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Nachliel E, Gutman M. Reaction within the coulomb-cage; science in retrospect. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184071. [PMID: 36244436 DOI: 10.1016/j.bbamem.2022.184071] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 08/01/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
The Coulomb-cage is defined as the space where the electrostatic interaction between two bodies is more intensive than the thermal energy (kBT). For small molecule, the Coulomb-cage is a small sphere, extending only few water molecules towards the bulk and its radius is sensitive to the ionic strength of the solution. For charged proteins or membranal structures, the Coulomb-cage can engulf large fraction of the surface and provides a preferred pathway for ion propagation along the surface. Similarly, electrostatic potential at the inner space of a channel can form preferential trajectories passage for ions. The dynamics of ions inside the Coulomb-cage of ions was formulated by the studies of proton-anion recombination of excited photoacids. In the present article, we recount the study of intra- Coulomb-cage reaction taking place on the surface of macro-molecular bodies like micelles, membranes, proteins and intra-protein cavities. The study progressed stepwise, tracing the dynamics of a proton ejected from a photo-acid molecule located at defined sites (on membrane, inter-membrane space, active site of enzyme, inside Large Pore Channels etc.). Accumulation of experimental observations encouraged us to study of the reaction mechanism by molecular dynamics simulations of ions within the Coulomb-cage of proteins surface or inside large pores. The intra-Coulomb-cage proton transfer events follows closely the fine structure of the electrostatic field inside the cage and reflects the shape of nearby dielectric boundaries, the temporal ordering of the solvent molecules and the structural fluctuations of the charged side chains. The article sums some 40 years of research, which in retrospect clarifies the intra-Coulomb-cage reaction mechanism.
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Affiliation(s)
- E Nachliel
- Laser Laboratory for Fast Reactions, Dep. Of Biochemistry and Molecular Biology, Life Sciences, Tel Aviv University, Israel
| | - M Gutman
- Laser Laboratory for Fast Reactions, Dep. Of Biochemistry and Molecular Biology, Life Sciences, Tel Aviv University, Israel.
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2
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Stuchebrukhov AA, Variyam AR, Amdursky N. Using Proton Geminate Recombination as a Probe of Proton Migration on Biological Membranes. J Phys Chem B 2022; 126:6026-6038. [PMID: 35921517 DOI: 10.1021/acs.jpcb.2c00953] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proton migration on biological membranes plays a major role in cellular respiration and photosynthesis, but it is not yet fully understood. Here we show that proton dissociation kinetics and related geminate recombination can be used as a probe of such proton migration mechanisms. We develop a simple model for the process and apply it to analyze the results obtained using a photo-induced proton release probe (chemically modified photoacid) tethered to phosphatidylcholine membranes. In our theoretical model, we apply approximate treatment for the diffusional cloud of the geminate proton around the dissociated photoacid and consider arbitrary dimension of the system, 1 < d < 3. We observe that in d > 2, there is a kinetic phase transition between an exponential and a power-law kinetic phases. The existence of an exponential decay phase at the beginning of the proton dissociation is a signature of d > 2 systems. In most other cases, the exponential decay phase is not present, and the kinetics follows a diffusional power-law P(t) ∼ t-d/2 that develops after a short initiation time. Specifically, in a 1D case, which corresponds to the desorption of a proton from the surface, the dissociation occurs by the slow power-law ∼1/t and explains the abnormally slow desorption rate reported recently in experiments.
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Affiliation(s)
- Alexei A Stuchebrukhov
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, United States
| | | | - Nadav Amdursky
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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3
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Morelli AM, Ravera S, Panfoli I. The aerobic mitochondrial ATP synthesis from a comprehensive point of view. Open Biol 2020; 10:200224. [PMID: 33081639 PMCID: PMC7653358 DOI: 10.1098/rsob.200224] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Most of the ATP to satisfy the energetic demands of the cell is produced by the F1Fo-ATP synthase (ATP synthase) which can also function outside the mitochondria. Active oxidative phosphorylation (OxPhos) was shown to operate in the photoreceptor outer segment, myelin sheath, exosomes, microvesicles, cell plasma membranes and platelets. The mitochondria would possess the exclusive ability to assemble the OxPhos molecular machinery so to share it with the endoplasmic reticulum (ER) and eventually export the ability to aerobically synthesize ATP in true extra-mitochondrial districts. The ER lipid rafts expressing OxPhos components is indicative of the close contact of the two organelles, bearing different evolutionary origins, to maximize the OxPhos efficiency, exiting in molecular transfer from the mitochondria to the ER. This implies that its malfunctioning could trigger a generalized oxidative stress. This is consistent with the most recent interpretations of the evolutionary symbiotic process whose necessary prerequisite appears to be the presence of the internal membrane system inside the eukaryote precursor, of probable archaeal origin allowing the engulfing of the α-proteobacterial precursor of mitochondria. The process of OxPhos in myelin is here studied in depth. A model is provided contemplating the biface arrangement of the nanomotor ATP synthase in the myelin sheath.
