Electron transfer pathways from quantum dynamics simulations.

This work explores the possibility of simulating an electron transfer process between a donor and an acceptor in real time using time-dependent density functional theory electron dynamics. To achieve this objective, a central issue to resolve is the definition of the initial state. This must be a non-equilibrium electronic state able to trigger the charge transfer dynamics; here, two schemes are proposed to prepare such states. One is based on the combination of the density matrices of the donor and acceptor converged separately with appropriate charges (for example, -1 for the donor and +1 for the acceptor). The second approach relied on constrained DFT to localize the charge on each fragment. With these schemes, electron transfer processes are simulated in different model systems of increasing complexity: an atomic hydrogen dimer, a polyacetylene chain, and the active site of the T. cruzi hybrid type A heme peroxidase, for which two possible electron transfer paths have been postulated. For the latter system, the present methodology applied in a hybrid Quantum Mechanics - Molecular Mechanics framework allows us to establish the relative probabilities of each path and provides insight into the inhibition of the electron transfer provoked by the substitution of tryptophan by phenylalanine in the W233F mutant.

Multiscale Modeling of Thiol Overoxidation in Peroxiredoxins by Hydrogen Peroxide.

In this work, we employ a multiscale quantum-classical mechanics (QM/MM) scheme to investigate the chemical reactivity of sulfenic acids toward hydrogen peroxide, both in aqueous solution and in the protein environment of the peroxiredoxin alkyl hydroperoxide reductase E from Mycobacterium tuberculosis (MtAhpE). The reaction of oxidation of cysteine with hydrogen peroxides, catalyzed by peroxiredoxins, is usually accelerated several orders of magnitude in comparison with the analogous reaction in solution. The resulting cysteine sulfenic acid is then reduced in other steps of the catalytic cycle, recovering the original thiol. However, under some conditions, the sulfenic acid can react with another equivalent of oxidant to form a sulfinic acid. This process is called overoxidation and has been associated with redox signaling. Herein, we employed a multiscale scheme based on density function theory calculations coupled to the classical AMBER force field, developed in our group, to establish the molecular basis of thiol overoxidation by hydrogen peroxide. Our results suggest that residues that play key catalytic roles in the oxidation of MtAhpE are not relevant in the overoxidation process. Indeed, the calculations propose that the process is unfavored by this particular enzyme microenvironment.

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

Human hemoglobin (Hb) Coimbra (ßAsp99Glu) is one of the seven ßAsp99 Hb variants described to date. All ßAsp99 substitutions result in increased affinity for O2 and decreased heme-heme cooperativity and their carriers are clinically characterized by erythrocytocis, caused by tissue hypoxia. Since ßAsp99 plays an important role in the allosteric α1ß2 interface and the mutation in Hb Coimbra only represents the insertion of a CH2 group in this interface, the present study of Hb Coimbra is important for a better understanding of the global impact of small modifications in this allosteric interface. We carried out functional, kinetic and dynamic characterization of this hemoglobin, focusing on the interpretation of these results in the context of a growth of the position 99 side chain length in the α1ß2 interface. Oxygen affinity was evaluated by measuring p50 values in distinct pHs (Bohr effect), and the heme-heme cooperativity was analyzed by determining the Hill coefficient (n), in addition to the effect of the allosteric effectors inositol hexaphosphate (IHP) and 2,3-bisphosphoglyceric acid (2,3-BPG). Computer simulations revealed a stabilization of the R state in the Coimbra variant with respect to the wild type, and consistently, the T-to-R quaternary transition was observed on the nanosecond time scale of classical molecular dynamics simulations.

Structural Plasticity in Globins: Role of Protein Dynamics in Defining Ligand Migration Pathways.

Globins are a family of proteins characterized by the presence of the heme prosthetic group and involved in variety of biological functions in the cell. Due to their biological relevance and widespread distribution in all kingdoms of life, intense research efforts have been devoted to disclosing the relationships between structural features, protein dynamics, and function. Particular attention has been paid to the impact of differences in amino acid sequence on the topological features of docking sites and cavities and to the influence of conformational flexibility in facilitating the migration of small ligands through these cavities. Often, tunnels are carved in the interior of globins, and ligand exchange is regulated by gating residues. Understanding the subtle intricacies that relate the differences in sequence with the structural and dynamical features of globins with the ultimate aim of rationalizing the thermodynamics and kinetics of ligand binding continues to be a major challenge in the field. Due to the evolution of computational techniques, significant advances into our understanding of these questions have been made. In this review we focus our attention on the analysis of the ligand migration pathways as well as the function of the structural cavities and tunnels in a series of representative globins, emphasizing the synergy between experimental and theoretical approaches to gain a comprehensive knowledge into the molecular mechanisms of this diverse family of proteins.

Molecular mechanism of myoglobin autoxidation: insights from computer simulations.

