ML/MM) framework. The implementation is designed as a general-purpose tool for the simu…
View article: Comparing thiol and selenol reactivity towards peroxynitrite by computer simulation
Comparing thiol and selenol reactivity towards peroxynitrite by computer simulation Open
Peroxynitrite is a very reactive species implicated in a variety of pathophysiological cellular processes. Particularly, peroxynitrite-mediated oxidation of cellular thiol-containing compounds such as cysteine residues is a key process whi…
View article: Kinetic and dynamical properties of truncated hemoglobins of the Antarctic bacterium <i>Pseudoalteromonas haloplanktis</i> TAC125
Kinetic and dynamical properties of truncated hemoglobins of the Antarctic bacterium <i>Pseudoalteromonas haloplanktis</i> TAC125 Open
Due to the low temperature, the Antarctic marine environment is challenging for protein functioning. Cold‐adapted organisms have evolved proteins endowed with higher flexibility and lower stability in comparison to their thermophilic homol…
View article: Proximal ligand tunes active site structure and reactivity in bacterial L. monocytogenes coproheme ferrochelatase
Proximal ligand tunes active site structure and reactivity in bacterial L. monocytogenes coproheme ferrochelatase Open
View article: Catalytic Mechanism of <i>Mycobacterium tuberculosis</i> Methionine Sulfoxide Reductase A
Catalytic Mechanism of <i>Mycobacterium tuberculosis</i> Methionine Sulfoxide Reductase A Open
The oxidation of Met to methionine sulfoxide (MetSO) by oxidants such as hydrogen peroxide, hypochlorite, or peroxynitrite has profound effects on protein function. This modification can be reversed by methionine sulfoxide reductases (msr)…
View article: ANI-aa-qmmm Data set
ANI-aa-qmmm Data set Open
This data set was constructed for our work entitled "Assessment of embedding schemes in a hybrid machine learning/classical potentials (ML/MM) approach" to provide an unbiased insight into the performance of different atomic partial charge…
View article: The carbonyl-lock mechanism underlying non-aromatic fluorescence in biological matter
The carbonyl-lock mechanism underlying non-aromatic fluorescence in biological matter Open
View article: A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1
A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1 Open
Coenzyme A (CoA) is a key cellular metabolite which participates in diverse metabolic pathways, regulation of gene expression and the antioxidant defense mechanism. Human NME1 (hNME1), which is a moonlighting protein, was identified as a m…
View article: The role of the distal cavity in carbon monoxide stabilization in the coproheme decarboxylase enzyme from C. diphtheriae
The role of the distal cavity in carbon monoxide stabilization in the coproheme decarboxylase enzyme from C. diphtheriae Open
View article: Multiple oxidative post-translational modifications of human glutamine synthetase mediate peroxynitrite-dependent enzyme inactivation and aggregation
Multiple oxidative post-translational modifications of human glutamine synthetase mediate peroxynitrite-dependent enzyme inactivation and aggregation Open
View article: The “Carbonyl-Lock” Mechanism Underlying Non-Aromatic Fluorescence in Biological Matter
The “Carbonyl-Lock” Mechanism Underlying Non-Aromatic Fluorescence in Biological Matter Open
Challenging the basis of our chemical intuition, recent experimental evidence reveals the presence of a new type of intrinsic fluorescence in biomolecules that exists even in the absence of aromatic or electronically conjugated chemical co…
View article: Possible molecular basis of the biochemical effects of cysteine-derived persulfides
Possible molecular basis of the biochemical effects of cysteine-derived persulfides Open
Persulfides (RSSH/RSS − ) are species closely related to thiols (RSH/RS − ) and hydrogen sulfide (H 2 S/HS − ), and can be formed in biological systems in both low and high molecular weight cysteine-containing compounds. They are key inter…
View article: Profiling the Site of Protein CoAlation and Coenzyme A Stabilization Interactions
