Theoretical studies on the influence of molecular interactions on the mechanism of electron transfer in photosynthetic reaction center ofRps. viridis

Based on the QM/MM optimized X-ray crystal structure of the photosynthetic reaction center (PRC) of purple bacteriaRhodopseudomonas (Rps.)viridis, quantum chemistry density functional method (DFT, B3LYP/6-31G) has been performed to study the interactions between the pigment molecules and either the surrounded amino acid residues or water molecules that are either axially coordinated or hydrogen bonded with the pigment molecules, leading to an explanation of the mechanism of the primary electron-transfer (ET) reactions in the PRC. Results show that the axial coordination of amino acid residues greatly raises theE _LUMO of pigment molecules and it is important for the possibility of ET to take place. Different hydrogen bonds between amino acid residues, water molecules and pigment molecules decrease theE _LUMO of the pigment molecules to different extents. It is crucial for the ET taking place from excited P along L branch and sustains that the ET is a one-step reaction without through accessory bacteriochlorophyll (ABChl b). It is insufficient to treat the whole protein surrounding as a homogeneous dielectric medium.     

Oxidation of methionine residues in aqueous solutions: free methionine and methionine in granulocyte colony-stimulating factor

The free energy barriers and a mechanism of the oxidation of the amino acid methionine in water and in granulocyte colony-stimulating factor (G-CSF) are analyzed via combined quantum mechanical and molecular mechanical (QM/MM) methods, constrained molecular dynamics, and committor probability calculations. The computed free energy barrier of free methionine amino acid is very close to the measured value (14.7 +/- 1.2 versus 15.5 +/- 0.02 kcal/mol). The reaction coordinate was found to be the difference between the O-O bond of H2O2 and the S-O bond, where the S is the sulfur atom of the methionine residue. It was confirmed by computing the committor probability distribution and the distribution of constrained forces that this coordinate is not coupled to the activation of other degrees of freedom. The computed free energies of the oxidation of methionine residues in G-CSF indicate that the protein environment has insignificant effects on the reaction barriers of oxidation. This result further validates our proposal that the access of solvent to methionine sites, as measured by the two-shell water coordination number, governs the kinetics of the oxidation reaction of methionine groups in a protein molecule. We also found that the number of hydrogen bonds between the distal oxygen of H2O2 and the water molecules near the methionine increases along the reaction coordinate as oxidation progresses, indicating that the charge separation developed during the oxidation by H2O2 is stabilized by specific interactions with water molecules, such as hydrogen bonding.     

酶切过程中肽段过烷基化对蛋白质定性和定量分析的影响

蛋白质的还原-烷基化是蛋白质酶切中的重要步骤,常用的烷基化试剂是碘乙酰胺(IAA),但是IAA除了和半胱氨酸发生反应,也可能和其他多种氨基酸发生副反应。我们模拟常规的酶切条件,系统地研究了蛋白质真实酶切时所有酶切肽段发生烷基化的情况。结果表明,多种氨基酸可以发生烷基化,其趋势为:半胱氨酸>肽段N端氨基酸>天冬氨酸>谷氨酸>组氨酸>天冬酰胺>赖氨酸>酪氨酸,同时也发现同一肽段上的氨基酸烷基化具有排他性和聚集性。根据定性结果,采用质谱多反应监测(MRM)技术对多个肽段进行了定量分析,评估了过烷基化对蛋白质定量分析的影响。该研究结果表明,过量的烷基化修饰对蛋白质的定性与定量分析都可能产生较大影响。在蛋白质组学研究的样本处理流程中,应避免样本的过烷基化。     

Secondary structure sensitivity of hydrogen bond lifetime dynamics in the protein hydration layer

The heterogeneous nature of a protein surface plays an essential role in its biological activity and molecular recognition, and this role is mediated at least partly through the surrounding water molecules. We have performed atomistic molecular dynamics simulations of an aqueous solution of HP-36 to investigate the correlation between the dynamics of the hydration layer water molecules and the lifetimes of protein-water hydrogen bonds. The nonexponential hydrogen bond lifetime correlation functions have been analyzed by using the formalism of Luzar and Chandler, which allowed identification of the quasi-bound states in the surface and quantification of the dynamic equilibrium between quasi-bound and free water molecules in terms of time-dependent rate of interconversion. It is noticed that, irrespective of the structural heterogeneity of different segments of the protein, namely the three alpha-helices, the positively charged amino acid residues form longer-lived hydrogen bonds with water. The overall relaxation behavior of protein-water hydrogen bonds is found to differ significantly among the three helices of the protein. Study of water number density fluctuation reveals that the hydration layer of helix-3 is much less rigid, which can be correlated with faster structural relaxation of the hydrogen bonds between its residues and water. This also agrees excellently with faster translational and rotational motions of water near helix-3, and hence the lower rigidity of its hydration layer. The lower rigidity of the helix-3 hydration layer also correlates well with the biological activity of the protein, as several of the active-site residues of HP-36 are located in helix-3.     

