Proton Wires Research Articles

Theoretical modelling of biomolecular systems I. Large-scale QM/MM calculations of hydrogen-bonding networks of the oxygen evolving complex of photosystem II

Quantum mechanical (QM)/molecular mechanics (MM) calculations by the use of a large-scale QM model (QM Model V) have been performed to elucidate hydrogen-bonding networks and proton wires for proton release pathways (PRP) of water oxidation reaction in the oxygen evolving complex (OEC) of photosystem II (PSII). Full geometry optimisations of PRP by the QM/MM model have been carried out starting from the geometry of heavy atoms determined by the recent high-resolution X-ray diffraction (XRD) experiment of PSII refined to 1.9 Å resolution. Computational results by the QM/MM calculations have elucidated the hydrogen-bonding O···O(N) and O···H distances and O(N)–H···O angles in PRP, together with the Cl–O(N) and Cl···H distances and O(N)–H···Cl angles for chloride anions. The optimised hydrogen-bonding networks are well consistent with the XRD results and available experiments such as extended X-ray absorption fine structure, showing the reliability of channel structures of OEC of PSII revealed by the XRD experiment. The QM/MM computations have elucidated possible roles of chloride anions in the OEC of PSII. The QM/MM computational results have provided useful information for understanding and explanation of accumulated mutation experiments of key amino acid residues in the OEC of PSII. Implications of the present results are discussed in relation to three steps for theoretical modelling of water oxidation in the OEC of PSII and bio-inspired working hypotheses for developments of artificial water oxidation systems by use of 3d transition-metal complexes.

Crystallographic and molecular dynamics simulation analysis of Escherichia coli dihydroneopterin aldolase.

BackgroundDihydroneopterin aldolase (DHNA) catalyzes the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-dihydropterin and also the epimerization of DHNP to 7,8-dihydromonapterin. Previously, we determined the crystal structure of Staphylococcus aureus DHNA (SaDHNA) in complex with the substrate analogue neopterin (NP). We also showed that Escherichia coli DHNA (EcDHNA) and SaDHNA have significantly different binding and catalytic properties by biochemical analysis. On the basis of these structural and functional data, we proposed a catalytic mechanism involving two proton wires.ResultsTo understand the structural basis for the biochemical differences and further investigate the catalytic mechanism of DHNA, we have determined the structure of EcDHNA complexed with NP at 1.07-Å resolution [PDB:2O90], built an atomic model of EcDHNA complexed with the substrate DHNP, and performed molecular dynamics (MD) simulation analysis of the substrate complex. EcDHNA has the same fold as SaDHNA and also forms an octamer that consists of two tetramers, but the packing of one tetramer with the other is significantly different between the two enzymes. Furthermore, the structures reveal significant differences in the vicinity of the active site, particularly in the loop that connects strands β3 and β4, mainly due to the substitution of nearby residues. The building of an atomic model of the complex of EcDHNA and the substrate DHNP and the MD simulation of the complex show that some of the hydrogen bonds between the substrate and the enzyme are persistent, whereas others are transient. The substrate binding model and MD simulation provide the molecular basis for the biochemical behaviors of the enzyme, including noncooperative substrate binding, indiscrimination of a pair of epimers as the substrates, proton wire switching during catalysis, and formation of epimerization product.ConclusionsThe EcDHNA and SaDHNA structures, each in complex with NP, reveal the basis for the biochemical differences between EcDHNA and SaDHNA. The atomic substrate binding model and MD simulation offer insights into substrate binding and catalysis by DHNA. The EcDHNA structure also affords an opportunity to develop antimicrobials specific for Gram-negative bacteria, as DHNAs from Gram-negative bacteria are highly homologous and E. coli is a representative of this class of bacteria.

Catalytic strategy used by the myosin motor to hydrolyze ATP.

Myosin is a molecular motor responsible for biological motions such as muscle contraction and intracellular cargo transport, for which it hydrolyzes adenosine 5'-triphosphate (ATP). Early steps of the mechanism by which myosin catalyzes ATP hydrolysis have been investigated, but still missing are the structure of the final ADP·inorganic phosphate (Pi) product and the complete pathway leading to it. Here, a comprehensive description of the catalytic strategy of myosin is formulated, based on combined quantum-classical molecular mechanics calculations. A full exploration of catalytic pathways was performed and a final product structure was found that is consistent with all experiments. Molecular movies of the relevant pathways show the different reorganizations of the H-bond network that lead to the final product, whose γ-phosphate is not in the previously reported HPγO4(2-) state, but in the H2PγO4(-) state. The simulations reveal that the catalytic strategy of myosin employs a three-pronged tactic: (i) Stabilization of the γ-phosphate of ATP in a dissociated metaphosphate (PγO3(-)) state. (ii) Polarization of the attacking water molecule, to abstract a proton from that water. (iii) Formation of multiple proton wires in the active site, for efficient transfer of the abstracted proton to various product precursors. The specific role played in this strategy by each of the three loops enclosing ATP is identified unambiguously. It explains how the precise timing of the ATPase activation during the force generating cycle is achieved in myosin. The catalytic strategy described here for myosin is likely to be very similar in most nucleotide hydrolyzing enzymes.

