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PubMed1992

An energy-based approach to packing the 7-helix bundle of bacteriorhodopsin.

Based on the heavy-atom coordinates determined by the electron microscopy for the seven main helical regions of bacteriorhodopsin with the all-trans retinal isomer, energy optimizations were carried out for helix bundles containing the all-trans retinal and 13-cis retinal chromophores, respectively. A combination of simulated annealing and energy minimization was utilized during the process of energy optimization. It was found that the 7-helix bundle containing the all-trans isomer is about 10 kcal/mol lower in conformational energy than that containing the 13-cis isomer. An energetic analysis indicates that such a difference in energy is consistent with the observation that absorption of a 570-nm proton is required for the conversion of a bacteriorhodopsin from its all-trans to 13-cis form. It was also found that the above conversion process is accompanied by a significant conformational perturbation around the chromophore, as reflected by the fact that the beta-ionone ring of retinal moves about 5.6 A along the direction perpendicular to the membrane plane. This is consistent with the observation by Fodor et al. (Fodor, S.P.A., Ames, J.B., Gebhard, R., van der Berg, E.M.M., Stoeckenius, W., Lugtenburg, J., & Mathies, R.A., 1988, Biochemistry 27, 7097-7101). Furthermore, it is interesting to observe that although the retinal chromophore undergoes a significant change in its spatial position, the orientation of its transition dipole changes only slightly, in accord with experimental observations. In other words, even though orientation of the retinal transition dipole is very restricted, there is sufficient room, and degrees of freedom, for the retinal chromophore to readjust its position considerably. This finding provides new insight into the subtle change of the retinal microenvironment, which may be important for revealing the proton-pumping mechanism of bacteriorhodopsin. The importance of electrostatic and nonbonded interactions in stabilizing the 7-helix bundle structure has also been analyzed. Electrostatic interactions favor an antiparallel arrangement among adjacent helices. Nonbonded interactions, however, drive most of the closely packed helices into an arrangement in which the packing angles lie around -160 degrees, a value very near the -154 degrees value computed earlier as the most favorable packing arrangement of two poly(Ala) alpha-helices (Chou, K.-C., Némethy, G., & Scheraga, H.A., 1983, J. Phys. Chem. 87, 2869-2881). The structural features of the 7-helix bundle and their relationship to those found in typical 4-helix bundle proteins are also discussed.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1977

Structural and spectroscopic characteristics of bacteriorhodopsin in air-water interface films.

A suspension of purple membrane fragments in a solution of soya phosphatidyl-choline in hexane is spread at an air-water interface. Surface pressure and surface potential measurements indicate that the membrane fragments and lipids organize at the interface as an insoluble film. Electron microscopy of shadow-cast replicas of the film reveal that in the bacteriorhodopsin to soya PC weight ratio range of 2:1 to 10:1, these films consist of nonoverlapping membrane fragments which occupy approximately 35% of the surface area and are separated by a lipid monolayer. Furthermore, the membrane fragments are oriented with their intracellular surface towards the aqueous subphase. Nearly all the bacteriorhodopsin molecules at the interface are spectroscopically intact and exhibit visible spectral characteristics identical to those in aqueous suspensions of purple membrane and in intact bacteria. In addition, bacteriorhodopsin in air-dried interface films show spectral changes upon dark-adaptation and upon flash illumination similar to those observed in aqueous suspensions of purple membrane, but with slower kinetics. The kinetics of the spectral changes in interface films can be made nearly the same as in aqueous suspension by immersing the films in water.

Air↗
PubMed1978

Influence of membrane lipids on the photochemistry of bacteriorhodopsin in the purple membrane of Halobacterium halobium.

Purple membrane fragments from Halobacterium halobium were reconstituted with the native lipids replaced by dipalmitoyl phosphatidylcholine and by egg lecithin. In parallel studies the temperature dependence of bacteriorhodopsin phototransient lifetime and absorption dichroism and of in situ lipid microviscosity were determined; the former two by, respectively, conventional and polarization flash photometry, and the latter by observation of emission depolarization of an embedded fluorescent dye, 1,6-diphenyl-1,3,5-hexatriene. Discontinuities in lipid microviscosity profiles in native and egg lecithin purple membrane were reflected in both the photochemical cycle frequency and bacteriorhodopsin chromophore rotational mobility. The influence exerted by membrane-lipid viscosity appears to be a secondary effect, and points to the bacteriorhodopsin chromophoric group being situated in the protein interior.

