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At least 55 records · Page 3

Influence of the size and protonation state of acidic residue 85 on the absorption spectrum and photoreaction of the bacteriorhodopsin chromophore

The consequences of replacing Asp-85 with glutamate in bacteriorhodopsin, as expressed in Halobacterium sp. GRB, were investigated. Similarly to the in vitro mutated and in Escherichia coli expressed protein, the chromophore was found to exist as a mixture of blue (absorption maximum 615 nm) and red (532 nm) forms, depending on the pH. However, we found two widely separated pKa values (about 5.4 and 10.4 without added salt), arguing for two blue and two red forms in separate equilibria. Both blue and red forms of the protein are in the two-dimensional crystalline state. A single pKa, such as in the E. coli expressed protein, was observed only after solubilization with detergent. The photocycle of the blue forms was determined at pH 4.0 with 610 nm photoexcitation, and that of the red forms at pH 10.5 and with 520 nm photoexcitation, in the time-range of 100 ns to 1 s. The blue forms produced no M, but a K- and an L-like intermediate, whose spectra and kinetics resembled those of blue wild-type bacteriorhodopsin below pH 3. The red forms produced a K-like intermediate, as well as M and N. Only the red forms transported protons. Specific perturbation of the neighborhood of the Schiff base by the replacement of Asp-85 with glutamate was suggested by (1) the shift and splitting of the pKa for what is presumably the protonation of residue 85, (2) a 36 nm blue-shift in the absorption of the all-trans red chromophore and a 25 nm red-shift of the 13-cis N chromophore, as compared to wild-type bacteriorhodopsin and its N intermediate, and (3) significant acceleration of the deprotonation of the Schiff base at pH 7, but not of its reprotonation and the following steps in the photocycle.

Non-NASA Center↗

Pathways of proton transfer in the light-driven pump bacteriorhodopsin

The mechanism of proton transport in the light-driven pump bacteriorhodopsin is beginning to be understood. Light causes the all-trans to 13-cis isomerization of the retinal chromophore. This sets off a sequential and directed series of transient decreases in the pKa's of a) the retinal Schiff base, b) an extracellular proton release complex which includes asp-85, and c) a cytoplasmic proton uptake complex which includes asp-96. The timing of these pKa changes during the photoreaction cycle causes sequential proton transfers which result in the net movement of a proton across the protein, from the cytoplasmic to the extracellular surface.

NASA Discipline Number 52-30↗

The rhodopsins: structure and function. Introduction

Nature makes use of the propensity of retinal for light-dependent double-bond isomerization in a number of systems and in a variety of ways. The common theme for light receptors based on this kind of chemistry is that (1) the retinal is bound in most cases to a small membrane protein via a protonated lysine-retinal Schiff base, (2) the absorption maximum in the visible is tuned to a suitable wavelength largely by electrostatic interaction with polar protein residues, and (3) the light-induced bond rotations and strains in the retinal set off reaction chains during which at least part of the excess free energy acquired is transferred to the protein and causes pK shifts of acidic residues and/or backbone conformational changes. The physiological consequence of the process initiated by absorption of light is either the activation of an information transfer chain (sensory and visual rhodopsins) or energy transduction which drives the electrogenic movement of ions across the membrane (ion-motive rhodopsins). Rhodopsins with these functions occur in bacteria and in higher organisms; from an evolutionary standpoint they are not related to one another. Nevertheless, all of these proteins are remarkably similar and form a distinct family.

NASA Discipline Number 52-30↗

Illumination-dependent changes in the intrinsic fluorescence of bacteriorhodopsin

The paper describes the intrinsic UV fluorescence of bacteriorhodopsin in some detail and determines the changes during the rapid cyclic reaction following light flashes. The results suggest that several tryptophan residues are affected in the protein, among them one or more exposed to aqueous medium. The kinetics of the fluorescence changes coincide closely with events involving the retinal residue during the deprotonation and reprotonation of the Schiff base group.

Bogomolni, R. A.↗

Photoenergy transduction in halobacterium halobium

The structure and function of a rhodopsin-like pigment bacteriorhodopsin, discovered and isolated from the membranes of the halophile Halobacterium halobium, were studied. Intermediatesm appearing in the cyclic photoreaction that drives the proton translocation, were spectroscopically characterized. The charge translocation in membrane monolayers and mulitlayers placed between electrodes were kinetically resolved. A model was developed for the proton translocation process, in which the isomerization of the retinal Schiff base decreases its pK to drive the proton off and simultaneaouly changes the connectivity from the cytoplasmic surface to the external surface. The stoichiometry of proton pumping in intact cells and the effect of the light generated electrochemical potential on the kinetics of the photoreaction cycle and the synthesis of ATP were investigated.