Solid-state magnetic switching triggered by proton-coupled electron-transfer assisted by long-distance proton-alkali cation transport.

Acidity of water molecules coordinated to Co ions in CoFe Prussian blue analogues (PBA) has been used to reversibly activate the Co(III)Fe(II) ↔ Co(II)Fe(III) electron transfer. The study of the structure and the electronic structure shows that the process implies an original PCET reaction between a solid-state porous coordination polymer and hydroxide ions in solution. The PCET reaction spreads throughout the solid network thanks to a long-range H(+) and Rb(+) transport within the pore channels of PBA taking advantage of the hydrogen-bonding network of zeolitic water molecules acting as proton wires.

Deciphering the infrared spectrum of the protonated water pentamer and the hybrid Eigen–Zundel cation

Traditionally, infrared band assignment for the protonated water clusters, such as H(+)(H2O)5, is based on their lowest energy isomer. Recent experiments extend the observation spectral window to lower frequencies, for which such assignment appears to be inadequate. Because this hydrogen-bonded system is highly anharmonic, harmonic spectral calculations are insufficient for reliable interpretation. Consequently, we have calculated the IR spectrum of several isomers of the protonated water pentamer using an inherently anharmonic methodology, utilizing dipole and velocity autocorrelation functions computed from ab initio molecular dynamic trajectories. While the spectrum of H(+)(H2O)5 is universally assumed to represent the branched Eigen isomer, we find a better agreement for a mixture of a ring and linear isomers. The first has an Eigen core and contributes at high frequencies, whereas the latter accounts for all prominent low-frequency bands. Interestingly, its core is neither a classical Eigen nor a Zundel cation, but rather has hybrid geometry. Such an isomer may play a role in proton conductance along short proton wires.

H+-type and OH- -type biological protonic semiconductors and complementary devices.

Proton conduction is essential in biological systems. Oxidative phosphorylation in mitochondria, proton pumping in bacteriorhodopsin, and uncoupling membrane potentials by the antibiotic Gramicidin are examples. In these systems, H+ hop along chains of hydrogen bonds between water molecules and hydrophilic residues – proton wires. These wires also support the transport of OH− as proton holes. Discriminating between H+ and OH− transport has been elusive. Here, H+ and OH− transport is achieved in polysaccharide- based proton wires and devices. A H+- OH− junction with rectifying behaviour and H+-type and OH−-type complementary field effect transistors are demonstrated. We describe these devices with a model that relates H+ and OH− to electron and hole transport in semiconductors. In turn, the model developed for these devices may provide additional insights into proton conduction in biological systems.

1.55 Å-resolution structure of ent-copalyl diphosphate synthase and exploration of general acid function by site-directed mutagenesis

BackgroundThe diterpene cyclase ent-copalyl diphosphate synthase (CPS) catalyzes the first committed step in the biosynthesis of gibberellins. The previously reported 2.25Å resolution crystal structure of CPS complexed with (S)-15-aza-14,15-dihydrogeranylgeranyl thiolodiphosphate (1) established the αβγ domain architecture, but ambiguities regarding substrate analog binding remained. MethodUse of crystallization additives yielded CPS crystals diffracting to 1.55Å resolution. Additionally, active site residues that hydrogen bond with D379, either directly or through hydrogen bonded water molecules, were probed by mutagenesis. ResultsThis work clarifies structure–function relationships that were ambiguous in the lower resolution structure. Well-defined positions for the diphosphate group and tertiary ammonium cation of 1, as well as extensive solvent structure, are observed. ConclusionsTwo channels involving hydrogen bonded solvent and protein residues lead to the active site, forming hydrogen bonded “proton wires” that link general acid D379 with bulk solvent. These proton wires may facilitate proton transfer with the general acid during catalysis. Activity measurements made with mutant enzymes indicate that N425, which donates a hydrogen bond directly to D379, and T421, which hydrogen bonds with D379 through an intervening solvent molecule, help orient D379 for catalysis. Residues involved in hydrogen bonds with the proton wire, R340 and D503, are also important. Finally, conserved residue E211, which is located near the diphosphate group of 1, is proposed to be a ligand to Mg2+ required for optimal catalytic activity. General significanceThis work establishes structure–function relationships for class II terpenoid cyclases.