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Affiliation(s)
- Alessandro Maria Morelli
- Pharmacy Department (DIFAR), Biochemistry Laboratory, University of Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Silvia Ravera
- Experimental Medicine Department (DIMES), University of Genova, Via De Toni, 14, 16132 Genova, Italy
| | - Isabella Panfoli
- Pharmacy Department (DIFAR), Biochemistry Laboratory, University of Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
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Vester M, Grueter A, Finkler B, Becker R, Jung G. Biexponential photon antibunching: recombination kinetics within the Förster-cycle in DMSO. Phys Chem Chem Phys 2016; 18:10281-8. [PMID: 27020473 DOI: 10.1039/c6cp00718j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Time-resolved experiments with pulsed-laser excitation are the standard approach to map the dynamic evolution of excited states, but ground-state kinetics remain hidden or require pump-dump-probe schemes. Here, we exploit the so-called photon antibunching, a purely quantum-optical effect related to single molecule detection to assess the rate constants for a chemical reaction in the electronic ground state. The measurement of the second-order correlation function g((2)), i.e. the evaluation of inter-photon arrival times, is applied to the reprotonation in a Förster-cycle. We find that the antibunching of three different photoacids in the aprotic solvent DMSO significantly differs from the behavior in water. The longer decay constant of the biexponential antibunching tl is linked to the bimolecular reprotonation kinetics of the fully separated ion-pair, independent of the acidic additives. The value of the corresponding bimolecular rate constant, kp = 4 × 10(9) M(-1) s(-1), indicates diffusion-controlled reprotonation. The analysis of tl also allows for the extraction of the separation yield of proton and the conjugated base after excitation and amounts to approximately 15%. The shorter time component ts is connected to the decay of the solvent-separated ion pair. The associated time constant for geminate reprotonation is approximately 3 ± 1 ns in agreement with independent tcspc experiments. These experiments verify that the transfer of quantum-optical experiments to problems in chemistry enables mechanistic conclusions which are hardly accessible by other methods.
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Affiliation(s)
- Michael Vester
- Biophysical Chemistry, Saarland University, 66123 Saarbrücken, Germany.
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5
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Amdursky N, Simkovitch R, Huppert D. Excited-State Proton Transfer of Photoacids Adsorbed on Biomaterials. J Phys Chem B 2014; 118:13859-69. [DOI: 10.1021/jp509153r] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Nadav Amdursky
- Department
of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Ron Simkovitch
- Raymond
and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dan Huppert
- Raymond
and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
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6
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Chung K, Fujiki I, Okabe S. Effect of formation of biofilms and chemical scale on the cathode electrode on the performance of a continuous two-chamber microbial fuel cell. BIORESOURCE TECHNOLOGY 2011; 102:355-360. [PMID: 20923722 DOI: 10.1016/j.biortech.2010.04.091] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Revised: 04/26/2010] [Accepted: 04/29/2010] [Indexed: 05/30/2023]
Abstract
A two-chamber MFC system was operated continuously for more than 500 days to evaluate effects of biofilm and chemical scale formation on the cathode electrode on power generation. A stable power density of 0.57 W/m(2) was attained after 200 days operation. However, the power density decreased drastically to 0.2 W/m(2) after the cathodic biofilm and chemical scale were removed. As the cathodic biofilm and chemical scale partially accumulated on the cathode, the power density gradually recovered with time. Microbial community structure of the cathodic biofilm was analyzed based on 16S rRNA clone libraries. The clones closely related to Xanthomonadaceae bacterium and Xanthomonas sp. in the Gammaproteobacteria subdivision were most frequently retrieved from the cathodic biofilm. Results of the SEM-EDX analysis revealed that the cation species (Na(+) and Ca(2+)) were main constituents of chemical scale, indicating that these cations diffused from the anode chamber through the Nafion membrane. However, an excess accumulation of the biofilm and chemical scale on the cathode exhibited adverse effects on the power generation due to a decrease in the active cathode surface area and an increase in diffusion resistance for oxygen. Thus, it is important to properly control the formation of chemical scale and biofilm on the cathode during long-term operation.
