Effect of hydrogen bonds on the energetics of electron transfer

For a model system consisting of a special pair of bacteriochlorophyll molecules (P) and a primary quinone with the nearest environment (QA) (which are acceptor and donor in the recombination reaction in Rhodobacter sphaeroides reaction center, respectively), energies of P+QA(-) and PQA states were calculated. Calculations were performed using several stable QA conformations differing by the positions of hydrogen bond protons. Essential influence of proton positions on the energy of vertical transition P+QA(-) --> PQA was shown.     

The influence of hydrogen bonds on electron transfer rate in photosynthetic RCs

Hydrogen bonds formed between photosynthetic reaction centers (RCs) and their cofactors were shown to affect the efficacy of electron transfer. The mechanism of such influence is determined by sensitivity of hydrogen bonds to electron density rearrangements, which alter hydrogen bonds potential energy surface. Quantum chemistry calculations were carried out on a system consisting of a primary quinone Q_A, non-heme Fe²⁺ ion and neighboring residues_. The primary quinone forms two hydrogen bonds with its environment, one of which was shown to be highly sensitive to the Q_A state. In the case of the reduced primary quinone two stable hydrogen bond proton positions were shown to exist on [Q_A-His^M219] hydrogen bond line, while there is only one stable proton position in the case of the oxidized primary quinone. Taking into account this fact and also the ability of proton to transfer between potential energy wells along a hydrogen bond, theoretical study of temperature dependence of hydrogen bond polarization was carried out. Current theory was successfully applied to interpret dark P⁺/Q_A⁻ recombination rate temperature dependence.     

Influence of the energy of H-bond protons on the electron transfer rate in photosynthetic reaction centers

We present here a theoretical interpretation of the temperature dependence of the rate of dark recombination between a primary quinone (Q_A) and a bacteriochlorophyll dimer in the reaction center of Rhodobacter sphaeroides. We were able to describe qualitatively the nonmonotonous character of this dependence using the energy of interaction between an excess electron and H-bond protons. We considered a molecular model of Q_A and two reaction center fragments that make H-bonds with Q_A: His(M219) and Asn(M259)-Ala(M260). We used the two-center approach with regard for electron-phonon interaction in order to calculate the characteristic time of electron tunneling during the recombination reaction. The energy of the phonon emitted/ absorbed during the electron tunneling was determined by the relative shift of donor and acceptor energy levels, the detuning of levels. The detuning was shown to depend on temperature nonmonotonously for H-bonds with double-well potential energy surface. The characteristic time (or the reaction rate) depended on temperature parametrically. The computed dependence was in qualitative agreement with the experimental one.     

Probing the nature of hydrogen bonds in DNA base pairs

Energy decomposition analyses based on the block-localized wave-function (BLW-ED) method are conducted to explore the nature of the hydrogen bonds in DNA base pairs in terms of deformation, Heitler–London, polarization, electron-transfer and dispersion-energy terms, where the Heitler–London energy term is composed of electrostatic and Pauli-exchange interactions. A modest electron-transfer effect is found in the Watson–Crick adenine–thymine (AT), guanine–cytosine (GC) and Hoogsteen adenine-thymine (H-AT) pairs, confirming the weak covalence in the hydrogen bonds. The electrostatic attraction and polarization effects account for most of the binding energies, particularly in the GC pair. Both theoretical and experimental data show that the GC pair has a binding energy (−25.4 kcal mol⁻¹ at the MP2/6-31G** level) twice that of the AT (−12.4 kcal mol⁻¹) and H-AT (−12.8 kcal mol⁻¹) pairs, compared with three conventional N-H···O(N) hydrogen bonds in the GC pair and two in the AT or H-AT pair. Although the remarkably strong binding between the guanine and cytosine bases benefits from the opposite orientations of the dipole moments in these two bases assisted by the π-electron delocalization from the amine groups to the carbonyl groups, model calculations demonstrate that π-resonance has very limited influence on the covalence of the hydrogen bonds. Thus, the often adopted terminology “resonance-assisted hydrogen bonding (RHAB)” may be replaced with “resonance-assisted binding” which highlights the electrostatic rather than electron-transfer nature of the enhanced stabilization, as hydrogen bonds are usually regarded as weak covalent bonds. Figure Electron density difference (EDD) maps for the GC pair: a shows the polarization effect (isodensity 1.2×10⁻³ a.u.); b shows the charge transfer effect (isodensity 2×10⁻⁴ a.u.) Dedicated to Professor Paul von Ragué Schleyer on the occasion of his 75th birthday     

