Reorientation Step Research Articles

Improving the systems for controlling ground-based sun orientation devices

The control system for terrestrial two-axis devices for orientation to the Sun has been improved with a high-speed microcontroller operation algorithm. A geomagnetic sensor was introduced into the system to increase the reliability of monitoring the positioning of solar cells. The basis of the algorithm is a simplified astronomical and geographical model of the movement of the Sun in the celestial sphere. The control system automatically tracks the trajectory of the Sun and calculates its angular coordinates for the current moment of time on any day of the year and for any point on the globe. The derived equations of the simplified mathematical model are suitable for calculations of orientation angles to the Sun in real time on 8-bit microcontrollers with low computing power. The control system by AVR-328 microcontrollers was studied. It was established that the use of the algorithm when programming microcontrollers for two-axis orientation systems ensures high stability and reliability of the tracker`s functioning process. The technical parameters of the AVR-328 microcontrollers in the case of using the developed algorithm ensure that the control system performs one reorientation step in a time interval of less than 2 seconds, which ensures the minimum technical period of the reorientation process by the tracker drive mechanisms which is about 5 seconds. Deviations of the calculated orientation angle from the exact value do not exceed 3°, which corresponds to the relative accuracy of recording the solar radiation intensity, which is less than 0.3 %. The microcontroller program written according to the developed simplified algorithm occupies about 35 % of its memory. Therefore, the use of the developed algorithm frees up the resources of AVR-328 microcontrollers for performing additional data processing operations and automatic control over various additional devices related to the process of orientation to the Sun. In the case of solar energy, the algorithm ensures the use of about 98 % of the power of solar radiation

Quality control for the geophone reorientation of ocean bottom seismic data using k‐means clustering

ABSTRACTDuring ocean bottom seismic acquisition, seafloor multicomponent geophones located in rugose and sloping water bottom can be affected by skewed energy distribution, such as leaked shear energy on the vertical geophones and leaked compressional energy on the horizontal geophones. To correct for the tilted energy distribution, which is one of most effective preprocessing steps, a geophone reorientation step is applied. This is a simple and straightforward process that applies a 3‐dimensional rotation matrix with respect to the orientation angles. Since the reorientation process highly affects the outcome of the entire data processing workflow, it has to be accompanied by a careful quality control process to verify its validity for the whole survey area. In this study, we propose a quality control workflow for the geophone reorientation by using unsupervised machine learning. A correlation analysis is employed to compare numerical versus analytical solutions of both the azimuth and the incidence angles for the direct arrivals. A comparison of both solutions aims to generate correlation coefficients that are indicative of the accuracy of geophone orientation. The correlation coefficients are subsequently investigated by the k‐means clustering algorithm to differentiate and identify normally and abnormally deployed/reoriented geophones. Numerical experiments on a field ocean bottom seismic data set confirm that the proposed workflow effectively provides reliable labels for normally and abnormally deployed/reoriented geophones. The labelling assigned by the proposed quality control workflow is a suitable indicator for abnormalities in the geophone reorientation step and will be helpful for further investigation, such as re‐correction or removal of abnormally reoriented geophones.

Proton-Assisted Mechanism of NO Reduction on a Dinuclear Ruthenium Complex.

