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PubMed1992

Cauliflower mosaic virus: a 420 subunit (T = 7), multilayer structure.

The structures of the Cabb-B and CM1841 strains of cauliflower mosaic virus (CaMV) have been solved to about 3 nm resolution from unstained, frozen-hydrated samples that were examined with low-irradiation cryo-electron microscopy and three-dimensional image reconstruction procedures. CaMV is highly susceptible to distortions. Spherical particles, with a maximum diameter of 53.8 nm, are composed of three concentric layers (I-III) of solvent-excluded density that surround a large, solvent-filled cavity (approximately 27 nm dia). The outermost layer (I) contains 72 capsomeric morphological units, with 12 pentavalent pentamers and 60 hexavalent hexamers for a total of 420 subunits (37-42 kDa each) arranged with T = 7 icosahedral symmetry. CaMV is the first example of a T = 7 virus that obeys the rules of stoichiometry proposed for isometric viruses by Caspar and Klug (1962, Cold Spring Harb. Symp. Quant. Biol. 27, 1-24), although the hexameric capsomers exhibit marked departure from the regular sixfold symmetry expected for a structure in which the capsid protein subunits are quasi-equivalently related. The double-stranded DNA genome is distributed in layers II and III along with a portion of the viral protein. The CaMV reconstructions are consistent with the model based on neutron diffraction studies (Kruse et al., 1987, Virology 159, 166-168) and, together, these structural models are discussed in relation to a replication-assembly model (Hull et al., 1987, J. Cell Sci. (Suppl.) 7, 213-229). Remarkable agreement between the reconstructions of CaMV Cabb-B and CM1841 suggests that other strains of CaMV adopt the same basic structure.

Capsid↗
PubMed2005

Investigations into the membrane interactions of m-calpain domain V.

m-calpain is a calcium-dependent heterodimeric protease implicated in a number of pathological conditions. The activation of m-calpain appears to be modulated by membrane interaction, which has been predicted to involve oblique-orientated alpha-helix formation by a GTAMRILGGVI segment located in domain V of the protein's small subunit. Here, we have investigated this prediction. Fourier transform infrared conformational analysis showed that VP1, a peptide homolog of this segment, exhibited alpha-helicity of approximately 45% in the presence of dimyristoylphosphatidylcholine/dimyristoylphosphatidylserine (DMPS) vesicles. The level of helicity was unaffected over a 1- to 8-mM concentration range and did not alter when the anionic lipid composition of these vesicles was varied between 1% and 10% DMPS. Similar levels of alpha-helicity were observed in trifluoroethanol and the peptide appeared to adopt alpha-helical structure at an air/water interface with a molecular area of 164 A(2) at the monolayer collapse pressure. VP1 was found to penetrate dimyristoylphosphatidylcholine/DMPS monolayers, and at an initial surface pressure of 30 mN m(-1), the peptide induced surface pressure changes in these monolayers that correlated strongly with their anionic lipid content (maximal at 4 mN m(-1) in the presence of 10% DMPS). Neutron diffraction studies showed VP1 to be localized at the hydrophobic core of model palmitoyloleylphosphatidylcholine/palmitoyloleylphosphatidylserine (10:1 molar ratio) bilayer structures and, in combination, these results are consistent with the oblique membrane penetration predicted for the peptide. It would also appear that although not needed for structural stabilization anionic lipid was required for membrane penetration.

Calpain↗
PubMed1995

Relationship of 13C NMR chemical shift tensors to diffraction structures.

