1
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Oliva R, Winter R. Harnessing Pressure-Axis Experiments to Explore Volume Fluctuations, Conformational Substates, and Solvation of Biomolecular Systems. J Phys Chem Lett 2022; 13:12099-12115. [PMID: 36546666 DOI: 10.1021/acs.jpclett.2c03186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Intrinsic thermodynamic fluctuations within biomolecules are crucial for their function, and flexibility is one of the strategies that evolution has developed to adapt to extreme environments. In this regard, pressure perturbation is an important tool for mechanistically exploring the causes and effects of volume fluctuations in biomolecules and biomolecular assemblies, their role in biomolecular interactions and reactions, and how they are affected by the solvent properties. High hydrostatic pressure is also a key parameter in the context of deep-sea and subsurface biology and the study of the origin and physical limits of life. We discuss the role of pressure-axis experiments in revealing intrinsic structural fluctuations as well as high-energy conformational substates of proteins and other biomolecular systems that are important for their function and provide some illustrative examples. We show that the structural and dynamic information obtained from such pressure-axis studies improves our understanding of biomolecular function, disease, biological evolution, and adaptation.
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Affiliation(s)
- Rosario Oliva
- Department of Chemistry and Chemical Biology, Physical Chemistry I, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Strasse 6, Dortmund44227, Germany
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126Naples, Italy
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Physical Chemistry I, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Strasse 6, Dortmund44227, Germany
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2
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Soloviov D, Borshchevskiy V, Chizhov I. Time-Resolved UV-VIS Spectroscopy of Microbial Rhodopsins. Methods Mol Biol 2022; 2501:169-179. [PMID: 35857228 DOI: 10.1007/978-1-0716-2329-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Absorption of light quanta by microbial rhodopsins (or more generally by retinal proteins) leads to conversion of the light energy to the generation of transmembrane anion or cation gradients, optically gated channels, or signal states in photoreception. All these processes are accompanied by series of reaction steps with half-times ranging from femtoseconds to seconds or longer (photocycles). The number of these steps and their kinetic and spectral properties are the essential experimental information required for determination of the mechanism of light energy conversion in these proteins. Here we describe experiments and data analysis providing this information.
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Affiliation(s)
- Dmytro Soloviov
- Institute for Safety Problems of Nuclear Power Plants, NAS of Ukraine, Chornobyl, Ukraine
- Faculty of Physics, Adam Mickiewicz University, Poznan, Poland
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Joint Institute for Nuclear Research, Dubna, Russia
| | - Igor Chizhov
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany.
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3
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Abstract
We review the combined effect of temperature and pressure on the structure, dynamics and phase behavior of lipid bilayers, differing in chain length, headgroup structure and composition as revealed by thermodynamic, spectroscopic and scattering experiments. The effect of additives, such as ions, cholesterol, and anaesthetics is discussed as well. Our data include also reports on the effect of pressure on the lateral organization of heterogeneous lipid membranes and lipid extracts from cellular membranes, as well as the influence of peptide and protein incorporation on the pressure-dependent structure and phase behavior of lipid membranes. Moreover, the effects of pressure on membrane protein function are summarized. Finally, we introduce pressure as a kinetic variable for studying the kinetics of various lipid phase transformations.