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Affiliation(s)
- Kyungmi Chung
- Department of Urban and Environmental Engineering, Graduate School of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo 060-8628, Japan
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7
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Zhuang L, Feng C, Zhou S, Li Y, Wang Y. Comparison of membrane- and cloth-cathode assembly for scalable microbial fuel cells: Construction, performance and cost. Process Biochem 2010. [DOI: 10.1016/j.procbio.2010.02.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Surface-coupled proton exchange of a membrane-bound proton acceptor. Proc Natl Acad Sci U S A 2010; 107:4129-34. [PMID: 20160117 DOI: 10.1073/pnas.0908671107] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proton-transfer reactions across and at the surface of biological membranes are central for maintaining the transmembrane proton electrochemical gradients involved in cellular energy conversion. In this study, fluorescence correlation spectroscopy was used to measure the local protonation and deprotonation rates of single pH-sensitive fluorophores conjugated to liposome membranes, and the dependence of these rates on lipid composition and ion concentration. Measurements of proton exchange rates over a wide proton concentration range, using two different pH-sensitive fluorophores with different pK(a)s, revealed two distinct proton exchange regimes. At high pH (> 8), proton association increases rapidly with increasing proton concentrations, presumably because the whole membrane acts as a proton-collecting antenna for the fluorophore. In contrast, at low pH (< 7), the increase in the proton association rate is slower and comparable to that of direct protonation of the fluorophore from the bulk solution. In the latter case, the proton exchange rates of the two fluorophores are indistinguishable, indicating that their protonation rates are determined by the local membrane environment. Measurements on membranes of different surface charge and at different ion concentrations made it possible to determine surface potentials, as well as the distance between the surface and the fluorophore. The results from this study define the conditions under which biological membranes can act as proton-collecting antennae and provide fundamental information on the relation between the membrane surface charge density and the local proton exchange kinetics.
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9
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Park K, Shin KJ, Kim H. Excited-state reversible geminate recombination in two dimensions. J Chem Phys 2009; 131:154105. [PMID: 20568845 DOI: 10.1063/1.3242273] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Excited-state reversible geminate recombination with two different lifetimes and quenching is investigated in two dimensions. From the exact Green function in the Laplace domain, analytic expressions of two-dimensional survival and binding probabilities are obtained at short and long times. We find that a new pattern of kinetic transition occurs in two dimensions. The long-time effective survival probabilities show a pattern of (ln t)(-1)-->constant-->e(t) depending on the rate constants while the effective binding probabilities show t(-1)(ln t)(-2)-->t(-1)-->e(t).
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Affiliation(s)
- Kihyun Park
- Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea
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10
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Fan Y, Hu H, Liu H. Sustainable power generation in microbial fuel cells using bicarbonate buffer and proton transfer mechanisms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2007; 41:8154-8158. [PMID: 18186352 DOI: 10.1021/es071739c] [Citation(s) in RCA: 161] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Phosphate buffer solution has been commonly used in MFC studiesto maintain a suitable pH for electricity-generating bacteria and/or to increase the solution conductivity. However, addition of a high concentration of phosphate buffer in MFCs could be expensive, especially for wastewater treatment. In this study, the performances of MFCs with cloth electrode assemblies (CEA) were evaluated using bicarbonate buffer solutions. A maximum power density of 1550 W/m3 (2770 mW/ m2) was obtained at a current density of 0.99 mA/cm2 using a pH 9 bicarbonate buffer solution. Such a power density was 38.6% higher than that using a pH 7 phosphate buffer at the same concentration of 0.2 M. Based on the quantitative comparison of free proton transfer rates, diffusion rates of pH buffer species, and the current generated, a facilitated proton transfer mechanism was proposed for MFCs in the presence of the pH buffers. The excellent performance of MFCs using bicarbonate as pH buffer and proton carrier indicates that bicarbonate buffer could be served as a low-cost and effective pH buffer for practical applications, especially for wastewater treatment.
