Comment on "An apparent general solution for the kinetic models of the bacteriorhodopsin photocycles".
Explore the source record for details and available documents.
Bacteriorhodopsins↗
Biomedical subjects
John F Nagle
Publications and source records attributed to John F Nagle.
Partial molecular volumes of lipids and cholesterol.
Volumetric measurements are reported for fully hydrated lipid/cholesterol bilayer mixtures using the neutral flotation method. Apparent specific volume data were obtained with the lipids DOPC, POPC and DMPC at T=30 degrees Celsius, DPPC at 50 degrees Celsius, and brain sphingomyelin (BSM) at 45 and 24 degrees Celsius for mole fractions of cholesterol x from 0 to 0.5. Unlike previous cholesterol mixture studies, we converted our raw data to partial molecular volume V(L) of the lipid and V(C) of the cholesterol. The partial molecular volumes were constant for POPC and DOPC as x was varied, but had sharp breaks for the other lipids at values of x(C) near 0.25+/-0.05. Results for x x(C) the values of the partial molecular volumes of cholesterol clustered near 630+/-10A(3) in all the lipids when measured for T>T(M); we suggest that this is the most appropriate measure of the bare volume of cholesterol in lipid bilayers.
Cholesterol↗
Closer look at structure of fully hydrated fluid phase DPPC bilayers.
X-ray data are presented for the benchmark dipalmitoylphosphatidylcholine lipid bilayer in the most biologically relevant state in which the bilayers are fully hydrated and in the fluid (liquid-crystalline) phase. Form factors F(q(z)) are obtained from a combination of two sample preparations, oriented stacks of bilayers for q(z) extending to 0.85 A(-1) and unilamellar vesicles for smaller q(z). Modeling obtains the electron density profile and values for the area per molecule, for the locations of the component groups, and for the different types of thicknesses of the bilayer, such as the hydrocarbon thickness and the steric thickness.
1,2-Dipalmitoylphosphatidylcholine↗
Structure of fully hydrated fluid phase lipid bilayers with monounsaturated chains.
Quantitative structures are obtained at 30 degrees C for the fully hydrated fluid phases of palmitoyloleoylphosphatidylcholine (POPC), with a double bond on the sn-2 hydrocarbon chain, and for dierucoylphosphatidylcholine (di22:1PC), with a double bond on each hydrocarbon chain. The form factors F(qz) for both lipids are obtained using a combination of three methods. (1) Volumetric measurements provide F(0). (2) X-ray scattering from extruded unilamellar vesicles provides /F(qz)/ for low q(z). (3) Diffuse X-ray scattering from oriented stacks of bilayers provides /F(qz)/ for high q(z). Also, data using method (2) are added to our recent data for dioleoylphosphatidylcholine (DOPC) using methods (1) and (3); the new DOPC data agree very well with the recent data and with (4) our older data obtained using a liquid crystallographic X-ray method. We used hybrid electron density models to obtain structural results from these form factors. The result for area per lipid (A) for DOPC 72.4 +/- 0.5 A(2) agrees well with our earlier publications, and we find A = 69.3 +/- 0.5 A2 for di22:1PC and A = 68.3 +/- 1.5 A2 for POPC. We obtain the values for five different average thicknesses: hydrophobic, steric, head-head, phosphate-phosphate and Luzzati. Comparison of the results for these three lipids and for our recent dimyristoylphosphatidylcholine (DMPC) determination provides quantitative measures of the effect of unsaturation on bilayer structure. Our results suggest that lipids with one monounsaturated chain have quantitative bilayer structures closer to lipids with two monounsaturated chains than to lipids with two completely saturated chains.
Fats, Unsaturated↗
Simulation-based methods for interpreting x-ray data from lipid bilayers.
