Structure of bacteriorhodopsin investigated using Fourier transform infrared spectroscopy and proteolytic digestion

Bacteriorhodopsin-ZnO hybrid as a potential sensing element for low-temperature detection of ethanol vapour

Zinc oxide (ZnO) and bacteriorhodopsin (bR) hybrid nanostructures were fabricated by immobilizing bR on ZnO thin films and ZnO nanorods. The morphological and spectroscopic analysis of the hybrid structures confirmed the ZnO thin film/nanorod growth and functional properties of bR. The photoactivity results of the bR protein further corroborated the sustainability of its charge transport property and biological activity. When exposed to ethanol vapour (reducing gas) at low temperature (70 °C), the fabricated sensing elements showed a significant increase in resistivity, as opposed to the conventional n-type behaviour of bare ZnO nanostructures. This work opens up avenues towards the fabrication of low temperature, photoactivated, nanomaterial-biomolecule hybrid gas sensors.

Quality assessment of recombinant proteins by infrared spectroscopy. Characterisation of a protein aggregation related band of the Ca2+-ATPase

FTIR spectroscopy detects aggregates of recombinantly produced protein and can therefore be used for quality control.

Surface chemical functionalization of single walled carbon nanotubes with a bacteriorhodopsin mutant

In this work, single walled carbon nanotubes (SWNTs) have been chemically functionalized at their walls with a membrane protein, namely the mutated bacteriorhodopsin D96N, integrated in its native archaeal lipid membrane. The modification of the SWNT walls with the mutant has been carried out in different buffer solutions, at pH 5, 7.5 and 9, to investigate the anchoring process, the typical chemical and physical properties of the component materials being dependent on the pH. The SWNTs modified by interactions with bacteriorhodopsin membrane patches have been characterized by UV-vis steady state, Raman and attenuated total reflection Fourier transform infrared spectroscopy and by atomic force and transmission electron microscopy. The investigation shows that the membrane protein patches wrap the carbon walls by tight chemical interactions undergoing a conformational change; such chemical interactions increase the mechanical strength of the SWNTs and promote charge transfers which p-dope the nano-objects. The functionalization, as well as the SWNT doping, is favoured in acid and basic buffer conditions; such buffers make the nanotube walls more reactive, thus catalysing the anchoring of the membrane protein. The direct electron communication among the materials can be exploited for effectively interfacing the transport properties of carbon nanotubes with both molecular recognition capability and photoactivity of the cell membrane for sensing and photoconversion applications upon integration of the achieved hybrid materials in sensors or photovoltaic devices.

Theoretical analysis of ultraviolet spectroscopic studies on the feathering of cream in coffee

Ultraviolet spectra of solutions of instant and filter coffees have been analysed as a linear combination of component Gaussian bands. We show that the ratio, R′, of two of these bands, one at 329 nm due almost entirely to chlorogenic acid, and the other at 272 nm due to a coffee component not appearing in the chlorogenic acid spectrum, is analogous to the ratio R (Hamboyan et al. 1989). The use of R which is easier to measure than R′ has therefore been justified on physical grounds, based on the existence of component spectral bands. Filter coffees appeared to exhibit behaviour similar to that of instant coffees.

The bacteriorhodopsin carboxyl-terminus contributes to proton recruitment and protein stability