13C chemical shift tensor measurements on single crystals provide a powerful method to study changes in the electron environment of nuclei with changes in molecular structure. Thus, diffraction structures are critical to an understanding of chemical shift tensors. This work explores the general reliability of using structural data to predict components of the symmetrical chemical shift tensor. Imprecision in the hydrogen positions introduces considerable scatter in the simulated 13C shift tensors, and optimized C-H bond distances in methyl-beta-D-glucopyranoside used with the X-ray positions of the heavier C and O atoms greatly improve the simulated chemical shifts. Acenaphthene, with two crystallographically different molecules per unit cell, offers an excellent example for comparing and contrasting structural differences in the two molecules. A recently improved X-ray structure of naphthalene obtained at low temperature provides chemical shift simulations which are comparable to those from neutron diffraction methods and appear to reflect breaks in the D2h symmetry measured in the NMR chemical shift tensors. These data illustrate the close relationship between NMR and diffraction structures.

Carbohydrate Conformation↗
PubMed2005

Electron-density distribution in cubic SrTiO3: a comparative gamma-ray diffraction study.

The electron density and atomic displacements in the perovskite SrTiO(3) have been studied using extensive and accurate gamma-ray diffraction data (lambda = 0.0392 A) at room temperature. The six strongest low-order structure factors have been determined under extinction-free conditions. Gram-Charlier series expansion of the thermal parameters have revealed no evidence for anharmonicity. The population of the 3d subshell on Ti is found to be close to zero, in agreement with the observed magnetic behaviour. The electronic properties at the bond critical points indicate ionic Ti-O and Sr-O interactions of different strengths, which is corroborated by the net charges of the atomic basins [q(Sr) = 1.18 |e|, q(Ti) = 3.10 |e|, q(O) = -1.42 |e|]. A critical comparison is made with earlier experimental results from laboratory X-ray, synchrotron X-ray, electron and neutron diffraction studies. Agreement and discrepancies are identified and resolved.

Journal Article↗
PubMed2005

Synthesis and characterization of a porous magnetic diamond framework, Co3(HCOO)6, and its N2 sorption characteristic.

[Co3(HCOO)6](CH3OH)(H2O) (1), the isostructural analogue of the porous magnet of coordination framework [Mn3(HCOO)6](CH3OH)(H2O), and its desolvated form [Co3(HCOO)6] (2) were prepared and characterized by X-ray and neutron diffraction methods, IR, thermal analyses, and BET, and their magnetic properties were measured. The parent compound, 1, crystallizes in the monoclinic system, space group P21/c, a = 11.254(2) A, b = 9.832(1) A, c = 18.108(3) A, beta = 127.222(2) degrees , V = 1595.5(4) A3, Z = 4, R1 = 0.0329 at 180 K. It possesses a unit cell volume that is 9% smaller than [Mn3(HCOO)6](CH3OH)(H2O) due to the smaller radius of Co2+ ion. Compared with the parent compound 1, the desolvated compound 2 has slightly larger lattice with cell parameters of a = 11.2858(4) A, b = 9.8690(4) A, c = 18.1797(6) A, beta = 127.193(2) degrees , V = 1613.0(1) A3, R1 = 0.0356 at 180 K. The cell parameters of 2, obtained from neutron powder data at 2 K, are a = 11.309(2) A, b = 9.869(1) A, c = 18.201(3) A, beta = 127.244(8) degrees , V = 1617.3(5) A3. The pore volume reduces from 33% to 30% by replacing Mn by Co. The material exhibits a diamond framework based on Co-centered CoCo4 tetrahedral nodes, in which all metal ions have octahedral coordination geometry and all HCOO groups link the metal ions in syn-syn/anti modes. It displays thermal stability up to 270 degrees C. The compound easily loses guest molecules without loss of crystallinity, and it partly reabsorbs water from the atmosphere. Significant N2 sorption was observed for the desolvated framework suggesting that the material possesses permanent porosity. The magnetic properties show a tendency to a 3D long-range magnetic ordering, probably antiferromagnetic with a spin canting arrangement below 2 K.

Journal Article↗
PubMed1992

Molecular basis for the inhibition of 1,4-dihydropyridine calcium channel drugs binding to their receptors by a nonspecific site interaction mechanism.