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Affiliation(s)
- Roland Winter
- Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, Otto-Hahn Str. 6, D-44227, Dortmund, Germany,
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4
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Krywka C, Krasnov I, Figuli R, Burghammer M, Müller M. Determination of Silkworm Silk Fibroin Compressibility Using High Hydrostatic Pressure with in Situ X-ray Microdiffraction. Macromolecules 2014. [DOI: 10.1021/ma501880h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christina Krywka
- Institute
for Applied and Experimental Physics, Universität Kiel, Leibnizstr. 19, D-24098 Kiel, Germnay
- Helmholtz Zentrum
Geesthacht, Max-Planck-Straße
1, D-21502 Geesthacht, Germnay
| | - Igor Krasnov
- Institute
for Applied and Experimental Physics, Universität Kiel, Leibnizstr. 19, D-24098 Kiel, Germnay
- Helmholtz Zentrum
Geesthacht, Max-Planck-Straße
1, D-21502 Geesthacht, Germnay
| | - Roxana Figuli
- Institute
for Experimental Physics, Universität Leipzig, Linnéstraße
5, D-04103 Leipzig, Germnay
| | - Manfred Burghammer
- European Synchrotron
Radiation Facility (ESRF), 6 Rue Jules
Horowitz, F-38043 Grenoble, France
| | - Martin Müller
- Helmholtz Zentrum
Geesthacht, Max-Planck-Straße
1, D-21502 Geesthacht, Germnay
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5
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Mukhopadhyay S, Cohen SR, Marchak D, Friedman N, Pecht I, Sheves M, Cahen D. Nanoscale electron transport and photodynamics enhancement in lipid-depleted bacteriorhodopsin monomers. ACS NANO 2014; 8:7714-7722. [PMID: 25003581 DOI: 10.1021/nn500202k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Potential future use of bacteriorhodopsin (bR) as a solid-state electron transport (ETp) material requires the highest possible active protein concentration. To that end we prepared stable monolayers of protein-enriched bR on a conducting HOPG substrate by lipid depletion of the native bR. The ETp properties of this construct were then investigated using conducting probe atomic force microscopy at low bias, both in the ground dark state and in the M-like intermediate configuration, formed upon excitation by green light. Photoconductance modulation was observed upon green and blue light excitation, demonstrating the potential of these monolayers as optoelectronic building blocks. To correlate protein structural changes with the observed behavior, measurements were made as a function of pressure under the AFM tip, as well as humidity. The junction conductance is reversible under pressure changes up to ∼300 MPa, but above this pressure the conductance drops irreversibly. ETp efficiency is enhanced significantly at >60% relative humidity, without changing the relative photoactivity significantly. These observations are ascribed to changes in protein conformation and flexibility and suggest that improved electron transport pathways can be generated through formation of a hydrogen-bonding network.
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6
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Liu Y, Edens GJ, Grzymski J, Mauzerall D. Volume and enthalpy changes of proton transfers in the bacteriorhodopsin photocycle studied by millisecond time-resolved photopressure measurements. Biochemistry 2008; 47:7752-61. [PMID: 18578542 DOI: 10.1021/bi800158x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The volume and enthalpy changes associated with proton translocation steps during the bacteriorhodopsin (BR) photocycle were determined by time-resolved photopressure measurements. The data at 25 degrees C show a prompt increase in volume followed by two further increases and one decrease to the original state to complete the cycle. These volume changes are decomposed into enthalpy and inherent volume changes. The positive enthalpy changes support the argument for inherent entropy-driven late steps in the BR photocycle [Ort, D. R., and Parson, W. M. (1979) Enthalpy changes during the photochemical cycle of bacteriorhodopsin. Biophys. J. 25, 355-364]. The volume change data can be interpreted by the electrostriction effect as charges are canceled and formed during the proton transfers. A simple glutamic acid-glutamate ion model or a diglutamate-arginine-protonated water charge-delocalized model for the proton-release complex (PRC) fit the data. A conformational change with a large positive volume change is required in the slower rise (M --> N of the optical cycle) step and is reversed in the decay (N --> O --> BR) steps. The large variation in the published values for both the volume and enthalpy changes is greatly ameliorated if the values are presented per absorbed photon instead of per mole of BR. Thus, it is the highly differing assumptions about the quantum or reaction yields that cause the variations in the published results.
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Affiliation(s)
- Yan Liu
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA.
