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  1. Mg2+ binding to coenzyme A

    Article • Archives of Biochemistry and Biophysics, January 2025, Elsevier

    Professor Dario A. Estrin

  2. ANI Neural Networks Meet Electrostatics: A ML/MM Implementation in Amber

    Article • October 2024, American Chemical Society (ACS)

    Professor Dario A. Estrin

  3. Kinetic and dynamical properties of truncated hemoglobins of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125

    Article • Protein Science, June 2024, Wiley

    Professor Dario A. Estrin

  4. Mechanism of Peroxynitrite Interaction with Ferric M. tuberculosis Nitrobindin: A Computational Study

    Article • Inorganic Chemistry, May 2024, American Chemical Society (ACS)

    Professor Dario A. Estrin

  5. Assessment of Embedding Schemes in a Hybrid Machine Learning/Classical Potentials (ML/MM) Approach

    Article • Journal of Chemical Information and Modeling, May 2024, American Chemical Society (ACS)

    Professor Dario A. Estrin

  6. Proximal ligand tunes active site structure and reactivity in bacterial L. monocytogenes coproheme ferrochelatase

    Article • Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy, May 2024, Elsevier

    Professor Dario A. Estrin

  7. Catalytic Mechanism of Mycobacterium tuberculosis Methionine Sulfoxide Reductase A

    Article • Biochemistry, January 2024, American Chemical Society (ACS)

    Professor Dario A. Estrin

  8. Assessment of embedding schemes in a hybrid machine learning/classical potentials (ML/MM) scheme

    Article • November 2023, American Chemical Society (ACS)

    Professor Dario A. Estrin

  9. The carbonyl-lock mechanism underlying non-aromatic fluorescence in biological matter

    Article • Nature Communications, November 2023, Springer Science + Business Media

    Professor Dario A. Estrin

  10. Nitric oxide binding to ferrous nitrobindins: A computer simulation investigation

    Article • Journal of Inorganic Biochemistry, November 2023, Elsevier

    Professor Dario A. Estrin

  11. Binding mechanism of disulfide species to ferric hemeproteins: The case of metmyoglobin

    Article • Journal of Inorganic Biochemistry, October 2023, Elsevier

    Professor Dario A. Estrin

  12. Disulfides form persulfides at alkaline pH leading to potential overestimations in the cold cyanolysis method

    Article • Free Radical Biology and Medicine, October 2023, Elsevier

    Professor Dario A. Estrin

  13. Minimum Free Energy Pathways of Reactive Processes with Nudged Elastic Bands

    Article • Journal of Chemical Theory and Computation, August 2023, American Chemical Society (ACS)

    Professor Dario A. Estrin

  14. Reduction of metmyoglobin by inorganic disulfide species

    Article • Journal of Inorganic Biochemistry, August 2023, Elsevier

    Professor Dario A. Estrin

  15. The role of the distal cavity in carbon monoxide stabilization in the coproheme decarboxylase enzyme from C. diphtheriae

    Article • Journal of Inorganic Biochemistry, August 2023, Elsevier

    Professor Dario A. Estrin

  16. Autocatalytic Mechanism in the Anaerobic Reduction of Metmyoglobin by Sulfide Species

    Article • Inorganic Chemistry, July 2023, American Chemical Society (ACS)

    Professor Dario A. Estrin

  17. A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1

    Article • International Journal of Molecular Sciences, May 2023, MDPI AG

    Professor Dario A. Estrin

  18. Multiple oxidative post-translational modifications of human glutamine synthetase mediate peroxynitrite-dependent enzyme inactivation and aggregation

    Article • Journal of Biological Chemistry, March 2023, Elsevier

    Professor Dario A. Estrin

  19. The “Carbonyl-Lock” Mechanism Underlying Non-Aromatic Fluorescence in Biological Matter

    Article • January 2023, American Chemical Society (ACS)

    Professor Dario A. Estrin

  20. Novel Lennard-Jones Parameters for Cysteine and Selenocysteine in the AMBER Force Field

    Article • Journal of Chemical Information and Modeling, January 2023, American Chemical Society (ACS)

    Professor Dario A. Estrin

  21. Computational evaluation of relevant species in inorganic sulfur biochemistry

    Article • Electronic Structure, December 2022, Institute of Physics Publishing

    Professor Dario A. Estrin

  22. Possible molecular basis of the biochemical effects of cysteine-derived persulfides

    Article • Frontiers in Molecular Biosciences, September 2022, Frontiers

    Professor Dario A. Estrin

  23. TD‐DFT modeling of electronic spectra of biliverdins in different environments

    Article • International Journal of Quantum Chemistry, August 2022, Wiley

    Professor Dario A. Estrin

  24. Profiling the Site of Protein CoAlation and Coenzyme A Stabilization Interactions

    Article • Antioxidants, July 2022, MDPI AG

    Professor Dario A. Estrin

  25. Insights into the product release mechanism of dengue virus NS3 helicase

    Article • Nucleic Acids Research, June 2022, Oxford University Press (OUP)

    Professor Dario A. Estrin

  26. Minimum free energy pathways with the nudged elastic band method in combination with a QM-MM Hamiltonian

    Article • June 2022, American Chemical Society (ACS)

    Professor Dario A. Estrin

  27. Mycobacterium tuberculosis DosS binds H2S through its Fe3+ heme iron to regulate the DosR dormancy regulon

    Article • Redox Biology, June 2022, Elsevier

    Professor Dario A. Estrin

  28. Distal lysine (de)coordination in the algal hemoglobin THB1: A combined computer simulation and experimental study

    Article • Journal of Inorganic Biochemistry, July 2021, Elsevier

    Professor Dario A. Estrin

  29. Reactivity of inorganic sulfide species towards a pentacoordinated heme model system

    Article • Journal of Inorganic Biochemistry, July 2021, Elsevier

    Professor Dario A. Estrin

  30. Mycobacterium tuberculosis DosS binds H2S through its Fe3+ heme iron to regulate the Dos dormancy regulon

    Article • June 2021, Cold Spring Harbor Laboratory Press

    Professor Dario A. Estrin

  31. Control of distal lysine coordination in a monomeric hemoglobin: A role for heme peripheral interactions

    Article • Journal of Inorganic Biochemistry, June 2021, Elsevier

    Professor Dario A. Estrin

  32. Electron transfer pathways from quantum dynamics simulations

    Article • The Journal of Chemical Physics, December 2020, American Institute of Physics