Bacteriorhodopsins↗
PubMed1978

Bacteriorhodopsin vesicles. An outline of the requirements for light-dependent H+ pumping.

A systematic study was performed to determine under which conditions bacteriorhodopsin can be applied as an energy generator in reconstituted systems. It is concluded that reconstitution of an active light-driven proton pump is possible over a wide range of conditions. High extents (per bacteriorhodopsin molecule) of proton uptake by reconstituted vesicles are found at a high lipid to protein ratio, after long sonication and at high pH. No active proton pump is obtained if reconstitution is attempted at high pH with neutral phospholipids or at low ionic strength with negatively charged lipids. Attention was also paid to the requirement of a crystalline array for active pumping; most likely, monomeric bacteriorhodopsin molecules can effectively pump protons.

Bacteriorhodopsins↗
PubMed1979

Enthalpy changes during the photochemical cycle of bacteriorhodopsin.

We have used a capacitor microphone calorimeter to measure rapid enthalpy changes that occur when bacteriorhodopsin-containing membrane fragments are excited with short flashes of light. We resolved the enthalpy changes into three phases. At about 100 microsecond after the flash, the bacteriorhodopsins converted into metastable states have an enthalpy about 15-20 kcal mol-1 greater than the enthalpy before excitation. Some of this energy (approximately 10 kcal) is then released to the surroundings as the membrane fragments release protons to the solution. After proton release and before proton rebinding, a large amount of heat is released to the surroundings, equivalent to about 40-45 kcal/mol of bacteriorhodopsin reacting. At this point the energy of the system is about 35 kcal/mol less than it was before the flash; i.e., the system has released all of the energy of the photon (49 kcal/E) plus an additional 35 kcal/mol. Nevertheless, the free energy of the system must still be greater than it was originally, because relaxation to the original state occurs spontaneously. An entropy decrease of at least 125 cal/mol per deg is required to compensate for the heat release. An entropy decrease of this magnitude implies a major increase in molecular order in the purple membrane.

Bacteriorhodopsins↗
PubMed1979

Time-resolved resonance Raman characterization of the bO640 intermediate of bacteriorhodopsin. Reprotonation of the Schiff base.

The resonance Raman spectrum of photolyzed bacteriorhodopsin under conditions known to increase the concentration of the bO640 intermediate in both H2O and D2O is presented. By use of computer subtraction techniques and a knowledge of the Raman spectra of the unphotolyzed bacteriorhodopsin as well as the other intermediates in the cycle, a qualitative spectrum of bO640 is determined. The shift of a band at 1630 cm-1 in H2O to 1616 cm-1 in D2O suggests that the Schiff base of bO640 is protonated. Additional bands at 947, 965, and 992 cm-1 that appear only in D2O suspensions confirm that a proton is coupled to the retinal chromophore of bO640. The reprotonation of the Schiff base thus occurs during the bM412 to bO640 step. The fingerprint region, sensitive to the isomeric configuration of the retinal chromophore of bO640, is dissimilar to the fingerprint regions of published model compounds and other forms of bacteriorhodopsin.

Bacteriorhodopsins↗
PubMed1977

Time-resolved resonance Raman spectroscopy of bacteriorhodopsin on the millisecond timescale.

A simple technique is described that uses a continuous wave laser with electromechanical modulation to obtain time-resolved Raman spectra of transient species on the millisecond timescale. The time behavior of the vibrational bands of the intermediates involved in the proton pumping of bacteriorhodopsin is determined. From these results, along with resonance enhancement and power dependence studies, the bands that appear in the continuous wave Raman spectrum of bacteriorhodopsin can be assigned to three intermediates in the photochemical cycle of bacteriorhodopsin, bR570, bL550, and bM412. The Raman spectra of bR570 and bM412 are compared with published spectra of model Schiff bases of all-trans and 13-cis retinal.

Bacteriorhodopsins↗
PubMed1977

Orientation of bacteriorhodopsin in Halobacterium halobium as studied by selective proteolysis.

