Dramatic in situ conformational dynamics of the transmembrane protein bacteriorhodopsin

Resolving Strategic Dilemmas in Ambidextrous Organizations: An Integrated Second-Order Factor Model Perspective

Drawing on relevant literature, this study investigates the process of realizing innovation ambidexterity (IA) by proposing a theoretical model and adopting a specifically integrated mechanism with the aim to resolve strategic dilemmas in ambidextrous organizations (AOs). We analyzed a sample of 136 cross-sectional surveys collected from business managers of 132 medium- and high-tech firms in China by employing a structural equation model combined with moderation analysis to test our hypotheses. Our findings indicate that the second-order theoretical model fits the data well and AO, represented by a higher-order construct, positively affects IA. Instead of structural ambidexterity, balanced contextual ambidexterity and radical performance management can be effectively applied as the factors of the second-order construct; the design comprising balanced contextual ambidexterity and performance management is thus helpful in resolving strategic dilemmas. Our findings demonstrate that Chinese firms, as technology latecomers, are more inclined to conduct near-radical innovation. The risk of exploration crowding out exploitation efforts exists in Chinese high-tech firms. Furthermore, we provides greater insights into the moderating impact of intra-organizational practice on IA based on the fact that performance measurement balance (PMB) did not directly influence the achievement of IA and clarifies the positive role that PMB plays in improving IA.

QHELIX: A Computational Tool for the Improved Measurement of Inter-Helical Angles in Proteins

Knowledge about the assembled structures of the secondary elements in proteins is essential to understanding protein folding and functionality. In particular, the analysis of helix geometry is required to study helix packing with the rest of the protein and formation of super secondary structures, such as, coiled coils and helix bundles, formed by packing of two or more helices. Here we present an improved computational method, QHELIX, for the calculation of the orientation angles between helices. Since a large number of helices are known to be in curved shapes, an appropriate definition of helical axes is a prerequisite for calculating the orientation angle between helices. The present method provides a quantitative measure on the irregularity of helical shape, resulting in discriminating irregular-shaped helices from helices with an ideal geometry in a large-scale analysis of helix geometry. It is also capable of straightforwardly assigning the direction of orientation angles in a consistent way. These improvements will find applications in finding a new insight on the assembly of protein secondary structure.

Infrared dichroism from the X-ray structure of bacteriorhodopsin

A detailed comparison with the three-dimensional protein structure provides a stringent test of the models and parameters commonly used in determining the orientation of the alpha-helices from the linear dichroism of the infrared amide bands, particularly in membranes. The order parameters of the amide vibrational transition moments are calculated for the transmembrane alpha-helices of bacteriorhodopsin by using the crystal structure determined at a resolution of 1.55 A (PDB accession number 1C3W). The dependence on the angle delta(M) that the transition moment makes with the peptide carbonyl bond is fit by the expression ((3)/(2)S(alpha) cos(2) alpha)cos(2)(delta(M) + beta) - 1/2S(alpha), where S(alpha) (0.91) is the order parameter of the alpha-helices, alpha (13 degrees ) is the angle that the peptide plane makes with the helix axis, and beta (11 degrees ) is the angle that the peptide carbonyl bond makes with the projection of the helix axis on the peptide plane. This result is fully consistent with the model of nested axial distributions commonly used in interpreting infrared linear dichroism of proteins. Comparison with experimental infrared dichroic ratios for bacteriorhodopsin yields values of Theta(A) = 33 +/- 1 degree, Theta(I) = 39.5 +/- 1 degree, and Theta(II) = 70 +/- 2 degrees for the orientation of the transition moments of the amide A, amide I, and amide II bands, respectively, relative to the helix axis. These estimates are close to those found for model alpha-helical polypeptides, indicating that side-chain heterogeneity and slight helix imperfections are unlikely to affect the reliability of infrared measurements of helix orientations.

Unravelling the folding of bacteriorhodopsin

The folding mechanism of integral membrane proteins has eluded detailed study, largely as a result of the inherent difficulties in folding these proteins in vitro. The seven-transmembrane helical protein bacteriorhodopsin has, however, allowed major advances to be made, not just on the folding of this particular protein, but also on the factors governing folding of transmembrane alpha-helical proteins in general. This review focusses on kinetic and equilibrium studies of bacteriorhodopsin folding in vitro. It covers what is currently known about secondary and tertiary structure formation as well as the events accompanying retinal binding, for protein in detergent and lipid systems, including native membrane samples.