    Professor Dario A. Estrin

  33. Computational Vibrational Spectroscopy: A Contemporary Perspective

    Article • December 2020, Royal Society of Chemistry

    Professor Dario A. Estrin

  34. Acidity and nucleophilic reactivity of glutathione persulfide

    Article • Journal of Biological Chemistry, November 2020, Elsevier

    Professor Dario A. Estrin

  35. Nucleotide-dependent dynamics of the Dengue NS3 helicase

    Article • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, August 2020, Elsevier

    Professor Dario A. Estrin

  36. Dioxygen Binding and Sensing Proteins

    Article • Antioxidants & Redox Signaling, June 2020, Mary Ann Liebert Inc

    Professor Dario A. Estrin

  37. Substrate and Product-Assisted Catalysis: Molecular Aspects behind Structural Switches along Organic Hydroperoxide Resistance Protein Catalytic Cycle

    Article • ACS Catalysis, May 2020, American Chemical Society (ACS)

    Professor Dario A. Estrin

  38. In Silico Insight into the Reductive Nitrosylation of Ferric Hemeproteins

    Article • Inorganic Chemistry, March 2020, American Chemical Society (ACS)

    Professor Dario A. Estrin

  39. Structure and function of crocodilian hemoglobins and allosteric regulation by chloride, ATP, and CO2

    Article • AJP Regulatory Integrative and Comparative Physiology, March 2020, American Physiological Society

    Professor Dario A. Estrin

  40. Conformational Flexibility Drives Cold Adaptation in Pseudoalteromonas haloplanktis TAC125 Globins

    Article • Antioxidants & Redox Signaling, February 2020, Mary Ann Liebert Inc

    Professor Dario A. Estrin

  41. Design, synthesis and biological evaluation of quinoxaline compounds as anti-HIV agents targeting reverse transcriptase enzyme

    Article • European Journal of Medicinal Chemistry, February 2020, Elsevier

    Professor Dario A. Estrin

  42. Hemeproteins as Targets for Sulfide Species

    Article • Antioxidants & Redox Signaling, February 2020, Mary Ann Liebert Inc

    Professor Dario A. Estrin

  43. 3-Nitrotyrosine and related derivatives in proteins: precursors, radical intermediates and impact in function

    Article • Essays in Biochemistry, February 2020, Portland Press Ltd.

    Professor Dario A. Estrin

  44. Reaction Path Analysis from Potential Energy Contributions Using Forces: An Accessible Estimator of Reaction Coordinate Adequacy

    Article • Journal of Chemical Theory and Computation, January 2020, American Chemical Society (ACS)

    Professor Dario A. Estrin

  45. Multiscale Modeling of Thiol Overoxidation in Peroxiredoxins by Hydrogen Peroxide

    Article • Journal of Chemical Information and Modeling, November 2019, American Chemical Society (ACS)

    Professor Dario A. Estrin

  46. Catalysis of Peroxide Reduction by Fast Reacting Protein Thiols

    Article • Chemical Reviews, September 2019, American Chemical Society (ACS)

    Professor Dario A. Estrin

  47. Ligand Binding Rate Constants in Heme Proteins Using Markov State Models and Molecular Dynamics Simulations

    Article • ChemPhysChem, August 2019, Wiley

    Professor Dario A. Estrin

  48. Evaluation of quinoxaline compounds as ligands of a site adjacent to S2 (AS2) of cruzain

    Article • Bioorganic & Medicinal Chemistry Letters, August 2019, Elsevier

    Professor Dario A. Estrin

  49. Gating in plant plasma membrane aquaporins: the involvement of leucine in the formation of a pore constriction in the closed state

    Article • FEBS Journal, May 2019, Wiley

    Professor Dario A. Estrin

  50. Lessons learned about steered molecular dynamics simulations and free energy calculations

    Article • Chemical Biology & Drug Design, February 2019, Wiley

    Professor Dario A. Estrin

  51. In Search of GABAA Receptor’s Neurosteroid Binding Sites

    Article • Journal of Medicinal Chemistry, December 2018, American Chemical Society (ACS)

    Professor Dario A. Estrin

  52. Thermal Stability of Globins: Implications of Flexibility and Heme Coordination Studied by Molecular Dynamics Simulations

    Article • Journal of Chemical Information and Modeling, December 2018, American Chemical Society (ACS)

    Professor Dario A. Estrin

  53. A computational investigation of the reactions of tyrosyl, tryptophanyl, and cysteinyl radicals with nitric oxide and molecular oxygen

    Article • Free Radical Research, November 2018, Taylor & Francis

    Professor Rafael Radi, Professor Dario A. Estrin

  54. Cold-Adaptation Signatures in the Ligand Rebinding Kinetics to the Truncated Hemoglobin of the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125

    Article • The Journal of Physical Chemistry B, September 2018, American Chemical Society (ACS)

    Professor Dario A. Estrin

  55. Mechanism of Sulfide Binding by Ferric Hemeproteins

    Article • Inorganic Chemistry, June 2018, American Chemical Society (ACS)

    Professor Dario A. Estrin

  56. Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO Code

    Article • Frontiers in Chemistry, March 2018, Frontiers

    Professor Dario A. Estrin

  57. Spectroscopy in Complex Environments from QM–MM Simulations

    Article • Chemical Reviews, March 2018, American Chemical Society (ACS)

    Professor Dario A. Estrin

  58. Understanding the molecular basis of the high oxygen affinity variant human hemoglobin Coimbra

    Article • Archives of Biochemistry and Biophysics, January 2018, Elsevier

    Professor Dario A. Estrin

  59. Tertiary and quaternary structural basis of oxygen affinity in human hemoglobin as revealed by multiscale simulations

