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PubMed1998

Magnetically aligned phospholipid bilayers with positive ordering: a new model membrane system.

A stable smectic phospholipid bilayer phase aligned with the director parallel to the magnetic field can be generated by the addition of certain trivalent paramagnetic lanthanide ions to a bicellar solution of dimyristoylphosphatidylcholine (DMPC) and dihexanoylphosphatidylcholine (DHPC) in water. Suitable lanthanide ions are those with positive anisotropy of their magnetic susceptibility, namely Eu3+, Er3+, Tm3+, and Yb3+. For samples doped with Tm3+, this phase extends over a wide range of Tm3+ concentrations (6-40 mM) and temperatures (35-90 degrees C) and appears to undergo a transition from a fluid nematic discotic to a fluid, but highly ordered, smectic phase at a temperature that depends on the thulium concentration. As a membrane mimetic, these new, positively ordered phospholipid phases have high potential for structural studies using a variety of techniques such as magnetic resonance (EMR and NMR), small-angle x-ray and neutron diffraction, as well as optical and infrared spectroscopy.

Dimyristoylphosphatidylcholine↗
PubMed2003

The distribution of toluene in intercalation complexes of a vermiculite and alkyl trimethylammonium bromides.

Neutron diffraction and isotopic labeling have been used to determine the distribution of toluene sorbed into the interlamellar space of complexes of vermiculite with alkyl trimethylammonium bromide complex of alkyl chain lengths C(12), C(14), and C(16) and in a mixed C(12)/C(16) complex. The toluene remains in a liquid-like form and fills and swells the interlamellar space space up to a point where there remains a small amount of overlap of the alkyl chains of the surfactant. If the complex is between vermiculite and one surfactant only this results in the toluene concentration being reduced in the center of the interlamellar space, with maxima on either side. On the other hand, in a complex of mixed-length surfactants, the toluene distribution reaches its maximum at the center of the interlamellar space.

Journal Article↗
PubMed2003

Layer-by-layer surface freezing of linear alcohols at the graphite/liquid interface.

Differential scanning calorimetry (DSC), incoherent elastic neutron scattering, and neutron diffraction are used to demonstrate the presence of adsorbed solid multilayers of linear alcohols at the graphite-liquid alcohol interface. All alcohols studied (C(5)-C(18)) are found to form at least one monolayer. In addition all the even alcohols investigated (C(6)OH to C(18)OH) show multilayer formation. However, only the short odd alcohols (C(5)OH to C(11)OH) clearly exhibit additional features indicating multilayer formation.

Journal Article↗
PubMed1983

Electron microscope structural study of modified fibrin and a related modified fibrinogen aggregate.

The structure of proteolytically modified fibrin and a closely related modified fibrinogen aggregate have been studied by analysis of electron microscope images. For both structures, we propose a model that consists of double-stranded, 2-fold helical protofibrils, which are associated laterally to form ordered fibrils, with a C222 space group: a = 44.0 nm, b = c = 9.4 nm. Each fibril is 80 nm or less in diameter, and twists along its length in a right-handed sense, with a pitch from 7 to 12 times the molecular length. The fibrils associate laterally to form bundles, which tend to twist in a left-handed sense, with a pitch of the order of 40 times the molecular length. The specific volume of modified fibrin calculated from this model is 3.9 A3 per dalton, which is comparable to the specific volume of 3.6 A3 per dalton for modified fibrinogen crystals but is lower than the 6 A3 per dalton determined for fibrin from light-scattering experiments. Comparison of our electron microscope results with X-ray and neutron diffraction data suggest a similar, but less well-ordered, structure for native fibrin, with a smaller fibril, approximately 18.4 nm wide, consisting of eight protofibrils.

Fibrin↗
PubMed1983

Exchange of individual hydrogens for a protein in a crystal and in solution.

A preliminary comparison of the solvent exchange of individual hydrogens of a protein in solution and in a crystal has been possible by using data for lysozyme from 1H nuclear magnetic resonance and neutron diffraction studies. It is suggested that this approach enables a direct comparison of local dynamical behaviour in the two states. The results indicate markedly similar behaviour for many residues, but significant differences are indicated in several regions of the protein.

Animals↗
PubMed1999

Changes in water structure induced by a hydrophobic solute probed by simulation of the water hydrogen bond angle and radial distribution functions.