Orientation of the infrared transition moments for an alpha-helix

Appropriate values for the orientation of the amide transition dipoles are essential to the growing use of isotopically edited vibrational spectroscopy generally in structural biology and to infrared dichroism measurements on membrane-associated alpha-helices, in particular. The orientations of the transition moments for the amide vibrations of an alpha-helix have been determined from the ratio of intensities of the A- and E(1)-symmetry modes in the infrared spectra of poly(gamma-methyl-L-glutamate)(x)-co-(gamma-n-octadecyl-L-glutamate)( y) oriented on silicon substrates. Samples possessing a high degree of alignment were used to facilitate band fitting. Consistent results were obtained from both attenuated total reflection and transmission experiments with polarized radiation, yielding values of Theta(I) = 38 degrees, Theta(II) = 73 degrees, and Theta(A) = 29 degrees, relative to the helix axis, for the amide I, amide II, and amide A bands, respectively. The measurements are discussed both in the context of the somewhat divergent older determinations, and in relation to the helix geometry and results on model amide compounds, to resolve current uncertainties in the literature.

Membrane helix orientation from linear dichroism of infrared attenuated total reflection spectra

Oriented multilamellar systems containing phospholipids and peptides have been formed on a germanium internal reflection element. Attenuated total reflection infrared spectra have been recorded and the linear dichroism of peptide amide I and amide II bands measured. Using peptides for which the orientation had been previously studied under similar experimental conditions by 15N solid-state nuclear magnetic resonance spectroscopy, important conclusions were drawn on the approach to be used to derive secondary structure orientation in a membrane from dichroic ratios. In particular, it is shown that the influence of the film thickness and refractive index on the orientation determination can be evaluated from the value of RATRiso, i.e., the dichroic ratio of a dipole oriented at the magic angle or with isotropic mobility. A series of peptides was used to test the validity of our suggestions on various helix orientations in the membrane. These include magainin 2 and hydrophobic (hPhi20) model peptides, the transmembrane segment of glycophorin (GLY), and LAH4, a designed peptide antibiotic that changes between a transmembrane and an in-plane orientation in a pH-dependent manner.

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.

Reconstitution of bacteriorhodopsin from the apoprotein and retinal studied by Fourier-transform infrared spectroscopy

The reconstitution of the retinal-containing protein bacteriorhodopsin (BR) from the apoprotein and retinal has been studied by Fourier-transform infrared (FTIR) difference spectroscopy. 9-cis-Retinal which occupies the binding site but does not reconstitute the chromophore was used as "caged retinal". Photoisomerization to the all-trans isomer triggers the reconstitution reaction. Absorption bands in the FTIR difference spectra of the educt and product of the reaction could be assigned by comparison with a 9-cis-retinal FTIR spectrum or an FT-Raman spectrum of BR and due to band shifts observed upon deuterium exchange. Specific difference bands were assigned to the protonated carboxyl groups of D96 and D115 by use of the mutants D115N and D96N. Both aspartic acids are protonated also in the apoprotein with pKa values above 10 and undergo a frequency shift toward higher wavenumbers indicating a more hydrophobic environment in the reconstituted protein. No indication was found for protonation changes of carboxyl groups or other protonatable residues when carrying out the reaction at pH values between 4 and 10. The pH-dependent protonation changes reported earlier [Fischer & Oesterhelt (1980) Biophys. J. 31, 139-146] therefore may be caused by protons in a hydrogen-bonded network. Mutations of E204, but not of D38 or E9, cancel proton uptake during reconstitution at high pH as well as proton release at low pH. It is concluded, that E204, without changing its protonation state itself, is part of a protonatable hydrogen-bonded network which changes its pKa during reconstitution thereby causing the observed protonation changes.