    Article • Scientific Reports, September 2017, Springer Science + Business Media

    Professor Dario A. Estrin

  60. Tyrosine oxidation and nitration in transmembrane peptides is connected to lipid peroxidation

    Article • Archives of Biochemistry and Biophysics, May 2017, Elsevier

    Professor Dario A. Estrin

  61. Naturally occurring fluorescence in frogs

    Article • Proceedings of the National Academy of Sciences, March 2017, Proceedings of the National Academy of Sciences

    Professor Dario A. Estrin

  62. Kinetics, subcellular localization, and contribution to parasite virulence of a Trypanosoma cruzi hybrid type A heme peroxidase ( Tc APx-CcP)

    Article • Proceedings of the National Academy of Sciences, February 2017, Proceedings of the National Academy of Sciences

    Dr Madia Trujillo, Professor Dario A. Estrin

  63. Role of Core Electrons in Quantum Dynamics Using TDDFT

    Article • Journal of Chemical Theory and Computation, December 2016, American Chemical Society (ACS)

    Professor Dario A. Estrin

  64. PrxQ B from Mycobacterium tuberculosis is a monomeric, thioredoxin-dependent and highly efficient fatty acid hydroperoxide reductase

    Article • Free Radical Biology and Medicine, December 2016, Elsevier

    Dr Madia Trujillo, Professor Dario A. Estrin

  65. Exploring the Catalytic Mechanism of Human Glutamine Synthetase by Computer Simulations

    Article • Biochemistry, October 2016, American Chemical Society (ACS)

    Professor Dario A. Estrin

  66. Experimental and Theoretical Study of the High-Temperature UV–Visible Spectra of Aqueous Hydroquinone and 1,4-Benzoquinone

    Article • The Journal of Physical Chemistry B, September 2016, American Chemical Society (ACS)

    Professor Dario A. Estrin

  67. Access and Binding of H2S to Hemeproteins: The Case of HbI of Lucina pectinata

    Article • The Journal of Physical Chemistry B, September 2016, American Chemical Society (ACS)

    Professor Dario A. Estrin

  68. Theoretical investigation of the mechanism of nitroxyl decomposition in aqueous solution

    Article • Journal of Inorganic Biochemistry, September 2016, Elsevier

    Professor Dario A. Estrin

  69. Coarse-Grained Simulations of Heme Proteins: Validation and Study of Large Conformational Transitions

    Article • Journal of Chemical Theory and Computation, June 2016, American Chemical Society (ACS)

    Professor Dario A. Estrin

  70. Impact of human galectin-1 binding to saccharide ligands on dimer dissociation kinetics and structure

    Article • Glycobiology, May 2016, Oxford University Press (OUP)

    Dr Madia Trujillo, Professor Dario A. Estrin

  71. Structural Study of a Flexible Active Site Loop in Human Indoleamine 2,3-Dioxygenase and Its Functional Implications

    Article • Biochemistry, April 2016, American Chemical Society (ACS)

    Professor Dario A. Estrin

  72. Structural Insights into the HWE Histidine Kinase Family: The Brucella Blue Light-Activated Histidine Kinase Domain

    Article • Journal of Molecular Biology, March 2016, Elsevier

    Professor Dario A. Estrin

  73. A quantitative model for oxygen uptake and release in a family of hemeproteins

    Article • Bioinformatics, February 2016, Oxford University Press (OUP)

    Professor Dario A. Estrin

  74. Evolutionary and Functional Relationships in the Truncated Hemoglobin Family

    Article • PLoS Computational Biology, January 2016, PLOS

    Professor Dario A. Estrin

  75. Mapping the protein-binding sites for iridium(iii)-based CO-releasing molecules

    Article • Dalton Transactions, January 2016, Royal Society of Chemistry

    Professor Dario A. Estrin

  76. Structural Plasticity in Globins

    Article • January 2016, Elsevier

    Professor Dario A. Estrin

  77. Destabilization of the torsioned conformation of a ligand side chain inverts the LXRβ activity

    Article • Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, December 2015, Elsevier

    Professor Dario A. Estrin

  78. Molecular Basis of Hydroperoxide Specificity in Peroxiredoxins: The Case of AhpE from Mycobacterium tuberculosis

    Article • Biochemistry, November 2015, American Chemical Society (ACS)

    Professor Dario A. Estrin

  79. The N-terminal pre-A region ofMycobacterium tuberculosis2/2HbN promotes NO-dioxygenase activity

    Article • FEBS Journal, November 2015, Wiley

    Professor Martino Bolognesi, Professor Dario A. Estrin

  80. Exploring the molecular basis of neurosteroid binding to the β3 homopentameric GABA A receptor

    Article • The Journal of Steroid Biochemistry and Molecular Biology, November 2015, Elsevier

    Professor Dario A. Estrin

  81. Ligand uptake in Mycobacterium tuberculosis truncated hemoglobins is controlled by both internal tunnels and active site water molecules

    Article • F1000Research, July 2015, Faculty of 1000, Ltd.

    Professor Dario A. Estrin

  82. Structural flexibility of the heme cavity in the cold-adapted truncated hemoglobin from the Antarctic marine bacteriumPseudoalteromonas haloplanktisTAC125

    Article • FEBS Journal, June 2015, Wiley

    Professor Martino Bolognesi, Professor Dario A. Estrin

  83. Insights into the mechanism of the reaction between hydrogen sulfide and peroxynitrite

    Article • Free Radical Biology and Medicine, March 2015, Elsevier

    Dr Madia Trujillo, Professor Dario A. Estrin

  84. Molecular Mechanism of Myoglobin Autoxidation: Insights from Computer Simulations

    Article • The Journal of Physical Chemistry B, January 2015, American Chemical Society (ACS)

    Professor Dario A. Estrin

  85. Ligand uptake in Mycobacterium tuberculosis truncated hemoglobins is controlled by both internal tunnels and active site water molecules

    Article • F1000Research, January 2015, Faculty of 1000, Ltd.

