Water and bacteriorhodopsin: structure, dynamics, and function

A wealth of information has been gathered during the past decades that water molecules do play an important role in the structure, dynamics, and function of bacteriorhodopsin (bR) and purple membrane. Light-induced structural alterations in bR as detected by X-ray and neutron diffraction at low and high resolution are discussed in relationship to the mechanism of proton pumping. The analysis of high resolution intermediate structures revealed photon-induced rearrangements of water molecules and hydrogen bonds concomitant with conformational changes in the chromophore and the protein. These observations led to an understanding of key features of the pumping mechanism, especially the vectoriality and the different modes of proton translocation in the proton release and uptake domain of bR. In addition, water molecules influence the function of bR via equilibrium fluctuations, which must occur with adequate amplitude so that energy barriers between conformational states can be overcome.

Reversible loss of crystallinity on photobleaching purple membrane in the presence of hydroxylamine

Structural changes of purple membrane during photobleaching in the presence of hydroxylamine were monitored using atomic force microscopy (AFM). The process of bleaching was associated with the disassembly of the purple membrane crystal into smaller crystals. Imaging steps of the photobleaching progress showed that disassembly proceeds until the sample is fully bleached and its crystallinity is almost lost. As revealed from high resolution AFM topographs, the loss of crystallinity was initiated by loss of lattice forming contact between the individual bacteriorhodopsin trimers. The bacteriorhodopsin molecules, however, remained assembled into trimers during the entire photobleaching process. Regeneration of the photobleached sample into intact purple membrane resulted in the reassembly of the bacteriorhodopsin trimers into the trigonal lattice of purple membrane. The data provide novel insights into factors triggering purple membrane formation and structure.

Dye removal, catalytic activity and 2D crystallization of chloroplast H(+)-ATP synthase purified by blue native electrophoresis

The proton-ATP synthase of thylakoid membranes from spinach chloroplasts (CF(O)F(1)) and its subcomplexes CF(O) and CF(1) were isolated by blue native electrophoresis (BN-PAGE) [Neff, D. and Dencher, N.A. (1999) Biochem. Biophys. Res. Commun. 259, 569-575] and subsequently electroeluted from the gel. A method was developed to remove most of the dye Coomassie G-250 (CBG) using gel filtration, a prerequisite for many biophysical investigations. The dye was removed from the electroeluted CF(O)F(1), CF(O) or CF(1) and exchanged with the detergent CHAPS. ATP hydrolysis activity of CF(1) and ATP synthesis activity of reconstituted CF(O)F(1) were determined before and after dye removal. The secondary structure of CF(O) was studied by CD spectroscopy in the presence and the absence of the dye. CBG neither abolishes the catalytic activity of the isolated CF(O)F(1) and CF(1) nor affects the subunit composition and the high alpha-helical content of CF(O). In crystallization attempts, 2D arrays of CF(O)F(1) and of CF(O) before and after dye removal were obtained. In the aggregates of CF(O), circular structures with a mean diameter of 6.7 nm were observed. Our results indicate that the combination of BN-PAGE and dye removal by gel filtration is a suitable approach to obtain catalytically active protein complexes for further functional and structural characterization.

Dye-ligand chromatographic purification of intact multisubunit membrane protein complexes: application to the chloroplast H+-FoF1-ATP synthase

n-Dodecyl-beta-D-maltoside was used as a detergent to solubilize the ammonium sulphate precipitate of chloroplast F(O)F(1)-ATP synthase, which was purified further by dye-ligand chromatography. Upon reconstitution of the purified protein complex into phosphatidylcholine/phosphatidic acid liposomes, ATP synthesis, driven by an artificial DeltapH/Deltapsi, was observed. The highest activity was achieved with ATP synthase solubilized in n-dodecyl-beta-D-maltoside followed by chromatography with Red 120 dye. The optimal dye for purification with CHAPS was Green 5. All known subunits were present in the monodisperse proton-translocating ATP synthase preparation obtained from chloroplasts.