Density-functional-theory (DFT) calculations are performed for the proposal of a plausible mechanism on the reduction of NO to N2O by a dinuclear ruthenium complex, reported by Arikawa and co-workers [J. Am. Chem. Soc. 2007, 129, 14160]. On the basis of the experimental fact that the reduction proceeds under strongly acidic conditions, the role of protons in the mechanistic pathways is investigated with model complexes, where one or two NO ligands are protonated. The reaction mechanism of the NO reduction is partitioned into three steps: reorientation of N2O2 (cis-NO dimer), O-N bond cleavage, and N2O elimination. A key finding is that the protonation of the NO ligand(s) significantly reduces the activation barrier in the rate-determining reorientation step. The activation energy of 43.1 kcal/mol calculated for the proton-free model is reduced to 30.2 and 17.6 kcal/mol for the mono- and diprotonated models, respectively. The protonation induces the electron transfer from the Ru(II)Ru(II) core to the O═N-N═O moiety to give a Ru(III)Ru(III) core and a hyponitrite (O-N═N-O)(2-) species. The formation of the hyponitrite species provides an alternative pathway for the N2O2 reorientation, resulting in the lower activation energies in the presence of proton(s). The protonation also has a marginal effect on the O-N bond cleavage and the N2O elimination steps. Our calculations reveal a remarkable role of protons in the NO reduction via N2O formation and provide new insights into the mechanism of NO reduction catalyzed by metalloenzymes such as nitric oxide reductase (NOR) that contains a diiron active site.

Elevator mechanism of aspartate (glutamate) transport across the membrane

Archaeal homologues of human neuronal glutamate transporter catalyze the coupled uptake of aspartate and three sodium ions. After the delivery of the substrate and sodium ions in the cytoplasm the empty binding site must reorient to the outward-facing conformation to reset the transporter. Here we present a crystal structure of the substrate-free transporter GltTk from Thermococcus kodakarensis, resolved at 3 Å resolution [1]. Despite the global similarity to the previously resolved structures of aspartate transporter GltPh, there are tremendous rearrangements in the substrate-binding site. The key binding residue Arg401 moves in and partially occupies the substrate's position, while the rotation of another conserved residue Met314 completely destroys the geometry of the sodium-binding sites. This structure provides direct structural insight in the mechanism of the essential reorientation step in the translocation cycle for this type of transporters.

Two-step polarization reversal in biased ferroelectrics

Polarization reversal in polycrystalline ferroelectrics is shown to occur via two distinct and sequential domain reorientation steps. This reorientation sequence, which cannot be readily discriminated in the overall sample polarization, is made apparent using time-resolved high-energy x-ray diffraction. Upon application of electric fields opposite to the initial poling direction, two unique and significantly different time constants are observed. The first (faster time constant) is shown to be derived by the release of a residual stress due to initial electrical biasing and the second (slower time constant) due to the redevelopment of residual stress during further domain wall motion. A modified domain reorientation model is given that accurately describes the domain volume fraction evolution during the reversal process.

Interactions of Phosphatase and Tensin Homologue (PTEN) Proteins with Phosphatidylinositol Phosphates: Insights from Molecular Dynamics Simulations of PTEN and Voltage Sensitive Phosphatase

The phosphatase and tensin homologue (PTEN) and the Ciona intestinalis voltage sensitive phosphatase (Ci-VSP) are both phosphatidylinositol phosphate (PIP) phosphatases that contain a C2 domain. PTEN is a tumor suppressor protein that acts as a phosphatase on PIP3 in mammalian cell membranes. It contains two principal domains: a phosphatase domain (PD) and a C2 domain. Despite detailed structural and functional characterization, less is known about its mechanism of interaction with PIP-containing lipid bilayers. Ci-VSP consists of an N-terminal transmembrane voltage sensor domain and a C-terminal PTEN domain, which in turn contains a PD and a C2 domain. The nature of the interaction of the PTEN domain of Ci-VSP with membranes has not been well established. We have used multiscale molecular dynamics simulations to define the interaction mechanisms of PTEN and of the Ci-VSP PTEN domains with PIP-containing lipid bilayers. Our results suggest a novel mechanism of association of the PTEN with such bilayers, in which an initial electrostatics-driven encounter of the protein and bilayer is followed by reorientation of the protein to optimize its interactions with PIP molecules in the membrane. Although a PIP3 molecule binds close to the active site of PTEN, our simulations suggest a further conformational change of the protein may be required for catalytically productive binding to occur. Ci-VSP interacted with membranes in an orientation comparable to that of PTEN but bound directly to PIP-containing membranes without a subsequent reorientation step. Again, PIP3 bound close to the active site of the Ci-VSP PD, but not in a catalytically productive manner. Interactions of Ci-VSP with the bilayer induced clustering of PIP molecules around the protein.