Modelling hydrogen bonds in NN-dimethylformamide

N, N-dimethylformamide (DMF) is a ‘universal’ solvent with the simplest amide structure. DMF has different interactions with many polymers and biomolecules. It is therefore necessary to study systematically the interactions in DMF itself first. In this study, both FT-IR and two molecular theoretical methods (MP2 and DFT/B3LYP) were used to study various hydrogen bonding interactions in DMF molecules based on its weak H-bonding donors CH/CH₃ and strong H-bonding acceptor C = O. The possible H-bonding donors and acceptors in DMF molecules were first analysed followed by modelling the effect of different structural environments on vC = O bands in infrared spectra. Finally, H-bonding properties including distance, angles and the energy as well as the probability of H-bonding patterns were obtained. The results showed that there exist five possible different weak types of H-bonding dimers; among them, three dimers consist of a pair of weak H-bonds, whereas two other dimers have two pairs of H-bonds, leading to 14 (including eight different) H-bonds. Two types of dimers were dominant, whereas three others can be omitted.     

微生物互营产甲烷过程中的种间电子传递

甲烷作为全球第二大温室气体,是典型的可再生清洁能源,也是碳循环中的重要物质组成。大气中约74%的甲烷由产甲烷古菌和其他微生物的互营产生,种间电子传递(interspecies electron transfer, IET)是微生物菌群降低热力学能垒、实现互营产甲烷的核心过程。IET可分为间接种间电子传递(mediated interspecies electron transfer,MIET)和直接种间电子传递(direct interspecies electron transfer, DIET)两种类型,其中MIET依赖氢气、甲酸等载体完成电子的远距离传输,而DIET则依赖导电菌毛、细胞色素c等膜蛋白,通过微生物的直接接触实现电子传递。本文将从IET的研究历程出发,从电子传递机制、微生物种类、生态多样性等方面对微生物互营产甲烷过程中的两种IET类型进行比较,最后对未来待探索的方向进行展望。本综述有助于加深对微生物互营产甲烷过程中IET的理解,为解决由甲烷引发的全球气候变暖等生态问题提供理论支撑。     

Geometric characteristics of hydrogen bonds involving sulfur atoms in proteins

Sulfur atoms have been known to participate in hydrogen bonds (H‐bonds) and these sulfur‐containing H‐bonds (SCHBs) are suggested to play important roles in certain biological processes. This study aims to comprehensively characterize all the SCHBs in 500 high‐resolution protein structures (≤1.8 Å). We categorized SCHBs into six types according to donor/acceptor behaviors and used explicit hydrogen approach to distinguish SCHBs from those of nonhydrogen bonding interactions. It is revealed that sulfur atom is a very poor H‐bond acceptor, but a moderately good H‐bond donor. In α‐helix, considerable SCHBs were found between the sulphydryl group of cysteine residue i and the carbonyl oxygen of residue i‐4, and these SCHBs exert effects in stabilizing helices. Although for other SCHBs, they possess no specific secondary structural preference, their geometric characteristics in proteins and in free small compounds are significantly distinct, indicating the protein SCHBs are geometrically distorted. Interestingly, sulfur atom in the disulfide bond tends to form bifurcated H‐bond whereas in cysteine‐cysteine pairs prefer to form dual H‐bond. These special H‐bonds remarkably boost the interaction between H‐bond donor and acceptor. By oxidation/reduction manner, the mutual transformation between the dual H‐bonds and disulfide bonds for cysteine‐cysteine pairs can accurately adjust the structural stability and biological function of proteins in different environments. Furthermore, few loose H‐bonds were observed to form between the sulphydryl groups and aromatic rings, and in these cases the donor H is almost over against the rim rather than the center of the aromatic ring. Proteins 2009. © 2008 Wiley‐Liss, Inc.     