Detergent effect on anion exchange perfusion chromatography and gel filtration of intact chloroplast H(+)-ATP synthase

To gain a pure enzyme preparation for functional and crystallization studies, an additional purification step in the isolation of the chloroplast ATP synthase (CF(0)F(1)) has been introduced. By applying gel filtration or anion exchange perfusion chromatography in presence of the detergents CHAPS and n-dodecyl-beta-d-maltoside, respectively, Rubisco and other contaminants were separated from CF(0)F(1). The purity and activity depended on the chromatographic method and the detergent employed. The highest purity and activity were achieved by anion exchange chromatography for the detergent dodecyl-maltoside and by gel filtration for the detergent CHAPS. The detergent Triton X-100, which is frequently used to solubilize CF(0)F(1), was found to be inadequate to stabilize the ATP synthase during chromatography.

Purification of multisubunit membrane protein complexes: isolation of chloroplast FoF1-ATP synthase, CFo and CF1 by blue native electrophoresis

The proton-ATP synthase of thylakoid membranes from chloroplasts (CFoF1) is composed of two parts with different structural and functional properties: the membrane-integral, proton-conducting complex CFo and the hydrophilic part, CF1 which catalyze the formation of adenosine-5'-triphosphate (ATP). To date it is difficult to isolate functional CFoF1 from thylakoids in high purity and yield. Blue native polyacrylamide gel electrophoresis (BN-PAGE) was therefore successfully employed to isolate CFoF1 in a one-step procedure from thylakoid membranes. Using a cathode buffer with low Coomassie Blue G-250 (CBG) concentration (0.002%), CFoF1 remains intact and can be obtained in high purity from solubilized, prepurified ATP synthase. Using BN-PAGE and a cathode buffer with 0.02% CBG, the ATP synthase bifurcates, and we were able to isolate both parts, CFo and CF1, separately. CFoF1, CFo, and CF1, respectively, were electroeluted nearly quantitatively electroeluted from the gel. BN-PAGE is a generally applicable method for the isolation and characterization of multisubunit membrane protein complexes in their native structure. However, the combination of neutral detergents and the negatively charged dye CBG seems to mimic properties of mild ionic detergents. This effect can lead to dissociation of labile subunits and subcomplexes, especially when delipidated membrane protein complexes are applied to BN-PAGE. By variation of the initial electrophoresis conditions, i.e., dye concentration in the cathode buffer, amount of lipid and detergent, BN-PAGE can be used for the isolation of either intact complexes or of subcomplexes.

X-ray diffraction from a single layer of purple membrane at the air/water interface

X-ray diffraction patterns have been recorded from a single layer of purple membrane ( approximately 50 A thickness) at the air/water interface in a Langmuir trough. Grazing-incidence X-ray diffraction is demonstrated to be a promising method for obtaining structural information on membrane proteins under physiological conditions. The method is so sensitive that diffraction can be measured from samples with only 10(13) protein molecules in the beam. Diffraction from hexagonal crystals of purple membrane with a lattice constant of 61. 3 A was observed up to the order {h,k}={4,3}, corresponding to a resolution of approximately 9 A. The work reported here is a first step towards a new way of protein crystallography using grazing-incidence X-ray diffraction at the air/water interface.

Molecular motions and hydration of purple membranes and disk membranes studied by neutron scattering

Fast stochastic equilibrium fluctuations (time scale: 10(-10)-10(-13) seconds) in purple membranes (MP) and in disk membranes (DM) have been measured with quasielastic incoherent neutron scattering. The comparison of predominantly stochastic motions occurring in purple membranes and in disk membranes revealed qualitatively similar dynamical behaviour. Models of internal motions within restricted volumes have been shown to be useful to fit the spectra from both samples. From fits using these models we found "amplitudes" 15 to 20% larger for motions in DM samples compared to PM samples. This indicates a higher internal flexibility of the DM. Because the dynamical behaviour is very sensitive to the hydration of the protein-lipid complex, we also performed neutron diffraction experiments to determine lamellar spacings as a measure of level of hydration and as a function of temperature. From these studies the interaction of solvent molecules with the surface of the protein-lipid complex appears to be qualitatively similar for both types of membranes.

