Detection of bacteriorhodopsin trimeric rotation at thermal phase transitions of purple membrane in suspension

Bacteriorhodopsin (bR) of purple membrane (PM) is a retinal protein that forms aggregates in the form of trimers constituting, together with archaeal lipids, the crystalline structure of PM. The rotary motion of bR inside PM may be pertinent in understanding the essence of the crystalline lattice. An attempt has been made to determine the rotation of bR trimers which has been found to be detected solely at thermal phase transitions of PM, namely lipid, crystalline lattice and protein melting phase transitions. The temperature dependences of dielectric versus electronic absorption spectra of bR have been determined. The results suggest that the rotation of bR trimers, together with concomitant bending of PM, are most likely brought by structural changes in bR which might be driven by retinal isomerization and mediated by lipid. The rupturing of the lipid-protein contact might consequently lead to rotation of trimers associated with bending, curling or vesicle formation of PM. So the retinal reorientation may underlie the concomitant rotation of trimers. Most importantly, rotation of trimers might play a role, in terms of the essence of the crystalline lattice, in the functional activity of bR and may serve physiological relevance.

Imaging DNA Equilibrated onto Mica in Liquid Using Biochemically Relevant Deposition Conditions

For over 25 years, imaging of DNA by atomic force microscopy has been intensely pursued. Ideally, such images are then used to probe the physical properties of DNA and characterize protein-DNA interactions. The atomic flatness of mica makes it the preferred substrate for high signal-to-noise ratio (SNR) imaging, but the negative charge of mica and DNA hinders deposition. Traditional methods for imaging DNA and protein-DNA complexes in liquid have drawbacks: DNA conformations with an anomalous persistence length ( p), low SNR, and/or ionic deposition conditions detrimental to preserving protein-DNA interactions. Here, we developed a process to bind DNA to mica in a buffer containing both MgCl₂ and KCl that resulted in high SNR images of equilibrated DNA in liquid. Achieving an equilibrated 2D configuration ( i. e., p = 50 nm) not only implied a minimally perturbative binding process but also improved data quality and quantity because the DNA's configuration was more extended. In comparison to a purely NiCl₂-based protocol, we showed that an 8-fold larger fraction (90%) of 680-nm-long DNA molecules could be quantified. High-resolution images of select equilibrated molecules revealed the right-handed structure of DNA with a helical pitch of 3.5 nm. Deposition and imaging of DNA was achieved over a wide range of monovalent and divalent ionic conditions, including a buffer containing 50 mM KCl and 3 mM MgCl₂. Finally, we imaged two protein-DNA complexes using this protocol: a restriction enzyme bound to DNA and a small three-nucleosome array. We expect such deposition of protein-DNA complexes at biochemically relevant ionic conditions will facilitate biophysical insights derived from imaging diverse protein-DNA complexes.

Potential Second-Harmonic Ghost Bands in Fourier Transform Infrared (FT-IR) Difference Spectroscopy of Proteins

Fourier transform infrared (FT-IR) difference absorption spectroscopy is a common method for studying the structural and dynamical aspects behind protein function. In particular, the 2800-1800 cm^-1 spectral range has been used to obtain information about internal (deuterated) water molecules, as well as site-specific details about cysteine residues and chemically modified and artificial amino acids. Here, we report on the presence of ghost bands in cryogenic light-induced FT-IR difference spectra of the protein bacteriorhodopsin. The presence of these ghost bands can be particularly problematic in the 2800-1900 cm^-1 region, showing intensities similar to O-D vibrations from water molecules. We demonstrate that they arise from second harmonics from genuine chromophore bands located in the 1400-850 cm^-1 region, generated by double-modulation artifacts caused from reflections of the IR beam at the sample and at the cryostat windows back to the interferometer (inter-reflections). The second-harmonic ghost bands can be physically removed by placing an optical filter of suitable cutoff in the beam path, but at the cost of losing part of the multiplexing advantage of FT-IR spectroscopy. We explored alternatives to the use of optical filters. Tilting the cryostat windows was effective in reducing the intensity of the second harmonic artifacts but tilting the sample windows was not, presumably by their close proximity to the focal point of the IR beam. We also introduce a simple numerical post-processing approach that can partially, but not fully, correct for second-harmonic ghost bands in FT-IR difference spectra.

Membrane proteomic analysis of Arabidopsis thaliana using alternative solubilization techniques

This study presents a comparative proteomic analysis of the membrane subproteome of whole Arabidopsis seedlings using 2% Brij-58 or 60% methanol to enrich and solubilize membrane proteins for strong cation exchange fractionation and reversed-phase liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 441 proteins were identified by our Brij-58 method, and 300 proteins were detected by our methanol-based solubilization approach. Although the total number of proteins obtained using the nonionic detergent was higher than the total obtained by organic solvent, the ratio of predicted membrane proteins to total proteins identified indicates up to an 18.6% greater enrichment efficiency using methanol. Using two different bioinformatics approaches, between 31.0 and 40.0% of the total proteins identified by the methanol-based method were classified as containing at least one putative transmembrane domain as compared to 22.0-23.4% for Brij-58. In terms of protein hydrophobicity as determined by the GRAVY index, it was revealed that methanol was more effective than Brij-58 for solubilizing membrane proteins ranging from -0.4 (hydrophilic) to +0.4 (hydrophobic). Methanol was also approximately 3-fold more effective than Brij-58 in identifying leucine-rich repeat receptor-like kinases. The ability of methanol to effectively solubilize and denature both hydrophobic and hydrophilic proteins was demonstrated using bacteriorhodopsin and cytochrome c, respectively, where both proteins were identified with at least 82% sequence coverage from a single reversed-phase LC-MS/MS analysis. Overall, our data show that methanol is a better alternative for identifying a wider range of membrane proteins than the nonionic detergent Brij-58.

Practical aspects of the maximum entropy inversion of the laplace transform for the quantitative analysis of multi-exponential data

The number, position, area, and width of the bands in a lifetime distribution give the number of exponentials present in time-resolved data and their time constants, amplitudes, and heterogeneities. The maximum entropy inversion of the Laplace transform (MaxEnt-iLT) provides a lifetime distribution from time-resolved data, which is very helpful in the analysis of the relaxation of complex systems. In some applications both positive and negative values for the lifetime distribution amplitudes are physical, but most studies to date have focused on positive-constrained solutions. In this work, we first discuss optimal conditions to obtain a sign-unrestricted maximum entropy lifetime distribution, i.e., the selection of the entropy function and the regularization value. For the selection of the regularization value we compared four methods: the chi2 criterion and Bayesian inference (already used in sign-restricted MaxEnt-iLT), and the L-curve and the generalized cross-validation methods (not yet used in MaxEnt-iLT to our knowledge). Except for the frequently used chi2 criterion, these methods recommended similar regularization values, providing close to optimum solutions. However, even when an optimal entropy function and regularization value are used, a MaxEnt lifetime distribution will contain noise-induced errors, as well as systematic distortions induced by the entropy maximization (regularization-induced errors). We introduce the concept of the apparent resolution function in MaxEnt, which allows both the noise and regularization-induced errors to be estimated. We show the capability of this newly introduced concept in both synthetic and experimental time-resolved Fourier transform infrared (FT-IR) data from the bacteriorhodopsin photocycle.