Mimicking the photosynthetic system with strong hydrogen bonds to promote proton electron concerted reactions

A Copper(2+) complex with a Cu^II–C bond containing sp³ configuration was used to investigate the role of strong hydrogen bonds in proton coupled electron transfer (PCET) reactions. The only example of a Cu^II–C system realized so far is that using tris-(pyridylthio)methyl (tptm) as a tetradentate tripodal ligand. Using this ligand, [CuF(tptm)] and [Cu(tptm)(OH)] have been prepared. The former complex forms supra-molecular arrays of layers of the complex between which hydroquinone is intercalated in the crystalline phase. This hydroquinone intercalation crystal was prepared via the photochemical conversion of quinone during the crystallization process. This conversion reaction probably involves a proton coupled electron transfer process. The nuclear magnetic resonance spectroscopic analysis of the reaction mixture shows the presence of Cu(III) during the conversion reaction. These results strongly suggest the presence of the molecular aggregate of the [CuF(tptm)] complex, water and quinone in the solution phase during the quinone to hydroquinone conversion. The presence of this type of aggregate requires a strong hydrogen bond between the [CuF(tptm)] complex and water. The presence of this particular hydrogen bond is a unique character of such a complex that has the Cu^II–C bond. This complex is used as a model for photosynthetic water splitting since the photoconversion of quinone to hydroquinone also involves the production of oxygen from water.     

High yield of secondary B-side electron transfer in mutant Rhodobacter capsulatus reaction centers

From the crystal structures of reaction centers (RCs) from purple photosynthetic bacteria, two pathways for electron transfer (ET) are apparent but only one pathway (the A side) operates in the native protein-cofactor complex. Partial activation of the B-side pathway has unveiled the true inefficiencies of ET processes on that side in comparison to analogous reactions on the A side. Of significance are the relative rate constants for forward ET and the competing charge recombination reactions. On the B side, these rate constants are nearly equal for the secondary charge-separation step (ET from bacteriopheophytin to quinone), relegating the yield of this process to < 50%. Herein we report efforts to optimize this step. In surveying all possible residues at position 131 in the M subunit, we discovered that when glutamic acid replaces the native valine the efficiency of the secondary ET is nearly two-fold higher than in the wild-type RC. The positive effect of M131 Glu is likely due to formation of a hydrogen bond with the ring V keto group of the B-side bacteriopheophytin leading to stabilization of the charge-separated state involving this cofactor. This change slows charge recombination by roughly a factor of two and affords the improved yield of the desired forward ET to the B-side quinone terminal acceptor.     

The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease

The hydrogen-bond network in various stages of the enzymatic reaction catalyzed by HIV-1 protease was studied through quantum-classical molecular dynamics simulations. The approximate valence bond method was applied to the active site atoms participating directly in the rearrangement of chemical bonds. The rest of the protein with explicit solvent was treated with a classical molecular mechanics model. Two possible mechanisms were studied, general-acid/general-base (GA/GB) with Asp 25 protonated at the inner oxygen, and a direct nucleophilic attack by Asp 25. Strong hydrogen bonds leading to spontaneous proton transfers were observed in both reaction paths. A single-well hydrogen bond was formed between the peptide nitrogen and outer oxygen of Asp 125. The proton was diffusely distributed with an average central position and transferred back and forth on a picosecond scale. In both mechanisms, this interaction helped change the peptide-bond hybridization, increased the partial charge on peptidyl carbon, and in the GA/GB mechanism, helped deprotonate the water molecule. The inner oxygens of the aspartic dyad formed a low-barrier, but asymmetric hydrogen bond; the proton was not positioned midway and made a slightly elongated covalent bond, transferring from one to the other aspartate. In the GA/GB mechanism both aspartates may help deprotonate the water molecule. We observed the breakage of the peptide bond and found that the protonation of the peptidyl amine group was essential for the peptide-bond cleavage. In studies of the direct nucleophilic mechanism, the peptide carbon of the substrate and oxygen of Asp 25 approached as close as 2.3 A.     

Strong and weak hydrogen bonds in the protein-ligand interface

The characteristics of N--H...O, O--H...O, and C--H...O hydrogen bonds and other weak intermolecular interactions are analyzed in a large and diverse group of 251 protein-ligand complexes using a new computer program that was developed in-house for this purpose. The interactions examined in the present study are those which occur in the active sites, defined here as a sphere of 10 A radius around the ligand. Notably, N--H...O and O--H...O bonds tend towards linearity. Multifurcated interactions are especially common, especially multifurcated acceptors, and the average degree of furcation is 2.6 hydrogen bonds per furcated acceptor. A significant aspect of this study is that we have been able to assess the reliability of hydrogen bond geometry as a function of crystallographic resolution. Thresholds of 2.3 and 2.0 A are established for strong and weak hydrogen bonds, below which hydrogen bond geometries may be safely considered for detailed analysis. Interactions involving water as donor or acceptor, and C--H...O bonds with Gly and Tyr as donors are ubiquitous in the active site. A similar trend was observed in an external test set of 233 protein-ligand complexes belonging to the kinase family. Weaker interactions like X--H...pi (X = C, N, O) and those involving halogen atoms as electrophiles or nucleophiles have also been studied. We conclude that the strong and weak hydrogen bonds are ubiquitous in protein-ligand recognition, and that with suitable computational tools very large numbers of strong and weak intermolecular interactions in the ligand-protein interface may be analyzed reliably. Results confirm earlier trends reported previously by us but the extended nature of the present data set mean that the observed trends are more reliable.     