Stoeckenius, W.↗

Accelerated heat-aging studies on fluororubber in various media

Heat-aging studies were conducted on fluororubber (copolymers of vinylidene fluoride and perfluoropropylene) using N,N-dicinnamylidene-1,6-hexanediamine, a Schiff's base of 1,6-hexanediamine, and MgO as acid acceptor. The principal technique employed was chemical stress relaxation for determining network changes brought about in the heat-aged fluororubber. This technique was backed up by swelling measurements, gel permeation chromatography, and IR spectroscopy. Stress relaxation curves are plotted for a wide range of variation in parameters (time, crosslinking density, state of curing, temperature, intermittent and continuous relaxation).

Kalfayan, S. H.↗

Structures of aspartic acid-96 in the L and N intermediates of bacteriorhodopsin: analysis by Fourier transform infrared spectroscopy

The light-induced difference Fourier transform infrared spectrum between the L or N intermediate minus light-adapted bacteriorhodopsin (BR) was measured in order to examine the protonated states and the changes in the interactions of carboxylic acids of Asp-96 and Asp-115 in these intermediates. Vibrational bands due to the protonated and unprotonated carboxylic acid were identified by isotope shift and band depletion upon substitution of Asp-96 or -115 by asparagine. While the signal due to the deprotonation of Asp-96 was clearly observed in the N intermediate, this residue remained protonated in L. Asp-115 was partially deprotonated in L. The C = O stretching vibration of protonated Asp-96 of L showed almost no shift upon 2H2O substitution, in contrast to the corresponding band of Asp-96 or Asp-115 of BR, which shifted by 9-12 cm-1 under the same conditions. In the model system of acetic acid in organic solvents, such an absence of the shift of the C = O stretching vibration of the protonated carboxylic acid upon 2H2O substitution was seen only when the O-H of acetic acid is hydrogen-bonded. The non-hydrogen-bonded monomer showed the 2H2O-dependent shift. Thus, the O-H bond of Asp-96 enters into hydrogen bonding upon conversion of BR to L. Its increased hydrogen bonding in L is consistent with the observed downshift of the O-H stretching vibration of the carboxylic acid of Asp-96.

NASA Discipline Exobiology↗

A superconducting gyroscope to test Einstein's general theory of relativity

Schiff (1960) proposed a new test of general relativity based on measuring the precessions of the spin axes of gyroscopes in earth orbit. Since 1963 a Stanford research team has been developing an experiment to measure the two effects calculated by Schiff. The gyroscope consists of a uniform sphere of fused quartz 38 mm in diameter, coated with superconductor, electrically suspended and spinning at about 170 Hz in vacuum. The paper describes the proposed flight apparatus and the current state of development of the gyroscope, including techniques for manufacturing and measuring the gyro rotor and housing, generating ultralow magnetic fields, and mechanizing the readout.

Everitt, C. W. F.↗

Foundations for a theory of gravitation theories

A foundation is laid for future analyses of gravitation theories. This foundation is applicable to any theory formulated in terms of geometric objects defined on a 4-dimensional spacetime manifold. The foundation consists of (1) a glossary of fundamental concepts; (2) a theorem that delineates the overlap between Lagrangian-based theories and metric theories; (3) a conjecture (due to Schiff) that the Weak Equivalence Principle implies the Einstein Equivalence Principle; and (4) a plausibility argument supporting this conjecture for the special case of relativistic, Lagrangian-based theories.

Thorne, K. S.↗

A computational examination of directional stability for smooth and chined forebodies at high-alpha

Computational Fluid Dynamics (CFD) has been used to study aircraft forebody flowfields at low-speed, angle-of-attack conditions with sideslip. The purpose is to define forebody geometries which provide good directional stability characteristics under these conditions. The flows over the experimentally investigated F-5A forebody and chine type configuration, previously computed by the authors, were recomputed with better grid topology and resolution. The results were obtained using a modified version of CFL3D (developed at NASA Langley) to solve either the Euler equations or the Reynolds equations employing the Baldwin-Lomax turbulence model with the Degani-Schiff modification to account for massive crossflow separation. Based on the results, it is concluded that current CFD methods can be used to investigate the aerodynamic characteristics of forebodies to achieve desirable high angle-of-attack characteristics. An analytically defined generic forebody model is described, and a parametric study of various forebody shapes was then conducted to determine which shapes promote a positive contribution to directional stability at high angle-of-attack. An unconventional approach for presenting the results is used to illustrate how the positive contribution arises. Based on the results of this initial parametric study, some guidelines for aerodynamic design to promote positive directional stability are presented.