Three-layer matrix/sample preparation method for MALDI MS analysis of low nanomolar protein samples

A robust and sensitive sample preparation method is presented for matrix-assisted laser desorption ionization (MALDI) mass spectrometric analysis of low nanomolar concentrations of proteins containing high amounts of common salts and buffers. This method involves the production of densely packed sub-micrometer matrix crystals by depositing a matrix solution on top of a matrix seed-layer prepared on a MALDI target. A sub-microliter aliquot of analyte solution is then directly added to the top of the matrix crystals to form a thin-layer. alpha-Cyano-4-hydroxycinnamic acid (4-HCCA) is used as matrix and demonstrated to give better performance than other commonly used matrices, such as 2,5-dihydroxybenzoic acid (DHB), 2-(4-hydroxy-phenylazo) benzoic acid (HABA), or sinapinic acid. This three-layer method is shown to be superior to the other MALDI sample preparation methods, particularly for handling low nanomolar protein solutions containing salts and buffers.

Simulation of fluorescence anisotropy experiments: probing protein dynamics

Time-resolved fluorescence anisotropy decay experiments on a protein-attached dye can probe local protein dynamics and steric restrictions, but are difficult to interpret at the structural level. Aiming at an atomistic description, we have carried out molecular dynamics simulations of such experiments. Our simulations describe an Alexa488 fluorescent dye maleimide derivative covalently attached via a single cysteine to the AB-loop of bacteriorhodopsin. Fluorescence anisotropy decay curves obtained from the simulations agree well with the measured ones. Three anisotropy decay components were resolved and assigned to: 1), the fast dynamics of the attached dye on the picosecond timescale; 2), the slower dynamics of the loop at the one nanosecond timescale; and 3), the overall tumbling of the molecule. For the biologically relevant 1-ns component we identified two processes from simulations, the motion of the flexible loop as well as slow conformational dynamics of the dye. These two processes are not separable by experiment alone. Furthermore, analysis of the correlation between the dye and the protein motion revealed which part and which motion of the protein is actually probed by the experiment. Finally, our simulations allowed us to test the usual and inevitable assumption underlying these types of spectroscopic measurements that the attached dye probe does not severely perturb the protein dynamics. For the case at hand, by comparison with a simulation of the dye-free protein, the perturbation was quantified and found to be small.

Microwave-assisted acid hydrolysis of proteins combined with liquid chromatography MALDI MS/MS for protein identification

Simple and efficient digestion of proteins, particularly hydrophobic membrane proteins, is of significance for comprehensive proteome analysis using the bottom-up approach. We report a microwave-assisted acid hydrolysis (MAAH) method for rapid protein degradation for peptide mass mapping and tandem mass spectrometric analysis of peptides for protein identification. It uses 25% trifluoroacetic acid (TFA) aqueous solution to dissolve or suspend proteins, followed by microwave irradiation for 10 min. This detergent-free method generates peptide mixtures that can be directly analyzed by liquid chromatography (LC) matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) without the need of extensive sample cleanup. LC-MALDI MS/MS analysis of the hydrolysate from 5 microg of a model transmembrane protein, bacteriorhodopsin, resulted in almost complete sequence coverage by the peptides detected, including the identification of two posttranslational modification sites. Cleavage of peptide bonds inside all seven transmembrane domains took place, generating peptides of sizes amenable to MS/MS to determine possible sequence errors or modifications within these domains. Cleavage specificity, such as glycine residue cleavage, was observed. Terminal peptides were found to be present in relatively high abundance in the hydrolysate, particularly when low concentrations of proteins were used for MAAH. It was shown that these peptides could still be detected from MAAH of bacteriorhodopsin at a protein concentration of 1 ng/microl or 37 fmol/microl. To evaluate the general applicability of this method, it was applied to identify proteins from a membrane protein enriched fraction of cell lysates of human breast cancer cell line MCF7. With one-dimensional LC-MALDI MS/MS, a total of 119 proteins, including 41 membrane-associated or membrane proteins containing one to 12 transmembrane domains, were identified by MS/MS database searching based on matches of at least two peptides to a protein.

Maximum entropy deconvolution of infrared spectra: use of a novel entropy expression without sign restriction

Absorbance and difference infrared spectra are often acquired aiming to characterize protein structure and structural changes of proteins upon ligand binding, as well as for many other chemical and biochemical studies. Their analysis requires as a first step the identification of the component bands (number, position, and area) and as a second step their assignment. The first step of the analysis is challenged by the habitually strong band overlap in infrared spectra. Therefore, it is useful to make use of a mathematical method able to narrow the component bands to the extent to eliminate, or at least reduce, the band overlap. Additionally, to be of general applicability this method should permit negative values for the solution. We present a maximum entropy deconvolution approach for the band-narrowing of absorbance and difference spectra showing the required characteristics, which uses the generalized negative Burg-entropy (Itakura-Saito discrepancy) generalized for difference spectra. We present results on synthetic noisy absorbance and difference spectra, as well as on experimental infrared spectra from the membrane protein bacteriorhodopsin.

Membrane lateral mobility obstructed by polymer-tethered lipids studied at the single molecule level

Obstructed long-range lateral diffusion of phospholipids (TRITC-DHPE) and membrane proteins (bacteriorhodopsin) in a planar polymer-tethered 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer is studied using wide-field single molecule fluorescence microscopy. The obstacles are well-controlled concentrations of hydrophobic lipid-mimicking dioctadecylamine moieties in the polymer-exposed monolayer of the model membrane. Diffusion of both types of tracer molecules is well described by a percolating system with different percolation thresholds for lipids and proteins. Data analysis using a free area model of obstructed lipid diffusion indicates that phospholipids and tethered lipids interact via hard-core repulsion. A comparison to Monte Carlo lattice calculations reveals that tethered lipids act as immobile obstacles, are randomly distributed, and do not self-assemble into large-scale aggregates for low to moderate tethering concentrations. A procedure is presented to identify anomalous subdiffusion from tracking data at a single time lag. From the analysis of the cumulative distribution function of the square displacements, it was found that TRITC-DHPE and W80i show normal diffusion at lower concentrations of tethered lipids and anomalous diffusion at higher ones. This study may help improve our understanding of how lipids and proteins in biomembranes may be obstructed by very small obstacles comprising only one or very few molecules.

Molecular force modulation spectroscopy revealing the dynamic response of single bacteriorhodopsins

Recent advances in atomic force microscopy allowed globular and membrane proteins to be mechanically unfolded on a single-molecule level. Presented is an extension to the existing force spectroscopy experiments. While unfolding single bacteriorhodopsins from native purple membranes, small oscillation amplitudes (6-9 nm) were supplied to the vertical displacement of the cantilever at a frequency of 3 kHz. The phase and amplitude response of the cantilever-protein system was converted to reveal the elastic (conservative) and viscous (dissipative) contributions to the unfolding process. The elastic response (stiffness) of the extended parts of the protein were in the range of a few tens pN/nm and could be well described by the derivative of the wormlike chain model. Discrete events in the viscous response coincided with the unfolding of single secondary structure elements and were in the range of 1 microNs/m. In addition, these force modulation spectroscopy experiments revealed novel mechanical unfolding intermediates of bacteriorhodopsin. We found that kinks result in a loss of unfolding cooperativity in transmembrane helices. Reconstructing force-distance spectra by the integration of amplitude-distance spectra verified their position, offering a novel approach to detect intermediates during the forced unfolding of single proteins.

