All Stories

  1. Exploring human carboxylesterases 1 and 2 selectivity of two families of substrates at an atomistic level
  2. Advancing Multiscale Molecular Modeling with Machine Learning-Derived Electrostatics
  3. Advancing Multiscale Molecular Modeling with Machine Learning-Derived Electrostatics
  4. Mechanistic aspects of the binding of acid–base ligands to ferric heme proteins
  5. Insights into the flexibility of the domain‐linking loop in actinobacterial coproheme decarboxylase through structures and molecular dynamics simulations
  6. Mg2+ binding to coenzyme A
  7. ANI Neural Networks Meet Electrostatics: A ML/MM Implementation in Amber
  8. Kinetic and dynamical properties of truncated hemoglobins of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125
  9. Mechanism of Peroxynitrite Interaction with Ferric M. tuberculosis Nitrobindin: A Computational Study
  10. Assessment of Embedding Schemes in a Hybrid Machine Learning/Classical Potentials (ML/MM) Approach
  11. Proximal ligand tunes active site structure and reactivity in bacterial L. monocytogenes coproheme ferrochelatase
  12. Catalytic Mechanism of Mycobacterium tuberculosis Methionine Sulfoxide Reductase A
  13. Assessment of embedding schemes in a hybrid machine learning/classical potentials (ML/MM) scheme
  14. The carbonyl-lock mechanism underlying non-aromatic fluorescence in biological matter
  15. Nitric oxide binding to ferrous nitrobindins: A computer simulation investigation
  16. Binding mechanism of disulfide species to ferric hemeproteins: The case of metmyoglobin
  17. Disulfides form persulfides at alkaline pH leading to potential overestimations in the cold cyanolysis method
  18. Minimum Free Energy Pathways of Reactive Processes with Nudged Elastic Bands
  19. Reduction of metmyoglobin by inorganic disulfide species
  20. The role of the distal cavity in carbon monoxide stabilization in the coproheme decarboxylase enzyme from C. diphtheriae
  21. Autocatalytic Mechanism in the Anaerobic Reduction of Metmyoglobin by Sulfide Species
  22. A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1
  23. Multiple oxidative post-translational modifications of human glutamine synthetase mediate peroxynitrite-dependent enzyme inactivation and aggregation
  24. The “Carbonyl-Lock” Mechanism Underlying Non-Aromatic Fluorescence in Biological Matter
  25. Novel Lennard-Jones Parameters for Cysteine and Selenocysteine in the AMBER Force Field
  26. Computational evaluation of relevant species in inorganic sulfur biochemistry
  27. Possible molecular basis of the biochemical effects of cysteine-derived persulfides
  28. TD‐DFT modeling of electronic spectra of biliverdins in different environments
  29. Profiling the Site of Protein CoAlation and Coenzyme A Stabilization Interactions
  30. Insights into the product release mechanism of dengue virus NS3 helicase
  31. Minimum free energy pathways with the nudged elastic band method in combination with a QM-MM Hamiltonian
  32. Mycobacterium tuberculosis DosS binds H2S through its Fe3+ heme iron to regulate the DosR dormancy regulon
  33. Distal lysine (de)coordination in the algal hemoglobin THB1: A combined computer simulation and experimental study
  34. Reactivity of inorganic sulfide species towards a pentacoordinated heme model system
  35. Mycobacterium tuberculosis DosS binds H2S through its Fe3+ heme iron to regulate the Dos dormancy regulon
  36. Control of distal lysine coordination in a monomeric hemoglobin: A role for heme peripheral interactions
  37. Electron transfer pathways from quantum dynamics simulations
  38. Computational Vibrational Spectroscopy: A Contemporary Perspective
  39. Acidity and nucleophilic reactivity of glutathione persulfide
  40. Nucleotide-dependent dynamics of the Dengue NS3 helicase
  41. Dioxygen Binding and Sensing Proteins