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7
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Abstract
The transport function of the Na pump (Na,K-ATPase) in cellular ion homeostasis involves both nucleotide binding reactions in the cytoplasm and alternating aqueous exposure of inward- and outward-facing ion binding sites. An osmotically active, nonpenetrating polymer (poly(ethyleneglycol); PEG) and a modifier of the aqueous viscosity (glycerol) were used to probe the overall and partial enzymatic reactions of membranous Na,K-ATPase from shark salt glands. Both inhibit the steady-state Na,K-ATPase as well as Na-ATPase activity, whereas the K(+)-dependent phosphatase activity is little affected by up to 50% of either. Both Na,K-ATPase and Na-ATPase activities are inversely proportional to the viscosity of glycerol solutions in which the membranes are suspended, in accordance with Kramers' theory for strong coupling of fluctuations at the active site to solvent mobility in the aqueous environment. PEG decreases the affinity for Tl(+) (a congener for K(+)), whereas glycerol increases that for the nucleotides ATP and ADP in the presence of NaCl but has little effect on the affinity for Tl(+). From the dependence on osmotic stress induced by PEG, the aqueous activation volume for the Na,K-ATPase reaction is estimated to be approximately 5-6 nm(3) (i.e., approximately 180 water molecules), approximately half this for Na-ATPase, and essentially zero for p-nitrophenol phosphatase. The change in aqueous hydrated volume associated with the binding of Tl(+) is in the region of 9 nm(3). Analysis of 15 crystal structures of the homologous Ca-ATPase reveals an increase in PEG-inaccessible water space of approximately 22 nm(3) between the E(1)-nucleotide bound forms and the E(2)-thapsigargin forms, showing that the experimental activation volumes for Na,K-ATPase are of a magnitude comparable to the overall change in hydration between the major E(1) and E(2) conformations of the Ca-ATPase.
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8
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Klare JP, Chizhov I, Engelhard M. Microbial rhodopsins: scaffolds for ion pumps, channels, and sensors. Results Probl Cell Differ 2007; 45:73-122. [PMID: 17898961 DOI: 10.1007/400_2007_041] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Microbial rhodopsins have been intensively researched for the last three decades. Since the discovery of bacteriorhodopsin, the scope of microbial rhodopsins has been considerably extended, not only in view of the large number of family members, but also their functional properties as pumps, sensors, and channels. In this review, we give a short overview of old and newly discovered microbial rhodopsins, the mechanism of signal transfer and ion transfer, and we discuss structural and mechanistic aspects of phototaxis.
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Affiliation(s)
- Johann P Klare
- Fachbereich Physik, University Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany
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9
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Maeda A, Morgan JE, Gennis RB, Ebrey TG. Water as a cofactor in the unidirectional light-driven proton transfer steps in bacteriorhodopsin. Photochem Photobiol 2007; 82:1398-405. [PMID: 16634652 DOI: 10.1562/2006-01-16-ir-779] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Recent evidence for involvement of internal water molecules in the mechanism of bacteriorhodopsin is reviewed. Water O-H stretching vibration bands in the Fourier transform IR difference spectra of the L, M and N intermediates of bacteriorhodopsin were analyzed by photoreactions at cryogenic temperatures. A broad vibrational band in L was shown to be due to formation of a structure of water molecules connecting the Schiff base to the Thr46-Asp96 region. This structure disappears in the M intermediate, suggesting that it is involved in transient stabilization of the L intermediate prior to proton transfer from the Schiff base to Asp85. The interaction of the Schiff base with a water molecule is restored in the N intermediate. We propose that water is a critical mobile component of bacteriorhodopsin, forming organized structures in the transient intermediates during the photocycle and, to a large extent, determining the chemical behavior of these transient states.