Physical detwinning of hemihedrally twinned hexagonal crystals of bacteriorhodopsin

Hexagonal crystals of the membrane protein bacteriorhodopsin of space group P6 3 grown in lipidic cubic phase are twinned hemihedrally. It was shown that slow changes of salt concentration in the mother liquor lead to a split of crystals so that the split parts preserved high diffraction quality. Analysis of diffraction data from split crystals by Yeates statistic and Britton plot showed that the split parts are free of twinning. It is concluded that crystals of bacteriorhodopsin are composed of several macroscopic twinning domains with sizes comparable to the original crystal. The appearance of twinning domains during crystal growth and the mechanism of splitting are discussed.

Development and applications of in-gel CNBr/tryptic digestion combined with mass spectrometry for the analysis of membrane proteins

Hydrophobic membrane proteins often have complex functions and are thus of great interest. However, their analysis presents a challenge because they are not readily soluble in polar solvents and often undergo aggregation. We present a sequential CNBr and trypsin in-gel digestion method combined with mass spectrometry for membrane protein analysis. CNBr selectively cleaves methionine residues. But due to the low number of methionines in proteins, CNBr cleavage produces a small number of large peptide fragments with MWs typically >2000, which are difficult to extract from gel pieces. To produce a larger number of smaller peptides than that obtained by using CNBr alone, we demonstrate that trypsin can be used to further digest the sample in gel. The use of n-octyl glucoside (n-OG) to enhance the digestion efficiency and peptide recovery was also studied. We demonstrate that the sensitivity of this membrane protein identification method is in the tens of picomole regime, which is compatible to the Coomassie staining gel-spot visualization method, and is more sensitive than other techniques reported in the literature. This CNBr/trypsin in-gel digestion method is also found to be very reproducible and has been successfully applied for the analysis of complex protein mixtures extracted from biological samples. The results are presented from a study of the analysis of bacteriorhodopsin, nitrate reductase 1 gamma chain, and a complex protein mixture extracted from the endoplasmic recticulum membrane of mouse liver.

Effect of beta-particles on the retinal chromophore in bacteriorhodopsin of Halobacterium salinarium

Bacteriorhodopsin (bR) is an attractive intelligent material. Understanding the mechanism of its light-driven proton pumping outward the cell implicates it in many technical applications, particularly, in what is called optical computers, and the biotechnology is waiting for this promised biological molecule. An ionizing radiation source handling could be computerized in radiation fields. The computer containing such biological material will not be out of reach of the fields of ionizing radiation. So it is interesting to report on the working of such biological computer if it is subjected to ionizing radiation. The functional unit in this molecule is retinal chromophore. In the present work, it is interested to assess the functionality of bR through determining the electronic transition dipole moment of its chromophore. Significant changes in the values of the absorption transition dipole moment were noticed at different doses of beta-particles in the range of 0.1-0.3 kGy. Ionizing radiation-induced changes in bR were followed by intrinsic fluorescence spectroscopy. An analysis of the fluorescence data bears on the tertiary structure of bR. The emission spectrum is, however, red shifted with an increase in intensity with the different doses; in the meanwhile, gradual decrease in the visible absorbance has occurred till almost complete loss is attained. This bleaching due to ionizing radiation may offer an alternative way of data processing in such optical devices based on bR. Nevertheless, bR has proofed to be used as a biological indicator of ionizing radiation. However, the potential of bR for use as a biosensor to detect ionizing radiation should be considered.

Thr-90 plays a vital role in the structure and function of bacteriorhodopsin

The role of Thr-90 in the bacteriorhodopsin structure and function was investigated by its replacement with Ala and Val. The mutant D115A was also studied because Asp-115 in helix D forms a hydrogen bond with Thr-90 in helix C. Differential scanning calorimetry showed a decreased thermal stability of all three mutants, with T90A being the least stable. Light-dark adaptation of T90A was found to be abnormal and salt-dependent. Proton transport monitored using pyranine signals was approximately 10% of wild type for T90A, 20% for T90V, and 50% for D115A. At neutral or alkaline pH, the M rise of these mutants was faster than that of wild type, whereas M decay was slower in T90A. Overall, Fourier transform infrared (FTIR) difference spectra of T90A were strongly pH-dependent. Spectra recorded on films adjusted at the same pH at 243 or 277 K, dry or wet, showed similar features. The D115A and T90V FTIR spectra were closer to WT, showing minor structural differences. The band at 1734 cm(-1) of the deconvoluted FTIR spectrum, corresponding to the carboxylate of Asp-115, was absent in all mutants. In conclusion, Thr-90 plays a critical role in maintaining the operative location and structure of helix C through three complementary interactions, namely an interhelical hydrogen bond with Asp-115, an intrahelical hydrogen bond with the peptide carbonyl oxygen of Trp-86, and a steric contact with the retinal. The interactions established by Thr-90 emerge as a general feature of archaeal rhodopsin proteins.

Efficient in-gel digestion procedure using 5-cyclohexyl-1-pentyl-beta-D-maltoside as an additive for gel-based membrane proteomics

A cycloalkyl aliphatic saccharide, 5-cyclohexyl-1-pentyl-beta-D-maltoside (CYMAL-5), was evaluated as a novel additive in a high-throughput in-gel protein digestion system using 96-well plates. Addition of 0.1% CYMAL-5 (final concentration) during trypsin treatment was compatible with both matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and liquid chromatography/tandem mass spectrometry (LC/MS/MS) analysis, and gave a better digestion efficiency than n-octylglucoside, which we previously reported. In-gel reduction and alkylation of Cys residues under denaturing conditions also improved the sequence coverage of peptides. In-gel tryptic digestion with the optimum combination of 0.5 mm thick gels, negative staining, alkylation under denaturing conditions (6 M guanidine hydrochloride), and digestion in the presence of CYMAL-5, gave excellent performance especially for membrane protein analysis, where recovery of hydrophobic peptides was markedly enhanced. The new protocol is simple and convenient, and should be widely applicable to gel-based proteomics.

On-Column Sample Enrichment for Capillary Electrophoresis Sheathless Electrospray Ionization Mass Spectrometry: Evaluation for Peptide Analysis and Protein Identification

Although several designs have been advanced for coupling sample enrichment devices to a sheathless electrospray ionization-mass spectrometry (MS) interface on a capillary electrophoresis (CE) column, most of these approaches suffer from difficulties in fabrication, and the CE separation efficiency is degraded as a result of the presence of coupling sleeves. We have developed a design that offers significant improvements in terms of ease of fabrication, durability, and maintenance of the integrity of the CE-separated analyte zones. Capillaries with different inside and outside diameters were evaluated to optimize the performance of the CE-MS system, resulting in a mass limit of detection of 500 amol for tandem MS analysis of a standard peptide using a 20-microm-i.d. capillary. The improved design incorporates an efficient method to preconcentrate a sample directly within the CE capillary followed by its electrophoretic separation and detection using a true zero dead-volume sheathless CE-MS interface. Testing of this novel CE-MS system showed its ability to characterize proteomic samples such as protein digests, in-gel-digested proteins, and hydrophobic peptides as well as to quantitate ICAT-labeled peptides.