  42. Substrate and Product-Assisted Catalysis: Molecular Aspects behind Structural Switches along Organic Hydroperoxide Resistance Protein Catalytic Cycle
  43. In Silico Insight into the Reductive Nitrosylation of Ferric Hemeproteins
  44. Structure and function of crocodilian hemoglobins and allosteric regulation by chloride, ATP, and CO2
  45. Conformational Flexibility Drives Cold Adaptation in Pseudoalteromonas haloplanktis TAC125 Globins
  46. Design, synthesis and biological evaluation of quinoxaline compounds as anti-HIV agents targeting reverse transcriptase enzyme
  47. Hemeproteins as Targets for Sulfide Species
  48. 3-Nitrotyrosine and related derivatives in proteins: precursors, radical intermediates and impact in function
  49. Reaction Path Analysis from Potential Energy Contributions Using Forces: An Accessible Estimator of Reaction Coordinate Adequacy
  50. Multiscale Modeling of Thiol Overoxidation in Peroxiredoxins by Hydrogen Peroxide
  51. Catalysis of Peroxide Reduction by Fast Reacting Protein Thiols
  52. Ligand Binding Rate Constants in Heme Proteins Using Markov State Models and Molecular Dynamics Simulations
  53. Evaluation of quinoxaline compounds as ligands of a site adjacent to S2 (AS2) of cruzain
  54. Gating in plant plasma membrane aquaporins: the involvement of leucine in the formation of a pore constriction in the closed state
  55. Lessons learned about steered molecular dynamics simulations and free energy calculations
  56. In Search of GABAA Receptor’s Neurosteroid Binding Sites
  57. Thermal Stability of Globins: Implications of Flexibility and Heme Coordination Studied by Molecular Dynamics Simulations
  58. A computational investigation of the reactions of tyrosyl, tryptophanyl, and cysteinyl radicals with nitric oxide and molecular oxygen
  59. Cold-Adaptation Signatures in the Ligand Rebinding Kinetics to the Truncated Hemoglobin of the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125
  60. Mechanism of Sulfide Binding by Ferric Hemeproteins
  61. Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO Code
  62. Spectroscopy in Complex Environments from QM–MM Simulations
  63. Understanding the molecular basis of the high oxygen affinity variant human hemoglobin Coimbra
  64. Tertiary and quaternary structural basis of oxygen affinity in human hemoglobin as revealed by multiscale simulations
  65. Tyrosine oxidation and nitration in transmembrane peptides is connected to lipid peroxidation
  66. Naturally occurring fluorescence in frogs
  67. Kinetics, subcellular localization, and contribution to parasite virulence of a Trypanosoma cruzi hybrid type A heme peroxidase ( Tc APx-CcP)
  68. Role of Core Electrons in Quantum Dynamics Using TDDFT
  69. PrxQ B from Mycobacterium tuberculosis is a monomeric, thioredoxin-dependent and highly efficient fatty acid hydroperoxide reductase
  70. Exploring the Catalytic Mechanism of Human Glutamine Synthetase by Computer Simulations
  71. Experimental and Theoretical Study of the High-Temperature UV–Visible Spectra of Aqueous Hydroquinone and 1,4-Benzoquinone
  72. Access and Binding of H2S to Hemeproteins: The Case of HbI of Lucina pectinata
  73. Theoretical investigation of the mechanism of nitroxyl decomposition in aqueous solution
  74. Coarse-Grained Simulations of Heme Proteins: Validation and Study of Large Conformational Transitions
  75. Impact of human galectin-1 binding to saccharide ligands on dimer dissociation kinetics and structure
  76. Structural Study of a Flexible Active Site Loop in Human Indoleamine 2,3-Dioxygenase and Its Functional Implications
  77. Structural Insights into the HWE Histidine Kinase Family: The Brucella Blue Light-Activated Histidine Kinase Domain
  78. A quantitative model for oxygen uptake and release in a family of hemeproteins
  79. Evolutionary and Functional Relationships in the Truncated Hemoglobin Family
  80. Mapping the protein-binding sites for iridium(iii)-based CO-releasing molecules