细菌胞际电子转移及其生态生理学意义研究进展

胞际电子转移是指细胞内电子以间接或直接的方式传递到细胞外,最终到达细胞周围电子受体的过程.胞际电子转移普遍存在于自然界,尤其存在于电子受体相对匮乏的环境中.胞际电子转移可分为间接和直接胞际电子转移.间接胞际电子转移(胞际基质转移)是主要借助氢、甲酸以及其他代谢产物的电子传递;而直接胞际电子转移则由胞内电子转移偶联胞外电子传递实现.胞际电子转移促进了细胞的基质代谢活性,拓展了细胞的作用空间,具有重要的生理意义.胞际电子转移产生了电流,实现了菌间能源共享,驱动了胞外物质(如重金属、腐殖质)转化,具体重大的生态意义.本文总结相关文献,对细菌胞际电子转移的过程、特点、机理及其生态生理学意义作了系统的分析和探讨.     

Mechanism of photoinduced electron transfer in photosystem II reaction centers

The shape of the EPR spectrum of the triplet state of photosystem II reaction centers with a singly reduced primary acceptor complex Q_AFe²⁺ was studied. It was shown that the spectroscopic properties do not significantly change when the relaxation of the primary acceptor is accelerated and when the magnetic interaction between the reduced quinone molecule Q_A and the nonheme iron ion Fe²⁺ is disrupted. This observation confirmed the earlier conclusion that the anisotropy of the quantum yield of the triplet state is the main cause of the anomalous shape of the EPR spectrum. A scheme of primary processes in photosystem II that is consistent with the observed properties of the EPR spectrum of the triplet state is discussed.     

Free energy dependence of the direct charge recombination from the primary and secondary quinones in reaction centers from Rhodobacter sphaeroides

The direct charge recombination rates from the primary quinone, k _AD (D⁺Q _A ^– DQ_A) and the secondary quinone, k _BD (D⁺Q _B ^– DQ_B), in reaction centers from Rhodobacter sphaeroides were measured as a function of the free energy differences for the processes, G _AD ⁰ and G _BD ⁰ , respectively. Measurements were performed at 21 °C on a series of mutant reaction centers that have a wide range of dimer midpoint potentials and consequently a large variation in G _AD ⁰ and G _BD ⁰ . As –G _AD ⁰ varied from 0.43 to 0.78 eV, k _AD varied from 4.6 to 28.6 s^–1. The corresponding values for the wild type are 0.52 eV and 8.9 s^–1. Observation of the direct charge recombination rate k _BD was achieved by substitution of the primary quinone with naphthoquinones in samples in which ubiquinone was present at the secondary quinone site, resulting specifically in an increase in the free energy of the D⁺Q _A ^– state relative to the D⁺Q_AQ _B ^– state. As –G _BD ⁰ varied from 0.37 to 0.67 eV, k _BD varied from 0.03 to 1.4 s^–1. The corresponding values for the wild type are 0.46 eV and 0.2 s^–1. A fit of the two sets of data to the Marcus theory for electron transfer yielded significantly different reorganization energies of 0.82 and 1.3 eV for k _AD and k _BD, respectively. In contrast, the fitted values for the coupling matrix element, or equivalently the maximum possible rate, were comparable (25 s^–1) for the two charge recombination processes. These results are in accord with Q_B having more interactions with dipoles, from both the surrounding protein and bound water molecules, than Q_A and with the primary determinant of the maximal rate being the quinone-donor distance.     