The orientation of bacteriorhodopsin in the purple membrane of Halobacterium halobium has been studied by proteolytic degradation of purple membrane sheets, reconstituted vesicles, and whole cells, with the following results: (i) Bacteriorhodopsin in purple membrane sheets is cleaved at a single site by Pronase or trypsin; a polypeptide segment of about 15 amino acids is lost from the carboxyl end. Carboxypeptidase A sequentially releases amino acids from the carboxyl end; the tetrapeptide sequence -Ala-Ala-Thr-Ser(COOH) was tentatively deduced for this terminus. (ii) The apomembrane, which lacks retinal, undergoes a second cleavage with trypsin releasing a fragment of approximately 6300 molecular weight from the amino terminus. (iii) Vesicles reconstituted from the purple membrane sheets and synthetic lecithins, in which the direction of proton pumping is opposite to that in the whole cells, have the carboxyl terminus of bacteriorhodopsin accessible to proteolysis. (iv) In envelope vesicles, which largely pump protons in the same direction as the whole cells, the carboxyl terminus is largely protected against proteolysis. (v) Treatment of whole cells with proteinase K hydrolyzes the cell wall proteins but has no effect on acteriorhodopsin. However, the same treatment after lysis of the cells results in degradation of the hydrophilic region at the carboxyl terminus. The results show that the carboxyl terminus as well as the additional cleavage site near the amino terminus observed in apomembrane are on the cytoplasmic side of the purple membrane.

Apoproteins↗
PubMed1979

Photoisomerization, energy storage, and charge separation: a model for light energy transduction in visual pigments and bacteriorhodopsin.

A simple model for the early events in visual pigments and bacteriorhodopsin is proposed. The model makes use of the likelihood that a negatively charged amino acid forms a salt bridge with the positively charged nitrogen of the retinylic chromophore. The photochemical event is a cis-trans isomerization in visual pigments and a trans-cis isomerization in bacteriorhodopsin, which in each case cleaves the salt bridge and thus separates charge in the interior of the protein. We propose that this is how the energy of a photon is transduced into chemical free energy of the primary photoproduct. The use of photoisomerization of a flexible chromophore to achieve charge separation provides a general mechanism which may be applicable to other systems. Our model explains many of the fundamental properties of visual pigments and their photoproducts. First, the extraordinarily low rate of thermally populating the ground state of the primary photoproduct, as determined from psychophysical and electrophysiological measurements, is seen as resulting from the large barrier to thermal isomerization about a double bond, perhaps enhanced by electrostatic attraction in the salt bridge. Second, the increase in energy and the spectral red shift that characterize the primary photochemical events are natural consequences of the separation of charge. Proton-dependent processes detected with picosecond techniques are proposed to be ground-state relaxation processes following the primary photochemical event. Finally, the charged groups of the salt bridge, repositioned by photoisomerization, provide a simple mechanism for vectorial proton translocation in bacteriorhodopsin.

Bacteriorhodopsins↗
PubMed1977

Light-induced formation of the 410 nm intermediate from reconstituted bacteriorhodopsin.

Light-induced formation of the 410 nm intermediate was investigated with reconstituted bacteriorhodopsin. Only bacteriorhodopsin with all-trans retinal formed the 410 nm intermediate in response to light excitation. In equilibrium in the dark, both native and reconstituted bacteriorhodopsin contained about equal amounts of the all-trans and 13-cis forms over a wide range of temperature.

Bacteriorhodopsins↗
PubMed1978

Proteolysis and flash photolysis of bacteriorhodopsin in purple membrane fragments.

Pronase treatment of aqueous suspensions of purple membrane fragments from H.halobium leads to the cleavage of bacteriorhodopsin. The protein fragments remaining in the membrane after treatment with relatively small concentrations of enzyme (2% w/w) in normal daylight range in molecular weight from 20,000--21,000 daltons, indicating that cleavage occurs mainly near the extremities of the protein chain. At higher enzyme concentrations the relative amounts of protein fragments having smaller molecular weight increase. Generally, the relative loss of retinal chromophore is larger than that of protein and thus the retinal binding site seems to be located near one of the chain ends that is cleaved off by enzyme. Irradiation with white light during the time of proteolysis (at both low and high enzyme concentrations) results in extensive cleavage, so that under certain conditions no high molecular weight components can be detected in SDS-polyacrylamide gels. It, therefore, appears that parts of the bacteriorhodopsin chain become more exposed to enzyme digestion when the purple membrane is illuminated. Enzyme treated aqueous purple membrane fragment suspensions still show photocycle activity. The main consequence of proteolysis is a pronounced appearance of biphasicity in the decay of M412 and the regeneration of bR570. Simultaneously the yield of O660 is reduced. As with untreated purple membrane, the correlation between the rates of decay of M412 and regeneration of bR570 is greatest when the yield of O660 is lowest.

Bacterial Proteins↗
PubMed1979

Bacteriorhodopsin in liposomes. I. A description using irreversible thermodynamics.