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Affiliation(s)
- Akio Maeda
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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10
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Lórenz-Fonfría VA, Kandori H. Bayesian maximum entropy (two-dimensional) lifetime distribution reconstruction from time-resolved spectroscopic data. APPLIED SPECTROSCOPY 2007; 61:428-43. [PMID: 17456263 DOI: 10.1366/000370207780466172] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Time-resolved spectroscopy is often used to monitor the relaxation processes (or reactions) of physical, chemical, and biochemical systems after some fast physical or chemical perturbation. Time-resolved spectra contain information about the relaxation kinetics, in the form of macroscopic time constants of decay and their decay associated spectra. In the present paper we show how the Bayesian maximum entropy inversion of the Laplace transform (MaxEnt-iLT) can provide a lifetime distribution without sign-restrictions (or two-dimensional (2D)-lifetime distribution), representing the most probable inference given the data. From the reconstructed (2D) lifetime distribution it is possible to obtain the number of exponentials decays, macroscopic rate constants, and exponential amplitudes (or their decay associated spectra) present in the data. More importantly, the obtained (2D) lifetime distribution is obtained free from pre-conditioned ideas about the number of exponential decays present in the data. In contrast to the standard regularized maximum entropy method, the Bayesian MaxEnt approach automatically estimates the regularization parameter, providing an unsupervised and more objective analysis. We also show that the regularization parameter can be automatically determined by the L-curve and generalized cross-validation methods, providing (2D) lifetime reconstructions relatively close to the Bayesian best inference. Finally, we propose the use of MaxEnt-iLT for a more objective discrimination between data-supported and data-unsupported quantitative kinetic models, which takes both the data and the analysis limitations into account. All these aspects are illustrated with realistic time-resolved Fourier transform infrared (FT-IR) synthetic spectra of the bacteriorhodopsin photocycle.
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Affiliation(s)
- Victor A Lórenz-Fonfría
- Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.
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11
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Maeda A, Morgan JE, Gennis RB, Ebrey TG. Water as a Cofactor in the Unidirectional Light-Driven Proton Transfer Steps in Bacteriorhodopsin. Photochem Photobiol 2006. [DOI: 10.1111/j.1751-1097.2006.tb09791.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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12
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Partridge JC, White EM, Douglas RH. The effect of elevated hydrostatic pressure on the spectral absorption of deep-sea fish visual pigments. J Exp Biol 2006; 209:314-9. [PMID: 16391353 DOI: 10.1242/jeb.01984] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The effect of hydrostatic pressure (0.1-54 MPa, equivalent to pressures experienced by fish from the ocean's surface to depths of ca. 5,400 m) on visual pigment absorption spectra was investigated for rod visual pigments extracted from the retinae of 12 species of deep-sea fish of diverse phylogeny and habitat. The wavelength of peak absorption (lambda(max)) was shifted to longer wavelengths by an average of 1.35 nm at 40 MPa (a pressure approximately equivalent to average ocean depth) relative to measurements made at one atmosphere (ca. 0.1 MPa), but with little evidence of a change in absorbance at the lambda(max). We conclude that previous lambda(max) measurements of deep-sea fish visual pigments, made at a pressure close to 0.1 MPa, provide a good indication of lambda(max) values at higher pressures when considering the ecology of vision in the deep-sea. Although not affecting the spectral sensitivity of the animal to any important degree, the observed shift in lambda(max) may be of interest in the context of understanding opsin-chromophore interaction and spectral tuning of visual pigments.
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Affiliation(s)
- J C Partridge
- School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK.
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13
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Jang H, Crozier PS, Stevens MJ, Woolf TB. How environment supports a state: molecular dynamics simulations of two states in bacteriorhodopsin suggest lipid and water compensation. Biophys J 2005; 87:129-45. [PMID: 15240452 PMCID: PMC1304336 DOI: 10.1529/biophysj.104.039602] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The light-driven proton pump bacteriorhodopsin (bR) is a transmembrane protein that uses large conformational changes for proton transfer from the cytoplasmic to the extracellular regions. Crystal structures, due to their solvent conditions, do not resolve the effect of lipid molecules on these protein conformational changes. To begin to understand the molecular details behind such large conformational changes, we simulated two conformations of wild-type bacteriorhodopsin, one of the dark-adapted state and the second of an intermediate (M(O)) state, each within an explicit dimyristoyl-phosphatidylcholine (DMPC) lipid bilayer. The simulations included all-hydrogen and all-atom representations of protein, lipid, and water and were performed for 20 ns. We investigate the equilibrium properties and the dynamic motions of the two conformations in the lipid setting. We note that the conformational state of the M(O) intermediate bR remains markedly different from the dark-adapted bR state in that the M(O) intermediate shows rearrangement of the cytoplasmic portions of helices C, F, and G, and nearby loops. This difference in the states remained throughout the simulations, and the results are stable on the molecular dynamics timescale and provide an illustration of the changes in both lipid and water that help to stabilize a particular state. Our analysis focuses on how the environment adjusts to these two states and on how the dynamics of the helices, loops, and water molecules can be related to the pump mechanism of bacteriorhodopsin. For example, water generally behaves in the same manner on the extracellular sides of both simulations but is decreased in the cytoplasmic region of the M(O) intermediate. We suspect that the different water behavior is closely related to the fluctuations of microcavities volume in the protein interior, which is strongly coupled to the collective motion of the protein. Our simulation result suggests that experimental observation can be useful to verify a decreased number of waters in the cytoplasmic regions of the late-intermediate stages by measuring the rate of water exchange with the interior of the protein.