Function and picosecond dynamics of bacteriorhodopsin in purple membrane at different lipidation and hydration

By neutron scattering experiments and time-resolved absorption spectroscopy we have investigated picosecond equilibrium fluctuations and the kinetics of the photocycle of bacteriorhodopsin (BR) in the purple membrane (PM). Natural PM samples composed of 75% BR (w/w) and 25% lipid (w/w) as well as delipidated PM having only 5% lipid (w/w) were measured at different levels of hydration. We observed a reduced 'flexibility', due to a diminished weight of stochastic large-amplitude motions occurring in the delipidated PM as compared to the natural PM. This effect is more pronounced for wet samples, indicating the importance of lipid hydration for protein dynamics. The reduced flexibility is accompanied by significantly larger time constants describing the decay of the M-intermediate. Therefore, a correlation between the dynamical behavior of the protein-lipid complex and BR function emerges.

Evidence for charge-controlled conformational changes in the photocycle of bacteriorhodopsin

The existence of two different M-state structures in the photocycle of the bacteriorhodopsin mutant ASP38ARG was proved. At pH 6.7 (0 to -6 degreesC) a spectroscopic M intermediate (M1) that does not differ significantly in its tertiary structure from the light-adapted ground state accumulates under illumination. At pH > 9 another state (M2), characterized by additional pronounced changes in the Fourier transform infrared difference spectrum in the region of the amide I and II bands, accumulates. The M2 intermediate trapped at pH 9.6 displays the same changes in the x-ray diffraction intensities under continuous illumination as previously described for x-ray experiments with the mutant ASP96ASN. These observations indicate that in this mutant the altered charge distribution at neutral pH controls the tertiary structural changes that seem to be necessary for proton translocation.

Dehydration of biological membranes by cooling: an investigation on the purple membrane

The lamellar spacing dl of purple membrane (PM) multilayer systems was investigated with neutron diffraction as a function of temperature and of the level of hydration. The observed large T-dependent variations of dl indicate that PM is partially dehydrated when cooled below a "hydration water freezing point". This phenomenon is reversible, but a hysteresis is observed when PM is rehydrated upon reheating. The hydration water remaining bound to the membrane below about 240 K is non-freezing. Its amount was found to be hnf=0.24(+/-0.02) g 2H2O/g BR for all samples equilibrated at room temperature in the presence of 2H2O vapour at >/=84% r.h. It is evident, that the dehydration/rehydration behaviour of PM is strongly correlated with the temperature-dependent behaviour of the dynamical structure factor. Above the well-known "dynamical transition" announcing the onset of localized diffusive molecular motions between 190 K and 230 K, a second dynamical transition is caused by the temperature-induced rehydration of the PM starting near 255 K. This is also correlated with the deviation from a pure Arrhenius law of the rate-limiting process in the photocycle, known to occur upon cooling beyond the ice point into the same temperature region. Our results suggest that the phenomenon of dehydration and rehydration induced by cooling and reheating, respectively, is a general property of biological membranes.

Structure and hydration of the M-state of the bacteriorhodopsin mutant D96N studied by neutron diffraction

Neutron diffraction from oriented purple membrane fragments at various hydration levels, coupled with H2O/2H2O exchange, was used to compare the structure and hydration of the light-adapted initial state (B-state) and the M photointermediate of bacteriorhodopsin mutant D96N. Diffraction patterns were recorded at 86%, 75% and 57% relative humidity (r.h.). Structural changes observed at 86% and 75% r.h. are absent at 57% r.h., showing that they are uncoupled from the deprotonation of the Schiff base during formation of the M-state. In a current model, the M-state consists of two substates, M1 and M2. Our data suggest that the state trapped at 57% r.h. is M1 and that M2 is trapped at the higher r.h. values. The observed structural changes are, therefore, associated with the M1-->M2 transition, which can only take place at higher r.h. The difference Fourier projections of exchangeable hydrogen atoms and water molecules in the membrane plane are very similar for the B and M-states at 75% and 86% r.h. This shows that contrary to certain models, the structural changes in the M-state are not correlated with major hydration changes in the proton channel projection.