    Professor Kanak L Dikshit, Professor Dario A. Estrin

  86. Bridging Theory and Experiment to Address Structural Properties of Truncated Haemoglobins

    Article • January 2015, Elsevier

    Professor Dario A. Estrin

  87. Engineered chimeras reveal the structural basis of hexacoordination in globins: A case study of neuroglobin and myoglobin

    Article • Biochimica et Biophysica Acta (BBA) - General Subjects, January 2015, Elsevier

    Professor Dario A. Estrin

  88. Reactivity of Inorganic Sulfide Species toward a Heme Protein Model

    Article • Inorganic Chemistry, December 2014, American Chemical Society (ACS)

    Professor Dario A. Estrin

  89. Interplay of the H-Bond Donor–Acceptor Role of the Distal Residues in Hydroxyl Ligand Stabilization of Thermobifida fusca Truncated Hemoglobin

    Article • Biochemistry, December 2014, American Chemical Society (ACS)

    Professor Dario A. Estrin

  90. Interaction between Proteins and Ir Based CO Releasing Molecules: Mechanism of Adduct Formation and CO Release

    Article • Inorganic Chemistry, September 2014, American Chemical Society (ACS)

    Professor Antonello Merlino, Professor Dario A. Estrin

  91. Mechanistic Insight into the Enzymatic Reduction of Truncated Hemoglobin N of Mycobacterium tuberculosis

    Article • Journal of Biological Chemistry, August 2014, Elsevier

    Professor Dario A. Estrin

  92. Molecular basis of thermal stability in truncated (2/2) hemoglobins

    Article • Biochimica et Biophysica Acta (BBA) - General Subjects, July 2014, Elsevier

    Professor Dario A. Estrin

  93. Ligand Uptake Modulation by Internal Water Molecules and Hydrophobic Cavities in Hemoglobins

    Article • The Journal of Physical Chemistry B, January 2014, American Chemical Society (ACS)

    Professor Dario A. Estrin

  94. Structural basis of redox-dependent modulation of galectin-1 dynamics and function

    Article • Glycobiology, January 2014, Oxford University Press (OUP)

    Dr Madia Trujillo, Professor Dario A. Estrin

  95. Thiol redox biochemistry: insights from computer simulations

    Article • Biophysical Reviews, January 2014, Springer Science + Business Media

    Dr Madia Trujillo, Professor Dario A. Estrin

  96. Coupling of tyrosine deprotonation and axial ligand exchange in nitrocytochrome c

    Article • Chemical Communications, January 2014, Royal Society of Chemistry

    Daniel Murgida, Professor Rafael Radi, Professor Dario A. Estrin

  97. The extraordinary catalytic ability of peroxiredoxins: a combined experimental and QM/MM study on the fast thiol oxidation step

    Article • Chemical Communications, January 2014, Royal Society of Chemistry

    Dr Madia Trujillo, Professor Dario A. Estrin

  98. Mechanism of cysteine oxidation by peroxynitrite: An integrated experimental and theoretical study

    Article • Archives of Biochemistry and Biophysics, November 2013, Elsevier

    Dr Madia Trujillo, Professor Dario A. Estrin

  99. H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin

    Article • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, September 2013, Elsevier

    Professor Dario A. Estrin

  100. Small ligand–globin interactions: Reviewing lessons derived from computer simulation

    Article • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, September 2013, Elsevier

    Professor Dario A. Estrin

  101. Molecular basis of the NO trans influence in quaternary T‐state human hemoglobin: A computational study

    Article • FEBS Letters, June 2013, Wiley

    Alessandro Vergara, Professor Antonello Merlino, Professor Dario A. Estrin

  102. Hydrophobic Effect Drives Oxygen Uptake in Myoglobin via Histidine E7

    Article • Journal of Biological Chemistry, March 2013, Elsevier

    Professor Dario A. Estrin

  103. Quaternary structure effects on the hexacoordination equilibrium in rice hemoglobin rHb1: Insights from molecular dynamics simulations

    Article • Proteins Structure Function and Bioinformatics, February 2013, Wiley

    Professor Dario A. Estrin

  104. The key role of water in the dioxygenase function of Escherichia coli flavohemoglobin

    Article • Journal of Inorganic Biochemistry, February 2013, Elsevier

    Professor Dario A. Estrin

  105. Conformational States of 2′-C-Methylpyrimidine Nucleosides in Single and Double Nucleic Acid Stranded Structures

    Article • The Journal of Physical Chemistry B, December 2012, American Chemical Society (ACS)

    Professor Dario A. Estrin

  106. Coordination of peroxide to the CuM center of peptidylglycine α-hydroxylating monooxygenase (PHM): structural and computational study

    Article • JBIC Journal of Biological Inorganic Chemistry, December 2012, Springer Science + Business Media

    Dr Leon Mario Amzel, Professor Dario A. Estrin

  107. Biophysical Characterisation of Neuroglobin of the Icefish, a Natural Knockout for Hemoglobin and Myoglobin. Comparison with Human Neuroglobin

    Article • PLOS One, December 2012, PLOS

    Professor Dario A. Estrin

  108. Role of PheE15 Gate in Ligand Entry and Nitric Oxide Detoxification Function of Mycobacterium tuberculosis Truncated Hemoglobin N

    Article • PLOS One, November 2012, PLOS

    Professor Dario A. Estrin

  109. pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4

    Article • PLoS Computational Biology, November 2012, PLOS

    Professor Dario A. Estrin

  110. Molecular basis of intramolecular electron transfer in proteins during radical-mediated oxidations: Computer simulation studies in model tyrosine–cysteine peptides in solution

    Article • Archives of Biochemistry and Biophysics, September 2012, Elsevier

    Daniel Murgida, Dr Madia Trujillo, Professor Dario A. Estrin

  111. Following Ligand Migration Pathways from Picoseconds to Milliseconds in Type II Truncated Hemoglobin from Thermobifida fusca

    Article • PLOS One, July 2012, PLOS

    Professor Dario A. Estrin

  112. The Caenorhabditis elegans DAF-12 nuclear receptor: Structure, dynamics, and interaction with ligands

    Article • Proteins Structure Function and Bioinformatics, May 2012, Wiley

    Professor Dario A. Estrin

  113. Molecular Basis of the Mechanism of Thiol Oxidation by Hydrogen Peroxide in Aqueous Solution: Challenging the SN2 Paradigm

    Article • Chemical Research in Toxicology, February 2012, American Chemical Society (ACS)