Ravi, Ramakrishnan↗

Turbulent Vortex-Flow Simulation Over a 65 deg Sharp and Blunt Leading-Edge Delta Wing at Subsonic Speeds

Turbulent thin-layer, Reynolds-Averaged Navier-Stokes solutions, based on a multi-block structured grid, are presented for a 65 deg delta wing having either a sharp leading edge (SLE) or blunt leading edge (BLE) geometry. The primary objective of the study is to assess the prediction capability of the method for simulating the leading-edge flow separation and the ensuing vortex flow characteristics. Computational results are obtained for two angles of attack of approximately 13 and 20 deg, at free-stream Mach number of 0.40 and Reynolds number of 6 million based on the wing mean aerodynamic chord. The effects of two turbulence models of Baldwin-Lomax with Degani-Schiff (BL/DS) and the Spalart-Allmaras (SA) on the numerical results are also discussed. The computations also explore the effects of two numerical flux-splitting schemes, i.e., flux difference splitting (fds) and flux vector splitting (fvs), on the solution development and convergence characteristics. The resulting trends in solution sensitivity to grid resolution for the selected leading-edge geometries, angles of attack, turbulence models and flux splitting schemes are also presented. The validity of the numerical results is evaluated against a unique set of experimental wind-tunnel data that was obtained in the National Transonic Facility at the NASA Langley Research Center.

Ghaffari, Farhad↗

Turbulence Model Comparisons and Reynolds Number Effects Over a High-Speed Aircraft at Transonic Speeds

This paper gives the results of a grid study, a turbulence model study, and a Reynolds number effect study for transonic flows over a high-speed aircraft using the thin-layer, upwind, Navier-Stokes CFL3D code. The four turbulence models evaluated are the algebraic Baldwin-Lomax model with the Degani-Schiff modifications, the one-equation Baldwin-Barth model, the one-equation Spalart-Allmaras model, and Menter's two-equation Shear-Stress-Transport (SST) model. The flow conditions, which correspond to tests performed in the NASA Langley National Transonic Facility (NTF), are a Mach number of 0.90 and a Reynolds number of 30 million based on chord for a range of angle-of-attacks (1 degree to 10 degrees). For the Reynolds number effect study, Reynolds numbers of 10 and 80 million based on chord were also evaluated. Computed forces and surface pressures compare reasonably well with the experimental data for all four of the turbulence models. The Baldwin-Lomax model with the Degani-Schiff modifications and the one-equation Baldwin-Barth model show the best agreement with experiment overall. The Reynolds number effects are evaluated using the Baldwin-Lomax with the Degani-Schiff modifications and the Baldwin-Barth turbulence models. Five angles-of-attack were evaluated for the Reynolds number effect study at three different Reynolds numbers. More work is needed to determine the ability of CFL3D to accurately predict Reynolds number effects.

Rivers, Melissa B.↗

Comparison of Turbulence Models for Nozzle-Afterbody Flows with Propulsive Jets

A numerical investigation was conducted to assess the accuracy of two turbulence models when computing non-axisymmetric nozzle-afterbody flows with propulsive jets. Navier-Stokes solutions were obtained for a Convergent-divergent non-axisymmetric nozzle-afterbody and its associated jet exhaust plume at free-stream Mach numbers of 0.600 and 0.938 at an angle of attack of 0 deg. The Reynolds number based on model length was approximately 20 x 10(exp 6). Turbulent dissipation was modeled by the algebraic Baldwin-Lomax turbulence model with the Degani-Schiff modification and by the standard Jones-Launder kappa-epsilon turbulence model. At flow conditions without strong shocks and with little or no separation, both turbulence models predicted the pressures on the surfaces of the nozzle very well. When strong shocks and massive separation existed, both turbulence models were unable to predict the flow accurately. Mixing of the jet exhaust plume and the external flow was underpredicted. The differences in drag coefficients for the two turbulence models illustrate that substantial development is still required for computing very complex flows before nozzle performance can be predicted accurately for all external flow conditions.

Compton, William B., III↗

Fourier functional analysis for unsteady aerodynamic modeling

A method based on Fourier analysis is developed to analyze the force and moment data obtained in large amplitude forced oscillation tests at high angles of attack. The aerodynamic models for normal force, lift, drag, and pitching moment coefficients are built up from a set of aerodynamic responses to harmonic motions at different frequencies. Based on the aerodynamic models of harmonic data, the indicial responses are formed. The final expressions for the models involve time integrals of the indicial type advocated by Tobak and Schiff. Results from linear two- and three-dimensional unsteady aerodynamic theories as well as test data for a 70-degree delta wing are used to verify the models. It is shown that the present modeling method is accurate in producing the aerodynamic responses to harmonic motions and the ramp type motions. The model also produces correct trend for a 70-degree delta wing in harmonic motion with different mean angles-of-attack. However, the current model cannot be used to extrapolate data to higher angles-of-attack than that of the harmonic motions which form the aerodynamic model. For linear ramp motions, a special method is used to calculate the corresponding frequency and phase angle at a given time. The calculated results from modeling show a higher lift peak for linear ramp motion than for harmonic ramp motion. The current model also shows reasonably good results for the lift responses at different angles of attack.

Lan, C. Edward↗