Mechanism of proton entry into the cytoplasmic section of the proton-conducting channel of bacteriorhodopsin

Bacteriorhodopsin is the light-driven proton-pumping protein of Halobacterium salinarum that extracts protons from the well-buffered cytoplasmic space within the time limits set by the photocycle turnover. The specific mechanism of the proton uptake by the cytoplasmic surface of the protein was investigated in this study by the laser-induced proton pulse technique. The purple membrane preparations were labeled by fluorescein at two residues (36 or 38) of the cytoplasmic surface of the protein, sites that are close to the orifice of the proton-conducting channel. The membranes were pulsed by protons discharged from photoexcited pyranine [Nachliel, E., Gutman, M., Kiryati, S., and Dencher, N.A. (1996) Proc. Nat Acad. Sci. U.S.A. 93, 10747-10752). The reaction of the discharged protons with the pyranine anion and the fluorescein was measured with sub-microsecond resolution. The experimental signals were reconstructed through numeric integration of differential rate equations which quantitated the rates of all proton transfer reactions between all reactants present in the system. The interaction of protons with the orifice of the cytoplasmic channel is enhanced by the exposed carboxylates of the protein. A cluster of three carboxylates acts as a strong proton attractor site while one carboxylate, identified as D36, acts as a mediator that delivers the proton to the channel. The combination of these reactions render the surface of the protein with properties of a proton-collecting antenna. The size of the collecting area is less than that of the protein's surface.

Picosecond molecular motions in bacteriorhodopsin from neutron scattering

The characteristics of internal molecular motions of bacteriorhodopsin in the purple membrane have been studied by quasielastic incoherent neutron scattering. Because of the quasihomogeneous distribution of hydrogen atoms in biological molecules, this technique enables one to study a wide variety of intramolecular motions, especially those occurring in the picosecond to nanosecond time scale. We performed measurements at different energy resolutions with samples at various hydration levels within a temperature range of 10-300 K. The analysis of the data revealed a dynamical transition at temperatures Td between 180 K and 220 K for all motions resolved at time scales ranging from 0.1 to a few hundred picoseconds. Whereas below Td the motions are purely vibrational, they are predominantly diffusive above Td, characterized by an enormously broad distribution of correlation times. The variation of the hydration level, on the other hand, mainly affects motions slower than a few picoseconds.

Chloroplast F0F1 ATP Synthase Imaged by Atomic Force Microscopy

The F0F1 ATP synthase of chloroplasts was imaged using atomic force microscopy (AFM) in contact mode under physiological conditions. Chloroplast (CF0F1) ATP synthases were reconstituted into liposomes. Liposomes were adsorbed on a mica surface where they spread and formed lipid bilayers containing CF0F1 ATP synthases which could be imaged. From these reconstituted CF0F1 ATP synthases, the CF1 part could be removed either by application of a chemical denaturant or less efficiently by mechanical stripping with the AFM tip. Embedded in the lipid bilayer were seen ring-like structures with a central dimple with outer diameters of 20 +/- 3 nm (chemical denaturant) and ca. 7 nm (mechanical stripping), respectively. Ring-like structures were also observed in a protein-free lipid bilayer. These had diameters of 30 +/- 5 nm and could be clearly distinguished from the structures observed after mechanical stripping. Hence, the ring-like structures observed after mechanical stripping might represent the intrinsic membrane domain CF0 or the oligomer of its subunit III. In addition, isolated CF1 adsorbed directly onto the mica surface was imaged. In accordance with the size known from electron microscopy, a diameter of 13 +/- 4 nm was measured.

The tertiary structural changes in bacteriorhodopsin occur between M states: X-ray diffraction and Fourier transform infrared spectroscopy

The tertiary structural changes occurring during the photocycle of bacteriorhodopsin (BR) are assigned by X-ray diffraction to distinct M states, M1 and M2. Purple membranes (PM) of the mutant Asp96Asn at 15, 57, 75 and 100% relative humidity (r.h.) were studied in a parallel X-ray diffraction and Fourier transform infrared (FTIR) spectroscopic investigation. Light-dependent conformational changes of BR-Asp96Asn are observed at high hydration levels (100 and 75% r.h.) but not in partially dehydrated samples (57 and 15% r.h.). The FTIR spectra of continuously illuminated samples at low and high hydration, despite some differences, are characteristic of the M intermediate. The changes in diffraction patterns of samples in the M2 state are of the same magnitude as those of wild-type samples trapped with GuaHCl in the M(G) state. Additional large changes in the amide bands of the FTIR spectra occur between M2 and M(G). This suggests, that the tertiary structural changes between M1 and M2 are responsible for the switch opening the cytoplasmic half-channel of BR for reprotonation to complete the catalytic cycle. These tertiary structural changes seem to be triggered by a charge redistribution which might be a common feature of retinal proteins also in signal transduction.