In order to better characterize changes in water structure induced by a hydrophobic solute the oxygen-oxygen and hydrogen-hydrogen radial distribution functions (goo(r), ghh(r)) and the hydrogen bond angle distribution function p(theta) for water molecules in the first hydration shell of the tetramethyl ammonium (TMA) cation were computed using Monte Carlo simulations. goo(r) and ghh(r) were corrected for the effect of solute volume exclusion on the local solvent density so that intrinsic structural changes independent of local solvent density variations could be detected. Comparison of ghh(r) of TMA's first hydration shell water with ghh(r) for bulk water shows subtle but clear evidence of structure formation induced by the ion. These changes in ghh(r) are very similar to those seen experimentally for larger tetra-alkyl ammonium ions in previous neutron diffraction experiments. Larger changes in p(theta) in the first hydration shell of TMA were seen. Comparison of changes in p(theta) with changes in goo(r) and ghh(r) show that the angle distribution function provides the most sensitive way to analyze water structure changes associated with hydrophobic solvation.

Algorithms↗
PubMed2003

Comparison of phase contrast transmission electron microscopy with optimized scanning transmission annular dark field imaging for protein imaging.

Henderson has already shown that electron microscopy should be superior to X-ray and neutron diffraction for determining protein structure with minimum radiation damage. Since the contrast for a molecule embedded in vitreous ice is very low, it is conceivable that dark field imaging would be superior to bright field phase contrast microscopy. A detailed analysis of contrast and signal/noise for both imaging modes is presented. Annular dark field scanning transmission microscopy gives improved contrast and equivalent signal/noise to phase contrast TEM when the molecule is the same thickness as a vitreous ice embedding medium. For a constant embedding medium thickness of 200 A the contrast is equivalent to phase contrast TEM but the signal/noise is 5 times worse. Even with an efficient detector that only excludes scattering less than 5 mrad there is insufficient signal at a dose of 5 electrons/A(2) to produce an image with more than 1 electron/per pixel. For larger molecules (>100 A thick which corresponds to 420 kDa for spherical molecules) the weak phase object approximation used to analyse a phase contrast image no longer applies at 100 kV. This limit could be extended to about 200 A (about 3 MDa) if a 400 kV microscope were used.

Algorithms↗
PubMed2000

Interaction of membrane proteins and lipids with solubilizing detergents.

Detergents are indispensable in the isolation of integral membrane proteins from biological membranes to study their intrinsic structural and functional properties. Solubilization involves a number of intermediary states that can be studied by a variety of physicochemical and kinetic methods; it usually starts by destabilization of the lipid component of the membranes, a process that is accompanied by a transition of detergent binding by the membrane from a noncooperative to a cooperative interaction already below the critical micellar concentration (CMC). This leads to the formation of membrane fragments of proteins and lipids with detergent-shielded edges. In the final stage of solubilization membrane proteins are present as protomers, with the membrane inserted sectors covered by detergent. We consider in detail the nature of this interaction and conclude that in general binding as a monolayer ring, rather than as a micelle, is the most probable mechanism. This mode of interaction is supported by neutron diffraction investigations on the disposition of detergent in 3-D crystals of membrane proteins. Finally, we briefly discuss the use of techniques such as analytical ultracentrifugation, size exclusion chromatography, and mass spectrometry relevant for the structural investigation of detergent solubilized membrane proteins.

Crystallography↗
PubMed1997

Correlations between 9Be magic-angle spinning nuclear magnetic resonance spectra and the geometry of beryllium containing framework structures.

A range of sodalite framework structures containing beryllium with general formula M8[BeZO4]6X2; M = Cd, Zn, Z = Si, Ge and X = S, Se or Te have been synthesised. The structures of these materials, which contain a single beryllium environment, have been refined from powder neutron diffraction or powder X-ray diffraction data and the compounds further characterised using 9Be magic-angle spinning nuclear magnetic resonance (MASNMR). Spectra show a single sharp resonance for 9Be(OSi)4 in the chemical shift range +/- 1 ppm from 0.1 M BeCl2. Correlations between the Be-O-Z bond angles and the 9Be chemical shift are reported and show upfield shifts for larger angles as seen previously in MASNMR spectra for 29Si and 27Al.

Beryllium↗
PubMed1995

The structure of OmpF porin in a tetragonal crystal form.