Studies of protein hydration in aqueous solution by high-resolution nuclear magnetic resonance spectroscopy

Individual hydration water molecules in aqueous protein solutions have been observed using experimental schemes for homonuclear two-dimensional and heteronuclear three-dimensional NMR experiments in H₂O solution, which do not require suppression of the solvent line by presaturation. In these experiments, the location of the hydration waters is determined from their nuclear Overhauser effects (NOE s) with individual hydrogen atoms of distinct amino acid residues. In the basic pancreatic trypsin inhibitor (BPTI ), four internal water molecules that had been reported in three different crystal forms were also found to be in the same locations in the solution structure, with lifetimes with respect to exchange of the water protons in excess of 0.3 ns. Additional NOE s with polypeptide protons located on the protein surface may involve either hydration water molecules or hydroxyl protons of amino acid side chains. Their total number is small compared to the number of NOE s expected from the hydration water molecules identified in the crystal structures of BPTI .     

Are pterins able to modulate oxidative stress?

Pterins (also known as pteridines) are common animal colorants that constitute heterocyclic compounds and have the highest nitrogen content of any pigment analyzed from animals. It has been reported that pterins modulate oxidative stress as these molecules are able to scavenge free radicals. Previous reports suggest three possible mechanisms that are responsible for scavenging free radicals; these are electron transfer (ET) reaction, hydrogen atom transfer (HAT) and radical addition. In this paper, the facility to scavenge free radicals (antiradical power) of pterins is analyzed, using density functional theory calculations and considering two possible mechanisms: ET and HAT. For the electron transfer process, considering the electron donor facility of the free radical scavenger molecules, vertical ionization energy of pterins indicates that the antiradical power of those pterins is lower than the antiradical power of any carotenoids (except for tetrahydrobiopterin). In terms of the HAT mechanism, the bond dissociation energy involved in the removal of one hydrogen atom from pterins is higher than for carotenoids (except for sepiapterin and 7,8-dihydrobiopterin). It can be expected that the most reactive molecules are those that have the smallest dissociation energy since the dissociation of the hydrogen atom is the first step of the reaction. This could indicate that some pterins are depicted as poorer antiradicals than carotenoids in terms of the HAT mechanism. Further studies focusing on the third mechanism (radical addition) and the kinetics of the reactions are necessary in order to fully understand the antiradical power of these substances. For this reason, work continues in order to clarify these aspects.     

Elucidation of Metal‐Ion Accumulation Induced by Hydrogen Bonds on Protein Surfaces by Using Porous Lysozyme Crystals Containing RhIII Ions as the Model Surfaces

Metal‐ion accumulation on protein surfaces is a crucial step in the initiation of small‐metal clusters and the formation of inorganic materials in nature. This event is expected to control the nucleation, growth, and position of the materials. There remain many unknowns, as to how proteins affect the initial process at the atomic level, although multistep assembly processes of the materials formation by both native and model systems have been clarified at the macroscopic level. Herein the cooperative effects of amino acids and hydrogen bonds promoting metal accumulation reactions are clarified by using porous hen egg white lysozyme (HEWL) crystals containing Rh^III ions, as model protein surfaces for the reactions. The experimental results reveal noteworthy implications for initiation of metal accumulation, which involve highly cooperative dynamics of amino acids and hydrogen bonds: i) Disruption of hydrogen bonds can induce conformational changes of amino‐acid residues to capture Rh^III ions. ii) Water molecules pre‐organized by hydrogen bonds can stabilize Rh^III coordination as aqua ligands. iii) Water molecules participating in hydrogen bonds with amino‐acid residues can be replaced by Rh^III ions to form polynuclear structures with the residues. iv) Rh^III aqua complexes are retained on amino‐acid residues through stabilizing hydrogen bonds even at low pH (≈2). These metal–protein interactions including hydrogen bonds may promote native metal accumulation reactions and also may be useful in the preparation of new inorganic materials that incorporate proteins.     

