Biomedical subjects

Norbert Kucerka

Publications and source records attributed to Norbert Kucerka.

9 recordsLinked to original sources

PubMed2006

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↗

PubMed2006

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↗

PubMed2006

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↗

PubMed2005

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↗

PubMed2005

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↗

PubMed2005

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↗

PubMed2004

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↗

PubMed2003

Determination of bilayer thickness and lipid surface area in unilamellar dimyristoylphosphatidylcholine vesicles from small-angle neutron scattering curves: a comparison of evaluation methods.

Small-angle neutron scattering (SANS) experiments were performed on unilamellar 1,2-dimyristoylphosphatidylcholine (DMPC) vesicles prepared in heavy water by extrusion through polycarbonate filters with 500 A pores. The data obtained at 30+/-0.1 degrees C were evaluated using a five-strip function model of the bilayer coherent neutron scattering length density, three different approximate form factors describing scattering from vesicles, and different methods of evaluation of the experimental data. It is shown that the results obtained from the SANS data in the range of scattering vector values 0.0316 A(-1)< q<0.0775 A(-1) are not sensitive to the vesicle form factor, nor to the evaluation method. Using the hollow sphere model of vesicles convoluted with the Gaussian distribution of their sizes, a constrained bilayer polar region thickness of 9 A and a DMPC headgroup volume of 325.5 A(3), it was possible to obtain from the experimental data the DMPC surface area as 58.9+/-0.8 A(2), the bilayer thickness as 44.5+/-0.3 A and the number of water molecules as 6.8+/-0.2 per DMPC located in the bilayer polar region.

Algorithms↗

PubMed2003

Small-angle neutron scattering study of the lipid bilayer thickness in unilamellar dioleoylphosphatidylcholine vesicles prepared by the cholate dilution method: n-decane effect.

Previous X-ray diffraction studies on fully hydrated fluid lamellar egg phosphatidylcholine phases indicated a approximately 10 A increase of bilayer thickness in the presence of excess n-decane [Biochim. Biophys. Acta 597 (1980) 455], while the small-angle neutron scattering (SANS) on unilamellar extruded dioleoylphosphatidylcholine (DOPC) vesicles detected substantially smaller 2.4+/-1.3 A bilayer thickness increase at n-decane/DOPC molar ratio of 1.2 [Biophys. Chem. 88 (2000) 165]. The purpose of the present study is to investigate the n-decane effect on the bilayer thickness in unilamellar DOPC vesicles prepared by the sodium cholate (NaChol) dilution method. Mixed DOPC+NaChol micelles at DOPC and NaChol concentrations of 0.1 mol/l were prepared in 2H(2)O containing 0.135 mol/l NaCl. This micellar solution was diluted in 0.135 mol/l NaCl in 2H(2)O to reach the final DOPC and NaChol concentrations of 0.008 mol/l. Thirty microliters of n-decane solution in methanol was added to 1 ml of this dispersion. After methanol evaporation, SANS was conducted on the dispersions. From the Kratky-Porod plot ln[I(Q)Q(2)] vs. Q(2) of SANS intensity I(Q) in the range of scattering vector values Q corresponding to interval 0.001 A(-2)<or=Q(2)<or=0.006 A(-2), the bilayer radius of gyration R(g) and the bilayer thickness parameter d(g)=12(0.5)R(g) were obtained. The values of d(g) indicate that the bilayer thickness increases by 2.4+/-0.9 A up to n-decane/DOPC molar ratio of 1.6. This result confirms the previous SANS findings obtained with extruded vesicles.

Alkanes↗