    Dr Madia Trujillo, Professor Dario A. Estrin

  114. Complete Reaction Mechanism of Indoleamine 2,3-Dioxygenase as Revealed by QM/MM Simulations

    Article • The Journal of Physical Chemistry B, January 2012, American Chemical Society (ACS)

    Professor Dario A. Estrin

  115. Fluoride as a Probe for H-Bonding Interactions in the Active Site of Heme Proteins: The Case of Thermobifida fusca Hemoglobin

    Article • Journal of the American Chemical Society, December 2011, American Chemical Society (ACS)

    Professor Dario A. Estrin

  116. Structural Model for p75NTR–TrkA Intracellular Domain Interaction: A Combined FRET and Bioinformatics Study

    Article • Journal of Molecular Biology, December 2011, Elsevier

    Professor Dario A. Estrin

  117. Ligand Migration in Methanosarcina acetivorans Protoglobin: Effects of Ligand Binding and Dimeric Assembly

    Article • The Journal of Physical Chemistry B, November 2011, American Chemical Society (ACS)

    Professor Martino Bolognesi, Professor Dario A. Estrin

  118. Molecular Basis for the Substrate Stereoselectivity in Tryptophan Dioxygenase

    Article • Biochemistry, November 2011, American Chemical Society (ACS)

    Professor Dario A. Estrin

  119. When Galectins Recognize Glycans: From Biochemistry to Physiology and Back Again

    Article • Biochemistry, September 2011, American Chemical Society (ACS)

    Professor Dario A. Estrin

  120. Protein dynamics and ligand migration interplay as studied by computer simulation

    Article • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, August 2011, Elsevier

    Professor Dario A. Estrin

  121. An Integrated Computational Analysis of the Structure, Dynamics, and Ligand Binding Interactions of the Human Galectin Network

    Article • Journal of Chemical Information and Modeling, July 2011, American Chemical Society (ACS)

    Professor Dario A. Estrin

  122. Aromatic–Aromatic Interactions in Proteins: Beyond the Dimer

    Article • Journal of Chemical Information and Modeling, June 2011, American Chemical Society (ACS)

    Professor Dario A. Estrin

  123. Comparing and combining implicit ligand sampling with multiple steered molecular dynamics to study ligand migration processes in heme proteins

    Article • Journal of Computational Chemistry, May 2011, Wiley

    Professor Dario A. Estrin

  124. Structural basis for ligand recognition in a mushroom lectin: solvent structure as specificity predictor

    Article • Carbohydrate Research, May 2011, Elsevier

    Professor Dario A. Estrin

  125. Role of the Distal Hydrogen-Bonding Network in Regulating Oxygen Affinity in the Truncated Hemoglobin III from Campylobacter jejuni

    Article • Biochemistry, April 2011, American Chemical Society (ACS)

    Professor Dario A. Estrin

  126. Tetrachlorocarbonyliridates: Water-Soluble Carbon Monoxide Releasing Molecules Rate-Modulated by the Sixth Ligand

    Article • Inorganic Chemistry, March 2011, American Chemical Society (ACS)

    Prof. Javier Alcides Ellena, Professor Dario A. Estrin

  127. Protonation of histidine 55 affects the oxygen access to heme in the alpha chain of the hemoglobin from the Antarctic fish Trematomus bernacchii

    Article • IUBMB Life, March 2011, Wiley

    Alessandro Vergara, Professor Antonello Merlino, Professor Dario A. Estrin

  128. Exploring the molecular basis of human manganese superoxide dismutase inactivation mediated by tyrosine 34 nitration

    Article • Archives of Biochemistry and Biophysics, March 2011, Elsevier

    Professor Dario A. Estrin

  129. Structure and dynamics of Antarctic fish neuroglobin assessed by computer simulations

    Article • IUBMB Life, March 2011, Wiley

    Professor Dario A. Estrin

  130. Coordinated nitroxyl anion is produced and released as nitrous oxide by the decomposition of iridium-coordinated nitrosothiols

    Article • Inorganica Chimica Acta, January 2011, Elsevier

    Professor Dario A. Estrin

  131. Ligand Migration in the Apolar Tunnel ofCerebratulus lacteusMini-Hemoglobin

    Article • Journal of Biological Chemistry, December 2010, American Society for Biochemistry & Molecular Biology (ASBMB)

    Professor Martino Bolognesi, Professor Dario A. Estrin

  132. Heme Pocket Structural Properties of a Bacterial Truncated Hemoglobin from Thermobifida fusca

    Article • Biochemistry, November 2010, American Chemical Society (ACS)

    Professor Dario A. Estrin

  133. The peculiar heme pocket of the 2/2 hemoglobin of cold-adapted Pseudoalteromonas haloplanktis TAC125

    Article • JBIC Journal of Biological Inorganic Chemistry, November 2010, Springer Science + Business Media

    Professor Dario A. Estrin

  134. Inhibitory effect of quercetin on matrix metalloproteinase 9 activity Molecular mechanism and structure–activity relationship of the flavonoid–enzyme interaction

    Article • European Journal of Pharmacology, October 2010, Elsevier

    Professor Dario A. Estrin

  135. Substrate stereo‐specificity in tryptophan dioxygenase and indoleamine 2,3‐dioxygenase

    Article • Proteins Structure Function and Bioinformatics, September 2010, Wiley

    Professor Dario A. Estrin

  136. Linking the Structure and Thermal Stability of β-Galactoside-Binding Protein Galectin-1 to Ligand Binding and Dimerization Equilibria

    Article • Biochemistry, August 2010, American Chemical Society (ACS)

    Professor Dario A. Estrin

  137. Role of Heme Distortion on Oxygen Affinity in Heme Proteins: The Protoglobin Case

    Article • The Journal of Physical Chemistry B, June 2010, American Chemical Society (ACS)

    Professor Dario A. Estrin

  138. The first step of the dioxygenation reaction carried out by tryptophan dioxygenase and indoleamine 2,3-dioxygenase as revealed by quantum mechanical/molecular mechanical studies

    Article • JBIC Journal of Biological Inorganic Chemistry, April 2010, Springer Science + Business Media

    Professor Dario A. Estrin

  139. Copper-Transfer Mechanism from the Human Chaperone Atox1 to a Metal-Binding Domain of Wilson Disease Protein

    Article • The Journal of Physical Chemistry B, February 2010, American Chemical Society (ACS)