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Affiliation(s)
- Yanzhen Fan
- Department of Biological and Ecological Engineering, Oregon State University, Corvallis, Oregon 97331, USA
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11
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Cohen-Hadar N, Wine Y, Nachliel E, Huppert D, Gutman M, Frolow F, Freeman A. Monitoring the stability of crosslinked protein crystals biotemplates: a feasibility study. Biotechnol Bioeng 2006; 94:1005-11. [PMID: 16572452 DOI: 10.1002/bit.20935] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Protein crystals, routinely prepared for the elucidation of protein 3D structures by X-ray crystallography, present an ordered and highly accurate 3D array of protein molecules. Inherent to the 3D arrangement of the protein molecules in the crystal is a complementary 3D array of voids made of interconnected cavities and exhibiting highly ordered porosity. The permeability of the porosity of chemically crosslinked enzyme protein crystals to low molecular weight solutes, was used for enzyme mediated organic synthesis and size exclusion chromatography. This permeability might be extended to explore new potential applications for protein crystals, for example, their use as bio-templates for the fabrication of novel, nano-structured composite materials. The quality of composites obtained from "filling" of the ordered voids in protein crystals and their potential applications will be strongly dependent upon an accurate preservation of the order in the original protein crystal 3D array during the "filling" process. Here we propose and demonstrate the feasibility of monitoring the changes in 3D order of the protein array by a step-by-step molecular level monitoring of a model system for hydrogel bio-templating by glutaraldehyde crosslinked lysozyme crystals. This monitoring is based on step-by-step comparative analysis of data obtained from (i) X-ray crystallography: resolution, unit cell dimensions and B-factor values and (ii) fluorescence decay kinetics of ultra-fast laser activated dye, impregnated within these crystals. Our results demonstrated feasibility of the proposed monitoring approach and confirmed that the stabilized protein crystal template retained its 3D structure throughout the process.
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Affiliation(s)
- Noa Cohen-Hadar
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
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12
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Saxena AM, Udgaonkar JB, Krishnamoorthy G. Protein dynamics control proton transfer from bulk solvent to protein interior: a case study with a green fluorescent protein. Protein Sci 2005; 14:1787-99. [PMID: 15937281 PMCID: PMC2253357 DOI: 10.1110/ps.051391205] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The kinetics of proton transfer in Green Fluorescent Protein (GFP) have been studied as a model system for characterizing the correlation between dynamics and function of proteins in general. The kinetics in EGFP (a variant of GFP) were monitored by using a laser-induced pH jump method. The pH was jumped from 8 to 5 by nanosecond flash photolysis of the "caged proton," o-nitrobenzaldehyde, and subsequent proton transfer was monitored by following the decrease in fluorescence intensity. The modulation of proton transfer kinetics by external perturbants such as viscosity, pH, and subdenaturing concentrations of GdnHCl as well as of salts was studied. The rate of proton transfer was inversely proportional to solvent viscosity, suggesting that the rate-limiting step is the transfer of protons through the protein matrix. The rate is accelerated at lower pH values, and measurements of the fluorescence properties of tryptophan 57 suggest that the enhancement in rate is associated with an enhancement in protein dynamics. The rate of proton transfer is nearly independent of temperature, unlike the rate of the reverse process. When the stability of the protein was either decreased or increased by the addition of co-solutes, including the salts KCl, KNO(3), and K(2)SO(4), a significant decrease in the rate of proton transfer was observed in all cases. The lack of correlation between the rate of proton transfer and the stability of the protein suggests that the structure is tuned to ensure maximum efficiency of the dynamics that control the proton transfer function of the protein.
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Affiliation(s)
- Anoop M Saxena
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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13
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Abstract
The dynamics of proton dissociation from an acidic moiety and its subsequent dispersion in the bulk is regulated by the physical chemical properties of the solvent. The solvent has to provide a potential well to accommodate the discharged proton, screen it from the negative charge of the conjugated base, and provide an efficient mode for the diffusion of the proton to the bulk. On measuring the dynamics of proton dissociation in the time-resolved domain, the kinetic analysis of the reaction can quantitate the properties of the immediate environment. In this review we implement the kinetic analysis for evaluating the properties of small cavities in proteins and the diffusion of protons within narrow channels. On the basis of this analysis,we discuss how the clustering of proton-binding sites on a surface can endow the surface with enhanced capacity to attract protons and to funnel them toward a specific site.