  81. Structural Plasticity in Globins
  82. Destabilization of the torsioned conformation of a ligand side chain inverts the LXRβ activity
  83. Molecular Basis of Hydroperoxide Specificity in Peroxiredoxins: The Case of AhpE from Mycobacterium tuberculosis
  84. The N-terminal pre-A region ofMycobacterium tuberculosis2/2HbN promotes NO-dioxygenase activity
  85. Exploring the molecular basis of neurosteroid binding to the β3 homopentameric GABA A receptor
  86. Ligand uptake in Mycobacterium tuberculosis truncated hemoglobins is controlled by both internal tunnels and active site water molecules
  87. Structural flexibility of the heme cavity in the cold-adapted truncated hemoglobin from the Antarctic marine bacteriumPseudoalteromonas haloplanktisTAC125
  88. Insights into the mechanism of the reaction between hydrogen sulfide and peroxynitrite
  89. Molecular Mechanism of Myoglobin Autoxidation: Insights from Computer Simulations
  90. Ligand uptake in Mycobacterium tuberculosis truncated hemoglobins is controlled by both internal tunnels and active site water molecules
  91. Bridging Theory and Experiment to Address Structural Properties of Truncated Haemoglobins
  92. Engineered chimeras reveal the structural basis of hexacoordination in globins: A case study of neuroglobin and myoglobin
  93. Reactivity of Inorganic Sulfide Species toward a Heme Protein Model
  94. Interplay of the H-Bond Donor–Acceptor Role of the Distal Residues in Hydroxyl Ligand Stabilization of Thermobifida fusca Truncated Hemoglobin
  95. Interaction between Proteins and Ir Based CO Releasing Molecules: Mechanism of Adduct Formation and CO Release
  96. Mechanistic Insight into the Enzymatic Reduction of Truncated Hemoglobin N of Mycobacterium tuberculosis
  97. Molecular basis of thermal stability in truncated (2/2) hemoglobins
  98. Ligand Uptake Modulation by Internal Water Molecules and Hydrophobic Cavities in Hemoglobins
  99. Structural basis of redox-dependent modulation of galectin-1 dynamics and function
  100. Thiol redox biochemistry: insights from computer simulations
  101. Coupling of tyrosine deprotonation and axial ligand exchange in nitrocytochrome c
  102. The extraordinary catalytic ability of peroxiredoxins: a combined experimental and QM/MM study on the fast thiol oxidation step
  103. Mechanism of cysteine oxidation by peroxynitrite: An integrated experimental and theoretical study
  104. H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin
  105. Small ligand–globin interactions: Reviewing lessons derived from computer simulation
  106. Molecular basis of the NO trans influence in quaternary T‐state human hemoglobin: A computational study
  107. Hydrophobic Effect Drives Oxygen Uptake in Myoglobin via Histidine E7
  108. Quaternary structure effects on the hexacoordination equilibrium in rice hemoglobin rHb1: Insights from molecular dynamics simulations
  109. The key role of water in the dioxygenase function of Escherichia coli flavohemoglobin
  110. Conformational States of 2′-C-Methylpyrimidine Nucleosides in Single and Double Nucleic Acid Stranded Structures
  111. Coordination of peroxide to the CuM center of peptidylglycine α-hydroxylating monooxygenase (PHM): structural and computational study
  112. Biophysical Characterisation of Neuroglobin of the Icefish, a Natural Knockout for Hemoglobin and Myoglobin. Comparison with Human Neuroglobin
  113. Role of PheE15 Gate in Ligand Entry and Nitric Oxide Detoxification Function of Mycobacterium tuberculosis Truncated Hemoglobin N
  114. pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4
  115. Molecular basis of intramolecular electron transfer in proteins during radical-mediated oxidations: Computer simulation studies in model tyrosine–cysteine peptides in solution
  116. Following Ligand Migration Pathways from Picoseconds to Milliseconds in Type II Truncated Hemoglobin from Thermobifida fusca