We examined functional and structural roles for the bacteriorhodopsin (bR) carboxyl-terminus. The extramembranous and intracellular carboxyl-terminus was deleted by insertion of premature translation stop codons. Deletion of the carboxyl-terminus had no effect on purple membrane (PM) lattice dimensions, sheet size, or the electrogenic environment of the ground-state chromophore. Removal of the distal half of the carboxyl-terminus had no effect on light-activated proton pumping, however, truncation of the entire carboxyl-terminus accelerated the rates of M-state decay and proton uptake approximately 3.7-fold and severely distorted the kinetics of proton uptake. Differential scanning calorimetry (DSC) and SDS denaturation demonstrated that removal of the carboxyl-terminus decreased protein stability. The DSC melting temperature was lowered by 6 degrees C and the calorimetric enthalpy reduced by 50% following removal of the carboxyl-terminus. Over the time range of milliseconds to hours at least 3 phases were required to describe the SDS denaturation kinetics for each bR construction. The fastest phases were indistinguishable for all bR's, and reflected PM solubilization. At pH 7.4, 20 degrees C, and in 0.3% SDS (w/v) the half-times of bR denaturation were 19.2 min for the wild-type, 12.0 min for the half-truncation and 3.6 min for the full-truncation. Taken together the results of this study suggest that the bR ground state exhibits two "domains" of stability: (1) a core chromophore binding pocket domain that is insensitive to carboxyl-terminal interactions and (2) the surrounding helical bundle whose contributions to protein stability and proton pumping are influenced by long-range interactions with the extramembranous carboxyl-terminus.

Nanoparticle-assisted micropatterning of active proteins on solid substrate

Micropatterning of proteins on silica substrate was achieved using a new method. Proteins were first immobilized onto silica nanoparticles which were then dispensed into arrayed microwells on silicon. Atomic force microscopy (AFM), fluorescence microscopy and Fourier transform infrared (FTIR) spectroscopy were used to characterize the samples. The results showed that, compared to a planar surface, curved surfaces of nanoparticles provide more space for attaching proteins and thus increases the intensity of fluorescence signal. Furthermore, after attaching to silica nanoparticles, bovine serum albumin (BSA) maintains its major structure and the cytokine IFN-gamma maintains its ability to bind to its antibody. Use of this method can be extended to micropatterning of other biomolecules, such as DNA and enzymes.

Bovine serum albumin observed by infrared spectrometry. I. Methodology, structural investigation, and water uptake

The results of preliminary infrared (IR) spectrometry experiments on bovine serum albumin (BSA) films are presented. An analysis of spectral variations due to raising the temperature and deuteration of N--H groups leads to the assignment of most IR bands of BSA. From this analysis we furthermore deduce that at 115 degrees C only hydrogen bonds established by N&bond;H groups on the still present H(2)O molecules, which are so strongly bound to the protein that they do not evaporate, are weakened, some of which are broken. These N--H...OH(2) groups represent some 5% of all N--H groups in the dried protein. Spectral changes due to hydration by water vapor are also analyzed and a precise method to measure the water-vapor pressure of the atmosphere surrounding the BSA film, or equivalently the relative humidity, is described. Various procedures to measure the number of H(2)O molecules embedded in BSA are then presented and evaluated. One of them is selected as the best one for proteins, because it matches previous measurements based on gravimetric methods. This procedure is subsequently used in a study that is devoted to the determination of the various hydrogen-bond configurations, or interaction configurations, which are adopted by H(2)O molecules during the various steps of hydration of BSA. This first analysis of hydration spectra allows the completion of the assignment of IR bands. The various spectral components of the amide I band, which are interchanged during the hydration process, cannot be assigned to various secondary structures, as is usually proposed. It suggests that this usual assignment should be used with care, especially by taking into account the state of hydration, when one wishes to obtain structural information from it.

Thermal stability and reversibility of secondary conformation of alpha-crystallin membrane during repeated heating processes

Reflectance FT-IR/DSC microspectroscopy was first used to study the structural conformation of alpha-crystallin membranes in the heating-cooling-reheating cycle. The thermotropic transition and the changes in secondary structure of alpha-crystallin membrane during heating and reheating processes were investigated. A thermal transition ranging between 50 and 70 degrees C with a midpoint at 60 degrees C for the alpha-crystallin membrane was easily obtained from the three-dimensional plots of the reflectance FT-IR spectra as a function of temperature. The secondary structural components of the alpha-crystallin membrane were modified step-by-step with the increase of temperature from 25 to 120 degrees C, but restored to original values after cooling to 25 degrees C. During the heating process, the compositions of the alpha-helix, random coil and beta-sheet structure decreased with temperature, but the content of the beta-turn structure increased, however, all of them were restored after cooling. The absence of significant alteration in the secondary structures for the alpha-crystallin membrane before and after the first-heating process strongly suggests the high thermal stability and reversibility of alpha-crystallin. Interestingly, the thermal behavior of the first-heated alpha-crystallin membrane during the reheating process exhibited a unique thermal behavior with two transitional temperatures at 35-50 and 55-70 degrees C. The reflectance FT-IR/DSC microscopic data indicated that alpha-crystallin in the membrane state had higher thermal stability and reversibility.