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Affiliation(s)
- M Gutman
- Laser Laboratory for Fast Reactions in Biochemical Systems, Department of Biochemistry, Tel-Aviv University, Tel-Aviv, Israel 69978
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14
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Bransburg-Zabary S, Nachliel E, Gutman M. Gauging of the PhoE channel by a single freely diffusing proton. Biophys J 2002; 83:2987-3000. [PMID: 12496072 PMCID: PMC1302380 DOI: 10.1016/s0006-3495(02)75305-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
In the present study we combined a continuum approximation with a detailed mapping of the electrostatic potential inside an ionic channel to define the most probable trajectory for proton propagation through the channel (propagation along a structure-supported trajectory (PSST)). The conversion of the three-dimensional diffusion space into propagation along a one-dimensional pathway permits reconstruction of an ion motion by a short calculation (a few seconds on a state-of-the-art workstation) rather than a laborious, time-consuming random walk simulations. The experimental system selected for testing the accuracy of this concept was the reversible dissociation of a proton from a single pyranine molecule (8-hydroxypyrene-1,2,3-trisulfonate) bound by electrostatic forces inside the PhoE ionic channel of the Escherichia coli outer membrane. The crystal structure coordinates were used for calculation of the intra-cavity electrostatic potential, and the reconstruction of the observed fluorescence decay curve was carried out using the dielectric constant of the intra-cavity space as an adjustable parameter. The fitting of past experimental observations (Shimoni, E., Y. Tsfadia, E. Nachliel, and M. Gutman. 1993. Biophys. J. 64:472-479) was carried out by a modified version of the Agmon geminate recombination program (Krissinel, E. B., and N. Agmon. 1996. J. Comp. Chem. 17:1085-1098), where the gradient of the electrostatic potential and the entropic terms were calculated by the PSST program. The best-fitted reconstruction of the observed dynamics was attained when the water in the cavity was assigned epsilon </= 55, corroborating the theoretical estimation of Sansom (Breed, J. R., I. D. Kerr, and M. S. P. Sansom. 1996. Biophys. J. 70:1643-1661). The dielectric constant calculated for reversed micelles of comparable size (Cohen, B., D. Huppert, K. M. Solntsev, Y. Tsfadia, E. Nachliel, and M. Gutman. 2002. JACS. 124:7539-7547) allows us to set a margin of epsilon = 50 +/- 5.
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Affiliation(s)
- Sharron Bransburg-Zabary
- Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
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15
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16
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Smondyrev AM, Voth GA. Molecular dynamics simulation of proton transport near the surface of a phospholipid membrane. Biophys J 2002; 82:1460-8. [PMID: 11867461 PMCID: PMC1301947 DOI: 10.1016/s0006-3495(02)75500-8] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The structural and dynamical properties of a hydrated proton near the surface of DMPC membrane were studied using a molecular dynamics simulation. The proton transport between water molecules was modeled using the second generation multistate empirical valence bond model. The proton diffusion was found to be inhibited at the membrane surface. The potential of mean force for the proton adsorption to the membrane surface and its release back into the bulk water was also determined, yielding a small barrier in each direction. An efficient algorithm for Ewald summation calculations for the multistate empirical valence bond model is also introduced.
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Affiliation(s)
- Alexander M Smondyrev
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
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17
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Affiliation(s)
- Boiko Cohen
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978, Israel
| | - Dan Huppert
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978, Israel
| | - Noam Agmon
- The Fritz Haber Research Center, Department of Physical Chemistry, The Hebrew University, Jerusalem 91904, Israel
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18
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Nachliel E, Pollak N, Huppert D, Gutman M. Time-resolved study of the inner space of lactose permease. Biophys J 2001; 80:1498-506. [PMID: 11222310 PMCID: PMC1301341 DOI: 10.1016/s0006-3495(01)76122-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Pyranine (8-hydroxy pyrene-1,3,6-trisulfonate) is a commonly used photoacid that discharges a proton when excited to its first electronic singlet state. Follow-up of its dissociation kinetics reveals the physicochemical properties of its most immediate environment. At vanishing ionic strength the dye adsorbs to the Escherichia coli lactose permease with stoichiometry of 1:1 and an association constant of 2.5 x 10(5) M(-1). The reversal of the binding at high ionic strength and the lower pK value of the bound dye imply that positive charge(s) stabilize the dye in its site. The fluorescence decay curve of the bound dye was measured by time-correlated single photon counting and the measured transient was subjected to kinetic analysis based on the geminate recombination model. The analysis indicated that the binding domain is a cleft (between 9 and 17 A deep) characterized by low activity of water (a((water)) = 0.71), reduced diffusivity of protons, and enhanced electrostatic potential. The binding of pyranine and a substrate are not mutually exclusive; however, when the substrate is added, the dye-binding environment is better solvated. These properties, if attributed to the substrate-conducting pathway, may explain some of the forces operating on the substrate in the cavity. The reduced activities of the water strips the substrate from some of its solvation water molecules and replace them by direct interaction with the protein. In parallel, the lower dielectric constant enhances the binding of the proton to the protein, thus keeping a tight seal that prevents protons from diffusing.