The "membrane bilayer" pathway (Rhodes, D. G., J. G. Sarmiento, and L. G. Herbette. 1985. Mol. Pharmacol. 27:612-623.) for 1,4-dihydropyridine calcium channel drug (DHP) binding to receptor sites in cardiac sarcolemmal membranes has been extended to include the interaction of amphiphiles within the lipid bilayer. These studies focused on the ability of the Class III antiarrhythmic agents bretylium and clofilium to nonspecifically inhibit DHP-receptor binding in canine cardiac sarcolemma. Clofilium was found to inhibit nimodipine binding with an inhibition constant of approximately 5 microM, whereas bretylium had no effect on nimodipine binding. Small angle x-ray diffraction was then used to examine the differential ability of these two Class III agents to inhibit DHP-receptor binding. The time-averaged locations of bretylium, clofilium, and nimodipine in bovine cardiac phosphatidylcholine (BCPC) bilayers (supplemented with 13 mol% cholesterol) were determined to a resolution of 9 A. The location of bretylium as dominated by its phenyl ring in BCPC bilayers was found to be at the hydrocarbon core/water interface, similar to that of the dihydropyridine ring of nimodipine. The location of clofilium as dominated by its phenyl ring was found to be below the hydrocarbon/core water interface within the hydrocarbon chain region of the bilayer, similar to that of the phenyl ring of nimodipine. The location of the dihydropyridine ring portion of nimodipine has previously been shown by neutron diffraction to be located at the hydrocarbon core/water interface of native sarcoplasmic reticulum, consistent with the small angle x-ray data from model membranes in this paper. Therefore, we speculate that the nonspecific inhibition arises from the interaction of clofilium's phenyl ring with the site on the calcium channel receptor where the phenyl ring portion of nimodipine must interact. The DHP-receptor binding pathway would then involve both nonspecific (membrane) and specific (protein) binding components, both of which are necessary for receptor binding.

Animals↗
PubMed1989

The nature of the hydrophobic binding of small peptides at the bilayer interface: implications for the insertion of transbilayer helices.

One method of obtaining useful information about the physical chemistry of peptide/bilayer interactions is to relate thermodynamic parameters of the interactions to structural parameters obtained by diffraction methods. We report here the results of the application of this approach to interactions of hydrophobic tripeptides of the form Ala-X-Ala-O-tert-butyl with lipid bilayers. The thermodynamic constants (delta Gt, delta Ht, and delta St) for the transfer of the tripeptides from water into DMPC vesicles were determined for X = Leu, Phe, and Trp and found to be consistent with those expected for hydrophobic interactions above the phase transition of DMPC. Combining these results with the earlier ones of Jacobs and White [(1986) Biochemistry 25, 2605-2612], the favorable free energies of transfer with different amino acids in the -X- position increase in the order Gly less than Ala less than Leu less than Phe less than Trp in agreement with the Nozaki and Tanford [(1971) J. Biol. Chem. 246, 2211-2217] hydrophobicity scale. Determination of the location of Ala-[2H5]Trp-Ala-O-tert-butyl in oriented DOPC bilayers by neutron diffraction shows that the most hydrophobic peptide of the series is confined to the bilayer headgroup/water region. Refinement of the diffraction measurements shows that only 13% of the tryptophan is associated with the hydrocarbon core. The distribution of the water tends to mirror that of the peptide. Unlike peptide-free bilayers, 5% of the water penetrates the hydrocarbon, which is about 100-fold greater than expected. A quantitative thermodynamic analysis of the interfacial binding of the peptides suggests that (1) the hydrophobic interactions are 60-70% complete upon binding at the bilayer interface, (2) the interface is likely to play an important role in helix formation and insertion, (3) the hydrogen bond status of amino acid side chains is crucial to insertion, and (4) an a priori lack of knowledge of the status of such bonds could limit the precision of hydrophobicity plots. We introduce an interfacial hydrophobicity scale, IFH(h), with a variable hydrogen bond parameter (h) that permits one to consider explicitly hydrogen bonding in transbilayer helix searches.