BACKGROUND: OmpF porin is a trimeric integral membrane protein responsible for the passive transport of small hydrophilic molecules, such as nutrients and waste products, across the outer membrane of Escherichia coli. Very few membrane proteins have been crystallized in three dimensions, yet this stable protein can be obtained in several crystal forms. Comparison of the structures of the same membrane protein in two different packing environments is of major interest, because it allows us to explore the integrity of the structure outside the natural membrane environment. RESULTS: The structure of OmpF porin in a tetragonal crystal form with two trimers per asymmetric unit has been determined at 3.2 A resolution and compared with that obtained previously in a trigonal crystal form. The lattice contacts involve only polar atoms, whereas extensive hydrophobic protein-protein interactions were found in the trigonal lattice. The trimer structure is virtually identical in both. CONCLUSIONS: Our comparison reveals that the overall structure of OmpF is not influenced by crystal lattice constraints and, thus, presumably bears close resemblance to the in vivo structure. The tetragonal crystal structure has provided the starting model for the phasing of neutron diffraction data obtained from this crystal form, as described in an accompanying article.

Amino Acid Sequence↗
PubMed1999

Crystal alignment of carbonated apatite in bone and calcified tendon: results from quantitative texture analysis.

Calcified tissue contains collagen associated with minute crystallites of carbonated apatite. In this study, methods of quantitative X-ray texture analysis were used to determine the orientation distribution and texture strength of apatite in a calcified turkey tendon and in trabecular and cortical regions of osteonal bovine ankle bone (metacarpus). To resolve local heterogeneity, a 2 or 10 microm synchrotron microfocus X-ray beam (lambda = 0.78 A) was employed. Both samples revealed a strong texture. In the case of turkey tendon, 12 times more c axes of hexagonal apatite were parallel to the fibril axis than perpendicular, and a axes had rotational freedom about the c axis. In bovine bone, the orientation density of the c axes was three times higher parallel to the surface of collagen fibrils than perpendicular to it, and there was no preferential alignment with respect to the long axis of the bone (fiber texture). Whereas half of the apatite crystallites were strongly oriented, the remaining half had a random orientation distribution. The synchrotron X-ray texture results were consistent with previous analyses of mineral orientation in calcified tissues by conventional X-ray and neutron diffraction and electron microscopy, but gave, for the first time, a quantitative description.

Animals↗
PubMed2000

Chemistry and physics of supramolecular magnetic materials.

The building of multidimensional magnetic materials obtained with the molecular precursor [Cu(opba)](2-) is described. The reaction with other paramagnetic species (3d or 4f metal ions, organic radicals) yielded one-dimensional, two-dimensional, and interlocked networks. The magnetic properties of these systems are reviewed using polarized neutron diffraction and magnetic measurements. It is shown that the spin density maps give a precise description of the ground state of such molecular magnetic species. Moreover, different long-range magnetic orderings (antiferro-, ferri-, and ferromagnetic) have been obtained.

Magnetics↗
PubMed1994

Ribosomal components neighboring the conserved 518-533 loop of 16S rRNA in 30S subunits.

We report the synthesis of a radioactive, photolabile oligodeoxyribonucleotide probe complementary to 16S rRNA nucleotides 518-526 and its exploitation in identifying 30S ribosomal subunit components neighboring its target site in 16S rRNA. Nucleotides 518-526 lie within an almost universally conserved single-stranded loop that has been linked to the decoding region of Escherichia coli ribosomes. On photolysis in the presence of activated 30S ribosomes, the probe site-specifically incorporates into proteins S3, S4, S7, and S12 (identified by SDS-PAGE, RP-HPLC, and immunological analysis); nucleotides C525, C526, and G527 adjacent to its target binding site; and the 3'-terminus of 16S rRNA. When the probe is photoincorporated into 30S subunits subjected to brief cold inactivation (SI subunits), S7 labeling is increased compared to activated subunit incorporation, while S3, S4, and S12 labeling is decreased, as is labeling to nucleotides C525, C526, and G527; labeling at the 16S rRNA 3'-terminus appears unchanged. Longer cold inactivation of the 30S subunits (LI subunits) leads to decreases in the labeling of all components. These results provide clear evidence that C526 lies within 24 A (the distance between C526 and the photogenerated nitrene) of proteins S3, S4, S7, and S12 and the 3'-terminus of 16S rRNA. The identity of the tryptic digestion patterns of S7 labeled with the probe complementary to 16S rRNA nucleotides 518-526 and with a probe complementary to nucleotides 1397-1405 [Muralikrishna, P., & Cooperman, B. S. (1994) Biochemistry 33, 1392-1398] also provides evidence for proximity between C526 and G1405. Our results support the conclusion of Dontsova et al. [Dontsova, O., et al. (1992) EMBO J. 11, 3105-3116] in placing the 530 loop in close proximity to the decoding center of the 30S subunit but are apparently inconsistent with some protein-protein distances determined by neutron diffraction [Capel, M. S., et al. (1988) J. Mol. Biol. 200, 65-87]. This inconsistency suggests that a multistate model of subunit conformation may be required to account for the totality of results pertaining to the internal structure of the 30S subunit.