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Affiliation(s)
- E Nachliel
- Department of Biochemistry, Laser Laboratory for Fast Reactions in Biology, George Wise Faculty of Life Science, Tel Aviv University, Tel Aviv 69978, Israel
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19
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Brandsburg-Zabary S, Fried O, Marantz Y, Nachliel E, Gutman M. Biophysical aspects of intra-protein proton transfer. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1458:120-34. [PMID: 10812028 DOI: 10.1016/s0005-2728(00)00063-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The passage of proton trough proteins is common to all membranal energy conserving enzymes. While the routes differ among the various proteins, the mechanism of proton propagation is based on the same chemical-physical principles. The proton progresses through a sequence of dissociation association steps where the protein and water molecules function as a solvent that lowers the energy penalty associated with the generation of ions in the protein. The propagation of the proton in the protein is a random walk, between the temporary proton binding sites that make the conducting path, that is biased by the intra-protein electrostatic potential. Kinetic measurements of proton transfer reactions, in the sub-ns up to micros time frame, allow to monitor the dynamics of the partial reactions of an overall proton transfer through a protein.
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Affiliation(s)
- S Brandsburg-Zabary
- Laser Laboratory for Fast reactions in Biology, Biochemistry, Tel Aviv University, Tel Aviv, Israel
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20
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Zaloj V, Agmon N. Electrostatics of multilamellar vesicles: Legendre expansion and reaction-field Brownian dynamics. J Chem Phys 1998. [DOI: 10.1063/1.475483] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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21
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van Voorthuysen T, Bulychev AA, Dassen HH, Snel JF, Vredenberg WJ. Flash-induced conductance changes in chloroplast thylakoid lamellae. A patch-clamp study. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0302-4598(97)00011-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Abstract
Binding kinetics of receptor arrays can differ dramatically from that of the isolated receptor. We simulate synaptic transmission using a microscopically accurate Brownian dynamics routine. We study the factors governing the rise and decay of the activation probability as a function of the number of transmitter molecules released. Using a realistic receptor array geometry, the simulation reproduces the time course of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor-mediated excitatory postsynaptic currents. A consistent interpretation of experimentally observed synaptic currents in terms of rebinding and spatial correlations is discussed.
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Affiliation(s)
- N Agmon
- Department of Physical Chemistry, Hebrew University, Jerusalem, Israel.
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Absence of kinetic barrier for transfer of protons from aqueous phase to membrane-water interface. J Biosci 1995. [DOI: 10.1007/bf02703298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Gutman M, Nachliel E. The dynamics of proton exchange between bulk and surface groups. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1995. [DOI: 10.1016/0005-2728(95)00074-s] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Kasianowicz JJ, Bezrukov SM. Protonation dynamics of the alpha-toxin ion channel from spectral analysis of pH-dependent current fluctuations. Biophys J 1995; 69:94-105. [PMID: 7545444 PMCID: PMC1236228 DOI: 10.1016/s0006-3495(95)79879-4] [Citation(s) in RCA: 170] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
To probe protonation dynamics inside the fully open alpha-toxin ion channel, we measured the pH-dependent fluctuations in its current. In the presence of 1 M NaCl dissolved in H2O and positive applied potentials (from the side of protein addition), the low frequency noise exhibited a single well defined peak between pH 4.5 and 7.5. A simple model in which the current is assumed to change by equal amounts upon the reversible protonation of each of N identical ionizable residues inside the channel describes the data well. These results, and the frequency dependence of the spectral density at higher frequencies, allow us to evaluate the effective pK = 5.5, as well as the rate constants for the reversible protonation reactions: kon = 8 x 10(9) M-1 s-1 and koff = 2.5 x 10(4) s-1. The estimate of kon is only slightly less than the diffusion-limited values measured by others for protonation reactions for free carboxyl or imidazole residues. Substitution of H2O by D2O caused a 3.8-fold decrease in the dissociation rate constant and shifted the pK to 6.0. The decrease in the ionization rate constants caused by H2O/D2O substitution permitted the reliable measurement of the characteristic relaxation time over a wide range of D+ concentrations and voltages. The dependence of the relaxation time on D+ concentration strongly supports the first order reaction model. The voltage dependence of the low frequency spectral density suggests that the protonation dynamics are virtually insensitive to the applied potential while the rate-limiting barriers for NaCl transport are voltage dependent. The number of ionizable residues deduced from experiments in H2O (N = 4.2) and D2O (N = 4.1) is in good agreement.