Structure of yeast plasma membrane H(+)-ATPase: comparison of activated and basal-level enzyme forms

Plasma membrane H(+)-ATPase of the yeast Saccharomyces cerevisiae was isolated and purified in its two forms, the activated A-ATPase from glucose-metabolising cells, and the basal-level B-ATPase from cells with endogenous metabolism only. Structure of the two enzyme forms and the effects of beta, gamma-imidoadenosine 5'-triphosphate (AMP-PNP) and of diethylstilbestrol (DES) thereon were analysed by FT-IR spectroscopy. IR spectra revealed the presence of two populations of alpha-helices with different exposure to the solvent in both the A-ATPase and B-ATPase. AMP-PNP did not affect the secondary structure of A-ATPase while DES affected the ratio of the two alpha-helix populations. Thermal denaturation experiments suggested a more stable structure in the B-form than in the A-form. AMP-PNP stabilised the A-ATPase structure while DES destabilised both enzyme forms. IR spectra showed that 60% of the amide hydrogens were exchanged for deuterium in both forms at 20 degrees C. The remaining 40% were exchanged at higher temperatures. The maximum amount of H/D exchange was observed at 50-55 degrees C for both enzyme forms, while in the presence of DES it was observed at lower temperatures. The data do not contradict the possibility that the activation of H(+)-ATPase is due to the C-terminus of the enzyme dissociating from the ATP-binding site which is covered by it in the less active form.

Temperature-dependent conformational change of bacteriorhodopsin as studied by solid-state 13C NMR

Cross-polarization and dipolar-decoupled magic-angle spinning 13C-NMR spectra of [3-13C]Ala-labelled bacteriorhodopsin were obtained for hydrated purple membrane in the temperatures range 23 degrees C to -110 degrees C. Well-resolved 13C-NMR signals were observed either at ambient temperature or at -20 degrees C but were broadened considerably at lower temperature below -40 degrees C. This situation was interpreted in terms of the presence of exchange processes with a rate constant of 10(2) s-1 at ambient temperature among several conformations slightly different from each other. We found that such an exchange process was strongly influenced by the manner of organization of the lipid bilayers depending upon the presence or absence of cations responsible for electric shielding of negative charge at the polar head groups. The manner of organization of the lipid bilayers was conveniently characterized by a characteristic temperature at which the methyl peaks of fatty acyl groups of lipids in the purple membrane were suppressed due to interference of motional frequency with the decoupling frequency (10-100 kHz) for preparations containing 10 mM NaCl or CaCl2. No such spectral change in the absence of these cations was noted even if a preparation was cooled to -110 degrees C. The secondary structures of [3-13C]Ala-labelled bacteriorhodopsin was not always identical at temperatures between ambient and low temperatures, since the 13C chemical shifts and relative peak intensities for purple membrane preparations containing these salts changed with temperature in the range -110 degrees C to 23 degrees C. In particular, we found that some residues involving Ala residues at the alpha II-helix and loop region were converted at temperatures below -60 degrees C to a conformation involving alpha 1-helix. In other words, some portion of the alpha-helical conformation of bacteriorhodopsin proposed from results obtained by cryo-electron microscopy, at very low temperatures, is not always retained at ambient temperature.