Backbone dynamics of bacteriorhodopsin as studied by (13)C solid-state NMR spectroscopy

The surface dynamics of bacteriorhodopsin was examined by measurements of site-specific (13)C-(1)H dipolar couplings in [3-(13)C]Ala-labeled bacteriorhodopsin. Motions of slow or intermediate frequency (correlation time <50 micro s) scale down (13)C-(1)H dipolar couplings according to the motional amplitude. The two-dimensional dipolar and chemical shift (DIPSHIFT) correlation technique was utilized to obtain the dipolar coupling strength for each resolved peak in the (13)C MAS solid-state NMR spectrum, providing the molecular order parameter of the respective site. In addition to the rotation of the Ala methyl group, which scales the dipolar coupling to 1/3 of the rigid limit value, fluctuations of the Calpha-Cbeta vector result in additional motional averaging. Typical order parameters measured for mobile sites in bacteriorhodopsin are between 0.25 and 0.29. These can be assigned to Ala103 of the C-D loop and Ala235 at the C-terminal alpha-helix protruded from the membrane surface, and Ala196 of the F-G loop, as well as to Ala228 and Ala233 of the C-terminal alpha-helix and Ala51 from the transmembrane alpha-helix. Such order parameters departing significantly from the value of 0.33 for rotating methyl groups are obviously direct evidence for the presence of fluctuation motions of the Ala Calpha-Cbeta vectors of intact preparations of fully hydrated, wild-type bacteriorhodopsin at ambient temperature. The order parameter for Ala160 from the expectantly more flexible E-F loop, however, is unavailable under highest-field NMR conditions, probably because increased chemical shift anisotropy together with intrinsic fluctuation motions result in an unresolved (13)C NMR signal.

Downstream coding region determinants of bacterio-opsin, muscarinic acetylcholine receptor and adrenergic receptor expression in Halobacterium salinarum

The aim of this work is to develop a prokaryotic system capable of expressing membrane-bound receptors in quantities suitable for biochemical and biophysical studies. Our strategy exploits the endogenous high-level expression of the membrane protein bacteriorhodopsin (BR) in the Archaeon Halobacterium salinarum. We attempted to express the human muscarinic acetylcholine (M(1)) and adrenergic (a2b) receptors by fusing the coding region of the m1 and a2b genes to nucleotide sequences known to direct bacterio-opsin (bop) gene transcription. The fusions included downstream modifications to produce non-native carboxyl-terminal amino acids useful for protein identification and purification. bop mRNA and BR accumulation were found to be tightly coupled and the carboxyl-terminal coding region modifications perturbed both. m1 and a2b mRNA levels were low, and accumulation was sensitive to both the extent of the bop gene fusion and the specific carboxyl-terminal coding sequence modifications included. Functional a2b adrenergic receptor expression was observed to be dependent on the downstream coding region. This work demonstrates that a critical determinant of expression resides in the downstream coding region of the wild-type bop gene and manipulation of the downstream coding region of heterologous genes may affect their potential for expression in H. salinarum.

THz time domain spectroscopy of biomolecular conformational modes

We discuss the use of terahertz time domain spectroscopy for studies of conformational flexibility and conformational change in biomolecules. Protein structural dynamics are vital to biological function with protein flexibility affecting enzymatic reaction rates and sensory transduction cycling times. Conformational mode dynamics occur on the picosecond timescale and with the collective vibrational modes associated with these large scale structural motions in the 1-100 cm(-1) range. We have performed THz time domain spectroscopy (TTDS) of several biomolecular systems to explore the sensitivity of TTDS to distinguish different molecular species, different mutations within a single species and different conformations of a given biomolecule. We compare the measured absorbances to normal mode calculations and find that the TTDS absorbance reflects the density of normal modes determined by molecular mechanics calculations, and is sensitive to both conformation and mutation. These early studies demonstrate some of the advantages and limitations of using TTDS for the study of biomolecules.

Lipid-protein stoichiometries in a crystalline biological membrane: NMR quantitative analysis of the lipid extract of the purple membrane

The lipid/protein stoichiometries of a naturally crystalline biological membrane, the purple membrane (PM) of Halobacterium salinarum, have been obtained by a combination of (31)P- and (1)H-NMR analyses of the lipid extract. In total, 10 lipid molecules per retinal were found to be present in the PM lipid extract: 2-3 molecules of phosphatidylglycerophosphate methyl ester (PGP-Me), 3 of glycolipid sulfate, 1 of phosphatidylglycerol, 1 of archaeal glycocardiolipin (GlyC), 2 of squalene plus minor amounts of phosphatidylglycerosulfate (PGS) and bisphosphatidylglycerol (archaeal cardiolipin) (BPG) and a negligible amount of vitamin MK8. The novel data of the present study are necessary to identify the lipids in the electron density map, and to shed light on the structural relationships of the lipid and protein components of the PM.

Electric signals of light excited bacteriorhodopsin mutant D96N

The study of mutant D96N played an important role in understanding proton translocation by light driven bacteriorhodopsin. Our measurement of photoelectric current for single and double flash illumination revealed new details of the photocycle of this mutant. With double flash excitation we found an intermediate absorbing near the wavelength of the ground state of bacteriorhodopsin (bR) but pumping in the opposite direction. This intermediate has the same lifetime as the species described by Zimányi et al. [Proc. Natl. Acad. Sci. USA 96 (1999) 4414-4419] and was assigned to early recovery of a fraction of the ground state after excitation. Because the electric response does not reconcile with that of the ground state, we tentatively assign it to the L intermediate or to an intermediate similar in absorption to bR (bR').

Extraction method for analysis of detergent-solubilized bacteriorhodopsin and hydrophobic peptides by electrospray ionization mass spectrometry

The analysis of integral membrane proteins or transmembrane peptides by electrospray ionization mass spectrometry (ESI-MS) is difficult since detergents, used to solubilize these hydrophobic proteins and peptides, severely suppress analyte ion formation. This problem has been addressed previously by precipitating the protein, removing the detergent, and resolubilizing the protein in a nonpolar solvent. Here, we demonstrate a method that avoids protein precipitation and resolubilization. Detergent-solubilized bacteriorhodopsin is extracted into a nonpolar solvent phase by adding a chloroform/methanol/water solvent mixture to the aqueous detergent solution. ESI mass spectra of the nonpolar, chloroform-rich phase were dominated by peaks due to bacterioopsin. Bacterioopsin precursors with partially cleaved leader sequences were seen in all mass spectra. Additional peaks were likely due to intact bacteriorhodopsin, i.e., bacterioopsin with the retinal prosthetic group attached, and to bacterioopsin associated with lipid molecules. A separation process that occurred in the fused-silica capillary leading to the electrospray tip was essential for obtaining ESI mass spectra of bacterioopsin. The extraction-into-chloroform procedure also worked well with hydrophobic, transmembrane-type peptides that were insoluble in other electrospray solvents, including 100% formic acid, and the method has application to transmembrane peptides formed from digests of integral membrane proteins.

Electrospray-ionization mass spectrometry of intact intrinsic membrane proteins

Membrane proteins drive and mediate many essential cellular processes making them a vital section of the proteome. However, the amphipathic nature of these molecules ensures their detailed structural analysis remains challenging. A versatile procedure for effective electrospray-ionization mass spectrometry (ESI-MS) of intact intrinsic membrane proteins purified using reverse-phase chromatography in aqueous formic acid/isopropanol is presented. The spectra of four examples, bacteriorhodopsin and its apoprotein from Halobacterium and the D1 and D2 reaction-center subunits from spinach thylakoids, achieve mass measurements that are within 0.01% of calculated theoretical values. All of the spectra reveal lesser quantities of other molecular species that can usually be equated with covalently modified subpopulations of these proteins. Our analysis of bovine rhodopsin, the first ESI-MS study of a G-protein coupled receptor, yielded a complex spectrum indicative of extensive molecular heterogeneity. The range of masses measured for the native molecule agrees well with the range calculated based upon variable glycosylation and reveals further heterogeneity arising from other covalent modifications. The technique described represents the most precise way to catalogue membrane proteins and their post-translational modifications. Resolution of the components of protein complexes provides insights into native protein/protein interactions. The apparent retention of structure by bacteriorhodopsin during the analysis raises the potential of obtaining tertiary structure information using more developed ESI-MS experiments.