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Affiliation(s)
- J J Kasianowicz
- National Institute of Standards and Technology, Biotechnology Division, Gaithersburg, Maryland 20899, USA
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Gabriel B, Prats M, Teissié J. Proton lateral conduction along a lipid monolayer spread on a physiological subphase. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1186:172-6. [PMID: 8043591 DOI: 10.1016/0005-2728(94)90176-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A localized lateral proton pathway is present along the phospholipid polar heads and bound water molecules when the lipids are spread in monolayers at the air/water interface. Conduction can be detected on concentrated buffers as found under physiological conditions if the lateral proton gradient is large enough. The localized movement supports the occurrence of microlocalized proton circuits along a membrane and of lateral proton gradients.
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Affiliation(s)
- B Gabriel
- Laboratoire de pharmacologie et toxicologie fondamentales du CNRS, Département III-Glycoconjugués et Biomembranes, Toulouse, France
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Teissié J, Gabriel B, Prats M. Lateral communication by fast proton conduction: a model membrane study. Trends Biochem Sci 1993; 18:243-6. [PMID: 8212130 DOI: 10.1016/0968-0004(93)90171-i] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Lateral communication of information along biological membranes is thought to be a key process for many cellular activities. Support for this hypothesis comes from physicochemical experiments that show that an efficient facilitated lateral proton conduction exists along lipid-water interfaces. The existence of a local two-dimensional hydrogen bond network between the lipid headgroups and their associated water molecules would explain this phenomenon.
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Affiliation(s)
- J Teissié
- Department of Glycoconjugates and Biomembranes, UPR 8221 du CNRS, Toulouse, France
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Shimoni E, Tsfadia Y, Nachliel E, Gutman M. Gaugement of the inner space of the apomyoglobin's heme binding site by a single free diffusing proton. I. Proton in the cavity. Biophys J 1993; 64:472-9. [PMID: 8384501 PMCID: PMC1262349 DOI: 10.1016/s0006-3495(93)81389-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Time resolved fluorimetry was employed to monitor the geminate recombination between proton and excited pyranine anion locked, together with less than 30 water molecules, inside the heme binding site of Apomyoglobin (sperm whale). The results were analyzed by a numerical reconstruction of the differential rate equation for time-dependent diffusion controlled reaction with radiating boundaries using N. Agmon's procedure (Huppert, Pines, and Agmon, 1990, J. Opt. Soc. Am. B., 7:1541-1550). The analysis of the curve provided the effective dielectric constant of the proton permeable space in the cavity and the diffusion coefficient of the proton. The electrostatic potential within the cavity was investigated by the equations given by Gilson et al. (1985, J. Mol. Biol., 183:503-516). According to this analysis the dielectric constant of the protein surrounding the site is epsilon prot < or = 6.5. The diffusion coefficient of the proton in the heme binding site of Apomyoglobin-pyranine complex is D = 4 x 10(-5) cm2/s. This value is approximately 50% of the diffusion coefficient of proton in water. The lower value indicates enhanced ordering of water in the cavity, a finding which is corroborated by a large negative enthropy of binding delta S0 = -46.6 cal.mole-1 deg-1. The capacity of a small cavity in a protein to retain a proton had been investigated through the mathematical reconstruction of the dynamics. It has been demonstrated that Coulombic attraction, as large as delta psi of energy coupling membrane, is insufficient to delay a free proton for a time frame comparable to the turnover time of protogenic sites.
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Affiliation(s)
- E Shimoni
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
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