The fully hydrated liquid crystalline phase of the dimyristoylphosphatidycholine lipid bilayer at 30 degrees C was simulated using molecular dynamics with the CHARMM potential for five surface areas per lipid (A) in the range 55-65 A(2) that brackets the previously determined experimental area 60.6 A(2). The results of these simulations are used to develop a new hybrid zero-baseline structural model, denoted H2, for the electron density profile, rho(z), for the purpose of interpreting x-ray diffraction data. H2 and also the older hybrid baseline model were tested by fitting to partial information from the simulation and various constraints, both of which correspond to those available experimentally. The A, rho(z), and F(q) obtained from the models agree with those calculated directly from simulation at each of the five areas, thereby validating this use of the models. The new H2 was then applied to experimental dimyristoylphosphatidycholine data; it yields A = 60.6 +/- 0.5 A(2), in agreement with the earlier estimate obtained using the hybrid baseline model. The electron density profiles also compare well, despite considerable differences in the functional forms of the two models. Overall, the simulated rho(z) at A = 60.7 A(2) agrees well with experiment, demonstrating the accuracy of the CHARMM lipid force field; small discrepancies indicate targets for improvements. Lastly, a simulation-based model-free approach for obtaining A is proposed. It is based on interpolating the area that minimizes the difference between the experimental F(q) and simulated F(q) evaluated for a range of surface areas. This approach is independent of structural models and could be used to determine structural properties of bilayers with different lipids, cholesterol, and peptides.
Computer Simulation↗
Swelling of phospholipids by monovalent salt.
Critical to biological processes such as membrane fusion and secretion, ion-lipid interactions at the membrane-water interface still raise many unanswered questions. Using reconstituted phosphatidylcholine membranes, we confirm here that multilamellar vesicles swell in salt solutions, a direct indication that salt modifies the interactions between neighboring membranes. By varying sample histories, and by comparing with data from ion carrier-containing bilayers, we eliminate the possibility that swelling is an equilibration artifact. Although both attractive and repulsive forces could be modified by salt, we show experimentally that swelling is driven primarily by weakening of the van der Waals attraction. To isolate the effect of salt on van der Waals interactions, we focus on high salt concentrations at which any possible electrostatic interactions are screened. By analysis of X-ray diffraction data, we show that salt does not alter membrane structure or bending rigidity, eliminating the possibility that repulsive fluctuation forces change with salt. By measuring changes in interbilayer separation with applied osmotic stress, we have determined, using the standard paradigm for bilayer interactions, that 1 M concentrations of KBr or KCl decrease the van der Waals strength by 50%. By weakening van der Waals attractions, salt increases energy barriers to membrane contact, possibly affecting cellular communication and biological signaling.
Algorithms↗
Areas of molecules in membranes consisting of mixtures.
The question has arisen in recent literature: how to partition the total area in simulations of membranes consisting of more than one kind of molecule into average areas for each kind of molecule. Several definitions have been proposed, each of which has arbitrary features. When applied to mixtures of cholesterol and DPPC, these definitions give different results. This note recalls that physical chemistry provides a canonical way to define molecular area, in analogy to the definition of partial-specific volume. Results for partial-specific area are obtained from simulations of DPPC/cholesterol bilayers and compared to the results from the other recent definitions. The partial-specific-area formalism dramatically demonstrates the condensing effect of cholesterol and this leads to the introduction of a specific model that accounts for the area of mixtures of cholesterol and lipid over the entire range of cholesterol concentrations.
1,2-Dipalmitoylphosphatidylcholine↗
Anomalous swelling of lipid bilayer stacks is caused by softening of the bending modulus.
Arrays of bilayers of the lipid dimyristoylphosphatidylcholine (DMPC) exhibit anomalous swelling as the temperature decreases from T=27 degrees C toward the main phase transition at T(M) =24 degrees C, within the fluid L(alpha) thermodynamic phase. Analysis of diffuse x-ray scattering data from oriented stacks of biological lipid bilayers now makes it possible to obtain the bending modulus K(C) and the bulk compressibility modulus B separately. We report results that show that the measured bending modulus K(C) for DMPC decreases by almost a factor of 2 between T=27 degrees C and the transition temperature at T(M) =24 degrees C, which is the same temperature range where the anomalous swelling occurs. We also report Monte Carlo simulations that show that the anomalous swelling can be fully accounted for by the measured decrease in K(C) with no changes in the van der Waals or hydration forces.
Compressive Strength↗
Structure of fully hydrated fluid phase DMPC and DLPC lipid bilayers using X-ray scattering from oriented multilamellar arrays and from unilamellar vesicles.