    Professor Dario A. Estrin

  140. High Protein Structural Flexibility Of A Truncated Hemoglobin From An Antarctic Cold-Adapted Bacterium

    Article • January 2010, American Institute of Physics

    Professor Dario A. Estrin

  141. Unraveling the molecular basis for ligand binding in truncated hemoglobins: The trHbO Bacillus subtilis case

    Article • Proteins Structure Function and Bioinformatics, November 2009, Wiley

    Professor Dario A. Estrin

  142. Molecular Basis for the Electric Field Modulation of Cytochrome c Structure and Function

    Article • Journal of the American Chemical Society, October 2009, American Chemical Society (ACS)

    Daniel Murgida, Professor Dario A. Estrin

  143. Evidence for a ferryl intermediate in a heme-based dioxygenase

    Article • Proceedings of the National Academy of Sciences, October 2009, Proceedings of the National Academy of Sciences

    Professor Dario A. Estrin

  144. Carbohydrate-Binding Proteins: Dissecting Ligand Structures through Solvent Environment Occupancy

    Article • The Journal of Physical Chemistry B, June 2009, American Chemical Society (ACS)

    Professor Dario A. Estrin

  145. Role of Pre-A Motif in Nitric Oxide Scavenging by Truncated Hemoglobin, HbN, of Mycobacterium tuberculosis

    Article • Journal of Biological Chemistry, May 2009, Elsevier

    Professor Dario A. Estrin

  146. The hemoglobins of the sub‐Antarctic fish Cottoperca gobio, a phyletically basal species – oxygen‐binding equilibria, kinetics and molecular dynamics

    Article • FEBS Journal, March 2009, Wiley

    Alessandro Vergara, Professor Dario A. Estrin

  147. Molecular Basis for the pH Dependent Structural Transition of Nitrophorin 4

    Article • The Journal of Physical Chemistry B, January 2009, American Chemical Society (ACS)

    Professor Dario A. Estrin

  148. pH-Dependent Mechanism of Nitric Oxide Release in Nitrophorins 2 and 4

    Article • The Journal of Physical Chemistry B, January 2009, American Chemical Society (ACS)

    Professor Dario A. Estrin

  149. Exploring the Nitric Oxide Detoxification Mechanism of Mycobacterium tuberculosis Truncated Haemoglobin N

    Article • January 2009, Springer Science + Business Media

    Professor Dario A. Estrin

  150. High pressure reveals structural determinants for globin hexacoordination: Neuroglobin and myoglobin cases

    Article • Proteins Structure Function and Bioinformatics, December 2008, Wiley

    Professor Dario A. Estrin

  151. Hemisuccinate of 21-Hydroxy-6,19-Epoxyprogesterone: A Tissue-Specific Modulator of the Glucocorticoid Receptor

    Article • ChemMedChem, December 2008, Wiley

    Professor Dario A. Estrin

  152. QM–MM investigation of the reaction products between nitroxyl and O2 in aqueous solution

    Article • Chemical Physics Letters, September 2008, Elsevier

    Professor Dario A. Estrin

  153. A Microscopic Study of the Deoxyhemoglobin-Catalyzed Generation of Nitric Oxide from Nitrite Anion

    Article • Biochemistry, August 2008, American Chemical Society (ACS)

    Professor Dario A. Estrin

  154. Dynamical Characterization of the Heme NO Oxygen Binding (HNOX) Domain. Insight into Soluble Guanylate Cyclase Allosteric Transition

    Article • Biochemistry, August 2008, American Chemical Society (ACS)

    Professor Dario A. Estrin

  155. Theoretical insight into the hydroxylamine oxidoreductase mechanism

    Article • Journal of Inorganic Biochemistry, July 2008, Elsevier

    Professor Dario A. Estrin

  156. A Unique Family of Stable and Water-Soluble S-Nitrosothiol Complexes

    Article • Inorganic Chemistry, May 2008, American Chemical Society (ACS)

    Professor Dario A. Estrin

  157. Structural determinants of ligand migration in Mycobacterium tuberculosis truncated hemoglobin O

    Article • Proteins Structure Function and Bioinformatics, April 2008, Wiley

    Professor Martino Bolognesi, Professor Dario A. Estrin

  158. Structural and Energetic Study of Cisplatin and Derivatives: Comparison of the Performance of Density Funtional Theory Implementations

    Article • Journal of Chemical Theory and Computation, April 2008, American Chemical Society (ACS)

    Professor Dario A. Estrin

  159. Synthesis, Structure, and Reactivity of Aliphatic Primary Nitrosamines Stabilized by Coordination to [IrCl5]2−

    Article • Organometallics, April 2008, American Chemical Society (ACS)

    Professor Dario A. Estrin

  160. Exploring the Molecular Basis of Action of the Passive Antiglucocorticoid 21-Hydroxy-6,19-epoxyprogesterone

    Article • Journal of Medicinal Chemistry, March 2008, American Chemical Society (ACS)

    Professor Dario A. Estrin

  161. Bond or Cage Effect:  How Nitrophorins Transport and Release Nitric Oxide

    Article • Journal of the American Chemical Society, January 2008, American Chemical Society (ACS)

    Professor Dario A. Estrin

  162. Mechanism of Product Release in NO Detoxification from Mycobacterium tuberculosis Truncated Hemoglobin N

    Article • Journal of the American Chemical Society, January 2008, American Chemical Society (ACS)

    Professor Dario A. Estrin

  163. Exploring the molecular basis of heme coordination in human neuroglobin

    Article • Proteins Structure Function and Bioinformatics, January 2008, Wiley

    Professor Martino Bolognesi, Professor Dario A. Estrin

  164. DFT study on the reactivity of iron porphyrins tuned by ring substitution

    Article • Journal of Inorganic Biochemistry, January 2008, Elsevier

    Professor Dario A. Estrin

  165. Nitric Oxide Reactivity with Globins as Investigated Through Computer Simulation

    Article • January 2008, Elsevier

    Professor Dario A. Estrin

  166. Electronic Perturbation in a Molecular Nanowire of [IrCl5(NO)]− Units

    Article • Chemistry - A European Journal, October 2007, Wiley

    Daniel Murgida, Professor Dario A. Estrin

  167. HNO trapping and assisted decomposition of nitroxyl donors by ferric hemes

    Article • Polyhedron, October 2007, Elsevier

    Prof. Dr. Sebastian A. Suarez, Professor Dario A. Estrin

  168. QM-MM Investigation of the Reaction of Peroxynitrite with Carbon Dioxide in Water

    Article • Journal of Chemical Theory and Computation, June 2007, American Chemical Society (ACS)