Myoglobin (Mb) and hemoglobin have the biological ability to carry/store oxygen (O2), a property which requires its heme iron atom to be in the ferrous--Fe(II)--state. However, the thermodynamically stable state in the presence of O2 is Fe(III) and thus the oxidation rate of a globin is a critical parameter related to its function. Mb has been extensively studied and many mutants have been characterized regarding its oxygen mediated oxidation (i.e., autoxidation) rates. Site directed mutants in residues 29 (B10), which shapes the distal cavity, and 64 (E7), the well-known histidine gate, have been shown to display a wide range of autoxidation rate constants. In this work, we have thoroughly studied the mechanism underlying the autoxidation process by means of state-of-the-art computer simulation methodologies, using Mb and site directed mutants as benchmark cases. Our results explain the observed autoxidation rate tendencies in different variants of Mb, L29F < wt < L29A = H64Q < H64F < H64A, and shed light on several aspects of the reaction at the atomic level. First, water access to the distal pocket is a key event and the observed acid catalysis relies on HisE7 protonation and opening of the His gate to allow water access, rather than protonation of the oxy heme itself. Our results also suggest that the basic mechanism, i.e., superoxide displacement by hydroxide anion, is energetically more feasible. Finally, we confirmed that distal hydrogen bonds protect the oxy complex from autoxidation.

Feasibility testing of an automated image-capture method to aid dietary recall.

BACKGROUND/OBJECTIVES: The accuracy of dietary recalls might be enhanced by providing participants with photo images of foods they consumed during the test period. SUBJECTS/METHODS: We examined the feasibility of a system (Image-Diet Day) that is a user-initiated camera-equipped mobile phone that is programmed to automatically capture and transmit images to a secure website in conjunction with computer-assisted, multipass, 24-h dietary recalls in 14 participants during 2007. Participants used the device during eating periods on each of the three independent days. Image processing filters successfully eliminated underexposed, overexposed and blurry images. The captured images were accessed by the participants using the ImageViewer software while completing the 24-h dietary recall on the following day. RESULTS: None of the participants reported difficulty using the ImageViewer. Images were deemed 'helpful' or 'sort of helpful' by 93% of participants. A majority (79%) of users reported having no technical problems, but 71% rated the burden of wearing the device as somewhat to very difficult, owing to issues such as limited battery life, self-consciousness about wearing the device in public and concerns about the field of view of the camera. CONCLUSION: Overall, these findings suggest that automated imaging is a promising technology to facilitate dietary recall. The challenge of managing the thousands of images generated can be met. Smaller devices with a broader field of view may aid in overcoming self-consciousness of the user with using or wearing the device.

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

The influence of pressure on the equilibrium between five-(5c) and six-coordination (6c) forms in neuroglobin (Ngb) and myoglobin (Mb) has been examined by means of molecular dynamics (MD) simulations at normal and high pressure. The results show that the main effect of high pressure is to reduce the protein mobility without altering the structure in a significant manner. Moreover, our data suggest that the equilibrium between 5c and 6c states in globins is largely controlled by the structure and dynamics of the C-D region. Finally, in agreement with the available experimental data, the free energy profiles obtained from steered MD for both proteins indicate that high pressure enhances hexacoordination. In Ngb, the shift in equilibrium is mainly related to an increase in the 6c-->5c transition barrier, whereas in Mb such a shift is primarily due to a destabilization of the 5c state.

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.

Vertical excitation and electron detachment energies associated with the optical absorption of iodide ions dissolved in supercritical ammonia at 420 K have been calculated in two limiting scenarios: as a solvated free I- ion and forming a K+I- contact ion pair (CIP). The evolution of the transition energies as a result of the gradual building up of the solvation structure was studied for each absorbing species as the solvent's density increased, i.e., changing the NH3 supercritical thermodynamic state. In both cases, if the solvent density is sufficiently high, photon absorption produces a spatially extended electron charge beyond the volume occupied by the solvated solute core; this excited state resembles a typical charge-transfer-to-solvent (CTTS) state. A combination of classical molecular dynamics simulations followed by quantum mechanical calculations for the ground, first-excited, and electron-detached electronic states have been carried out for the system consisting of one donor species (free I- ion or K+I- CIP) surrounded by ammonia molecules. Vertical excitation and electron detachment energies were obtained by averaging 100 randomly chosen microconfigurations along the molecular dynamics trajectory computed for each thermodynamic condition (fluid density). Short- and long-range contributions of the solvent-donor interaction upon the CTTS states of I- and K+I- were identified by performing additional electronic structure calculations where only the solvent interaction due to the first neighbor molecules was taken into account. These computations, together with previous experimental evidence that we collected for the system, have been used to analyze the solvent effects on the CTTS transition. In this paper we have established the following: (i) the CTTS electron of free I- ion or K+I- CIP presents similar features, and it gradually localizes in close proximity of the iodine parent atom when the ammonia density is increased; (ii) for the free I- ion, the short-range solvent interaction contributes to the stabilization of the ground state more than it does for the CTTS excited state, which is evidenced experimentally as a blueshift in the maximum absorption of the CTTS transition when the density is increased; (iii) this effect is less noticeable for the K+I- ion pair, because in this case a tight solvation structure, formed by four NH3 molecules wedged between the ions, appears at very low density and is very little affected by changes in the density; (iv) the long-range contribution to the solvent stabilization can be neglected for the K+I- CIP, since the main features of its electronic transition can be explained on the basis of the vicinity of the cation; (v) however, the long-range solvent field contribution is essential for the free I- ion to become an efficient CTTS donor upon photoexcitation, and this establishes a difference in the CTTS behavior of I- in bulk and in clusters.