Fourier transform infrared spectroscopy study of the secondary structure of the gastric H+,K+-ATPase and of its membrane-associated proteolytic peptides

Membrane topology of the H+,K+-ATPase has been studied after proteolytic degradation of the protein by proteinase K. Proteinase K had access to either the cytoplasmic part of the protein or to both sides of the membrane. Fourier transform infrared attenuated total reflection spectroscopy indicated that membrane-associated domain of the protein represented about 55% of the native protein, meanwhile the cytoplasmic part represented only 27% of the protein. The secondary structure of the ATPase and of its membrane-associated domains was investigated by infrared spectroscopy. The secondary structure of the membrane-associated structures and of the entire protein was quite similar (alpha-helices, 35%; beta-sheets, 35%; turns, 20%; random, 15%). These data were in agreement with 10 alpha-helical transmembrane segments but suggested a participation of beta-sheet structures in the membrane-associated part of the protein. Polarized infrared spectroscopy indicated that the alpha-helices were oriented nearly perpendicular to the membrane plane. No preferential orientation could be attributed to the beta-sheets. Monitoring the amide hydrogen/deuterium exchange kinetics demonstrated that the membrane associated part of the ATPase molecule is characterized by a relatively high accessibility to the solvent, quite different from that observed for bacteriorhodopsin membrane segments.

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.

Conformation and dynamics of [3-13C]Ala- labeled bacteriorhodopsin and bacterioopsin, induced by interaction with retinal and its analogs, as studied by 13C nuclear magnetic resonance

13C nuclear magnetic resonance (NMR) spectra of [3-13C]Ala-labeled bacteriorhodopsin (bR), bacterioopsin (bO), and regenerated bR with retinal or bO complex with retinal analogs were recorded in order to gain insights into how the conformation and dynamics of apoprotein (bO) vary with or without retinal or its analogs. First, we assigned the 13C NMR peak resonating at 16.3 ppm to Ala 53 of both bR and bO, which appears to contact the side chain of Lys 216 at the site of the Schiff base in the former, utilizing the 13C NMR peaks of A53V and A53G proteins in comparison with those of wild-type bR and bO. Characteristic spectral differences between the apoprotein and bR were observed upon removal of the retinal: the changes of the peak intensities at 16.4, 15.9, and 16.9 ppm are notable. We found that the loops (17.4 ppm) and transmembrane alpha II helical region (15.9 ppm) acquired motional freedom with a correlation time of 10(-5)s when the retinal was removed, as detected by proton spin-lattice relaxation times in the rotating frame. A 13C NMR spectrum very similar to that of native bR was recorded when bR was regenerated by addition of retinal to bO. On the other hand, the addition of the retinal analogs retinol or beta-ionone, which are bound in the retinal binding site but are incapable of forming a Schiff base to the apoprotein, caused distinct spectral changes different from those of bR, as manifested from the displacements of 13C chemical shifts. These spectral changes must be ascribed to significant conformational changes of apoprotein at various locations in the protein, including the site of Ala 53 induced by modified interaction between the apoprotein and chromophore.

Backbone dynamics of (1-71)- and (1-36)bacterioopsin studied by two-dimensional (1)H- (15)N NMR spectroscopy

The backbone dynamics of uniformly (15)N-labelled fragments (residues 1-71 and 1-36) of bacterioopsin, solubilized in two media (methanol-chloroform (1:1), 0.1 M (2)HCO(2)NH(4), or SDS micelles) have been investigated using 2D proton-detected heteronuclear (1)H-(15)N NMR spectroscopy at two spectrometer frequencies, 600 and 400 MHz. Contributions of the conformational exchange to the transverse relaxation rates of individual nitrogens were elucidated using a set of different rates of the CPMG spin-lock pulse train and were essentially suppressed by the high-frequency CPMG spin-lock. We found that most of the backbone amide groups of (1-71)bacterioopsin in SDS micelles are involved in the conformational exchange process over a rate range of 10(3) to 10(4) s(-1). This conformational exchange is supposed to be due to an interaction between two α-helixes of (1-71)bacterioopsin, since the hydrolysis of the peptide bond in the loop region results in the disappearance of exchange line broadening. (15)N relaxation rates and (1)H-(15)N NOE values were interpreted using the model-free approach of Lipari and Szabo [Lipari, G. and Szabo, A. (1982) J. Am. Chem. Soc., 104, 4546-4559]. In addition to overall rotation of the molecule, the backbone N-H vectors of the peptides are involved in two types of internal motions: fast, on a time scale <20 ps, and intermediate, on a time scale close to 1 ns. The intermediate dynamics in the α-helical stretches was mostly attributed to bending motions. A decrease in the order parameter of intermediate motions was also observed for residues next to Pro(50), indicating an anisotropy of the overall rotational diffusion of the molecule. Distinctly mobile regions are identified by a large decrease in the order parameter of intermediate motions and correspond to the N- and C-termini, and to a loop connecting the α-helixes of (1-71)bacterioopsin. The internal dynamics of the α-helixes on the millisecond and nanosecond time scales should be taken into account in the development of a model of the functioning bacteriorhodopsin.