Quantitative structures of the fully hydrated fluid phases of dimyristoylphosphatidylcholine (DMPC) and dilauroylphosphatidylcholine (DLPC) were obtained at 30 degrees C. Data for the relative form factors F(q(z)) for DMPC were obtained using a combination of four methods. 1), Volumetric data provided F(0). 2), Diffuse x-ray scattering from oriented stacks of bilayers provided relative form factors |F(q(z))| for high q(z), 0.22 < q(z) < 0.8 A(-1). 3), X-ray scattering from extruded unilamellar vesicles with diameter 600 A provided |F(q(z))| for low q(z), 0.1 < q(z) < 0.3 A(-1). 4), Previous measurements using a liquid crystallographic x-ray method provided |F(2 pi h/D)| for h = 1 and 2 for a range of nearly fully hydrated D-spacings. The data from method 4 overlap and validate the new unilamellar vesicles data for DMPC, so method 4 is not required for DLPC or future studies. We used hybrid electron density models to obtain structural results from these form factors. Comparison of the model electron density profiles with that of gel phase DMPC provides areas per lipid A, 60.6 +/- 0.5 A(2) for DMPC and 63.2 +/- 0.5 A(2) for DLPC. Constraints on the model provided by volume measurements and component volumes obtained from simulations put the electron density profiles rho(z) and the corresponding form factors F(q(z)) on absolute scales. Various thicknesses, such as the hydrophobic thickness and the steric thickness, are obtained and compared to literature values.
Biophysics↗
Thermodynamic and structural characterization of amino acid-linked dialkyl lipids.
Using differential scanning calorimetry (DSC), X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR), we determined some thermodynamic and structural parameters for a series of amino acid-linked dialkyl lipids containing a glutamic acid-succinate headgroup and di-alkyl chains: C12, C14, C16 and C18 in CHES buffer, pH 10. Upon heating, DSC shows that the C12, C14 and annealed C16 lipids undergo a single transition which XRD shows is from a lamellar, chain ordered subgel phase to a fluid phase. This single transition splits into two transitions for C18, and FTIR shows that the upper main transition is predominantly the melting of the hydrocarbon chains whereas the lower transition involves changes in the headgroup ordering as well as changes in the lateral packing of the chains. For short incubation times at low temperature, the C16 lipid appears to behave like the C18 lipid, but appropriate annealing at low temperatures indicates that its true equilibrium behavior is like the shorter chain lipids. XRD shows that the C12 lipid readily converts into a highly ordered subgel phase upon cooling and suggests a model with untilted, interdigitated chains and an area of 77.2A(2)/4 chains, with a distorted orthorhombic unit subcell, a=9.0A, b=4.3A and beta=92.7 degrees . As the chain length n increases, subgel formation is slowed, but untilted, interdigitated chains prevail.
Amino Acids↗
Models to analyze small-angle neutron scattering from unilamellar lipid vesicles.
Small-angle scattering has been employed to study the structure of lipid bilayers in unilamellar vesicles. This paper evaluates the use of a model approach for the analysis of such data. A long molecular dynamics simulation of a dipalmitoylphosphatidylcholine bilayer in the L(alpha) phase provides detailed structural information from which scattering length density profiles and scattering intensity are obtained. A sequence of increasingly realistic models are defined and then fit to the simulated scattering intensity data for values of q that are experimentally accessible. The models are evaluated by how well they fit the intensity data and the structural parameters of the simulation. Although the conventional approach that extracts only the radius of gyration from a Kratky-Porod plot provides a reasonable fit to much of the data, the available experimental q range supports refined models with two independent parameters. Of the many two-parameter models, we propose that particular choices should be inspired by the functional form of the scattering length density profile of simulations. Constraints that limit realistic models to two independent parameters are described in detail. The analysis supports the proposition that reliable results for area/lipid and hydrocarbon thickness can be obtained from small-angle neutron scattering of unilamellar vesicles.
1,2-Dipalmitoylphosphatidylcholine↗
Diffuse scattering provides material parameters and electron density profiles of biomembranes.
Fully hydrated stacks of DOPC lipid bilayer membranes generate large diffuse x-ray scattering that corrupts the Bragg peak intensities that are used in conventional biophysical structural analysis, but the diffuse scattering actually contains more information. Using an efficient algorithm for fitting extensive regions of diffuse data to classical smectic liquid crystalline theory we first obtain the compressional modulus B= 10(13) erg/ cm(4), which involves interactions between membranes, and the bending modulus K(c) =8x 10(-13) erg of the membranes. The membrane form factor F ( q(z) ) is then obtained for most values of q(z) up to 0.8 A(-1). The electron density profile rho(z) is obtained by fitting models to F( q(z) ). Constraining the models to conform to other measurements provides structural quantities such as area A=72.1+/-0.5 A(2) per lipid at the interface.