Mechanism of intramolecular electron transfer in the photoexcited Zn-substituted cytochrome c: theoretical and experimental perspective

Photoinduced electron transfer (ET) in zinc-substituted cytochrome c (Zn-cyt c) has been utilized in many studies on the long-range ET in protein. Attempting to understand its ET mechanism in terms of electronic structure of the molecule, we have calculated an all-electron wave function for the ground-state of Zn-cyt c on the basis of density functional theory (DFT). The four molecular orbitals (MOs) responsible for excitation by UV-vis light (Gouterman's 4-orbitals) are assigned on the basis of the excited states of chromophore model for Zn-porphine complex calculated with the time-dependent DFT method. ET rates between each Gouterman's 4-orbitals and other MOs were estimated using Fermi's golden rule. It appeared that the two occupied MOs of the 4-orbitals show exclusively higher ET rate from/to particular MOs that localize on outermost amino acid residues (Lys 7 or Asn 54), respectively, whereas ET rates involving the two unoccupied MOs of the 4-orbitals are much slower. These results imply that the intramolecular ET in photoexcited Zn-cyt c is governed by the hole transfer through occupied MOs. The couplings of MOs between zinc porphyrin core and specific amino acid residues on the protein surface have been demonstrated in Zn-cyt c immobilized on an Au electrode via carboxylic acid group-terminated self-assembled monolayer. The Zn-cyt c-modified electrode showed photocurrents responsible for photoillumination. The action spectrum of the photocurrent was identical with the absorption spectrum of Zn-cyt c, indicating photoinduced electron conduction via occupied MOs. The voltage dependence of the photocurrent appeared to be linear and bidirectional like a photoconductor, which strongly supports the intramolecular ET mechanism in Zn-cyt c proposed on the basis of the theoretical calculations.     

1D radical motion in protein pocket: proton-coupled electron transfer in human serum albumin

Photoinduced, proton-coupled electron transfer (ET) between 9,10-anthraquinone-2,6-disulfonate (ADQS) and an amino acid residue of tryptophan in human serum albumin (HSA) was observed using time-resolved electron paramagnetic resonance (TREPR). The ET reaction reduces the protein binding affinity of the ligand. TREPR chemically induced dynamic electron polarization (CIDEP) spectra establish that photoinduced ET takes place from the tryptophan residue (W214) to the excited triplet state of AQDS2- while bound in subdomain IIA, a protein cleft of HSA. The TREPR CIDEP signals also reveal that the anion radical of the ligand escapes toward the bulk water region by a one-dimensional translation diffusion process within the protein's pocket area. This pilot study of HSA demonstrates how TREPR CIDEP can provide significant means to investigate dynamic characteristics of protein-surface reactions.     

Electron transfer in a radical ion pair: quantum calculations of the solvent reorganization energy

Results are presented for an investigation of intermolecular electron transfer (ET) in solution by means of quantum calculations. The two molecules that are involved in the ET reaction form a solvent-separated radical ion pair. The solvent plays an important role in the ET between the two molecules. In particular, it can give rise to specific solute-solvent interactions with the solutes. An example of specific interactions is the formation of a hydrogen bond between a protic solvent and one of the molecules involved in the ET. We address the study of this system by means of quantum calculations on the solutes immersed in a continuum solvent. However, when the solvent can give rise to hydrogen bond formation with the negatively charged ion after ET, we explicitly consider solvent molecules in the solute cavity, determining the hydrogen bond energetic contribution to the overall interaction energy. Solute-solvent pair distribution functions, showing the different arrangement of solvent molecules before and after ET in the first solvation shell, are reported. We provide results of the solvent reorganization energy from quantum calculations for both the two isolated fragments and the ion pair in solution. Results are in agreement with available experimental data.     

Effect of solvents on the rate of oxidation of acetaldehyde by peroxyacetic acid from the point of view of intermolecular hydrogen bonding

Summary It was shown that retardation of reaction found in some solvents is due to the blocking effect of solvent molecules hydrogen-bonded to peroxyacetic acid molecules. The presence of hydrogen bonds between peroxyacetic acid molecules and solvent molecules (nitromethane, acetone) was established by the determination of infrared absorption spectra.     

On the mechanism of hydrogen evolution at GaAs electrodes

The hydrogen evolution reaction at n- and p-GaAs electrodes has been reinvestigated. As in the case of metal electrodes, hydrogen evolution can occur in two ways: at ?0.5 V (SCE) hydronium ions are reduced, at ?1.25 V (SCE) reduction of water molecules takes place. It is confirmed that in both cases conduction band electrons are responsible for the two reduction steps, forming adsorbed hydrogen atoms in the first and hydrogen molecules in the second step. Hole injection can occur only to a negligible extent, although it appears energetically feasible.     