Protonation dynamics of the extracellular and cytoplasmic surface of bacteriorhodopsin in the purple membrane

The dynamics of proton binding to the extracellular and the cytoplasmic surfaces of the purple membrane were measured by laser-induced proton pulses. Purple membranes, selectively labeled by fluorescein at Lys-129 of bacteriorhodopsin, were pulsed by protons released in the aqueous bulk from excited pyranine (8-hydroxy-1,3,6-pyrenetrisulfonate) and the reaction of protons with the indicators was measured. Kinetic analysis of the data imply that the two faces of the membrane differ in their buffer capacities and in their rates of interaction with bulk protons. The extracellular surface of the purple membrane contains one anionic proton binding site per protein molecule with pK = 5.1. This site is within a Coulomb cage radius (approximately 15 A) from Lys-129. The cytoplasmic surface of the purple membrane bears 4-5 protonable moieties (pK = 5.1) that, due to close proximity, function as a common proton binding site. The reaction of the proton with this cluster is at a very fast rate (3.10(10) M-1.s-1). The proximity between the elements is sufficiently high that even in 100 mM NaCl they still function as a cluster. Extraction of the chromophore retinal from the protein has a marked effect on the carboxylates of the cytoplasmic surface, and two to three of them assume positions that almost bar their reaction with bulk protons. The protonation dynamics determined at the surface of the purple membrane is of relevance both for the vectorial proton transport mechanism of bacteriorhodopsin and for energy coupling, not only in halobacteria, but also in complex chemiosmotic systems such as mitochondrial and thylakoid membranes.

Internal molecular motions of bacteriorhodopsin: hydration-induced flexibility studied by quasielastic incoherent neutron scattering using oriented purple membranes

Quasielastic incoherent neutron scattering from hydrogen atoms, which are distributed nearly homogeneously in biological molecules, allows the investigation of diffusive motions occurring on the pico- to nanosecond time scale. A quasielastic incoherent neutron scattering study was performed on the integral membrane protein bacteriorhodopsin (BR), which is a light-driven proton pump in Halobacterium salinarium. BR is embedded in lipids, forming patches in the cell membrane of the organism, which are the so called purple membranes (PMs). Measurements were carried out at room temperature on oriented PM-stacks hydrated at two different levels (low hydration, h = 0.03 g of D2O per g of PM; high hydration, h = 0.28 g of D2O per g of PM) using time-of-flight spectrometers. From the measured spectra, different diffusive components were identified and analyzed with respect to the influence of hydration. This study supports the idea that a decrease in hydration results in an appreciable decrease in internal molecular flexibility of the protein structure. Because it is known from studies on the function of BR that the pump activity is reduced if the hydration level of the protein is insufficient, we conclude that the observed diffusive motions are essential for the function of this protein. A detailed analysis and classification of the different kinds of diffusive motions, predominantly occurring in PMs under physiological conditions, is presented.

Impaired plasticity of neurons in aging. Biochemical, biophysical, and behavioral studies

Age-related correlation of impaired plasticity of neurons (biochemical and biophysical aspects) and behavioral alterations were investigated in young (3.5 months) and extremely aged (approximately 40 months) female Wistar rats. Age-dependent significant differences in second messenger (cAMP and Ins (1,4,5)P3) concentration and signal transduction via muscarinic and dopaminergic receptors were found. The results point to the specifically impaired coupling between dopamine D1 receptor and GS protein, which underlies normal brain aging. However, cholinergic neurotransmission may be modulated at another level in extremely aged rats. Thus, it appears that the site of affection in coupling of receptor and G protein and/or G protein-dependent signal transduction in aging cannot be generalized. This indicates that alterations in the coupling of signal transduction depend on diverse neurotransmitter receptors with advanced age. The age-dependent alterations in the cAMP and PI signal pathways could be due to changes in the physical properties of the membranes. To support this hypothesis, age-dependent changes in the physical state and the biochemical composition of synaptosomal membranes from the cortex, cerebellum, and striatum were examined by measuring the steady-state fluorescence amisotropy of the membrane probes 1,6-diphenyl-1,3,5-hexatriene (DPH), trimethylammonium-DPH (TMA-DPH), and trimethylammoniumpropyl-DPH (TMAP-DPH). Significant differences in the physical properties of the synaptosomal membranes existed between young and very aged rats, expressed by a higher anisotropy in the 40-month-old rat brain tissue. The changes in the physical properties of the membranes were in line with the determined age-dependent alterations in the chemical composition, e.g., the increase in cholesterol content of the aged membranes.