Nitrosation of melatonin by nitric oxide: a computational study.

Melatonin is being increasingly promoted as a therapeutic agent for the treatment of jet lag and insomnia, and is an efficient free radical scavenger. We have recently characterized a product for the reaction of melatonin with nitric oxide (NO), N-nitrosomelatonin. In the present work, reaction pathways with N1, C2, C4, C6 and C7 as possible targets for its reaction with NO that yield the respective nitroso derivatives have been investigated using semiempirical AM1 computational tools, both in vacuo and aqueous solution. Specifically, two different pathways were studied: a radical mechanism involving the hydrogen atom abstraction to yield a neutral radical followed by NO addition, and an ionic mechanism involving addition of nitrosonium ion to the indolic moiety. Our results show that the indolic nitrogen is the most probable site for nitrosation by the radical mechanism, whereas different targets are probable considering the ionic pathway. These results are in good agreement with previous experimental findings and provide a coherent picture for the interaction of melatonin with NO.

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.

Reaction pathways for the one- and two-electron reductions of [Fe(CN)(5)NO](2)(-) have been investigated by means of a density functional theory (DFT) approach combined with the polarized continuum model (PCM) of solvation. In addition, UV-vis spectroscopic data were obtained using ZINDO/S calculations including a point-charge model simulation of solvent effects. DFT methodologies have been used to assess the thermodynamical feasibility of protonation and cyanide-release processes for the reduced species. We conclude that [Fe(CN)(5)NO](3)(-) is a stable species in aqueous solution but may release cyanide yielding [Fe(CN)(4)NO](2)(-), consistent with experimental results. On the other hand, the [Fe(CN)(5)NO](4)(-) complex turns out to be unstable in solution, yielding the product of cyanide release, [Fe(CN)(4)NO](3)(-), and/or the protonated HNO complex. All the structural and spectroscopic (IR, UV-vis) predictions for the [Fe(CN)(5)HNO](3)(-) ion are consistent with the scarce but significant experimental evidence of its presence as an intermediate in nitrogen redox interconversion chemistry. Our computed data support an Fe(II)(LS) + NO(+) assignment for [Fe(CN)(5)NO](2)(-), an Fe(II)(LS) + NO assignment for the one-electron reduction product, but an Fe(I)(LS) + NO(+) for the one-electron product after dissociation of an axial cianide, and an Fe(II) + singlet NO(-) for the two-electron reduction species.

Nitric oxide binding to ferric cytochrome P450: a computational study.

The interaction between nitric oxide (NO) and the active site of ferric cytochrome P450 was studied by means of density functional theory (DFT), at the generalized gradient approximation level, and of the SAM1 semiempirical method. The electrostatic effects of the protein environment were included in our DFT scheme by using a hybrid quantum classical approach. The active-site model consisted of an iron(III) porphyrin, the adjacent cysteine residue, and one coordinated water molecule. For this system, spin populations and relative energies for selected spin states were computed. Interestingly, the unpaired electron density, the HOMO, and the LUMO were found to be highly localized on the iron and in an appreciable extent on the sulfur coordinated to the metal. This provides central information about the reactivity of nitric oxide with the active site. Since the substitution of a molecule of H2O by NO has been proposed as being responsible for the inhibition of the cytochrome in the presence of nitric oxide, we have analyzed the thermodynamic feasibility of the ligand exchange process. The structure of the nitrosylated active site was partially optimized using SAM1. A low-spin ground state was obtained for the nitrosyl complex, with a linear Fe-N-O angle. The trends found in Fe-N-O angles and Fe-N lengths of the higher energy spin states provided a notable insight into the electronic configuration of the complex within the framework of the Enemark and Feltham formalism. In relation to the protein environment, it was assessed that the electrostatic field has significant effects on several computed properties. However, in both vacuum and protein environments, the ligand exchange reaction turned out to be exergonic and the relative orders of spin states of the relevant species were the same.

Reactions of melatonin and related indoles with free radicals: a computational study.

Melatonin is being increasingly promoted as a therapeutic agent for the treatment of jet lag and insomnia and has been recently suggested to act as an efficient free-radical scavenger. In the present work, its mechanisms of action for scavenging hydroxyl radicals have been investigated using semiempirical AM1 and density functional theory (DFT) computational tools. Two different reactions were proposed as follows: one involving the abstraction of an indolic hydrogen to yield a neutral radical and another involving the addition of the hydroxyl radical to the indolic moiety. Our results show that, from a thermodynamical standpoint, melatonin may directly scavenge hydroxyl radicals both in vacuum and in aqueous solution. The structural requirements for free-radical-trapping ability have been examined comparing melatonin with related indoles. Computational data suggest that 5-methoxy and N-acetyl groups of melatonin do not significantly affect its thermodynamical capacity of free-radical trapping. The present results support experimental data on the potential of melatonin as a physiological or pharmacological antioxidant agent.