    Professor Dario A. Estrin

  169. Characterization of the Galectin-1 Carbohydrate Recognition Domain in Terms of Solvent Occupancy

    Article • The Journal of Physical Chemistry B, May 2007, American Chemical Society (ACS)

    Professor Dario A. Estrin

  170. Short-range and long-range solvent effects on charge-transfer-to-solvent transitions of I− and K+I− contact ion pair dissolved in supercritical ammonia

    Article • The Journal of Chemical Physics, May 2007, American Institute of Physics

    Professor Dario A. Estrin

  171. Dynamical Regulation of Ligand Migration by a Gate-Opening Molecular Switch in Truncated Hemoglobin-N from Mycobacterium tuberculosis

    Article • Journal of the American Chemical Society, May 2007, American Chemical Society (ACS)

    Professor Dario A. Estrin

  172. Oxygen affinity controlled by dynamical distal conformations: The soybean leghemoglobin and the Paramecium caudatum hemoglobin cases

    Article • Proteins Structure Function and Bioinformatics, April 2007, Wiley

    Professor Dario A. Estrin

  173. Electric field effects on the reactivity of heme model systems

    Article • Chemical Physics Letters, January 2007, Elsevier

    Daniel Murgida, Professor Dario A. Estrin

  174. The Catalytic Mechanism of Peptidylglycine α-Hydroxylating Monooxygenase Investigated by Computer Simulation

    Article • Journal of the American Chemical Society, October 2006, American Chemical Society (ACS)

    Dr Leon Mario Amzel, Professor Dario A. Estrin

  175. Heme Protein Oxygen Affinity Regulation Exerted by Proximal Effects

    Article • Journal of the American Chemical Society, September 2006, American Chemical Society (ACS)

    Professor Dario A. Estrin

  176. Ligand-induced dynamical regulation of NO conversion in Mycobacterium tuberculosis truncated hemoglobin-N

    Article • Proteins Structure Function and Bioinformatics, May 2006, Wiley

    Professor Martino Bolognesi, Professor Dario A. Estrin

  177. Dioxygen affinity in heme proteins investigated by computer simulation

    Article • Journal of Inorganic Biochemistry, April 2006, Elsevier

    Professor Dario A. Estrin

  178. A Surprisingly Stable S-Nitrosothiol Complex

    Article • Journal of the American Chemical Society, February 2006, American Chemical Society (ACS)

    Professor Dario A. Estrin

  179. Free Energy Calculations with Non-Equilibrium Methods: Applications of the Jarzynski Relationship

    Article • Theoretical Chemistry Accounts, January 2006, Springer Science + Business Media

    Professor Dario A. Estrin

  180. Modeling heme proteins using atomistic simulations

    Article • Physical Chemistry Chemical Physics, January 2006, Royal Society of Chemistry

    Professor Dario A. Estrin

  181. Two distinct heme distal site states define Cerebratulus lacteus mini-hemoglobin oxygen affinity

    Article • Proteins Structure Function and Bioinformatics, December 2005, Wiley

    Professor Martino Bolognesi, Professor Dario A. Estrin

  182. Solvent Effects on Peroxynitrite Structure and Properties from QM/MM Simulations

    Article • The Journal of Physical Chemistry A, October 2005, American Chemical Society (ACS)

    Professor Dario A. Estrin

  183. Proximal effects in the modulation of nitric oxide synthase reactivity: a QM-MM study

    Article • JBIC Journal of Biological Inorganic Chemistry, August 2005, Springer Science + Business Media

    Professor Dario A. Estrin

  184. Mechanisms of NO Release by N1-Nitrosomelatonin:  Nucleophilic Attack versus Reducing Pathways

    Article • The Journal of Organic Chemistry, June 2005, American Chemical Society (ACS)

    Professor Dario A. Estrin

  185. Solvation and Structure of LiAlH4 in Ethereal Solvents

    Article • Inorganic Chemistry, June 2005, American Chemical Society (ACS)

    Professor Dario A. Estrin

  186. Nitric Oxide Interaction with Cytochromec‘ and Its Relevance to Guanylate Cyclase. Why Does the Iron Histidine Bond Break?

    Article • Journal of the American Chemical Society, May 2005, American Chemical Society (ACS)

    Professor Dario A. Estrin

  187. Multiple-Steering QM−MM Calculation of the Free Energy Profile in Chorismate Mutase

    Article • Journal of the American Chemical Society, April 2005, American Chemical Society (ACS)

    Professor Dario A. Estrin

  188. Discrimination of Nitroxyl and Nitric Oxide by Water-Soluble Mn(III) Porphyrins

    Article • Journal of the American Chemical Society, March 2005, American Chemical Society (ACS)

    Professor Dario A. Estrin

  189. Theoretical Study of the Truncated Hemoglobin HbN:  Exploring the Molecular Basis of the NO Detoxification Mechanism

    Article • Journal of the American Chemical Society, March 2005, American Chemical Society (ACS)

    Professor Dario A. Estrin

  190. Transnitrosation of Nitrosothiols:  Characterization of an Elusive Intermediate

    Article • Journal of the American Chemical Society, December 2004, American Chemical Society (ACS)

    Professor Dario A. Estrin

  191. NMR and molecular dynamics studies of the interaction of melatonin with calmodulin

    Article • Protein Science, November 2004, Wiley

    Professor Dario A. Estrin

  192. QM−MM Study of Nitrite Reduction by Nitrite Reductase of Pseudomonas aeruginosa

    Article • The Journal of Physical Chemistry B, October 2004, American Chemical Society (ACS)