Autoradiography↗
PubMed1991

Mean field stochastic boundary molecular dynamics simulation of a phospholipid in a membrane.

Computer simulations of phospholipid membranes have been carried out by using a combined approach of molecular and stochastic dynamics and a mean field based on the Marcelja model. First, the single-chain mean field simulations of Pastor et al. [(1988) J. Chem. Phys. 89, 1112-1127] were extended to a complete dipalmitoylphosphatidylcholine molecule; a 102-ns Langevin dynamics simulation is presented and compared with experiment. Subsequently, a hexagonally packed seven-lipid array was simulated with Langevin dynamics and a mean field at the boundary and with molecular dynamics (and no mean field) in the center. This hybrid method, mean field stochastic boundary molecular dynamics, reduces bias introduced by the mean field and eliminates the need for periodic boundary conditions. As a result, simulations extending to tens of nanoseconds may be carried out by using a relatively small number of molecules to model the membrane environment. Preliminary results of a 20-ns simulation are reported here. A wide range of motions, including overall reorientation with a nanosecond decay time, is observed in both simulations, and good agreement with NMR, IR, and neutron diffraction data is found.

Computer Simulation↗
PubMed1994

Spectroscopic study of Ser92 mutants of human myoglobin: hydrogen bonding effect of Ser92 to proximal His93 on structure and property of myoglobin.

Neutron diffraction studies have demonstrated that the hydroxyl group oxygen of Ser92(F7) is hydrogen bonded to the proximal His93(48) N epsilon H proton in myoglobin (Mb) [Cheng, X., & Shoenborn, B. P. (1991) J. Mol. Biol. 220, 381-399]. In order to examine the importance of this hydrogen bond, Ser92 was replaced with Ala and Asp in human Mb. By comparing the optical, 1H-NMR, resonance Raman, and IR spectra of Mb(S92A) in several spin and oxidation states with those of wild-type Mb, it was found that the mutation causes a structural change on the heme proximal side but not on the distal side. Comparison of the NMR spectra of the cyanomet form of Mb(S92A) and Mb(WT) suggests that the imidazole plane of His93 rotates somewhat around the Fe-N delta (His93) bond upon loss of the hydrogen bond between His93 and Ser92. The 2D 1H-NMR measurements of the CO complexes show that mutation of Ser92 to Ala changes the relative position of the His97 imidazole group to the heme plane, but the change is not so drastic as reported in the crystal data of Ser92 mutant of pig Mb [Smerdon et al. (1993) Biochemistry 32, 5132-5138]. On the other hand, ligand (CO, O2) binding is only slightly affected by this mutation. From these results, we conclude that the Ser92-His93 hydrogen bond maintains the protein structure of the proximal heme pocket, but it does not strongly affect the electronic structure of the heme as well as of the His93 imidazole ring.(ABSTRACT TRUNCATED AT 250 WORDS)

Carbon Monoxide↗
PubMed1986

Structural changes in lipid bilayers and biological membranes caused hydrostatic pressure.

By use of neutron diffraction, the structural parameters of oriented multilayers of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine with deuteriocarbon chains/cholesterol (molar ratio 70:30), multilamellar lipid vesicles composed of pure lipids and lipid/cholesterol mixtures, and crystalline purple membrane patches from Halobacterium halobium have been measured at pressures up to 2 kbar. Pressurization of the oriented 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine/cholesterol multilayers results in an in-plane compression with the mean deuteriocarbon chain spacing of 4.44 A obtained under ambient conditions decreasing by 3-7% at 1.9 kbar. The thickness for this bilayer increases by approximately equal to 1.5 A, but the net bilayer volume decreases and the isothermal compressibility is estimated to be in the range (-0.1 to -0.6) X 10(-4)/bar at 19.0 degrees C. The d spacings for multilamellar vesicles composed of lipids in the liquid crystalline state and lipid/cholesterol mixtures increase linearly as a function of pressure, suggesting that these bilayers are also compressed in the membrane plane. For 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine and 1,2-distearoyl-sn-glycero-3-phosphatidylcholine MLVs in the gel state, the d spacing decreases with pressure. For 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine, the hexagonally packed chains are anisotropically compressed in the bilayer plane, resulting in a pseudohexagonal chain packing at 1.9 kbar. The bilayer compressibility is (-0.4 or -0.5) X 10(-4)/bar depending on whether the chain tilt increases with pressure or terminal methyl groups of apposing lipid monolayers approach each other.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacteriorhodopsins↗
PubMed1989

Vitamin B12 monocarboxylic acids: unambiguous isomer assignments by modern two-dimensional NMR spectroscopy.