Adsorption Optimization of Lead (II) Using Saccharum Bengalense as a Non-Conventional Low Cost Biosorbent: Isotherm and Thermodynamics Modeling

In the present study a novel biomass, derived from the pulp of Saccharum bengalense, was used as an adsorbent material for the removal of Pb (II) ions from aqueous solution. After 50 minutes contact time, almost 92% lead removal was possible at pH 6.0 under batch test conditions. The experimental data was analyzed using Langmuir, Freundlich, Timken and Dubinin-Radushkevich two parameters isotherm model, three parameters Redlich—Peterson, Sip and Toth models and four parameters Fritz Schlunder isotherm models. Langmuir, Redlich—Peterson and Fritz-Schlunder models were found to be the best fit models. Kinetic studies revealed that the sorption process was well explained with pseudo second-order kinetic model. Thermodynamic parameters including free energy change (ΔG°), enthalpy change (ΔH°) and entropy change (ΔS°) have been calculated and reveal the spontaneous, endothermic and feasible nature of the adsorption process. The thermodynamic parameters of activation (ΔG #, ΔH #and ΔS #) were calculated from the pseudo-second order rate constant by using the Eyring equation. Results showed that Pb (II) adsorption onto SB is an associated mechanism and the reorientation step is entropy controlled.

Separated topologies—A method for relative binding free energy calculations using orientational restraints

Orientational restraints can improve the efficiency of alchemical free energy calculations, but they are not typically applied in relative binding calculations, which compute the affinity difference been two ligands. Here, we describe a new "separated topologies" method, which computes relative binding free energies using orientational restraints and which has several advantages over existing methods. While standard approaches maintain the initial and final ligand in a shared orientation, the separated topologies approach allows the initial and final ligands to have distinct orientations. This avoids a slowly converging reorientation step in the calculation. The separated topologies approach can also be applied to determine the relative free energies of multiple orientations of the same ligand. We illustrate the approach by calculating the relative binding free energies of two compounds to an engineered site in Cytochrome C Peroxidase.

Nonequilibrium Adsorption and Reorientation Dynamics of Molecules at Electrode/Electrolyte Interfaces Probed via Real-Time Second Harmonic Generation

Nonequilibrium adsorption and subsequent reorientation of organic molecules at electrode/electrolyte interfaces are important steps in electrochemical reactions and other interfacial processes, yet real-time quantitative characterization and monitoring of these processes, particularly for the reorientation step, are still challenging experimentally. Herein, we investigated the nonequilibrium adsorption process of 4-(4-(diethylamino)styryl)-N-methyl-pyridinium iodide (D289) molecules from acetonitrile solution onto a polycrystalline platinum electrode surface using real-time second harmonic generation (SHG) in combination with the potential step method. The time-dependent SHG curves exhibit two distinct regimes, which were interpreted with a two-step adsorption model consisting of a fast adsorption and a slow reorientation step for D289 on the surface. D289 was assumed to initially adsorb in an orientation perpendicular to the surface and then reorient to a parallel orientation. We derived a quantitative mathematical expression containing a biexponential function to fit the temporal SHG curves and obtain the rate constants for the two steps. The rate constants for fast adsorption and the slower reorientation processes show similar potential-dependent behavior: the rate decreases with an increase in the negative potential. We further proposed a molecular mechanism involving the displacement of D289 and CH3CN molecules adsorbed on the electrode interface to explain this potential-dependent behavior. On the basis of such analysis, we obtained a detailed picture of the adsorption of D289 molecules on the Pt electrode/CH3CN electrolyte, which consists of three consecutive steps: diffusion, adsorption, and reorientation. The results of this study may shed light on adsorption mechanisms at the electrode/electrolyte interface as well as at biological and other functional material interfaces.