Fourier transform infrared spectroscopy investigations of protein structure

Infrared spectroscopy can provide insight into protein structure. This technique is sensitive to the backbone amide arrangement of peptide and protein molecules. In many cases, complementary as well as more expansive information is obtained as opposed to information obtained by other methods that examine the molecule's environmental surroundings, require molecular probes, or perhaps cannot investigate the molecule in its native environment. The foundation for spectroscopic differences between the various secondary structures arises not only from geometrical differences and hydrogen bond variations but also transition dipole coupling between neighboring oscillators. Theoretical predictions of protein spectra have been made using normal mode analysis and combined with experimental data. At present the amide I band has provided the most insight into secondary structure. Even more convincing results are obtained when both H2O and D2O are used as solvents. Recent advances in computerized technology and mathematical techniques have expanded the potential contributions of infrared spectroscopy in the area of protein structural determination. However, the limitations of resolution enhancement and curve-fitting techniques must be taken into consideration. The parameters must be carefully and optimally chosen and evaluated on a case-by-case basis. The subjectivity of these techniques makes a thorough understanding of the algorithms necessary, especially those commercially available. Infrared spectroscopy continues to provide insight into protein and peptide structures under biologically relevant conditions that enable the structure-function relationships for such molecules to be better understood.

13C NMR study on conformation and dynamics of the transmembrane alpha-helices, loops, and C-terminus of [3-13C]Ala-labeled bacteriorhodopsin

We have recorded 13C CP-MAS and DD-MAS NMR spectra of untreated and deionized [3-13C]-Ala-labeled bacteriorhodopsin (bR) and those cleaved with carboxypeptidase A and papain to gain insight into the conformation and dynamics of the transmembrane alpha-helices, loops, and C-terminus. It turned out that the C-terminus does not contribute to the 13C CP-MAS NMR spectra of [3-13C]Ala-bR recorded at ambient temperature owing to its rapid reorientational motions, since the relative peak intensities were unchanged in spite of the enzymatic cleavages. Therefore, the 13C CP-MAS NMR peaks of bR should be ascribed both to the transmembrane alpha-helices and loops. We further distinguished the peaks of the alpha II-helix form at 16.3 ppm (60%) from those of the alpha I-helix form at 14.9 ppm (20%) by deconvolution of the respective peaks of the hydrated [3-13C]Ala-bR, as referred to the 13C chemical shift of polyalanine in hexafluoroisopropyl alcohol. The remaining CP-MAS NMR peak of [3-13C]Ala-bR at 17.2 ppm was ascribed to the loops (20%) taking a variety of turn structures. In contrast, the 13C NMR signals from the C-terminal residues were significantly enhanced by recording the dipolar-decoupled (DD)-MAS NMR spectra. Conformational features of the two different portions of the C-terminus, residues 245-248 and 231-244, were revealed by the conformation-dependent 13C signals of bR successively cleaved by carboxypeptidase A and papain, respectively. The terminal end, residues 245-248, containing two Ala residues is virtually disordered and undergoing rapid motions.(ABSTRACT TRUNCATED AT 250 WORDS)

Fourier transform infrared study of the rod outer segment disk and plasma membranes of vertebrate retina

Phospholipid composition and structure of disk and plasma membranes purified from bovine rod outer segments (ROS) are examined using Fourier transform infrared spectroscopy. Vibrational data indicate that both disk and plasma membranes lack sphingophospholipids, in contrast to the lens membranes. The hydrocarbon chains of the disk lipids are unsaturated by a factor of 5 over the acyl chains of the plasma lipids. The plasma lipids with 3-fold higher cholesterol and 5-fold higher saturation melt at a higher temperature (26 degrees C) than the disk lipids which melt at 16 degrees C. The transition temperature decreases by more than 20 degrees C in going from disk lipids to disk membrane, indicating a large drop in the enthalpy of the ROS membrane-matrix, presumably due to enhanced rhodopsin-lipid interaction. The lipid composition predisposes the disk and plasma membranes to be fluid and structurally disordered (about 84%) around physiological temperature. The fluid phospholipid environment of the disk membrane (i.e., just a few degrees above subzero temperatures) is considered to be vital for the ROS photoreceptor function. The amide I band profile of rhodopsin indicates an extensive alpha-helical (53%) peptide chain, with little beta-sheet (21%) and beta-turns (18%) in ROS membranes. This structure and/or conformation is conserved between 0-60 degrees C even though disk and plasma lipids undergo a phase change. The H-D exchange data indicate that as much as 84% of the peptide residues of ROS membranes in partially bleached retinas is accessible to D2O solvent after 1 h.(ABSTRACT TRUNCATED AT 250 WORDS)