The three cyanocobalaminmonocarboxylic acid isomers known to be produced by the mild acid hydrolysis of the b-, d-, and e-propionamide side chains of vitamin B12 have been unambiguously assigned by modern 2D NMR methods. Previously, structural assignments had been made by less definitive NMR methods, and both X-ray and neutron diffraction studies had failed to locate unambiguously the position of the carboxyl group. The b and e isomers were structurally assigned in this study, on the basis of the assignment of the 13C NMR signal of the carboxyl group from HMBC (1H-detected heteronuclear multiple-bond correlation) spectra. The carboxyl group resonances exhibited the greatest changes in chemical shift between the protonated (pH 2) and deprotonated (pH greater than 7) forms of the acids. The d isomer was assigned by difference. Since the HMBC experiments required the assignments of side-chain CH2 signals, homonuclear Hartmann-Hahn, 2D homonuclear correlation, 2D nuclear Overhauser effect, 1H-detected heteronuclear multiple quantum coherence, and HMBC spectroscopies were used to assign completely the 1H and 13C NMR spectra of the b and e isomers at pH approximately 7. By comparison with the 13C NMR spectra of the b and e isomers, nearly one-fourth of the resonances of the 13C NMR spectrum of vitamin B12 have been reassigned. The sites of incorporation of 13C-labeled precursors in B12 biosynthesis found in previous studies have been verified by a comparison of 13C assignments. The results of studies using cobalamins modified at the b-, d-, and e-propionamide side chains in which the incorrect structural assignments were used (before 1980), particularly studies of B12-dependent enzymes, require reinterpretation using the correct structural assignments.

Carboxylic Acids↗
PubMed1978

Spectroscopic studies of specifically deuterium labeled membrane systems. Nuclear magnetic resonance investigation of the effects of cholesterol in model systems.

Deuterium nuclear magnetic resonance spectra of dimyristoylphosphatidylcholines specifically labeled in positions 2', 3', 4', 6', 8', 10', 12', and 14', of the 2 chain, of an N-deuteriomethylphosphatidylcholine, and of cholesterol-3alpha-d1, have been obtained by the Fourier transform method at 5.46 and 3.52 T on two "home-built" widebore superconducting magnet spectrometers, as a function of temperature and composition. Data on the specifically deuterium-labeled cholesterol molecule (in nonsonicated membrane systems) permits an estimate of the most probable angle of tilt of the sterol in the membrane, and evaluation of the order parameter (Salpha) describing rigid body motions in the bilayer. Segmental order parameters derived from the data presented allow calculation of individual chain segment projections onto the director axis and, consequently, estimation of effective chain length. It is shown that mathematical models which include chain tilt as well as those which neglect this type of rigid body motion give essentially identical results when applied to the dimyristoylphosphatidylcholine and dimyristoylphosphatidylcholine-cholesterol bilayer systems (in excess water, between 23 and 60 degrees C). Results of calculations of chain length and membrane thickness of a dimyristoylphosphatidylcholine-30 mol % cholesterol membrane system at 23 degrees C give excellent agreement when compared with recent high-resolution neutron diffraction data obtained on specifically deuterium labeled lecithin-cholesterol systems. No evidence for formation of lecithin-cholesterol complexes having lifetimes of approximately 30 ms has been found. Below the pure-lipid gel-liquid crystal phase transition temperature Tc but in the presence of cholesterol, we have obtained further evidence for 1-chain/2-chain nonequivalence. At 10 degrees C, the 2' segment of the 2 chain, but not the 2' segment of the 1 chain or the 3', 6', or 12' segments of the 2 chain, is broadened almost beyond detection. These results are in agreement with similar effects reported recently for the dipalmitoylphosphatidylcholine-cholesterol system and may indicate a bent configuration for the 2 chain, in the lecithin-cholesterol system. Further cooling below Tc results in loss of the 1-chain 2'-position signal intensity plus 2-chain 3', 6', and 12' signals simultaneously. The increase in length of the 2 chain of dimyristoylphosphatidylcholine upon addition of 30 mol % cholesterol of 23 degrees C is about 2.3 A. Addition of cholesterol to a choline-labeled lecithin results in complex behavior of the head group deuterium quadrupole splitting as a function of temperature, and cholesterol mole fraction. Above approximately 20 mol % cholesterol, the main effect is a decrease in quadrupole splitting as cholesterol content increases, the opposite effect to that observed with hydrocarbon chains.

Cholesterol↗