D38 is an essential part of the proton translocation pathway in bacteriorhodopsin

At present, almost no knowledge exists about the functional relevance of the amino acid residues at the cytoplasmic (CP) surface of the light-driven proton pump bacteriorhodopsin (BR) although a prerequisite for efficient vectorial proton translocation is the efficient capture of protons from the alkaline cytoplasm of the cell. To identify residues involved in the proton transfer reaction steps in the CP part of BR, the aspartic and glutamic amino acids D36, D38, D102, D104, and E161 were replaced by cysteine and arginine (i.e., a negatively charged residue by a neutral or positive one at the pH of investigation). The effect of these replacements on the photo- and transport cycle was examined by time-resolved visible and infrared spectroscopy, biochemical modification studies, and activity assays in intact cells. Of the five CP amino acids studied, only the replacement of D38 resulted in severe alterations of the reaction steps in BR during the second half of the photocycle. Our data show that D38, which seemed to be a freely accessible CP surface residue lacking functional importance, is an essential part of the CP proton uptake pathway connecting the membrane surface with the Schiff base of BR, probably as the first amino acid residue at the CP entrance. D38 influences the late steps in the functional cycle, such as the occurrence of the intermediates N and O, the modulation of the hydrogen-network, the conformational changes in the protein moiety, and the deprotonation/reprotonation of D96. Opposed to this function, the surface-exposed amino acids D36, D102, D104, and E161 seem to efficiently collect protons from the aqueous bulk phase and funnel them to the entrance of the CP proton pathway.

Light-induced isomerization causes an increase in the chromophore tilt in the M intermediate of bacteriorhodopsin: a neutron diffraction study

Bacteriorhodopsin (BR) was regenerated with two selectively deuterated retinals, one with 11 deuterons in the beta-ionone ring (D11) and the other with 5 deuterons (D5) at the end of the polyene chain closest to the Schiff base at carbon atoms C-14, C-15, and C-20. Both label positions (centers of deuteration) were obtained from difference Fourier maps of projections onto the plane of the membrane by neutron diffraction at 90 K, both in the light-adapted ground-state BR568 and in the photocycle intermediate M412. To retard the decay of M412, purple membrane films were soaked in 0.1 M or 1 M guanidine hydrochloride at pH 9.6. M412 was produced by illuminating oriented membrane films at physiological temperature (278 K), followed by rapid cooling to 90 K in the absence of light. The results show that in the projected structure the ring position is unaltered during the transition from BR568 to M412, whereas the position of the D5 label shifts by 1.4 +/- 0.9 A toward the ring. The shortened interlabel distance in the projected structure for the M412 state implies that as a result of the all-trans/13-cis isomerization, the C-5 to C-13 part of the polyene chain tilts out of the plane of the membrane toward the cytoplasm by about 11 degrees +/- 6 degrees. Pairwise comparison of data sets with the same retinal for the two photocycle states M412 and BR568 leads to four difference-density maps for the protein, which are in agreement with previous work. They show changes in the protein density near helices G and F.

Proton migration along the membrane surface and retarded surface to bulk transfer

Since the proposal of the chemiosmotic theory there has been a continuing debate about how protons that have been pumped across membranes reach another membrane protein that utilizes the established pH gradient. Evidence has been gathered in favour of a 'delocalized' theory, in which the pumped protons equilibrate with the aqueous bulk phase before being consumed, and a 'localized' one, in which protons move exclusively along the membrane surface. We report here that after proton release by an integral membrane protein, long-range proton transfer along the membrane surface is faster than proton exchange with the bulk water phase. The rate of lateral proton diffusion can be calculated by considering the buffer capacity of the membrane surface. Our results suggest that protons can efficiently diffuse along the membrane surface between a source and a sink (for example H(+)-ATP synthase) without dissipation losses into the aqueous bulk.