Oxidative breakdown of acid orange 7 by a manganese oxide containing mine waste: Insight into sorption, kinetics and reaction dynamics

The reaction rates and orders of azo dye, acid orange 7 (AO 7), oxidation by a Mn oxide containing mine tailings were determined. The reaction is pseudo-first order with respect to the tailings surface area concentration [SA] and pseudo-fractional (0.6) order with respect to AO 7 concentration. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy was used to probe surface sorption and oxidation of AO 7 on a synthetic manganite surface. Sorption is rapid, pH dependent and predominantly outer-sphere. At pH 2.7 a distinct lag phase of 8min has been observed between dye sorption and the initiation of oxidation. This lag phase suggests that either transfer of the first electron is rate limiting or there is a time consuming re-orientation and inner-sphere sorption step prior to electron transfer.

The B‐matrix must be rotated when correcting for subject motion in DTI data

To estimate diffusion tensor MRI (DTI) measures, such as fractional anisotropy and fiber orientation, reliably, a large number of diffusion-encoded images is needed, preferably cardiac gated to reduce pulsation artifacts. However, the concomitant longer acquisition times increase the chances of subject motion adversely affecting the estimation of these measures. While correcting for motion artifacts improves the accuracy of DTI, an often overlooked step in realigning the images is to reorient the B-matrix so that orientational information is correctly preserved. To the best of our knowledge, most research groups and software packages currently omit this reorientation step. Given the recent explosion of DTI applications including, for example, neurosurgical planning (in which errors can have drastic consequences), it is important to investigate the impact of neglecting to perform the B-matrix reorientation. In this work, a systematic study to investigate the effect of neglecting to reorient the B-matrix on DTI data during motion correction is presented. The consequences for diffusion fiber tractography are also discussed.

Removal of copper(II) from aqueous solution by pine and base modified pine cone powder as biosorbent

Pine cone, a popular agricultural waste in South Africa has been studied for its potential application as a biosorbent in its raw and sodium hydroxide modified form. Surface modification were carried out using sodium hydroxide solution of concentration ranging from 0.01 to 0.15 mol L −1and the samples characterized. Batch kinetics were carried out on the biosorption of copper(II) from aqueous solution using the prepared samples and varying biosorption parameters such as solution pH, dose and biosorption temperature. The results revealed that pine cone surface was modified by sodium hydroxide treatment, carboxylic and phenolic functional groups were mostly affected as seen from Boehm's titration and FTIR analysis. Surface modification reduced pH PZC from 7.49 to 2.55 and also increased the internal surface of pine cone powder. Copper(II) biosorption studies revealed that optimum solution pH and biosorbent dose for copper(II) removal was pH 5 and 8.0 g L −1, for the untreated and treated samples. Copper(II) uptake followed the pseudo-second order kinetic model and the intraparticle diffusion model. Copper(II) removal increased with NaOH modification and higher NaOH concentration. Biosorption temperature was found to increase copper(II) uptake for all samples indicating that copper(II) biosorption is endothermic in nature. Activation energy computed from the pseudo-second order rate constant increased with NaOH modification from 18.22 to 21.39 kJ mol −1. The thermodynamic parameters of activation (Δ G*, Δ H* and Δ S*) were computed using Erying equation and the results show that the reorientation step is mostly entropy controlled at the activation state and the contribution of entropy to the reorientation step of activation tends to decrease with NaOH washing and with increase in NaOH concentration.

Path Integral Treatment of Proton Transport Processes inBaZrO3

Nuclear quantum effects on proton transfer and reorientation in BaZrO3 is investigated theoretically using the ab initio path-integral molecular-dynamics simulation technique. The result demonstrates that adding quantum fluctuations has a large effect on, in particular, the transfer barrier. The corresponding rates and diffusion coefficient are evaluated using the path-centroid transition state theory. In contrast with what is found assuming classical mechanics for the nuclear motion, the reorientation step becomes rate limiting below 600 K.