Reinvestigation of tricyclic acyclovir: characterization of a `proton-wire' model

The crystal structure of a dihydrate of the title compound, 3-[(2-hydroxyethoxy)methyl]-6-methyl-3H-imidazolo[1,2-a]-purin-9(5H)-one, C11H13N5O3·2H2O, has been reinvestigated. The asymmetric unit contains two molecules of tricyclic acyclovir and four molecules of water. The structure consists of a three-dimensional network of strong hydrogen bonds that integrates all of the components. While the crystal structure and the formation of an (H2O)8 solvent water molecule cluster through a disordered strong hydrogen bond [O···O = 2.807 (3) Å] between two water molecules across an inversion centre has been described previously [Suwińska, Golankiewicz & Zielenkiewicz (2001). Acta Cryst. C57, 767-769], the disorder was incompletely modelled. In this work, the disorder model is extended and includes disorder of one tricyclic acyclovir hydroxy group across another inversion centre [O···O = 2.644 (4) Å]. The resulting infinite O-H···O hydrogen-bonded water-hydroxy chains, analogous to the `proton wires' found in the membrane protein gramicidin A, are discussed and an unusual disorder model involving infinite concerted chains of O-H···O hydrogen bonds is provided.

Proton transfer through the water gossamer

The diffusion of protons through water is understood within the framework of the Grotthuss mechanism, which requires that they undergo structural diffusion in a stepwise manner throughout the water network. Despite long study, this picture oversimplifies and neglects the complexity of the supramolecular structure of water. We use first-principles simulations and demonstrate that the currently accepted picture of proton diffusion is in need of revision. We show that proton and hydroxide diffusion occurs through periods of intense activity involving concerted proton hopping followed by periods of rest. The picture that emerges is that proton transfer is a multiscale and multidynamical process involving a broader distribution of pathways and timescales than currently assumed. To rationalize these phenomena, we look at the 3D water network as a distribution of closed directed rings, which reveals the presence of medium-range directional correlations in the liquid. One of the natural consequences of this feature is that both the hydronium and hydroxide ion are decorated with proton wires. These wires serve as conduits for long proton jumps over several hydrogen bonds.

Charge transport along proton wires

Using density functional theory we look at the quantum mechanics of charge transport along water wires both with free ends and donor/acceptor terminated. With the intermediate geometries in the DFT iterations we can follow the charge transfer mechanism and also construct the energy landscape explicitly. It shows activation barriers when a proton is transferred from one water molecule to the next. This, together with snapshots of intermediate geometries, leads to a justification and further elucidation of the Grotthuss mechanism and the Bjerrum effect. The charge transfer times and the conductivity of the proton wire are obtained in agreement with experimental results.

Theoretical insight in to hydrogen-bonding networks and proton wire for the CaMn4O5 cluster of photosystem II. Elongation of Mn–Mn distances with hydrogen bonds

Quantum mechanical (QM) and QM/molecular mechanics (MM) calculations of three different cluster models have been performed to shed light on hydrogen bonding networks and proton wires for proton release pathways (PRP) of water oxidation reactions in the oxygen evolving complex (OEC) of photosystem II (PSII). Positions of all the hydrogen atoms in an extended QM Model III including the second coordination sphere for the active-site CaMn4O5 complex of OEC of PSII have been optimized assuming the geometry of heavy atoms determined by the recent high-resolution X-ray diffraction (XRD) experiment of PSII refined to 1.9 A resolution. Full geometry optimizations of the first coordination sphere model (QM Model I) embedded in the Model III and QM (QM Model I plus seven water molecules, namely QM Model II)/MM models, together with full QM Model III, have also been conducted to elucidate confinement effects for geometrical parameters of the CaMn4O5 cluster by proteins. Computational results by these methods have elucidated the O⋯O(N), O⋯H distances and O(N)–H⋯O angles for hydrogen bonds in proton release paths (PRP) I and II that construct a proton wire from Asp61 toward His190. The hydrogen-bonding structures revealed have also been examined in relation to the possibilities of protonation of bridge oxygen dianions within the CaMn4O5 cluster. The optimized inter-atomic distances by QM Models I and III, together with QM(Model II)/MM, have elucidated the elongation of the Mn–Mn distances with hydrogen bonds and variations of the Mnd–O(5) length with confinement effects by protein. Implications of the computational results are discussed in relation to the available EXAFS experiments, and internal, semi-internal and external reductions of Mn ions and long Mn–Mn distances of the high-resolution (SP8) XRD, and rational design of artificial catalysts for water oxidation that are current topics in the field of OEC of PSII.