The effect of glutamic acid side chain on acidity constant of lysine in beta-sheet: A density functional theory study

In this work, the possibility of proton transfer between side chain of lysine and glutamic acid in peptide of Glu^?-Ala-Lys⁺ was demonstrated using density functional theory (DFT). We have shown that the proton transfer takes place between side chain of glutamic and lysine residues through the hydrogen bond formation. The structures of transition state for proton transfer reaction were detected in gas and solution phases. Our kinetic studies show that the proton transfer reaction rate in gas phase is higher than solution phase. The ionization constant (pK _a) value of lysine residue in peptide was estimated 1.039 which is lower than intrinsic pK _a of lysine amino acid.     

Catalysis of Hydrogen Evolution by Polylysine,Polyarginine and Polyhistidine at Mercury Electrodes

Protein catalyzed hydrogen evolution reaction at mercury‐containing electrodes controlled by constant‐current chronopotentiometric stripping (CPS) is representing a new tool useful in protein research. The resulting CPS peak H is sensitive to changes in the protein structure and its amino acid composition. Besides CPS, cyclic voltammetry appears to be useful for study of poly(amino acids) as an intermediate model system between peptides and macromolecular proteins. Here we show that similarly as arginine in polyarginine and lysine in polylysine also histidine residues in polyhistidine contribute to the catalysis of hydrogen evolution under the given conditions. Peak potentials of individual poly(amino acids) are different and depend on the type of amino acid residues.     

Carbonic anhydrase activators. Activation of isozymes I, II, IV, VA, VII, and XIV with l- and d-histidine and crystallographic analysis of their adducts with isoform II: engineering proton-transfer processes within the active site of an enzyme

Activation of six human carbonic anhydrases (CA, EC 4.2.1.1), that is, hCA I, II, IV, VA, VII, and XIV, with l- and d-histidine was investigated through kinetics and by X-ray crystallography. l-His was a potent activator of isozymes I, VA, VII, and XIV, and a weaker activator of hCA II and IV. d-His showed good hCA I, VA, and VII activation properties, being a moderate activator of hCA XIV and a weak activator of hCA II and IV. The structures as determined by X-ray crystallography of the hCA II-l-His/d-His adducts showed the activators to be anchored at the entrance of the active site, contributing to extended networks of hydrogen bonds with amino acid residues/water molecules present in the cavity, explaining their different potency and interaction patterns with various isozymes. The residues involved in l-His recognition were His64, Asn67, Gln92, whereas three water molecules connected the activator to the zinc-bound hydroxide. Only the imidazole moiety of l-His interacted with these amino acids. For the d-His adduct, the residues involved in recognition of the activator were Trp5, His64, and Pro201, whereas two water molecules connected the zinc-bound water to the activator. Only the COOH and NH(2) moieties of d-His participated in hydrogen bonds with these residues. This is the first study showing different binding modes of stereoisomeric activators within the hCA II active site, with consequences for overall proton-transfer processes (rate-determining for the catalytic cycle). The study also points out differences of activation efficiency between various isozymes with structurally related activators, convenient for designing alternative proton-transfer pathways, useful both for a better understanding of the catalytic mechanism and for obtaining pharmacologically useful derivatives, for example, for the management of Alzheimer's disease.     

Molecular dynamics study of the solvation of an alpha-helical transmembrane peptide by DMSO

A 10-ns molecular dynamics study of the solvation of a hydrophobic transmembrane helical peptide in dimethyl sulfoxide (DMSO) is presented. The objective is to analyze how this aprotic polar solvent is able to solvate three groups of amino acid residues (i.e., polar, apolar, and charged) that are located in a stable helical region of a transmembrane peptide. The 25-residue peptide (sMTM7) used mimics the cytoplasmic proton hemichannel domain of the seventh transmembrane segment (TM7) from subunit a of H(+)-V-ATPase from Saccharomyces cerevisiae. The three-dimensional structure of peptide sMTM7 in DMSO has been previously solved by NMR spectroscopy. The radial and spatial distributions of the DMSO molecules surrounding the peptide as well as the number of hydrogen bonds between DMSO and the side chains of the amino acid residues involved are extracted from the molecular dynamics simulations. Analysis of the molecular dynamics trajectories shows that the amino acid side chains are fully embedded in DMSO. Polar and positively charged amino acid side chains have dipole-dipole interactions with the oxygen atom of DMSO and form hydrogen bonds. Apolar residues become solvated by DMSO through the formation of a hydrophobic pocket in which the methyl groups of DMSO are pointing toward the hydrophobic side chains of the residues involved. The dual solvation properties of DMSO cause it to be a good membrane-mimicking solvent for transmembrane peptides that do not unfold due to the presence of DMSO.     