Fourier transform infrared spectroscopy study of the secondary structure of the reconstituted Neurospora crassa plasma membrane H(+)-ATPase and of its membrane-associated proteolytic peptides

We reconstituted purified plasma membrane H(+)-ATPase from Neurospora crassa into soybean phospholipid vesicles (lipid/ATPase ratio of 5:1 w/w). The proteoliposomes contained an active ATPase, oriented inside-out. They were subjected to proteolysis by using Pronase, proteinase K, trypsin, and carboxypeptidase Y. Fourier transform infrared attenuated total reflection spectroscopy indicates that the amount of protein remaining after hydrolysis and elimination of the extramembrane domain of ATPase represents about 43% of the intact protein. The secondary structure of intact ATPase and of the membrane-associated domain of ATPase was determined by infrared spectroscopy. The membrane domain shows a typical alpha-helix and beta-sheet absorption. Polarized infrared spectroscopy reveals that the orientation of the helices is about perpendicular to the membrane. Amide hydrogen/deuterium exchange kinetics performed for the intact H(+)-ATPase and for the membrane-associated domain demonstrate that this part of ATPase shows less accessibility to the solvent than the entire protein but remains much more accessible to the solvent than bacteriorhodopsin membrane segments.

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.

Evidence for unbenignant nature of glucose as a replacement for water in purple membranes

The net angle (theta(alpha)) between the seven helical segments of the bacteriorhodopsin (bR) polypeptide and the normal to the membrane plane of the purple membrane (PM) is approximately 0 degrees when determined by oriented far-ultraviolet (UV) circular dichroism (OCD) and midinfrared linear dichroism (IRLD). However, theta(alpha) is approximately 11 degrees when determined by high-resolution electron cryo-microscopy and electron diffraction (EMD). The spectral studies are made with fresh hydrated PM films at ambient temperature, whereas diffraction studies are made with aged glucose-embedded PM at -120 to -268 degrees . The current study presents oriented far-UV OCD results of hydrated PM films embedded with glucose, which can best be interpreted as a change in the magnitude of theta(alpha) (Deltatheta(alpha)) from 0 to 23 degrees as a consequence of glucose embedment. Possible alternative explanations contrary to this conclusion are discussed and ruled out. Therefore, it is suggested that a theta(alpha) of approximately 11 degrees as determined by the EMD method may not be an intrinsic structural characteristic of the native PM but an induced one. The differences in the Deltatheta(alpha) value due to glucose embedment as determined by the two different approaches (23 vs. 11 degrees ) may be attributed to the drastic differences in the experimental conditions used, especially temperature. It is expected that at extremely low temperatures protein dynamics would be highly restricted and Deltatheta(alpha) relatively curtailed. It is concluded that glucose may not be as benign to biological structures as has been assumed in the past.

1H-15N-NMR studies of bacteriorhodopsin Halobacterium halobium. Conformational dynamics of the four-helical bundle

Series of uniformly and selectively 15N-labeled bacteriorhodopsins of Halobacterium halobium (strain ET 1001) were obtained and a 1H-15N-NMR study was performed in methanol/chloroform (1:1) and 0.1 M NH4CHOO, medium which mimics that in the membrane in vivo. Less than half of the cross-peaks expected from the amino acid sequence of uniformly 15N-labeled bacteriorhodopsin were observed, using heteronuclear 1H-15N coherence spectroscopy. In order to assign the observed cross-peaks, a selective 15N-labeling of amino acid residues (Tyr, Phe, Trp, Lys, Gly, Leu, Val or Ile) was carried out and 1H-15N-NMR spectra of bacteriorhodopsin and its fragments C1 (residues (72-231), C2 (residues 1-71), B1 (residues 1-155) and BP2 (residues 163-231) were investigated. By this procedure, all observed 1H-15N cross-peaks of the entire bacteriorhodopsin were found to belong to the transmembrane segments A, B and G. The cross-peaks from four (C, D, E and F) helical bundles (79-189 residues) were missed. These results clearly indicate that dynamic processes occur in the four helice bundle. The significance of this, in respect to bacteriorhodopsin functioning, is discussed.