Structural investigation of transglutaminase by Fourier transform infrared spectroscopy

The secondary structure of transglutaminase was investigated by Fourier transform infrared spectroscopy. Spectra of the protein in both H2O and 2H2O were analyzed by deconvolution and second derivative methods in order to observe the overlapping components of the amide-I band. The quantitative analysis of the amide-I-band components was made by a curve-fitting procedure. The protein was studied in the absence and in the presence of 1 mM GTP, 1 mM Ca2+ and 1 mM GTP/1 mM Ca2+. The quantitative analysis of infrared spectra revealed that no remarkable changes in the secondary structure of the enzyme are induced by GTP, Ca2+ or Ca2+/GTP. Major changes, however were observed in the thermal-denaturation behavior of the protein. The protein showed maximum of denaturation at temperatures over 50-55 degrees C in the absence or in the presence of 1 mM Ca2+ and over 55-60 degrees C in the presence of 1 mM GTP or 1 mM Ca2+/1 mM GTP. The results obtained indicate that GTP induces a stabilization of the tertiary structure of the enzyme, even in the presence of 1 mM Ca2+. The thermal denaturation patterns of the protein suggest the occurrence of Ca(2+)-dependent aggregation.

The role of retinal in the thermal stability of the purple membrane

Differential scanning calorimetry demonstrates that the bleached form of the purple membrane does not possess any measurable thermal transition in water, up to 105 degrees C, whereas in 0.1 M phosphate pH 7.5 it shows a transition at about 82 degrees C, with an enthalpy of 110 kJ/mol. In the latter medium, the native membrane shows the main transition at 97 degrees C, with an enthalpy of 390 kJ/mol. The reduced form of the purple membrane shows two small transitions in water, as well as in 0.1 M phosphate, which do not seem to be related to the main thermal transition of the native membrane. Fourier-transform infrared spectra in D2O show that the two modified samples, as well as the native one, undergo similar secondary structural changes upon thermal denaturation. These changes appear to extend through a wide temperature range for both modified forms, particularly for the bleached one. The results suggest that the main thermal transition in the purple membrane is due to a cooperative conformational change involving the disruption of the network of electrostatic and hydrogen-bonding interactions which originate from the protonated Schiff base. In the two modified membranes, these conformational changes appear to proceed smoothly through a rather low or non-cooperative process. The thermal behaviour of the bleached membrane in water resembles that of the molten globule state described for several globular proteins.

Structural and functional relationships in 5'-nucleotidase from bull seminal plasma. A Fourier transform infrared study

Fourier transform infrared spectroscopy (FTIR) was used to investigate the secondary structure of 5'-nucleotidase from bull seminal plasma (BSP). Spectra of protein in both D2O and H2O were analyzed by deconvolution and second derivative methods in order to observe the overlapping components of the amide I band. The protein, which is made up of two apparently identical subunits and which contains two zinc atoms, was studied in its native form, in the presence of dithiotreitol (DTT) and after removal of the two zinc atoms by means of nitrilotriacetic acid (NTA). Deconvolved and second derivative spectra of amide I band showed that the native protein contains mostly beta-sheet structure with a minor content of alpha-helix. The quantitative analysis of the amide I components was performed by a curve-fitting procedure which revealed 54% beta-sheet, 18% alpha-helix, 22% beta-turns and 6% unordered structure. The second derivative and deconvolved spectra of amide I band showed that no remarkable changes in the secondary structure of 5'-nucleotidase were induced by either DTT or NTA. These results were confirmed by the curve-fitting analysis where little or no changes occurred in the relative content of amide I components when the protein was treated with DTT or with NTA. Major changes, however, were observed in the thermal denaturation behavior of the protein. The native protein showed denaturation at temperatures between 70 and 75 degrees C, while the maximum of denaturation was observed between 65 and 70 degrees C and between 55 and 60 degrees C in the presence of NTA and DTT, respectively. The results obtained indicate that the two separate subunits of the protein have essentially the same secondary structure as that of the native enzyme.