A comprehensive description of light-induced ion transport in bacteriorhodopsin liposomes is presented. Linear irreversible thermodynamics and the chemiosmotic theory serve as theoretical bases for the formulation of a limited number of fundamental equations. In these equations mechanistic parameters characterize the dependence of ion movement and flux through the photochemical cycle of bacteriorhodopsin on electrochemical potential differences and a so-called light affinity. By making appropriate steady-state assummptions and carrying out mathematical reduction experimentally testable expressions, still containing the mechanistic parameters, are obtained. In the accompanying article rigid trials to falsify these expressions are shown to be unsuccessful.

Bacteriorhodopsins↗
PubMed1979

Bacteriorhodopsin (BR570) bathochromic band shift in an external electric field.

In dry films of bacteriorhodopsin-containing purple membranes from Halobacterium halobium the external electric field (10(4) -- 10(5) V . cm-1) induces the appearance of a product spectrally close to the initial intermediate of bacteriorhodopsin (BR) photochromic cycle (bathoform, K). This result and also preliminary data of the electret-thermal analysis of the preparations suggest that the dielectric polarization in chromophore-protein-lipid complexes might be an essential step of the primary stabilization of light energy in photo-bioenergetic processes.

Bacteriorhodopsins↗
PubMed1976

A measurement of the proton pump current generated by bacteriorhodopsin in black lipid membranes.

The light-induced electrical current generated by black lipid membranes containing bacteriorhodopsin from Halobacterium halobium has been measured directly. It is shown that a measurement of membrane potential can also be used to obtain the proton pump current developed during illumination. Evidence is presented that the charge movement across the membrane is associated with the release of protons in the photoreaction cycle of bacteriorhodopsin. The time variation of the pump current when the light is turned on suggests the rapid depopulation of some initially occupied state.

Bacteriorhodopsins↗
PubMed1976

Thermal denaturation and photochemistry of bacteriorhodopsin from Halobacterium cutirubrum as monitored by resonance Raman spectroscopy.

Resonance Raman studies of the thermal denaturation of bacteriorhodopsin from Halobacterium cutirubrum show that the N-retinylidenelysine moiety present in the chromophore is N-protonated. This corroborates an earlier suggestion of Lewis et al. ((1974) Proc. Natl. Acad. Sci. U.S., 71, 4462-4466). The widely differing excitation profiles of two -C=C- stretching modes are explained in terms of the light-initiated reaction cycle in the molecule. Glutaraldehyde fixation of bacteriorhodopsin has no effect on the intensity ratio of the two modes, suggesting that no large motion of the protein is necessary for the photoreaction cycle to occur.

Bacteriorhodopsins↗
PubMedDate not supplied

Characterization of the conformational change in the M1 and M2 substates of bacteriorhodopsin by the combined use of visible and infrared spectroscopy.

A combination of visible and Fourier transform infrared (FTIR) spectroscopies is used to characterize the formation of the M1 and M2 substates of the bacteriorhodopsin photocycle in glucose-embedded, hydrated thin films. Difference FTIR bands in the amide I region verify the previously reported existence of a significant peptide backbone conformational change in the transition from M1 to M2. The visible absorption spectra demonstrate that contamination of the M-intermediate samples by L, N, or other non-M species should contribute negligibly to the observed changes in the amide I region, and this conclusion is supported by comparison of specific carboxyl group peaks with corresponding bands in published L and N FTIR difference spectra. Based upon spectroscopic results, an extension of the C-T Model (Fodor, S., Ames, J., Gebhard, R., van den Berg, E., Stoeckenius, W., Lugtenberg, J., and Mathies, R. (1988) Biochemistry 27, 7097-7101) is presented. The results of this work suggest that protein structural changes should be clearly visible in M-bR, difference Fourier density maps and that these structural changes may in turn elucidate how bacteriorhodopsin actively pumps ions across the purple membrane of Halobacterium halobium.

Bacteriorhodopsins↗
PubMed1976

A method for measuring picosecond phenomena in photolabile species: the emission lifetime of bacteriorhodopsin.

We have measured the emission lifetime of bacteriorhodopsin at physiological temperatures to be 15 +/- 3 ps using a technique which employs a mode-locked dye laser, a sum frequency light gate, and a continuous flow system. We observe no concentration dependence of the lifetime over the range of 1.1 X 10(-4) M to 1.0 X 10(-5) M. We conclude that the emission which we observe comes from bacteriorhodopsin and not one of its photochemically produced intermediates, and that the emission cannot originate from the state into which light is absorbed.

Bacteriorhodopsins↗