互营氧化产甲烷微生物种间电子传递研究进展

甲烷是重要的温室气体,也是典型的可再生性生物质能源。目前约70%的大气甲烷排放来源于产甲烷微生物过程。在产甲烷环境中,产甲烷菌与互营细菌形成互营关系,从而克服有机质厌氧分解反应的热力学能垒,实现短链脂肪酸和醇类物质的互营氧化产甲烷过程。该过程中,种间电子传递是关键步骤。本文首先概述了甲烷的研究意义及微生物互营降解有机质产甲烷的过程,然后分别综述了种间H2转移、种间甲酸转移和种间直接电子传递这3种种间电子传递机制的起源、发展、研究现状和未来所需要解决的研究问题。     

On unsatisfied hydrogen bonds in the N-terminal subdomain of villin headpiece

Villin headpiece is a small autonomously folding protein that has emerged as a model system for understanding the fundamental tenets governing protein folding. In this communication, we employ NMR and X-ray crystallography to characterize a point mutant, H41F, which retains actin-binding activity, is more thermostable but, interestingly, does not exhibit the partially folded intermediate observed of either wild-type or other similar point mutants.     

How hydrogen bonds impact P-glycoprotein transport and permeability

The requirement to cross a biological membrane can be a complex process especially if multidrug transporters such as P-gp must be considered. Drug partitioning into the lipid membrane and efflux by P-gp are tightly coupled processes wherein H-bonding interactions play a key role. All H-bond donors and acceptors are not equal in terms of the strength of the H-bonds that they form, hence it is important to consider their relative strength. Using various examples from literature, we illustrate the benefits of considering the relative strengths of individual H-bonds and introducing intramolecular H-bonds to increase membrane permeability and/or decrease P-gp efflux.     

微生物种间电子传递的研究进展

种间电子传递可促进微生物发生共代谢,因而在地球生物化学循环和环境污染修复中具有重要意义。根据电子传递方式的不同可将种间电子传递分为直接种间电子传递（direct interspecies electron transfer,DIET）和间接种间电子传递（mediated interspecies electron transfer,MIET）,其中,直接种间电子传递由于易发生、效率高而受到更加广泛的关注。本文总结了近年来关于种间电子传递的研究进展,阐述了种间电子传递的途径,比较了DIET和MIET的优缺点,并对开发更多具有种间电子传递功能的微生物提出了建议,以期加深人们对于种间电子传递的理解,并对未来该领域的研究提供参考。     

The influence of hydrogen bonds on electron transfer rate in photosynthetic RCs

Hydrogen bonds formed between photosynthetic reaction centers (RCs) and their cofactors were shown to affect the efficacy of electron transfer. The mechanism of such influence is determined by sensitivity of hydrogen bonds to electron density rearrangements, which alter hydrogen bonds potential energy surface. Quantum chemistry calculations were carried out on a system consisting of a primary quinone Q(A), non-heme Fe(2+) ion and neighboring residues(.) The primary quinone forms two hydrogen bonds with its environment, one of which was shown to be highly sensitive to the Q(A) state. In the case of the reduced primary quinone two stable hydrogen bond proton positions were shown to exist on [Q(A)-His(M219)] hydrogen bond line, while there is only one stable proton position in the case of the oxidized primary quinone. Taking into account this fact and also the ability of proton to transfer between potential energy wells along a hydrogen bond, theoretical study of temperature dependence of hydrogen bond polarization was carried out. Current theory was successfully applied to interpret dark P(+)/Q(A)(-) recombination rate temperature dependence.     

On the efficiency of energy transfer and the different pathways of electron transfer in mutant reaction centers of Rhodobacter sphaeroides

The efficiency of energy transfer from the monomeric pigments to the primary donor was determined from 77 K steady-state fluorescence excitation spectra of three mutant reaction centers, YM210L, YM210F and LM160H / FM197H. For all three reaction centers this efficiency was not 100% and ranged between 55 and 70%. For the YM210L mutant it was shown using pump-probe spectroscopy with B band excitation at 798 nm that the excitations which are not transferred to P give rise to efficient charge separation. The results can be interpreted with a model in which excitation of the B absorbance band leads to direct formation of the radical pair state B_A ⁺H _A ^– in addition to energy transfer to P. It is also possible that some P⁺B_A ^– is formed from B^*. In previous publications we have demonstrated the operation of such alternative pathways for transmembrane electron transfer in a YM210W mutant reaction center [van Brederode et al. (1996) The Reaction center of Photosynthetic Bacteria, pp 225–238; (1997a,b) Chem Phys Lett 268: 143–149; Biochemistry 36: 6855–6861]. The results presented here demonstrate that these alternative mechanisms are not peculiar to the YM210W reaction center.