Amino Acids↗
PubMed1985

Hexane dissolved in dioleoyllecithin bilayers has a partial molar volume of approximately zero.

Neutron diffraction has been used to measure the amount and distribution of hexane incorporated from the vapor phase into oriented dioleoylphosphatidylcholine bilayers at 66% relative humidity. We reported earlier that hexane at low concentrations is located largely in a zone 10 A wide at the center of the bilayer [White, S. H., King, G. I., & Cain, J. E. (1981) Nature (London) 290, 161-163]. Extending these studies to high hexane concentrations, we find no readily apparent change in the volume of the hydrocarbon region of the bilayer even though more than one hexane molecule per lipid enters the region. The hexane partial molar volume in the bilayer hydrocarbon region is thus approximately zero. Within our statistical confidence limits, the partial molar volume is certainly no greater than one-third the molecular volume of the hexane. Further, analysis of the data suggests that the mass density of the bilayer is considerably less than 1 in the absence of hexane. These findings are in conflict with the assumptions usually made about lipid bilayers and their interaction with nonpolar hydrophobic molecules. In the course of these experiments, we found that standard methods of interpreting diffraction results were not suitable for our purposes. We thus developed several new methods which are summarized in the text and two appendixes. One of these methods allows us to define with precision the width of the hydrocarbon core of the bilayer. The other provides a means of calculating the effects of changes in the absolute scaling of the bilayers with changes in composition without placing the structures on an absolute scattering length density scale.

Hexanes↗
PubMed1983

Organization of calcium pump protein dimers in the isolated sarcoplasmic reticulum membrane.

The arrangement of the calcium pump protein in the isolated sarcoplasmic reticulum (SR) membrane was examined by optical diffraction of freeze-fracture electron micrographs. Several states of protein particle organization were observed: random, hexagonal and tetragonal packing, and a mixture of hexagonal and tetragonal packing. This suggests that the time-averaged positions of protein particles in the plane of the SR membrane are weakly defined. In addition, there appears to be a greater degree of local or short-range order compared to long-range order within the field of freeze-fracture particles. We utilized measurements from tetragonally or hexagonally packed arrays to determine a unit cell area occupied by each freeze-fracture particle and its associated lipid matrix. When these unit cell areas and the stereologically determined area per freeze-fracture particle were compared to the cross-sectional area occupied by a single calcium pump protein and its associated lipid, obtained by x-ray and neutron diffraction methods, we concluded that each freeze-fracture particle probably represents a dimer of pump protein molecules in the plane of the SR membrane.

Animals↗
PubMed2001

Low-resolution detergent tracing in protein crystals using xenon or krypton to enhance X-ray contrast.

Xenon and krypton show different solubilities in polar versus apolar solvents. Therefore, these noble gases should accumulate in apolar regions of protein crystals. Specifically, they should accumulate in lipid and detergent solvent regions within crystals of membrane proteins, which can be used as a basis for contrast-variation experiments to distinguish such apolar solvent regions from the aqueous phase by a low-resolution X-ray diffraction experiment. This possibility was explored with the OmpF porin, one of the general diffusion pores of the Escherichia coli outer membrane. Trigonal crystals were exposed to elevated pressures of the two noble gases (up to 10(7) Pa) for several minutes and subsequently flash-cooled to liquid-nitrogen temperatures. Both rare gases bind to a number of 'specific' sites, which can be classified as 'typical' noble-gas binding sites. Compared with a representative water-soluble protein, they are however much more abundant in OmpF. In addition, a very large number of weakly populated sites are observed which accumulate in the region of the 'detergent belt' for crystals exposed to xenon. After application of a Fourier-filtering protocol, low-resolution images of the detergent belt can be obtained. The resulting maps are similar to maps obtained from low-resolution neutron diffraction experiments on contrast-matched crystals.

Crystallography, X-Ray↗
PubMed1998

The lipase/colipase complex is activated by a micelle: neutron crystallographic evidence.