Density-functional calculations of prefactors and activation energies for H diffusion inBaZrO3

Density-functional calculations are used to investigate hydrogen diffusion in the solid-state proton conductor $\mathrm{Ba}\mathrm{Zr}{\mathrm{O}}_{3}$. Activation energies and prefactors for the rate of proton transfer and reorientation are evaluated for a defect-free region of this simple cubic perovskite-structured oxide. Both semiclassical over-barrier jumps and phonon-assisted tunneling transitions between sites are considered. It is found that the classical barriers for the elementary transfer and reorientation steps are both of the order of $0.2\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$. The quantum-mechanical zero-point motion effects are found to be sizable, to effectively reduce the barrier heights, and to make the prefactors similar for the transfer and reorientation steps. The Flynn-Stoneham model [Phys. Rev. B 1, 3966 (1970)] of phonon-assisted tunneling yields an activation energy of around $0.2\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$ and a very small prefactor for proton transfer, whereas the corresponding adiabatic model gives a similar activation energy but a much larger prefactor. It is suggested that the effect of other defects such as dopants has to be included for a proper description of hydrogen diffusion in this material.

Enhancing Glutamate Transport: Mechanism of Action of Parawixin1, a Neuroprotective Compound from Parawixia bistriata Spider Venom

Previous studies have shown that a compound purified from the spider Parawixia bistriata venom stimulates the activity of glial glutamate transporters and can protect retinal tissue from ischemic damage. To understand the mechanism by which this compound enhances transport, we examined its effects on the functional properties of glutamate transporters after solubilization and reconstitution in liposomes and in transfected COS-7 cells. Here, we demonstrate in both systems that Parawixin1 promotes a direct and selective enhancement of glutamate influx by the EAAT2 transporter subtype through a mechanism that does not alter the apparent affinities for the cosubstrates glutamate or sodium. In liposomes, we observed maximal enhancement by Parawixin1 when extracellular sodium and intracellular potassium concentrations are within physiological ranges. Moreover, the compound does not enhance the reverse transport of glutamate under ionic conditions that favor efflux, when extracellular potassium is elevated and the sodium gradient is reduced, nor does it alter the exchange of glutamate in the absence of internal potassium. These observations suggest that Parawixin1 facilitates the reorientation of the potassium-bound transporter, the rate-limiting step in the transport cycle, a conclusion further supported by experiments showing that Parawixin1 does not stimulate uptake by an EAAT2 transport mutant (E405D) defective in the potassium-dependent reorientation step. Thus, Parawixin1 enhances transport through a novel mechanism targeting a step in the transport cycle distinct from substrate influx or efflux and provides a basis for the design of new drugs that act allosterically on transporters to increase glutamate clearance.

Diffusion mechanisms for silicon di-interstitials

Tight-binding molecular dynamics and density-functional simulations on silicon seeded with a di-interstitial reveal its detailed diffusion mechanisms. The lowest-energy di-interstitial performs a translation/rotation diffusion-step with a barrier of $0.3\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$ and a prefactor of $11\phantom{\rule{0.3em}{0ex}}\mathrm{THz}$ followed by a reorientation diffusion step with a $90\phantom{\rule{0.3em}{0ex}}\mathrm{meV}$ barrier and a $2300\phantom{\rule{0.3em}{0ex}}\mathrm{THz}$ prefactor. The intermediate reorientation steps allow di-interstitials to diffuse isotropically along all possible ⟨111⟩ bond directions in the diamond lattice. The dominating diffusion barrier of $0.3\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$ is not inconsistent with the experimental value of $0.6\ifmmode\pm\else\textpm\fi{}0.2\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$. In addition, this lowest energy di-interstitial may diffuse to neighboring sites through an intermediate structure which is the bound state of two single interstitials. The process in which migrating single interstitials combine into a di-interstitial is exothermic with almost zero energy barrier.