  117. The Caenorhabditis elegans DAF-12 nuclear receptor: Structure, dynamics, and interaction with ligands
  118. Molecular Basis of the Mechanism of Thiol Oxidation by Hydrogen Peroxide in Aqueous Solution: Challenging the SN2 Paradigm
  119. Complete Reaction Mechanism of Indoleamine 2,3-Dioxygenase as Revealed by QM/MM Simulations
  120. Fluoride as a Probe for H-Bonding Interactions in the Active Site of Heme Proteins: The Case of Thermobifida fusca Hemoglobin
  121. Structural Model for p75NTR–TrkA Intracellular Domain Interaction: A Combined FRET and Bioinformatics Study
  122. Ligand Migration in Methanosarcina acetivorans Protoglobin: Effects of Ligand Binding and Dimeric Assembly
  123. Molecular Basis for the Substrate Stereoselectivity in Tryptophan Dioxygenase
  124. When Galectins Recognize Glycans: From Biochemistry to Physiology and Back Again
  125. Protein dynamics and ligand migration interplay as studied by computer simulation
  126. An Integrated Computational Analysis of the Structure, Dynamics, and Ligand Binding Interactions of the Human Galectin Network
  127. Aromatic–Aromatic Interactions in Proteins: Beyond the Dimer
  128. Comparing and combining implicit ligand sampling with multiple steered molecular dynamics to study ligand migration processes in heme proteins
  129. Structural basis for ligand recognition in a mushroom lectin: solvent structure as specificity predictor
  130. Role of the Distal Hydrogen-Bonding Network in Regulating Oxygen Affinity in the Truncated Hemoglobin III from Campylobacter jejuni
  131. Tetrachlorocarbonyliridates: Water-Soluble Carbon Monoxide Releasing Molecules Rate-Modulated by the Sixth Ligand
  132. Protonation of histidine 55 affects the oxygen access to heme in the alpha chain of the hemoglobin from the Antarctic fish Trematomus bernacchii
  133. Exploring the molecular basis of human manganese superoxide dismutase inactivation mediated by tyrosine 34 nitration
  134. Structure and dynamics of Antarctic fish neuroglobin assessed by computer simulations
  135. Coordinated nitroxyl anion is produced and released as nitrous oxide by the decomposition of iridium-coordinated nitrosothiols
  136. Ligand Migration in the Apolar Tunnel ofCerebratulus lacteusMini-Hemoglobin
  137. Heme Pocket Structural Properties of a Bacterial Truncated Hemoglobin from Thermobifida fusca
  138. The peculiar heme pocket of the 2/2 hemoglobin of cold-adapted Pseudoalteromonas haloplanktis TAC125
  139. Inhibitory effect of quercetin on matrix metalloproteinase 9 activity Molecular mechanism and structure–activity relationship of the flavonoid–enzyme interaction
  140. Substrate stereo‐specificity in tryptophan dioxygenase and indoleamine 2,3‐dioxygenase
  141. Linking the Structure and Thermal Stability of β-Galactoside-Binding Protein Galectin-1 to Ligand Binding and Dimerization Equilibria
  142. Role of Heme Distortion on Oxygen Affinity in Heme Proteins: The Protoglobin Case
  143. 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
  144. Copper-Transfer Mechanism from the Human Chaperone Atox1 to a Metal-Binding Domain of Wilson Disease Protein
  145. High Protein Structural Flexibility Of A Truncated Hemoglobin From An Antarctic Cold-Adapted Bacterium
  146. Unraveling the molecular basis for ligand binding in truncated hemoglobins: The trHbO Bacillus subtilis case
  147. Molecular Basis for the Electric Field Modulation of Cytochrome c Structure and Function
  148. Evidence for a ferryl intermediate in a heme-based dioxygenase
  149. Carbohydrate-Binding Proteins: Dissecting Ligand Structures through Solvent Environment Occupancy
  150. Role of Pre-A Motif in Nitric Oxide Scavenging by Truncated Hemoglobin, HbN, of Mycobacterium tuberculosis
  151. The hemoglobins of the sub‐Antarctic fish Cottoperca gobio, a phyletically basal species – oxygen‐binding equilibria, kinetics and molecular dynamics