Determination of protein secondary structure using factor analysis of infrared spectra

A method is presented for determining the secondary structural composition of a protein in aqueous solution from its infrared spectrum. A factor analysis approach is used to analyze the infrared spectra of 18 proteins whose crystal structures are known from X-ray studies. Factor analysis followed by multiple linear regression identifies those eigenspectra that correlate with the variation in properties described by the calibration set. The properties of interest in this study are % alpha-helix, % beta-sheet, and % turns. In the analysis of an unknown, the factor loadings required to reproduce its spectrum are substituted in the regression equation for each property to predict its secondary structural composition. The accuracy of the method was determined by removing each standard, in turn, from the calibration set and using a calibration set generated from the remainder to predict its composition. By this method we obtain standard errors of prediction of 3.9% for alpha-helix, 8.3% for beta-sheet, and 6.6% for turns. The method may also be applied to the spectra of proteins in 2H2O. The method has important advantages over those currently in use for the quantitative analysis of the infrared spectra of proteins. Manipulation of the spectrum is kept to a minimum, no curve-fitting is necessary, and the several amide I band components need not be assigned.

Fourier-transform infrared studies on cation binding to native and modified purple membranes

Fourier-transform infrared spectroscopy has been used to examine the structural differences in the protein moiety between the native purple and the deionized blue membranes, both at pH 5.0. The spectra demonstrate that deionization of purple membrane decreases the content of the distorted alpha II-helices in favor of the more common alpha I-helices. Changes in the signals from beta-turns are also observed. The changes corresponding to the carboxyl groups suggest that deionization leads to a decrease in the strength of the hydrogen bonds involving carboxyl groups. Most of these effects are reversed progressively upon binding of one to five Mn2+ per bacteriorhodopsin to the deionized membrane. Binding of Hg2+ to the deionized membranes does not restore the purple color but induces global changes similar to, but less intense than, those brought about by Mn2+ binding. However, the effects attributed to the carboxyl groups are opposite to those found for Mn2+. Schiff base reduction or bleaching induces a decrease of the content of the alpha II-helix in favor of the alpha I-helix and a decrease in the strength of hydrogen bonds to carboxyl groups. Deionization of these modified membranes leads to a further loss in the alpha II content. These results indicate a conformational rearrangement of the protein structure between the native purple membrane and the deionized membrane, which could arise from surface potential changes elicited by bound cations. The changes observed in the carboxyl groups suggest that some of them are located structurally close to the retinal environment and may be involved in cation binding.

Fourier transform infrared spectroscopic investigation of rhodopsin structure and its comparison with bacteriorhodopsin

FT-IR spectroscopy has been used to investigate the conformation of rhodopsin in bovine rod outer segment membranes, dispersed in aqueous suspension in both 2H2O and H2O. Detailed analysis of the amide I band was made, using second-derivative and deconvolution procedures. The frequency of the major amide I component is consistent with the presence of predominantly alpha-helices within the rhodopsin structure. A spectroscopic change occurs at acidic pH with the membranes in both 2H2O and H2O. The results for the membranes dispersed in H2O at pH 7 were used to estimate a value of 0.67 for w (amide II/amide I intensity ratio in H2O). This value of w gives an estimate of the unexchanged amide protons, in rhodopsin, of 51%. The extent of amide proton exchange at acidic p2H (p2H 5 and 2), in 2H2O was also determined. The conformation of rhodopsin in its unbleached and bleached states was investigated but no significant difference in the secondary structure was observed. A comparison, after second-derivative and deconvolution analysis, of the spectra of rhodopsin with that of bacteriorhodopsin shows that both proteins exhibit a similar number of amide I components. However, with bacteriorhodopsin the amide I band occurs at a higher frequency. Bacteriorhodopsin under similar conditions, in 2H2O, has 20% more unexchanged amide protons than does rhodopsin.