The Catalytic Mechanism of Fluoroacetate Dehalogenase: A Computational Exploration of Biological Dehalogenation

The biological dehalogenation of fluoroacetate carried out by fluoroacetate dehalogenase is discussed by using quantum mechanical/molecular mechanical (QM/MM) calculations for a whole‐enzyme model of 10 800 atoms. Substrate fluoroacetate is anchored by a hydrogen‐bonding network with water molecules and the surrounding amino acid residues of Arg105, Arg108, His149, Trp150, and Tyr212 in the active site in a similar way to haloalkane dehalogenase. Asp104 is likely to act as a nucleophile to attack the α‐carbon of fluoroacetate, resulting in the formation of an ester intermediate, which is subsequently hydrolyzed by the nucleophilic attack of a water molecule to the carbonyl carbon atom. The cleavage of the strong C? F bond is greatly facilitated by the hydrogen‐bonding interactions between the leaving fluorine atom and the three amino acid residues of His149, Trp150, and Tyr212. The hydrolysis of the ester intermediate is initiated by a proton transfer from the water molecule to His271 and by the simultaneous nucleophilic attack of the water molecule. The transition state and produced tetrahedral intermediate are stabilized by Asp128 and the oxyanion hole composed of Phe34 and Arg105.     

Site-selective photoinduced electron transfer from alcoholic solvents to the chromophore facilitated by hydrogen bonding: a new fluorescence quenching mechanism

Solute-solvent intermolecular photoinduced electron transfer (ET) reaction was proposed to account for the drastic fluorescence quenching behaviors of oxazine 750 (OX750) chromophore in protic alcoholic solvents. According to our theoretical calculations for the hydrogen-bonded OX750-(alcohol)(n) complexes using the time-dependent density functional theory (TDDFT) method, we demonstrated that the ET reaction takes place from the alcoholic solvents to the chromophore and the intermolecular ET passing through the site-specific intermolecular hydrogen bonds exhibits an unambiguous site selectivity. In our motivated experiments of femtosecond time-resolved stimulated emission pumping fluorescence depletion spectroscopy (FS TR SEP FD), it could be noted that the ultrafast ET reaction takes place as fast as 200 fs. This ultrafast intermolecular photoinduced ET is much faster than the diffusive solvation process, and even significantly faster than the intramolecular vibrational redistribution (IVR) process of the OX750 chromophore. Therefore, the ultrafast intermolecular ET should be coupled with the hydrogen-bonding dynamics occurring in the sub-picosecond time domain. We theoretically demonstrated for the first time that the selected hydrogen bonds are transiently strengthened in the excited states for facilitating the ultrafast solute-solvent intermolecular ET reaction.     

Water effects on electron transfer in azurin dimers

Recent experimental and theoretical analyses indicate that water molecules between or near redox partners can significantly affect their electron-transfer (ET) properties. Here, we study the effects of intervening water molecules on the electron self-exchange reaction of azurin (Az) by using a newly developed ab-initio method to calculate transfer integrals between molecular sites. We show that the insertion of water molecules in the gap between the copper active sites of Az dimers slows down the exponential decay of the ET rates with the copper-to-copper distance. Depending on the distance between the redox sites, water can enhance or suppress the electron-transfer kinetics. We show that this behavior can be ascribed to the simultaneous action of two competing effects: the electrostatic interaction of water with the protein subsystem and its ability to mediate ET coupling pathways.     

Amino acid end-group in commercial heparin. II. Reaction kinetics of the amino end groups with 2,4,6-trinitrobenzenesulfonic acid

Three different commercial heparins were trinitophenylated with 2,4,6-trinitrobenzenesulfonic acid (TNBS) under aqueous conditions. The reaction kinetics of amino groups in heparin with TNBS showed that the reactivities of amino groups were significantly different for free amino groups on heparin, compared to reactivities in peptides and amino acid residues attached to heparin molecules. With TNBS, unreactive amino groups were always present during the reaction.