    Professor Dario A. Estrin

  193. Ab Initio Study of NMR 15N Chemical Shift Differences Induced by Ca2+ Binding to EF-Hand Proteins

    Article • Biochemistry, May 2004, American Chemical Society (ACS)

    Professor Dario A. Estrin

  194. Fast Nitroxyl Trapping by Ferric Porphyrins

    Article • Journal of the American Chemical Society, November 2003, American Chemical Society (ACS)

    Professor Dario A. Estrin

  195. Modulation of the NO trans effect in heme proteins: implications for the activation of soluble guanylate cyclase

    Article • JBIC Journal of Biological Inorganic Chemistry, March 2003, Springer Science + Business Media

    Professor Dario A. Estrin

  196. Electronic spectra of indolyl radicals: a time-dependent DFT study

    Article • Chemical Physics Letters, October 2002, Elsevier

    Professor Dario A. Estrin

  197. Solvent-induced symmetry breaking of nitrate ion in aqueous clusters: A quantum-classical simulation study

    Article • The Journal of Chemical Physics, July 2002, American Institute of Physics

    Professor Dario A. Estrin

  198. Physiological concentrations of melatonin inhibit the nitridergic pathway in the Syrian hamster retina

    Article • Journal of Pineal Research, July 2002, Wiley

    Professor Dario A. Estrin

  199. Reaction pathways of 2,2,2-trifluoroethylamine and n-butylamine with [Ru(bpy)2(NO)Cl]2+

    Article • Tetrahedron, May 2002, Elsevier

    Professor Dario A. Estrin

  200. Molecular structure effects on the kinetics of hydroxyl radical addition to azo dyes

    Article • Journal of Physical Organic Chemistry, March 2002, Wiley

    Professor Dario A. Estrin

  201. Thermal and solvent effects on the coordination structure of LiAlH4: a computational study

    Article • Chemical Physics Letters, February 2002, Elsevier

    Professor Dario A. Estrin

  202. Environment effects on chemical reactivity of heme proteins

    Article • International Journal of Quantum Chemistry, January 2002, Wiley

    Professor Dario A. Estrin

  203. Structure and spin‐state energetics of an iron porphyrin model: An assessment of theoretical methods

    Article • International Journal of Quantum Chemistry, January 2002, Wiley

    Professor Dario A. Estrin

  204. Molecular relaxation and metalloenzyme active site modeling

    Article • International Journal of Quantum Chemistry, January 2002, Wiley

    Professor Dario A. Estrin

  205. Nitrosation of melatonin by nitric oxide: a computational study

    Article • Journal of Pineal Research, September 2001, Wiley

    Professor Dario A. Estrin

  206. Hydrogen Bonding and O2Affinity of Hemoglobins

    Article • Journal of the American Chemical Society, August 2001, American Chemical Society (ACS)

    Professor Dario A. Estrin

  207. Theoretical Investigation on the Electronic Structure of Pentacyano(L)ferrate(II) Complexes with NO+, NO, and NO- Ligands. Redox Interconversion, Protonation, and Cyanide-Releasing Reactions

    Article • Inorganic Chemistry, July 2001, American Chemical Society (ACS)

    Professor Dario A. Estrin

  208. Structure, solvation, and bonding in pentacyano(L)ferrate(II) ions (L=aliphatic amine): a density functional study

    Article • Journal of Molecular Modeling, July 2001, Springer Science + Business Media

    Professor Dario A. Estrin

  209. Scavenging of NO by Melatonin

    Article • Journal of the American Chemical Society, October 2000, American Chemical Society (ACS)

    Professor Dario A. Estrin

  210. Computer simulation study of HNO3 dissociation in aqueous clusters

    Article • Chemical Physics Letters, August 2000, Elsevier

    Professor Dario A. Estrin

  211. Concertedness and solvent effects in multiple proton transfer reactions: The formic acid dimer in solution

    Article • The Journal of Chemical Physics, June 2000, American Institute of Physics

    Professor Dario A. Estrin

  212. N-Nitrosomelatonin

    Article • Acta Crystallographica Section C Crystal Structure Communications, June 2000, International Union of Crystallography

    Professor Dario A. Estrin

  213. Nitric Oxide Binding to Ferric Cytochrome P450:  A Computational Study

    Article • Inorganic Chemistry, May 2000, American Chemical Society (ACS)

    Professor Dario A. Estrin

  214. Hybrid Quantum Classical Molecular Dynamics Simulation of the Proton-Transfer Reaction of HO- with HBr in Aqueous Clusters

    Article • The Journal of Physical Chemistry A, June 1999, American Chemical Society (ACS)

    Professor Dario A. Estrin

  215. Reactions of Melatonin and Related Indoles with Free Radicals:  A Computational Study

    Article • Journal of Medicinal Chemistry, August 1998, American Chemical Society (ACS)

    Professor Dario A. Estrin

  216. Solvent effects in density functional calculations of uracil and cytosine tautomerism

    Article • International Journal of Quantum Chemistry, December 1995, Wiley

    Professor Dario A. Estrin

  217. Time scales and other problems in linking simulations of simple chemical systems to more complex ones

    Article • International Journal of Quantum Chemistry, January 1993, Wiley

    Professor Dario A. Estrin

  218. Accurate non-local electron—argon pseudopotential for condensed phase simulation

    Article • Chemical Physics Letters, October 1991, Elsevier

    Sherwin J. Singer Singer, Professor Dario A. Estrin

  219. On the Hill determinant method

    Article • Journal of Physics A General Physics, June 1990, Institute of Physics Publishing

    Professor Dario A. Estrin

  220. Potential energy curves of diatomic molecules from the Hill determinant method

    Article • Journal of Mathematical Chemistry, June 1990, Springer Science + Business Media

    Professor Dario A. Estrin

  221. Alternative treatment of rotational quantum systems

    Article • Zeitschrift für Physik D, March 1989, Springer Science + Business Media

    Professor Dario A. Estrin

  222. Generalized Hill determinant method

    Article • Physics Letters A, July 1988, Elsevier

    Professor Dario A. Estrin

  223. Vibrational-rotational energy levels of diatomic molecules from the hill determinant method

    Article • Journal of Molecular Structure THEOCHEM, June 1988, Elsevier

    Professor Dario A. Estrin