Mass spectrometric analysis of integral membrane proteins: application to complete mapping of bacteriorhodopsins and rhodopsin

Integral membrane proteins have not been readily amenable to the general methods developed for mass spectrometric (or internal Edman degradation) analysis of soluble proteins. We present here a sample preparation method and high performance liquid chromatography (HPLC) separation system which permits online HPLC-electrospray ionization mass spectrometry (ESI-MS) and -tandem mass spectrometry (MS/MS) analysis of cyanogen bromide cleavage fragments of integral membrane proteins. This method has been applied to wild type (WT) bacteriorhodopsin (bR), cysteine containing mutants of bR, and the prototypical G-protein coupled receptor, rhodopsin (Rh). In the described method, the protein is reduced and the cysteine residues pyridylethylated prior to separating the protein from the membrane. Following delipidation, the pyridylethylated protein is cleaved with cyanogen bromide. The cleavage fragments are separated by reversed phase HPLC using an isopropanol/acetonitrile/aqueous TFA solvent system and the effluent peptides analyzed online with a Finnigan LCQ Ion Trap Mass Spectrometer. With the exception of single amino acid fragments and the glycosylated fragment of Rh, which is observable by matrix assisted laser desorption ionization (MALDI)-MS, this system permits analysis of the entire protein in a single HPLC run. This methodology will enable pursuit of chemical modification and crosslinking studies designed to probe the three dimensional structures and functional conformational changes in these proteins. The approach should also be generally applicable to analysis of other integral membrane proteins.

Localization of glycolipids in membranes by in vivo labeling and neutron diffraction

Evidence is accumulating for the lateral organization of cell membrane lipids and proteins in the context of sorting or intracellular signaling. So far, however, information has been lacking on the details of protein-lipid interactions in such aggregates. Purple membranes are patches made up of lipids and the protein bacteriorhodopsin in the plasma membrane of certain Archaea. Naturally crystalline, they provide a unique opportunity to study the structure of a natural membrane at submolecular resolution by diffraction methods. We present a direct structural determination of the glycolipids with respect to bacteriorhodopsin in these membranes. Deuterium labels incorporated in vivo into the sugar moieties of the major glycolipid were localized by neutron diffraction. The data suggest a role for specific aromatic residue-carbohydrate stacking interactions in the formation of the purple membrane crystalline patches.

Determination of the amount of native structural bacteriorhodopsin in purple membrane Langmuir-Blodgett films by a spectroscopic surface denaturation quantifying technique

Purple membrane (PM) shows denaturation when spread over an air/water interface. We established a technique, which we call the spectroscopic surface denaturation quantifying (SSDQ) technique, that uses infrared linear dichroism to determine the amount of native structural bacteriorhodopsin (BR) in PM Langmuir-Blodgett (LB) films. Using the SSDQ technique we found that the conformational change after surface denaturation of BR was the same as that caused by ethanol treatment. By extrapolating the data of the amount of non-denatured BR molecules in PM LB films vs. the area of a single BR molecule on an air/water interface, we also found that the surface area of a single non-denatured BR molecule was 11.5 nm2, which is consistent with that determined by high-resolution electron cryo-microscopy and electron diffraction (EMD). These results demonstrate that the SSDQ technique is effective in quantifying the amount of native structural BR in PM LB films. The SSDQ technique is also applicable to other types of protein consisting of alpha-helical conformation.

Novel bacterial rhodopsins from Haloarcula vallismortis

New bacterial rhodopsins of the cruxrhodopsin (cR) tribe were identified in a type strain Haloarcula vallismortis. The genes encoding a bacteriorhodopsin-like ion pump (named cR-3), a halorhodopsin-like ion pump (chR-3) and a sensor rhodopsin (csR-3) were cloned and sequenced. Together with the data for vsRII (Seidel et al., Proc. Natl. Acad. Sci. USA 92, 3036-3040 (1995); cpR-3 in our notation), the primary structures of a set of four rhodopsins are now all known only in this species. They are separated by almost the same distances in homology, suggesting that they have derived from a single ancestral rhodopsin. The degree of conservation in the amino acid sequence of each helix showed that helices C and G are relatively well conserved in all rhodopsins, whereas helices DEF are conserved especially in sensor rhodopsin-I, possibly because these helices are needed for interaction with the transducer protein (Htr).

Retained activities of some membrane proteins in stable lipid bilayers on a solid support

Highly stable lipid bilayers, composed of biologically relevant lipids such as phosphatidylcholine, phosphatidylethanolamine and cholesterol, were formed on platinum surfaces. Bacteriorhodopsin isolated from purple membrane (PM) from Halobacterium halobium, cytochrome oxidase from bovine heart, acetylcholinesterase from bovine brain and the nicotinic acetylcholine receptor from Torpedo electric organ were also incorporated into these reconstituted membranes. The proteins retained their biological activities. Some of them were active several weeks after the reconstitution and after several cycles of assay, washing and storage.

Backbone dynamics of (1-71)bacterioopsin studied by two-dimensional 1H-15N NMR spectroscopy

The backbone dynamics of a uniformly 15N-labelled proteolytic fragment (residues 1-71) of bacteriorhodopsin, solubilized in two media [methanol/chloroform (1:1), 0.1 M 2HCO2NH4 and SDS micelles] have been investigated using two-dimensional proton-detected heteronuclear 1H-15N NMR spectroscopy. A set of longitudinal and transverse relaxation rates of 15N nuclei and 1H-15N NOE were obtained for 61 backbone amide groups. The contribution of the conformational exchange to transverse relaxation rates of individual nitrogens was elucidated using a set of different rates of the Carr-Purcell-Meiboom-Gill (CPMG) spin-lock pulse train. We found that most of the backbone amide groups are involved in the co-operative exchange process over the rate range 10(3)-10(4) s-1, with the chemical-shift dispersion near 1 ppm. Contributions of conformational exchange to the measured transverse relaxation were essentially suppressed by the 3-kHz (spin-echo period tau = 0.083 ms) CPMG spin-lock. Under these conditions, the measured longitudinal, transverse relaxation rates and NOE values were interpreted using the model-free approach of Lipari and Szabo [Lipari, G. & Szabo, A. (1982) J. Am. Chem. Soc. 104, 4546-4559]. In both media used, the protein exhibits very similar dynamic properties, and has overall rotational correlation times of 7.0 ns and 6.6 ns in organic mixture and in SDS micelles, respectively. In addition to overall rotation of the molecule, the backbone N-H vectors are involved in two types of internal motions; fast, on a time scale of < 20 ps, and intermediate, close to 1 ns. Distinctly mobile regions are identified by a large decrease in the overall order parameter and correspond to N-terminal residues (residues 1-7 both for organic solvent and micelles), C-terminal residues (residues 65-71 and 69-71 for organic solvent and micelles, respectively) and residues connecting alpha helices (residues 33-41 and 33-38, for organic solvent and micelles, respectively). A decrease in the order parameter was also observed for residues next to Pro50, indicating a higher flexibility in this region. Thus, backbone dynamic parameters of (1-71)bacterioopsin are in good correspondence with its spatial structure [Pervushin, K. V., Orekhov, V. Yu., Popov, A., Musina, L. Yu., Arseniev, A. S., (1994) Eur. J. Biochem., in the press]. The observed conformational exchange behavior of alpha helices seems to be induced by the flickering helix-helix interaction and could be important for the functioning of bacteriorhodopsin.