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Affiliation(s)
- Hyunbum Jang
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
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14
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Lee AG. How lipids affect the activities of integral membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2005; 1666:62-87. [PMID: 15519309 DOI: 10.1016/j.bbamem.2004.05.012] [Citation(s) in RCA: 884] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2004] [Accepted: 05/28/2004] [Indexed: 11/30/2022]
Abstract
The activities of integral membrane proteins are often affected by the structures of the lipid molecules that surround them in the membrane. One important parameter is the hydrophobic thickness of the lipid bilayer, defined by the lengths of the lipid fatty acyl chains. Membrane proteins are not rigid entities, and deform to ensure good hydrophobic matching to the surrounding lipid bilayer. The structure of the lipid headgroup region is likely to be important in defining the structures of those parts of a membrane protein that are located in the lipid headgroup region. A number of examples are given where the conformation of the headgroup-embedded region of a membrane protein changes during the reaction cycle of the protein; activities of such proteins might be expected to be particularly sensitive to lipid headgroup structure. Differences in hydrogen bonding potential and hydration between the headgroups of phosphatidycholines and phosphatidylethanolamines could be important factors in determining the effects of these lipids on protein activities, as well as any effects related to the tendency of the phosphatidylethanolamines to form a curved, hexagonal H(II) phase. Effects of lipid structure on protein aggregation and helix-helix interactions are also discussed, as well as the effects of charged lipids on ion concentrations close to the surface of the bilayer. Interpretations of lipid effects in terms of changes in protein volume, lipid free volume, and curvature frustration are also described. Finally, the role of non-annular, or 'co-factor' lipids, tightly bound to membrane proteins, is described.
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Affiliation(s)
- Anthony G Lee
- Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Southampton SO16 7PX, UK.
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15
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Nicolini C, Ravindra R, Ludolph B, Winter R. Characterization of the temperature- and pressure-induced inverse and reentrant transition of the minimum elastin-like polypeptide GVG(VPGVG) by DSC, PPC, CD, and FT-IR spectroscopy. Biophys J 2004; 86:1385-92. [PMID: 14990468 PMCID: PMC1303976 DOI: 10.1016/s0006-3495(04)74209-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
We investigated the temperature- and pressure-dependent structure and phase behavior of a solvated oligopeptide, GVG(VPGVG), which serves as a minimalistic elastin-like model system, over a large region of the thermodynamic phase field, ranging from 2 to 120 degrees C and from ambient pressure up to approximately 10 kbar, applying various spectroscopic (CD, FT-IR) and thermodynamic (DSC, PPC) measurements. We find that this octapeptide behaves as a two-state system which undergoes the well-known inverse-temperature folding transition occurring at T approximately 36 degrees C, and, in addition, a slow trend reversal at higher temperatures, finally leading to a reentrant unfolding close to the boiling point of water. Furthermore, the pressure-dependence of the folding/unfolding transition was studied to yield a more complete picture of the p, T-stability diagram of the system. A molecular-level picture of these processes, in particular on the role of water for the folding and unfolding events of the peptide, presented with the help of molecular-dynamics simulations, is presented in a companion article in this issue.