  152. Molecular Basis for the pH Dependent Structural Transition of Nitrophorin 4
  153. pH-Dependent Mechanism of Nitric Oxide Release in Nitrophorins 2 and 4
  154. Exploring the Nitric Oxide Detoxification Mechanism of Mycobacterium tuberculosis Truncated Haemoglobin N
  155. High pressure reveals structural determinants for globin hexacoordination: Neuroglobin and myoglobin cases
  156. Hemisuccinate of 21-Hydroxy-6,19-Epoxyprogesterone: A Tissue-Specific Modulator of the Glucocorticoid Receptor
  157. QM–MM investigation of the reaction products between nitroxyl and O2 in aqueous solution
  158. A Microscopic Study of the Deoxyhemoglobin-Catalyzed Generation of Nitric Oxide from Nitrite Anion
  159. Dynamical Characterization of the Heme NO Oxygen Binding (HNOX) Domain. Insight into Soluble Guanylate Cyclase Allosteric Transition
  160. Theoretical insight into the hydroxylamine oxidoreductase mechanism
  161. A Unique Family of Stable and Water-Soluble S-Nitrosothiol Complexes
  162. Structural determinants of ligand migration in Mycobacterium tuberculosis truncated hemoglobin O
  163. Structural and Energetic Study of Cisplatin and Derivatives: Comparison of the Performance of Density Funtional Theory Implementations
  164. Synthesis, Structure, and Reactivity of Aliphatic Primary Nitrosamines Stabilized by Coordination to [IrCl5]2−
  165. Exploring the Molecular Basis of Action of the Passive Antiglucocorticoid 21-Hydroxy-6,19-epoxyprogesterone
  166. Bond or Cage Effect:  How Nitrophorins Transport and Release Nitric Oxide
  167. Mechanism of Product Release in NO Detoxification from Mycobacterium tuberculosis Truncated Hemoglobin N
  168. Exploring the molecular basis of heme coordination in human neuroglobin
  169. DFT study on the reactivity of iron porphyrins tuned by ring substitution
  170. Nitric Oxide Reactivity with Globins as Investigated Through Computer Simulation
  171. Electronic Perturbation in a Molecular Nanowire of [IrCl5(NO)]− Units
  172. HNO trapping and assisted decomposition of nitroxyl donors by ferric hemes
  173. QM-MM Investigation of the Reaction of Peroxynitrite with Carbon Dioxide in Water
  174. Characterization of the Galectin-1 Carbohydrate Recognition Domain in Terms of Solvent Occupancy
  175. 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
  176. Dynamical Regulation of Ligand Migration by a Gate-Opening Molecular Switch in Truncated Hemoglobin-N from Mycobacterium tuberculosis
  177. Oxygen affinity controlled by dynamical distal conformations: The soybean leghemoglobin and the Paramecium caudatum hemoglobin cases
  178. Electric field effects on the reactivity of heme model systems
  179. The Catalytic Mechanism of Peptidylglycine α-Hydroxylating Monooxygenase Investigated by Computer Simulation
  180. Heme Protein Oxygen Affinity Regulation Exerted by Proximal Effects
  181. Ligand-induced dynamical regulation of NO conversion in Mycobacterium tuberculosis truncated hemoglobin-N
  182. Dioxygen affinity in heme proteins investigated by computer simulation
  183. A Surprisingly Stable S-Nitrosothiol Complex
  184. Free Energy Calculations with Non-Equilibrium Methods: Applications of the Jarzynski Relationship
  185. Modeling heme proteins using atomistic simulations
  186. Two distinct heme distal site states define Cerebratulus lacteus mini-hemoglobin oxygen affinity
  187. Solvent Effects on Peroxynitrite Structure and Properties from QM/MM Simulations
  188. Proximal effects in the modulation of nitric oxide synthase reactivity: a QM-MM study
  189. Mechanisms of NO Release by N1-Nitrosomelatonin:  Nucleophilic Attack versus Reducing Pathways
  190. Solvation and Structure of LiAlH4 in Ethereal Solvents
  191. Nitric Oxide Interaction with Cytochromec‘ and Its Relevance to Guanylate Cyclase. Why Does the Iron Histidine Bond Break?