Analysis of hydrophobic proteins and peptides by electrospray ionization mass spectrometry

During the last decade mass spectrometry has become an essential tool for the analysis of peptides and proteins. Electrospray ionization mass spectrometry (ESIMS) is one of several recently developed techniques for the determination of accurate molecular masses of proteins, peptides, and other biopolymers up to > 100 kDa. Up to the present, analyses have been performed mainly on biopolymers that are soluble in aqueous solutions. Mass spectrometric analyses of very hydrophobic species, such as membrane proteins, have seldom been reported in the literature. This is mainly due to the incompatibility between most mass spectrometric techniques and detergents and/or salts which are required to retain such proteins in solution. Hydrophobic proteins (for example, bacterioopsin) and peptides are in general not soluble in the solutions (methanol/water or acetonitrile/water) typically used for ESIMS, and most detergents and chaotropes interfere with the analysis. We have developed sample handling protocols and solvent systems that are compatible with instrumental requirements and also are capable of retaining very hydrophobic peptides and proteins in solution. Chloroform/methanol/water mixtures were found to work well with, e.g., bacterioopsin, and also to be compatible with samples dissolved in hexafluoroisopropanol and 70-95% formic acid.

Segregation of modified bacteriorhodopsin aggregations in reconstituted vesicle membrane induced by the change of thermodynamical parameters

It was clearly shown that the change in thermodynamical parameters could cause the segregation of membrane protein aggregations in the phospholipid membrane. At first, reconstituted vesicles were prepared with a membrane protein, bacteriorhodopsin and a constituent phospholipid of biomembranes, L-alpha-dimyristoyl phosphatidylcholine. When the temperature of the suspension was decreased or the osmotic pressure was increased by adding poly(ethylene glycol) to this vesicle suspension at 23 degrees, the circular dichroism spectra showed a typical band indicating bacteriorhodopsin trimer formation implying their aggregation. This suggests that the aggregation of trimers proceeded by adding poly(ethylene glycol) into vesicle suspension, just as it proceeded by decreasing the temperature. Next, vesicles were prepared with fluorescein isothiocyanate-labeled bacteriorhodopsin, photoemissive bacteriorhodopsin and L-alpha-dimyristoyl phosphatidylcholine. The excitation energy transfer between the two modified proteins was measured by fluorescence spectroscopy. In this case, however, when poly(ethylene glycol) was added into the suspension, the yield of the excitation energy transfer decreased. This result indicates that modified proteins aggregate separately in a segregated form in the vesicle membrane.

Peptide building blocks from bacteriorhodopsin: isolation and physicochemical characterization of two individual transmembrane segments

For protein engineering purposes, transmembrane segments of the structurally stable protein bacteriorhodopsin have been isolated and chemically characterized. Bacteriorhodopsin was cleaved by protease V8 from Staphylococcus aureus to two fragments, V-1 and V-2. The V-2 fragment was separated by gel filtration in organic solvents and purified by reversed-phase FPLC. The fragment has been identified as the C-terminal, partially truncated double-loop of bacteriorhodopsin, including amino acids Val-167-Glu-232/4. Cleavage of V-2 by cyanogen bromide at the single Met-209 yielded two subfragments, which were purified to homogeneity by FPLC procedures. The N-terminal subfragment psi, consisted of a single transmembrane segment (helix F) of bacteriorhodopsin (Val-167-Met(Hse)-209). The C-terminal amphipathic subfragment omega, (Val-210-Glu-232/4) was identified as part of the C-terminal seventh helix of bacteriorhodopsin. Secondary structures of V-2, psi, and omega were investigated in organic solvents and micellar solutions. Native helical structures were partially retained in the solvent systems mentioned.

The interaction of Triton X-100 with purple membranes. Detergent binding, spectral changes and membrane solubilization

The interaction of the non-ionic surfactant Triton X-100 with Halobacterium purple membranes has been examined at sublytic and lytic surfactant concentrations. These membranes present a number of important peculiarities in their behaviour towards the surfactant. Although solubilization is a very slow process, with a half-time of the order of hours, detergent binding appears to occur at the same fast rate as that found in other membranes. Lipids are solubilized more easily than proteins, so that hardly any protein is solubilized at surfactant concentrations at which about 75% of the lipid is in the form of detergent-mixed micelles; once started, protein solubilization takes place within a narrow range of surfactant concentrations. Retinal provides a built-in probe to monitor detergent-induced conformational changes by spectroscopy in the visible range. No spectral variation is detected at the prelytic stage, i.e. when detergent is incorporated into the membrane in monomeric form. Membrane disruption is accompanied by a blue shift in the absorption maximum, retinal isomerization (from all-trans to 13-cis), and a decrease in specific absorbance (bleaching). Increasing detergent concentrations after solubilization is completed do not produce further shifts in the spectral maximum, but the specific absorbance is progressively decreased. It is shown that Triton X-100 has a complex effect on the retinal chromophore, modifying its configuration and microenvironment (changes in maximum wavelength) and promoting hydrolysis of the retinal-bacteriorhopsin Schiff's base (bleaching).

Effect of partial delipidation of purple membrane on the photodynamics of bacteriorhodopsin

The effect of lipid-protein interaction on the photodynamics of bacteriorhodopsin (bR) was investigated by using partially delipidated purple membrane (pm). When pm was incubated with a mild detergent, Tween 20, the two major lipid components of pm, phospholipids and glycolipids, were released in different ways: the amount of phospholipids released was proportional to the logarithm of the incubation time; the release of glycolipids became noticeable after the release of approximately 2 phospholipids/bR, but soon leveled off at approximately 50% of the initial content. It was found that the thermal decay of the photocycle intermediate N560 was inhibited by the removal of less than 2 phospholipids per bR. This inhibition was partly explained by an increase in the local pH near the membrane surface. More significant changes in the bR photoreactions were observed when greater than 2 phospholipids/bR were removed: (1) the extent of light adaptation became much smaller, and this reduction correlated with the release of glycolipids; (2) N560 became difficult to detect; (3) the M412 intermediate, which is characterized by a pH-insensitive lifetime, was replaced by a long-lived M-like photoproduct with a pH-sensitive lifetime. The heavy delipidation apparently altered the mechanism by which the deprotonated Schiff base receives a proton. An important conformational change in the protein moiety is suggested to take place during the M412 state, this conformational change being inhibited in the rigid lipid environment.

The transverse location of the retinal chromophore in the purple membrane by diffusion-enhanced energy transfer

We have used fluorescence energy transfer in the rapid-diffusion limit (RDL) to estimate the trans-membrane depth of retinal in the purple membrane (PM). Chelates of Tb(III) are excellent energy donors for the retinal chromophore of PM, having a maximum Ro value for Förster energy transfer of approximately 62 A (assuming a donor quantum yield of 1). Energy transfer rates were measured from the time-resolved emission kinetics of the donor. The distance of closest approach between chelates and the chromophore was estimated by simulating RDL energy-transfer rate constants according to geometric models of either PM sheets or membrane vesicles. The apparent rate constant for RDL energy transfer between Tb(III)HED3A and retinal in PM sheets is 1.5(+/- 0.1) x 10(6) M-1 s-1, corresponding to a depth of approximately 10 +/- 2 A for the retinal chromophore. Cell envelope vesicles (CEVs) from Halobacterium halobium were studied by using RDL energy transfer to assess the proximity of retinal to either the extracellular or intracellular face of the PM. The estimated depth of retinal from the extravesicular face of the PM is 10 +/- 3 A, based on the RDL energy-transfer rate constant. Energy-transfer levels to retinal in the PM were estimated by an indirect method with energy donors trapped in the inner-aqueous space of CEVs. The rate constants derived for this arrangement are too low to be consistent with the shortest depth of retinal deduced for PM sheets. Thus, the intravesticular face of CEVs, corresponding to the cytoplasmic face of cells, is the more distant surface from the chromophore of bacteriorhodopsin.