Profiling the Site of Protein CoAlation and Coenzyme A Stabilization Interactions Open
Coenzyme A (CoA) is a key cellular metabolite known for its diverse functions in metabolism and regulation of gene expression. CoA was recently shown to play an important antioxidant role under various cellular stress conditions by forming…
View article: Insights into the product release mechanism of dengue virus NS3 helicase
Insights into the product release mechanism of dengue virus NS3 helicase Open
The non-structural protein 3 helicase (NS3h) is a multifunctional protein that is critical in RNA replication and other stages in the flavivirus life cycle. NS3h uses energy from ATP hydrolysis to translocate along single stranded nucleic …
View article: Minimum free energy pathways with the nudged elastic band method in combination with a QM-MM Hamiltonian
Minimum free energy pathways with the nudged elastic band method in combination with a QM-MM Hamiltonian Open
The optimization of minimum free energy pathways (MFEP) is one of the most widely used strategies to study activated processes. For chemical reactions, this requires the use of quantum mechanics. Using quantum mechanics molecular mechanics…
View article: Mycobacterium tuberculosis DosS binds H2S through its Fe3+ heme iron to regulate the DosR dormancy regulon
Mycobacterium tuberculosis DosS binds H2S through its Fe3+ heme iron to regulate the DosR dormancy regulon Open
View article: <i>Mycobacterium tuberculosis</i> DosS binds H<sub>2</sub>S through its Fe<sup>3+</sup> heme iron to regulate the Dos dormancy regulon
<i>Mycobacterium tuberculosis</i> DosS binds H<sub>2</sub>S through its Fe<sup>3+</sup> heme iron to regulate the Dos dormancy regulon Open
Mycobacterium tuberculosis ( Mtb ) senses and responds to host-derived gasotransmitters NO and CO via heme-containing sensor kinases DosS and DosT and the response regulator DosR. Hydrogen sulfide (H 2 S) is an important signaling molecule…
View article: Author Index
Author Index Open
View article: Acidity and nucleophilic reactivity of glutathione persulfide
Acidity and nucleophilic reactivity of glutathione persulfide Open
Persulfides (RSSH/RSS-) participate in sulfur trafficking and metabolic processes, and are proposed to mediate the signaling effects of hydrogen sulfide (H2S). Despite their growing relevance, their chemical propertie…
View article: Substrate and Product-Assisted Catalysis: Molecular Aspects behind Structural Switches along Organic Hydroperoxide Resistance Protein Catalytic Cycle
Substrate and Product-Assisted Catalysis: Molecular Aspects behind Structural Switches along Organic Hydroperoxide Resistance Protein Catalytic Cycle Open
Bacteria contain a large repertoire of enzymes to decompose oxidants, such as hydroperoxides. Among them, organic hydroperoxide resistance (Ohr) proteins play central roles in the bacterial response to fatty acid peroxides and peroxynitrit…
View article: Dioxygen Binding and Sensing Proteins
Dioxygen Binding and Sensing Proteins Open
Oxygen binding proteins (O2BIP) have been actively investigated for the past five decades due to their rich redox chemistry and function as O2 carriers in blood cells, as well as their function as gasotransmitters and…
View article: Structure and function of crocodilian hemoglobins and allosteric regulation by chloride, ATP, and CO<sub>2</sub>
Structure and function of crocodilian hemoglobins and allosteric regulation by chloride, ATP, and CO<sub>2</sub> Open
Hemoglobins (Hbs) of crocodilians are reportedly characterized by unique mechanisms of allosteric regulatory control, but there are conflicting reports regarding the importance of different effectors, such as chloride ions, organic phospha…
View article: Electrostatics and the Control of Endogenous Heme Ligation by pH in a Hemoglobin
Electrostatics and the Control of Endogenous Heme Ligation by pH in a Hemoglobin Open
View article: Design, synthesis and biological evaluation of quinoxaline compounds as anti-HIV agents targeting reverse transcriptase enzyme
Design, synthesis and biological evaluation of quinoxaline compounds as anti-HIV agents targeting reverse transcriptase enzyme Open