Evaluation of the Quantitative Gated SPECT (QGS) software program in the presence of large perfusion defects

To evaluate the reproducibility and operator dependence for the quantitative regional left ventricular functional parameters (LVFP) assessed by Cedars-Sinai's Quantitative automated gated SPECT (QGS) software. The QGS algorithm was reviewed in detail and potential operator dependencies were defined. Series of prototypes were selected, consisting of (a) normal perfusion, (b) perfusion defects in all perfusion regions, (c) perfusion studies of patients with angiographic confirmed normal coronary arteries, proximal (>or=70% stenoses) single and multiple vessel disease, and (d) spurious activity in close proximity. While defining and re-orienting the volume containing the left ventricle, the operator adjusted 8 variables/degrees of freedom (DF). The software was used without further operator interventions. Results were expressed as a coefficient of variation (COV). Separate COV were calculated per distinct DF. A segment was considered not robust when the COV did exceed 20% in a single DF, 15% in at least 2 DF, or 10% in at least 3 DF. Regional left ventricular EF and volumes showed excellent reproducibility. Normal perfusion and the vessel disease prototypes showed an excellent COV (for all re-orientation steps [33/prototype]) mostly below 5% for LVFP. However, regional wall motion and thickening became less reliable in the presence of large perfusion defects or artifacts. Quantitative estimates for regional left ventricular functional data show excellent reproducibility using automated gated SPECT. However, there may be substantial operator dependency in the presence of large defects or spurious activity in close proximity.

Acetylcholine binding site in the vesicular acetylcholine transporter.

This study sought primarily to locate the acetylcholine (ACh) binding site in the vesicular acetylcholine transporter (VAChT). The design of the study also allowed us to locate residues linked to (a) the binding site for the allosteric inhibitor vesamicol and (b) the rates of the two transmembrane reorientation steps of a transport cycle. In more characterized proteins, ACh is known to be bound in part through cation-pi solvation by tryptophan, tyrosine, and phenylalanine residues. Each of 11 highly conserved W, Y, and F residues in putative transmembrane domains (TMDs) of rat VAChT was mutated to A and a different aromatic residue to test for loss of cation-pi solvation. Mutated VAChTs were expressed in PC12(A123.7) cells and characterized with the goal of determining whether mutations widely perturbed structure. The thermodynamic affinity for ACh was determined by displacement of trace [(3)H]-(-)-trans-2-(4-phenylpiperidino)cyclohexanol (vesamicol) with ACh, and Michaelis-Menten parameters were determined for [(3)H]ACh transport. Expression levels were determined with [(3)H]vesamicol saturation curves and Western blots, and they were used to normalize V(max) values. "Microscopic" parameters for individual binding and rate steps in the transport cycle were calculated on the basis of a published kinetics model. All mutants were expressed adequately, were properly glycosylated, and bound ACh and vesamicol. Subcellular mistargeting was shown not to be responsible for poor transport by some mutants. Mutation of residue W331, which lies in the beginning of TMD VIII proximal to the vesicular lumen, produced 5- and 9-fold decreased ACh affinities and no change in other parameters. This residue is a good candidate for cation-pi solvation of bound ACh. Mutation of four other residues decreased the ACh affinity up to 6-fold and also affected microscopic rate constants. The roles of these residues in ACh binding and transport thus are complex. Nine mutations allowed us to resolve the ACh and vesamicol binding sites from each other. Other mutations affected only the rates of the transmembrane reorientation steps, and four mutations increased the rate of one or the other. Two mutations increased the value of K(M) up to 5-fold as a result of rate effects with no ACh affinity effect. The results demonstrate that analysis of microscopic kinetics is required for the correct interpretation of mutational effects in VAChT. Results also are discussed in terms of recently determined three-dimensional structures for other transporters in the major facilitator superfamily.