Transient spectroscopy of bacterial rhodopsins with an optical multichannel analyzer. 1. Comparison of the photocycles of bacteriorhodopsin and halorhodopsin

We used a gated optical multichannel analyzer to measure transient flash-induced absorption changes in bacteriorhodopsin (BR) and halorhodopsin (HR) and developed criteria for calculating the absorption spectra of the photocycle intermediates and the kinetics of their rise and decay. The results for BR agree with data reported by a large number of other authors. The results for HR in the presence of chloride are consistent with earlier data and reveal an additional intermediate, not previously seen, in the submicrosecond time scale. Although an M412-like intermediate is not in the HR photocycle, a one-by-one comparison of the rest of the intermediates observed for BR and HR indicates a striking similarity between the photocycles of the two bacterial rhodopsins. This was previously not apparent, perhaps because the experimental approaches to the spectroscopy of the two pigments were different and the data were thus more fragmented.

Transient spectroscopy of bacterial rhodopsins with an optical multichannel analyzer. 2. Effects of anions on the halorhodopsin photocycle

We find that the photocycle of halorhodopsin (HR) in the presence of nitrate (but not chloride) consists of two parallel series of reactions. The first is essentially the same as that which occurs in the presence of chloride: HRhv----HRK----HRKL----HRL----HRO----HR. The second photocycle, however, which we describe as HRhv----HR'K----HRKO----HRO----HR, seems characteristic of what one would observe in the absence of chloride. Absorption spectra are calculated for all species but HRK and HR'K, which occur at shorter times (less than 60 ns) than we can resolve. At nitrate concentrations between 0.1 and 1 M, the proportion of HR which enters the first kind of photocycle increases in such a way as to suggest that nitrate can substitute for chloride, but much less effectively. At lower anion concentrations, the two photocycles are independent of one another, but at higher concentrations, they interact; i.e., the reaction HRKO----HRO----HRL can be observed. Thus, HRO must be common to the two photocycles. Kinetic fitting of the time dependence of HRL and HRO at different chloride concentrations provides evidence for the participation of chloride in the interconversion of HRL and HRO. The results are consistent with a model in which the photoreaction is influenced by the binding of an anion (either chloride or nitrate) to site II in HR: when an anion is bound, the HRK-initiated HRL-type photocycle is observed, but when the site is not occupied, the HR'K-initiated HRO-type photocycle is seen.

Synthesis and characterization of 6-O-(N-heptylcarbamoyl)-methyl-alpha-D-glucopyranoside, a new surfactant for membrane studies

A new surfactant, 6-O-(N-heptylcarbamoyl)-methyl-alpha-D-glucopyranoside (HECAMEG, molar mass 335.38 g), was synthesized by a simple and low cost procedure from methyl-alpha-D-glucopyranoside. This surfactant is characterized by a high solubility in water (even at 0 degree C), ultraviolet light transparency in the region useful for protein detection, and a high critical micellar concentration (CMC = 19.5 mM), permitting fast elimination by dialysis. Furthermore, the surfactant is colorimetrically titratable by the anthrone technique and its weak interference in protein titration by the Lowry et al. procedure and the bicinchoninic method is easy to overcome. Two membrane proteins (NADH oxidase and succinate dehydrogenase) and a soluble enzyme (lactoperoxidase) retained full activity in the presence of HECAMEG below or above its CMC. The partial inhibition of beta-lactamase (soluble form) by HECAMEG above the CMC was probably only apparent and due to an interference of the surfactant with the substrate rather than a direct effect on the enzyme. HECAMEG was capable of extracting up to 75% of bacteriorhodopsin from the purple membrane of Halobacterium halobium in a nondenatured form as indicated by the spectral properties of the protein. It also solubilized spiralin from the Spiroplasma melliferum membrane with a great selectivity and efficiency, without detectable loss of antigenic properties. These data show that HECAMEG is a very mild surfactant, useful for membrane protein studies.

An investigation of the electrochemical cycle of bacteriorhodopsin analogs with the modified ring

5,6-Epoxy-, 4-methoxy-, 4-hydroxy-, and 3,4-dehydrobacteriorhodopsins can generate delta psi coupled to a photochemical cycle with intermediate M. The kinetics of delta psi comprises three main electrogenic phases: the fast small negative, the microsecond, and the millisecond positive phases. The photocycle efficiency is lower in all the analogs. The photocycle is modified insignificantly only in 3,4-dehydrobacteriorhodopsin. In the other pigments the decay of the flash-induced bleaching in the chromophore main absorption band is slower than the decay of M or long-wave intermediates, especially in the 4-hydroxy analog. In the latter analog, such distinctions, according to delta pH measurements, are partly due to deceleration of the decay of the novel intermediate (P). In 5,6-epoxybacteriorhodopsin, at all wavelengths, the decay of the intermediates takes seconds upon M formation. According to our and literature data, no bacteriorhodopsin analogs are known to have a cycle which preserves the M-intermediate and does not transport a proton.

Topography of surface-exposed amino acids in the membrane protein bacteriorhodopsin determined by proteolysis and micro-sequencing

The topography of membrane-surface-exposed amino acids in the light-driven proton pump bacteriorhodopsin (BR) was studied. By limited proteolysis of purple membrane with papain or proteinase K, domains were cleaved, separated by SDS-PAGE, and electroblotted onto polyvinylidene difluoride (PVDF) membranes. Fragments transferred were sequenced in a gas-phase sequencer. Papain cleavage sites at Gly-65, Gly-72, and Gly-231, previously only deduced from the apparent molecular weight of the digestion fragments, could be confirmed by N-terminal micro-sequencing. By proteinase K, cleavage occurred at Gln-3, Phe-71, Gly-72, Tyr-131, Tyr-133, and Ser-226, i.e., in regions previously suggested to be surface-exposed. Additionally, proteinase-K cleavage sites at Thr-121 and Leu-127 were identified, which are sites predicted to be in the alpha-helical membrane-spanning segment D. Our results, especially that the amino acids Gly-122 to Tyr-133 are protruding into the aqueous environment, place new constraints on the amino-acid folding of BR across the purple membrane. The validity of theoretical prediction methods of the secondary structure and polypeptide folding for membrane proteins is challenged. The results on BR show that micro-sequencing of peptides separated by SDS-PAGE and blotted to PVDF can be successfully applied to the study of membrane proteins.