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Affiliation(s)
- C Nicolini
- Department of Chemistry, University of Dortmund, Dortmund, Germany
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16
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Calimet N, Ullmann GM. The Influence of a Transmembrane pH Gradient on Protonation Probabilities of Bacteriorhodopsin: The Structural Basis of the Back-Pressure Effect. J Mol Biol 2004; 339:571-89. [PMID: 15147843 DOI: 10.1016/j.jmb.2004.03.075] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2003] [Revised: 12/22/2003] [Accepted: 03/22/2004] [Indexed: 11/21/2022]
Abstract
Bacteriorhodopsin pumps protons across a membrane using the energy of light. The proton pumping is inhibited when the transmembrane proton gradient that the protein generates becomes larger than four pH units. This phenomenon is known as the back-pressure effect. Here, we investigate the structural basis of this effect by predicting the influence of a transmembrane pH gradient on the titration behavior of bacteriorhodopsin. For this purpose we introduce a method that accounts for a pH gradient in protonation probability calculations. The method considers that in a transmembrane protein, which is exposed to two different aqueous phases, each titratable residue is accessible for protons from one side of the membrane depending on its hydrogen-bond pattern. This method is applied to several ground-state structures of bacteriorhodopsin, which residues already present complicated titration behaviors in the absence of a proton gradient. Our calculations show that a pH gradient across the membrane influences in a non-trivial manner the protonation probabilities of six titratable residues which are known to participate in the proton transfer: D85, D96, D115, E194, E204, and the Schiff base. The residues connected to one side of the membrane are influenced by the pH on the other side because of their long-range electrostatic interactions within the protein. In particular, D115 senses the pH at the cytoplasmic side of the membrane and transmits this information to D85 and the Schiff base. We propose that the strong electrostatic interactions found between D85, D115, and the Schiff base as well as the interplay of their respective protonation states under the influence of a transmembrane pH gradient are responsible for the back-pressure effect on bacteriorhodopsin.
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Affiliation(s)
- Nicolas Calimet
- IWR-Computational Molecular Biophysics, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
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17
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Friedman R, Nachliel E, Gutman M. The role of small intraprotein cavities in the catalytic cycle of bacteriorhodopsin. Biophys J 2003; 85:886-96. [PMID: 12885636 PMCID: PMC1303210 DOI: 10.1016/s0006-3495(03)74528-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The last phase of the proton transfer cycle of bacteriorhodopsin calls for a passage of a proton from D38 to D96. This reaction utilizes a narrow shaft approximately 10-A long that connects the two carboxylates that cross through a very hydrophobic domain. As the shaft is too narrow to be permanently hydrated, there are two alternatives for the proton propagation into the channel. The proton may propagate through the shaft without solvation at the expense of a high electrostatic barrier; alternatively, the shaft will expand to accommodate some water molecules, thus lowering the Born energy for the insertion of the charge into the protein (B. Schätzler, N. A. Dencher, J. Tittor, D. Oesterhelt, S. Yaniv-Checover, E. Nachliel, and G. Gutman, 2003, BIOPHYS: J. 84:671-686). A comparative study of nine published crystal-structures of bacteriorhodopsin identified, next to the shaft, microcavities in the protein whose position and surrounding atoms are common to the reported structures. Some of the cavities either shrink or expand during the photocycle. It is argued that the plasticity of the cavities provides a working space needed for the transient solvation of the shaft, thus reducing the activation energy necessary for the solvation of the shaft. This suggestion is corroborated by the recent observations of Klink et al. (B. U. Klink, R. Winter, M. Engelhard, and I. Chizhov, 2002, BIOPHYS: J. 83:3490-3498) that the late phases of the photocycle (tau >/=1 ms) are strongly inhibited by external pressure.
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Affiliation(s)
- Ran Friedman
- Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, Tel Aviv University, Tel Aviv 69978, Israel
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