Absorptiometry, Photon↗
Lipid bilayers: thermodynamics, structure, fluctuations, and interactions.
This article, adapted from our acceptance speech of the Avanti Award in Lipids at the 47th Biophysical Society meeting in San Antonio, 2003, summarizes over 30 years of research in the area of lipid bilayers. Beginning with a theoretical model of the phase transition (J.F.N.), we have proceeded experimentally using dilatometry and density centrifugation to study volume, differential scanning calorimetry to study heat capacity, and X-ray scattering techniques to study structure of lipid bilayers as a function of temperature. Electron density profiles of the gel and ripple phases have been obtained as well as profiles from several fluid phase lipids, which lead to many structural results that compliment molecular dynamics simulations from other groups. Using the theory of liquid crystallography plus oriented lipid samples, we are the first group to obtain both material parameters (KC and B) associated with the fluctuations in fluid phase lipids. This allows us to use fully hydrated lipid samples, as in vivo, to obtain the structure.
Calorimetry, Differential Scanning↗
Structure and fluctuations of charged phosphatidylserine bilayers in the absence of salt.
Using x-ray diffraction and NMR spectroscopy, we present structural and material properties of phosphatidylserine (PS) bilayers that may account for the well documented implications of PS headgroups in cell activity. At 30 degrees C, the 18-carbon monounsaturated DOPS in the fluid state has a cross-sectional area of 65.3 A(2) which is remarkably smaller than the area 72.5 A(2) of the DOPC analog, despite the extra electrostatic repulsion expected for charged PS headgroups. Similarly, at 20 degrees C, the 14-carbon disaturated DMPS in the gel phase has an area of 40.8 A(2) vs. 48.1 A(2) for DMPC. This condensation of area suggests an extra attractive interaction, perhaps hydrogen bonding, between PS headgroups. Unlike zwitterionic lipids, stacks of PS bilayers swell indefinitely as water is added. Data obtained for osmotic pressure versus interbilayer water spacing for fluid phase DOPS are well fit by electrostatic interactions calculated for the Gouy-Chapman regime. It is shown that the electrostatic interactions completely dominate the fluctuational pressure. Nevertheless, the x-ray data definitively exhibit the effects of fluctuations in fluid phase DOPS. From our measurements of fluctuations, we obtain the product of the bilayer bending modulus K(C) and the smectic compression modulus B. At the same interbilayer separation, the interbilayer fluctuations are smaller in DOPS than for DOPC, showing that B and/or K(C) are larger. Complementing the x-ray data, (31)P-chemical shift anisotropy measured by NMR suggest that the DOPS headgroups are less sensitive to osmotic pressure than DOPC headgroups, which is consistent with a larger K(C) in DOPS. Quadrupolar splittings for D(2)O decay less rapidly with increasing water content for DOPS than for DOPC, indicating greater perturbation of interlamellar water and suggesting a greater interlamellar hydration force in DOPS. Our comparisons between bilayers of PS and PC lipids with the same chains and the same temperature enable us to focus on the effects of these headgroups on bilayer properties.
Lipid Bilayers↗
Structure of gel phase DMPC determined by X-ray diffraction.
The structure of fully hydrated gel phase dimyristoylphosphatidylcholine lipid bilayers was obtained at 10 degrees C. Oriented lipid multilayers were used to obtain high signal-to-noise intensity data. The chain tilt angle and an estimate of the methylene electron density were obtained from wide angle reflections. The chain tilt angle is measured to be 32.3 +/- 0.6 degrees near full hydration, and it does not change as the sample is mildly dehydrated from a repeat spacing of D = 59.9 A to D = 56.5 A. Low angle diffraction peaks were obtained up to the tenth order for 17 samples with variable D and prepared by three different methods with different geometries. In addition to the usual Fourier reconstructions of the electron density profiles, model electron density profiles were fit to all the low angle data simultaneously while constraining the model to include the wide-angle data and the measured lipid volume. Results are obtained for area/lipid (A = 47.2 +/- 0.5 A(2)), the compressibility modulus (K(A) = 500 +/- 100 dyn/cm), various thicknesses, such as the hydrocarbon thickness (2D(C) = 30.3 +/- 0.2 A), and the head-to-head spacing (D(HH) = 40.1 +/- 0.1 A).
Cell Membrane↗