Structure and thermal stability of monomeric bacteriorhodopsin in mixed phospholipid/detergent micelles

Thermal unfolding experiments on bacteriorhodopsin in mixed phospholipid/detergent micelles were performed. Bacteriorhodopsin was extracted from the purple membrane in a denatured state and then renatured in the micellar system. The purpose of this study was to compare the changes, if any, in the structure and stability of a membrane protein that has folded in a nonnative environment with results obtained on the native system, i.e., the purple membrane. The purple membrane crystalline lattice is an added factor that may influence the structural stability of bacteriorhodopsin. Micelles containing bacteriorhodopsin are uniformly sized disks 105 +/- 13 A in diameter (by electron microscopy) and have an estimated molecular mass of 210 kDa (by gel filtration HPLC). The near-UV CD spectra (which is indicative of tertiary structure) for micellar bacteriorhodopsin and the purple membrane are very similar. In the visible CD region of retinal absorption, the double band seen in the spectrum of the purple membrane is replaced with a broad positive band for micellar bacteriorhodopsin, indicating that in micelles, bacteriorhodopsin is monomeric. The plot of denaturational temperature vs. pH for micellar bacteriorhodopsin is displaced downward on the temperature axis, illustrating the lower thermal stability of micellar bacteriorhodopsin when compared to the purple membrane at the same pH. Even though micellar bacteriorhodopsin is less stable, similar changes in response to pH and temperature are seen in the visible absorption spectra of micellar bacteriorhodopsin and the purple membrane. This demonstrates that changes in the protonation state or temperature have a similar affect on the local environment of the chromophore and the protein conformation.(ABSTRACT TRUNCATED AT 250 WORDS)

Tritium thermal activation study of bacteriorhodopsin topography

The action of thermally activated tritium on the purple membrane and delipidated bacteriorhodopsin fragments has been studied, tritium incorporation into specified amino acid residues being quantified by Edman degradation. The membrane environment was found to affect the accessibility of amino acid residues for tritium. Bacteriorhodopsin fragments 14-31, 45-63, 81-89, 171-179, and 210-225 were localized to the membrane interior while fragments 4-12, 32-44, 64-65, 73-80, and 156-170 should lie outside or close to membrane surface. It was demonstrated that the peptide fragments joining transmembrane rods are not fully exposed to the solution.

[The similarity of the primary structure and homology of rhodopsin, beta-adrenoreceptor and muscarinic cholinoceptor]

Computer analysis has been made of the primary structure of 6 different types of receptor proteins: rhodopsin, adrenoreceptor, muscarinic acetylcholine receptor, insulin receptor, nicotinic cholinoreceptor, and bacteriorhodopsin. The aim of the present investigation was to elucidate, at least partially, to what extent insignificant similarity in the primary structure of rhodopsin, muscarinic cholinoreceptor and adrenoreceptor is due to divergent, but not convergent, evolution. Nicotinic cholinoreceptor, bacteriorhodopsin and insulin receptor were chosen for comparison with rhodopsin, adrenoreceptor and muscarinic cholinoreceptor since each of these proteins exhibits this or that structural or functional property which is common for rhodopsin, adrenoreceptor or muscarinic cholinoreceptor; on the other hand, nicotinic cholinoreceptor, bacteriorhodopsin and insulin receptor differ from other receptor proteins by their molecular mechanisms. Comparison of the primary structure of rhodopsin, adrenoreceptor and muscarinic cholinoreceptor on the one hand, and insulin receptor, nicotinic cholinoreceptor and bacteriorhodopsin on the other indicates that only the former exhibit similar primary structure, whereas insulin receptor, nicotinic cholinoreceptor and bacteriorhodopsin show no similarity neither in their primary structure, nor in the primary structure of rhodopsin and other receptor proteins which are similar to the latter with respect to their mode of action. The data obtained indicate that similarity in the primary structure between rhodopsin, muscarinic cholinoreceptor and adrenoreceptor is a consequence of divergent, not convergent, evolution; in other words, these receptor proteins are homologous.

Methoxyretinals in bacteriorhodopsin. Absorption maxima, cis-trans isomerization and retinal protein interaction

Analogue bacteriorhodopsins (BRs) were reconstituted from bacterioopsin and 9-, 11-, or 13-methoxyretinals or their demethyl derivatives, respectively. In organic solvents the retinals occur as cis isomers of the respective double bonds carrying the methoxy group. 9-Methoxyretinal, present as the 9-cis isomer, does not form an analogue BR with bacterioopsin in the dark. Upon illumination, a BR is produced with an absorbance maximum at 560 nm. This compound is thermally unstable, and converts back into the 9-cis-containing complex (lambda max = 410 nm) in the dark. Removal of the 13-methyl group from this compound (= 9-methoxy 13-demethyl retinal) does not change the 9-cis configuration of the free retinal, but allows the reconstitution of a thermally stable chromoprotein absorbing around 500 nm with a proton translocation rate of about 10% of the BR value, comparable to the 13-demethyl BR value [Gärtner, W., Towner, P., Hopf, H. & Oesterhelt, D. (1983) Biochemistry 22, 2637-2644]. 11-Methoxy BRs (13-demethyl and 9,13-didemethyl) absorb around 530 nm and are inactive. 13-Methoxy retinal (13-cis isomer) reconstitutes a chromoprotein with an absorbance maximum at 515 nm, which can be photoconverted to a thermostable 460-nm-absorbing complex. For the 515-nm-absorbing species of 13-methoxy BR a light-induced proton translocation was not detected in measurements with cell vesicles (detection of pH changes in the vesicle preparation). Only by photocurrent measurements in a bilayer experiment could a very diminished photocurrent be detected, about 1-2% of BR, [Fendler et al. (1987) Biochim. Biophys. Acta 893, 60-68]. The reconstitution rate of 13-methoxy BR from 13-methoxy retinal and bacterioopsin is slower by a factor of 40 compared to 13-ethyl BR, although both substituents are of similar size. The position 13 of retinal was found to be most sensitive for regulation of the absorption maximum and the formation and stability of the all-trans isomer, which is the active form for light-induced proton translocation. The results suggest that an electronic interaction with a charged residue of the binding site exists around position 13 of retinal, which is disturbed when a methoxy group replaces the methyl or ethyl group at that position. This electronic interaction is essential for maintaining the active all-trans configuration of retinal.

The orientation of halorhodopsin in the cell membrane of halobacteria

The orientation of the light-driven chloride pump, halorhodopsin, in the membrane was determined using antibodies directed against a synthetic peptide which represents the C-terminal segment of the protein. Antibodies against this decapeptide did not bind to right-side-out cell vesicles. Partial inversion by sonication or lysis under low salt conditions exposed this COOH-terminal antigenic site. Antibody binding was removed by preincubation with the decapeptide. The COOH terminus of the molecule is therefore located on the cytoplasmic surface of the membrane.

2-Hydroxy-5-nitrobenzyl bromide as a specific reagent for tryptophan residues in membrane proteins: bacteriorhodopsin as an example

The use of 2-hydroxy-5-nitrobenzyl bromide for the modification of tryptophan residues in integral membrane proteins is exemplified by its application to bacteriorhodopsin from Halobacterium halobium. Complete elimination of the unreacted reagent requires delipidation of the sample with detergents and posterior chromatography. This method also allows separation of the modified from the unmodified bacteriorhodopsin molecules. Modified molecules have lost the retinal, and are thus bleached, whereas the unmodified molecules appear to retain all the characteristics of solubilized native bacteriorhodopsin.

Images of purple membrane at 2.8 A resolution obtained by cryo-electron microscopy

Improvements in technique have produced electron micrographs of purple membrane that provide, after computer analysis, reproducibly measurable diffraction peaks extending to 2.8 A (1 A = 0.1 nm). The improvements include better specimen preparation, a more stable cryo-electron microscope with better alignment and the addition of an image-processing step, which gives weights to local areas of the image according to the local strength of the periodic component of the image. These improvements have enabled the calculation of a directly phased projection map at 2.8 A resolution.