Transition State Analysis of the Coupling of Drug Transport to ATP Hydrolysis by P-glycoprotein

ATPase activity associated with P-glycoprotein (Pgp) is characterized by three drug-dependent phases: basal (no drug), drug-activated, and drug-inhibited. To understand the communication between drug-binding sites and ATP hydrolytic sites, we performed steady-state thermodynamic analyses of ATP hydrolysis in the presence and absence of transport substrates. We used purified human Pgp (ABCB1, MDR1) expressed in Saccharomyces cerevisiae (Figler, R. A., Omote, H., Nakamoto, R. K., and Al-Shawi, M. K. (2000) Arch. Biochem. Biophys. 376, 34-46) as well as Chinese hamster Pgp (PGP1). Between 23 and 35 degrees C, we obtained linear Arrhenius relationships for the turnover rate of hydrolysis of saturating MgATP in the presence of saturating drug concentrations (kcat), from which we calculated the intrinsic enthalpic, entropic, and free energy terms for the rate-limiting transition states. Linearity of the Arrhenius plots indicated that the same rate-limiting step was being measured over the temperature range employed. Using linear free energy analysis, two distinct transition states were found: one associated with uncoupled basal activity and the other with coupled drug transport activity. We concluded that basal ATPase activity associated with Pgp is not a consequence of transport of an endogenous lipid or other endogenous substrates. Rather, it is an intrinsic mechanistic property of the enzyme. We also found that rapidly transported substrates bound tighter to the transition state and required fewer conformational alterations by the enzyme to achieve the coupling transition state. The overall rate-limiting step of Pgp during transport is a carrier reorientation step. Furthermore, Pgp is optimized to transport drugs out of cells at high rates at the expense of coupling efficiency. The drug inhibition phase was associated with low affinity drug-binding sites. These results are consistent with an expanded version of the alternating catalytic site drug transport model (Senior, A. E., Al-Shawi, M. K., and Urbatsch, I. L. (1995) FEBS Lett. 377, 285-289). A new kinetic model of drug transport is presented.

Molecular Mechanism of H + Conduction in the Single-File Water Chain of the Gramicidin Channel

The conduction of protons in the hydrogen-bonded chain of water molecules (or “proton wire”) embedded in the lumen of gramicidin A is studied with molecular dynamics free energy simulations. The process may be described as a “hop-and-turn” or Grotthuss mechanism involving the chemical exchange (hop) of hydrogen nuclei between hydrogen-bonded water molecules arranged in single file in the lumen of the pore, and the subsequent reorganization (turn) of the hydrogen-bonded network. Accordingly, the conduction cycle is modeled by two complementary steps corresponding respectively to the translocation 1) of an ionic defect (H +) and 2) of a bonding defect along the hydrogen-bonded chain of water molecules in the pore interior. The molecular mechanism and the potential of mean force are analyzed for each of these two translocation steps. It is found that the mobility of protons in gramicidin A is essentially determined by the fine structure and the dynamic fluctuations of the hydrogen-bonded network. The translocation of H + is mediated by spontaneous (thermal) fluctuations in the relative positions of oxygen atoms in the wire. In this diffusive mechanism, a shallow free-energy well slightly favors the presence of the excess proton near the middle of the channel. In the absence of H +, the water chain adopts either one of two polarized configurations, each of which corresponds to an oriented donor-acceptor hydrogen-bond pattern along the channel axis. Interconversion between these two conformations is an activated process that occurs through the sequential and directional reorientation of water molecules of the wire. The effect of hydrogen-bonding interactions between channel and water on proton translocation is analyzed from a comparison to the results obtained previously in a study of model nonpolar channels, in which such interactions were missing. Hydrogen-bond donation from water to the backbone carbonyl oxygen atoms lining the pore interior has a dual effect: it provides a coordination of water molecules well suited both to proton hydration and to high proton mobility, and it facilitates the slower reorientation or turn step of the Grotthuss mechanism by stabilizing intermediate configurations of the hydrogen-bonded network in which water molecules are in the process of flipping between their two preferred, polarized states. This mechanism offers a detailed molecular model for the rapid transport of protons in channels, in energy-transducing membrane proteins, and in enzymes.