Autocatalytic and Cooperatively Stabilized Dissociation of Water on a Stepped Platinum Surface

Water-metal interfaces are ubiquitous and play a key role in many chemical processes, from catalysis to corrosion. Whereas water adlayers on atomically flat transition metal surfaces have been investigated in depth, little is known about the chemistry of water on stepped surfaces, commonly occurring in realistic situations. Using first-principles simulations, we study the adsorption of water on a stepped platinum surface. We find that water adsorbs preferentially at the step edge, forming linear clusters or chains, stabilized by the cooperative effect of chemical bonds with the substrate and hydrogen bonds. In contrast with their behavior on flat Pt, at steps water molecules dissociate, forming mixed hydroxyl/water structures, through an autocatalytic mechanism promoted by H-bonding. Nuclear quantum effects contribute to stabilize partially dissociated cluster and chains. Together with the recently demonstrated behavior of water chains adsorbed on stepped Pt surfaces to transfer protons via thermally activated hopping, these findings make these systems viable candidates for proton wires.

Protonated sugars: vibrational spectroscopy and conformational structure of protonated O-methyl α-D-galactopyranoside

‘Bridging’ protons provide a common structural motif in biological assemblies such as proton wires and proton-bound dimers. Here we present a ‘proof-of-principle’ computational and vibrational spectroscopic investigation of an ‘intra-molecular proton-bound dimer,’ O-methyl α-D-galactopyranoside (αMeGal-H+), generated in the gas phase through photo-ionisation of its complex with phenol in a molecular beam. Its vibrational spectrum corresponds well with a classical molecular dynamics simulation conducted ‘on-the-fly’ and also with the lowest-energy structures predicted by DFT and ab initio calculations. They reveal proton-bound structures that bridge neighbouring pairs of oxygen atoms, preferentially O6 and O4, linked together within the carbohydrate scaffold. Motivated by the possibility of an entry into the microscopic mechanism of its acid (or enzyme)-catalysed hydrolysis, we also report the corresponding predictions for its singly hydrated complex.

Ionization of dimethyluracil dimers leads to facile proton transfer in the absence of hydrogen bonds

Proton transfer is ubiquitous in chemistry and biology, occurring, for example, in proteins, enzyme reactions and across proton channels and pumps. However, it has always been described in the context of hydrogen-bonding networks ('proton wires') acting as proton conduits. Here, we report efficient intramolecular ionization-induced proton transfer across a 1,3-dimethyluracil dimer, a model π-stacked system with no hydrogen bonds. Upon photoionization by tunable vacuum ultraviolet synchrotron radiation, the dimethyluracil dimer undergoes proton transfer and dissociates to produce a protonated monomer. Deuterated dimethyluracil experiments confirm that proton transfer occurs from the methyl groups and not from the aromatic C-H sites. Calculations reveal qualitative differences between the proton transfer reaction coordinate in the π-stacked and hydrogen-bonded base pairs, and that proton transfer in methylated dimers involves significant rearrangements of the two fragments, facilitating a relatively low potential energy barrier of only 0.6 eV in the ionized dimer.

Modeling Nonaqueous Proton Wires Built from Helical Peptides: Biased Proton Transfer Driven by Helical Dipoles

We report gas-phase electronic structure calculations on helical peptides that act as scaffolds for imidazole-based hydrogen-bonding networks (proton wires). We have modeled various 21-residue polyalanine peptides substituted at regular intervals with histidines (imidazole-bearing amino acids), using a hybrid approach with a semiempirical method (AM1) for peptide scaffolds and density functional theory (B3LYP) for proton wires. We have computed energy landscapes including barriers for Grotthuss-shuttling-type proton motions though wires supported on 3(10)-, α- and π-helical structures, showing the 3(10)- and α-helices to be attractive targets in terms of high proton affinities, low Grotthuss shuttling barriers, and high stabilities. Moreover, bias forces provided by the helical dipole moments were found to promote unidirectional proton translocation.