Effect of lipid-protein interaction on the color of bacteriorhodopsin

Detergent solubilization and subsequent delipidation of bacteriorhodopsin (bR) results in the formation of a new species absorbing maximally at 480 nm (bR480). Upon lowering the pH, its absorption shifts to 540 nm (bR540). The pK of this equilibrium is 2.6, with the higher pH favoring bR480 (Baribeau, J. and Boucher, F. (1987) Biochim. Biophysica Acta, 890, 275-278). Resonance Raman spectroscopy shows that bR480, like the native bR, contains a protonated Schiff base (PSB) linkage between the chromophore and the protein. However, the Schiff base vibrational frequency in bR480, and its shift upon deuteration, are quite different from these in the native bR, suggesting changes in the Schiff base environment upon delipidation. Infrared absorption and circular-dichroism (CD) spectral studies do not show any net change in the protein secondary structure upon formation of bR480. It is shown that deprotonation of the Schiff base is not the only mechanism of producing hypsochromic shift in the absorption maximum of bR-derived pigments, subtle changes in the protein tertiary structure, affecting the Schiff base environment of the chromophore, may play an equally significant role in the color regulation of bR-derived pigments.

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.

Peak locater for multicomponent spectra

A sliding pivot technique capable of locating component peak maxima of multicomponent spectra is presented. The locations of peak maxima obtained in this way are shown to be the same as those of the minima in the second derivative. A major advantage over the second-derivative test is simply that derivative spectra are not needed. The sliding pivot technique requires only the original spectrum to locate the component peak maxima and consequently reduces the noise enhancement factor. The deconvoluted Fourier transform infrared spectrum of purple membrane is analyzed and compared to a Gaussian analysis and a second-derivative analysis. The sliding pivot technique identifies a band missed by second-derivative analysis.

Fourier transform infrared spectra of the polypeptide alamethicin and a possible structural similarity with bacteriorhodopsin

FTIR spectra of alamethicin have been obtained in KBr disk, methanol and in aqueous lipid dispersion (above and below the lipid phase transition). The solution structure of this polypeptide in methanol has been shown by recent studies (Esposito et al. (1987) Biochemistry 26, 1043-1050) using NMR spectroscopy to be predominantly alpha-helical in content. It may therefore be regarded as a model structure for the interpretation of the spectra of certain biomembrane proteins. A comparison of the spectra with that obtained with bacteriorhodopsin shows spectral similarities, e.g. the presence of a high-frequency amide I maximum at 1661-1663 cm-1 and shoulders near 1640 cm-1 and 1620 cm-1.

Circular dichroism studies of distorted alpha-helices, twisted beta-sheets, and beta turns

Theoretical models for calculating the circular dichroism (CD) of biopolymers have been constructed which allow the evaluation of the effects of geometric distortions within regular secondary structures. Outward tilting of the carbonyl group within alpha-helical structures yields calculated CD spectra with diminished intensity and a red-shifted maximum near 190 nm. The alpha II-helix provides an extreme example of this type of alpha-helix distortion. It is predicted that a mixture of alpha and alpha II structures in bacteriorhodopsin can account for its anomalous CD spectrum. The minimum length of alpha-helix required to produce an alpha-helix-like CD spectrum is calculated to be two to three turns (seven to eleven residues), while helices greater than 30 residues should provide adequate models of an infinite helix. Twisting of beta-sheets is predicted to lead to an increase in CD intensity and significant shifts in band position. Calculated CD spectra for beta-turn models are accurate for types II and II', but appear to be inadequate for type I turns.