  192. Multiple-Steering QM−MM Calculation of the Free Energy Profile in Chorismate Mutase
  193. Discrimination of Nitroxyl and Nitric Oxide by Water-Soluble Mn(III) Porphyrins
  194. Theoretical Study of the Truncated Hemoglobin HbN:  Exploring the Molecular Basis of the NO Detoxification Mechanism
  195. Transnitrosation of Nitrosothiols:  Characterization of an Elusive Intermediate
  196. NMR and molecular dynamics studies of the interaction of melatonin with calmodulin
  197. QM−MM Study of Nitrite Reduction by Nitrite Reductase of Pseudomonas aeruginosa
  198. Ab Initio Study of NMR 15N Chemical Shift Differences Induced by Ca2+ Binding to EF-Hand Proteins
  199. Fast Nitroxyl Trapping by Ferric Porphyrins
  200. Modulation of the NO trans effect in heme proteins: implications for the activation of soluble guanylate cyclase
  201. Electronic spectra of indolyl radicals: a time-dependent DFT study
  202. Solvent-induced symmetry breaking of nitrate ion in aqueous clusters: A quantum-classical simulation study
  203. Physiological concentrations of melatonin inhibit the nitridergic pathway in the Syrian hamster retina
  204. Reaction pathways of 2,2,2-trifluoroethylamine and n-butylamine with [Ru(bpy)2(NO)Cl]2+
  205. Molecular structure effects on the kinetics of hydroxyl radical addition to azo dyes
  206. Thermal and solvent effects on the coordination structure of LiAlH4: a computational study
  207. Environment effects on chemical reactivity of heme proteins
  208. Structure and spin‐state energetics of an iron porphyrin model: An assessment of theoretical methods
  209. Molecular relaxation and metalloenzyme active site modeling
  210. Nitrosation of melatonin by nitric oxide: a computational study
  211. Hydrogen Bonding and O2Affinity of Hemoglobins
  212. 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
  213. Structure, solvation, and bonding in pentacyano(L)ferrate(II) ions (L=aliphatic amine): a density functional study
  214. Scavenging of NO by Melatonin
  215. Computer simulation study of HNO3 dissociation in aqueous clusters
  216. Concertedness and solvent effects in multiple proton transfer reactions: The formic acid dimer in solution
  217. N-Nitrosomelatonin
  218. Nitric Oxide Binding to Ferric Cytochrome P450:  A Computational Study
  219. Hybrid Quantum Classical Molecular Dynamics Simulation of the Proton-Transfer Reaction of HO- with HBr in Aqueous Clusters
  220. Reactions of Melatonin and Related Indoles with Free Radicals:  A Computational Study
  221. An ab initio path integral Monte Carlo simulation method for molecules and clusters: Application to Li4 and Li5+
  222. Theoretical and Experimental Study of Medium Effects on the Structure and Spectroscopy of the [Fe(CN)5NO]2-Ion
  223. Solvent effects in density functional calculations of uracil and cytosine tautomerism
  224. Time scales and other problems in linking simulations of simple chemical systems to more complex ones
  225. Electronic spectra of NaAr4and NaAr6: Isomerization and melting
  226. Is aluminum-argon (AlAr12) icosahedral?
  227. Accurate non-local electron—argon pseudopotential for condensed phase simulation
  228. On the Hill determinant method
  229. Potential energy curves of diatomic molecules from the Hill determinant method
  230. Alternative treatment of rotational quantum systems
  231. Generalized Hill determinant method
  232. Vibrational-rotational energy levels of diatomic molecules from the hill determinant method