Proton Transfer and Dissociation of GlyLysH+ following O–H and N–H Stretching Mode Excitations: Dynamics Simulations

Proton transfer and dissociation processes following excitation of the OH or NH stretching modes of the proton-bound complex GlyLysH(+) are studied by classical trajectories. "On the fly" simulations with the PM3 semiempirical electronic structure method for the potential surface are used. Initial conditions are sampled to correspond to the v=1 excited state of the OH or NH stretching modes. Five different conformers of the complex are studied as initial structures. The main findings are (1) Photoinduced proton transfer is on the picosecond time scale. (2) Proton transfer is much faster than the processes of dissociation. (3) Proton transfer involves different sites. Most trajectories show sequences of two proton transfer events. (4) The proton transfer events show high selectivity with regard to the initially excited vibration and the initial structure. (5) Photodissociation of the complex occurs on a typical time scale of 100 ps. (6) Conformational transitions are found to be often faster than proton transfer. These results have implications for the mass spectrometry of complexes, for dynamics of proton wires, and for proton migration in proteins.

Proton Wires via One-Dimensional Water Chains Adsorbed on Metallic Steps.

The process of proton transfer is here analyzed for one-dimensional water chains adsorbed on metallic steps. When the water chain contains a hydronium and a hydroxyl ion, two different mechanisms are possible, depending on the metal substrate. On coinage metals (Ag, Au), recombination is observed through a spontaneous Grotthuss mechanism. On more reactive surfaces (Pd and Pt), the hydronium ion is unstable and releases a proton that adsorbs onto the metal, leaving the negatively charged OH(-) unbalanced. In this case, the negative charge can be transferred along the wire with very low activation barriers.

Modeling Energy Landscapes of Proton Motion in Nonaqueous, Tethered Proton Wires

We have modeled structures and energetics of anhydrous proton-conducting wires: tethered hydrogen-bonded chains of the form ···HX···HX···HX···, with functional groups HX = imidazole, triazole, and formamidine; formic, sulfonic, and phosphonic acids. We have applied density functional theory (DFT) to model proton wires up to 19 units long, where each proton carrier is linked to an effective backbone to mimic polymer tethering. This approach allows the direct calculation of hydrogen bond strengths. The proton wires were found to be stabilized by strong hydrogen bonds (up to 50 kJ/mol) whose strength correlates with the proton affinity of HX [related to pK(b)(HX)] and not to pK(a)(HX) as is often assumed. Geometry optimizations and ab initio molecular dynamics near 400 K on imidazole-based proton wires both predict that adding a proton to the end of such wires causes the excess charge to embed into the interior segments of these wires. Proton translocation energy landscapes for imidazole-based wires are sensitive to the imidazole attachment point (head or feet) and to wire architecture (linear or interdigitated). Linear imidazole wires with head-attachment exhibit low barriers for intrawire proton motion, rivaling proton diffusion in liquid imidazole. Excess charge relaxation from the edge of wires is found to be dominated by long-range Grotthuss shuttling for distances as long as 42 Å, especially for interdigitated wires. For imidazole, we predict that proton translocation is controlled by the energetics of desorption from the proton wire, even for relatively long wires (600 imidazole units). Proton desorption energies show no correlation with functional group properties, suggesting that proton desorption is a collective process in proton wires.

Hydrogen-bond strengths by magnetically induced currents

We present here a "non-invasive" computational method to estimate the strength of individual hydrogen bonds using magnetically induced currents. The method is calibrated using H-bonding dimers, and applied on Watson-Crick DNA base pairs and proton wires in carbonic anhydrase.

Visualizing Proton Antenna in a High-Resolution Green Fluorescent Protein Structure

"Proton-collecting antenna" are conjectured to consist of several carboxylates within hydrogen-bond (HB) networks on the surface of proteins, which funnel protons to the orifice of an internal proton wire leading to the protein's active site. Yet such constructions were never directly visualized. Here we report an X-ray structure of green fluorescent protein (GFP) of the highest resolution to date (0.9 A). It allows the identification of some pivotal hydrogen atoms pertinent to uncertainties concerning the protonation state of the chromophore. Applying a computer algorithm for mapping proton wires in proteins reveals the previously observed "active site wire" connecting Glu222 with the surface carboxylate Glu5. In addition, it is now possible to identify what appears to be a proton-collecting apparatus of GFP. It consists of a negative surface patch containing carboxylates, threonines, and water molecules, connected by a HB network to Glu5. Furthermore, we detect exit points via Asn146 and His148 to a hydrophobic surface region. The more extensive HB network of the present structure, as compared with earlier GFP structures, is not accidental. A systematic investigation of over 100 mutants shows a clear correlation between the observed water content of GFP X-ray structures and their resolution. With increasing water content, the proton wires become progressively larger. These findings corroborate the scenario in which the photodissociated proton from wild-type GFP can leak outside, whereafter another proton is recruited via the proton-collecting apparatus reported herein.