The catalytic activity of most lipases depends on the aggregation state of their substrates. It is supposed that lipase activation requires the unmasking and structuring of the enzyme's active site through conformational changes involving the presence of oil-in-water droplets. This phenomenon has been called interfacial activation. Here, we report the crystal structure of the pancreatic activated lipase/colipase/micelle complex as determined using the D2O/H2O contrast variation low resolution neutron diffraction method. We find that a disk-shaped micelle interacts extensively with the concave face of colipase (CL) and the distal tip of the C-terminal domain of lipase away from the active site of the enzyme. Such interaction appears to help stabilizing the lipase-CL interaction. Consequently, we conclude that lipase activation is not interfacial but occurs in the aqueous phase and it is mediated by CL and a micelle.

Animals↗
PubMedDate not supplied

Effect of protein packing structure on side-chain methyl rotor conformations.

Protein molecules undergo a series of conformational fluctuations ranging in degree from atomic vibrations to transient denaturation, even in physiological conditions. The rotational motions of amino acid side chains form an important subset of the types of fluctuation a protein can undergo. NMR and molecular dynamics have shown that methyl groups in proteins are not held in fixed positions, but spin rapidly around their rotor axes. The question then arises as to whether methyl groups in proteins predominantly adopt the 'staggered' conformation, favoured by the intrinsic barrier to rotation of these groups, or whether cooperative packing effects in the folded protein perturb the average configurations to higher torsional energy. We report here an investigation of the rotational conformations of the methyl groups of aliphatic side chains in the protein crambin by neutron diffraction. We find that in the time-averaged structure of this protein, the majority of methyl rotors adopt the staggered conformation. This is consistent with rotation being a quantized event consisting of rapid reorientations of approximately 120 degrees steps to positions of highest stability. The fact that the local environment does not dictate the low energy state of methyl groups suggests that within the seemingly close-packed interior structure of a protein, mutual packing accommodation occurs as a consequence of the inherent flexibility and small packing defects in protein structures.

Motion↗
PubMed1995

An atomic model of the unregulated thin filament obtained by X-ray fiber diffraction on oriented actin-tropomyosin gels.

We present a model of the actin-tropomyosin complex in which the radial and azimuthal position of tropomyosin was adjusted to fit the X-ray fiber diffraction patterns from oriented actin-tropomyosin gels at a resolution of 1/8 A-1. We used the recently published atomic F-actin model for the calculations. The atomic model of tropomyosin was obtained by model-building a coiled coiled-coil structure from the tropomyosin sequence. The resulting atomic model is strongly preferred and shows strong electrostatic interactions between charged side-chains of tropomyosin residues and actin residues in subdomain 3 and subdomain 4. Furthermore, calculations of enthalpies based upon electrostatic interactions indicate that there is a favored rotational position of the tropomyosin core at the calculated azimuthal and radial position given by the X-ray refinement. Rotations of the tropomyosin strand out of this position turn strongly attractive electrostatic interactions into repulsive forces. The resulting binding radius of 39 A and the determined azimuthal position of tropomyosin are in good agreement with electron microscopy reconstructions and neutron diffraction experiments. Furthermore, the calculated position of tropomyosin would still partly block the rigor interaction of myosin cross-bridges with actin, whereas it very likely allows undisturbed binding of the cross-bridges in a weak binding state.

Actins↗
PubMed1984

Neutron scattering shows that cytochrome b5 penetrates deeply into the lipid bilayer.

Cytochrome b5 was asymmetrically reconstituted into small lipid vesicles made of a highly deuterated phospholipid. Small-angle neutron diffraction patterns were collected in a series of H2O-D2O mixtures from vesicles consisting of lipid and native or trypsinized cytochrome b5. The second moment of the radial distribution of scattering density in the vesicles was derived from these data and was compared to values calculated from three proposed models, which differ by the degree that cytochrome b5 penetrates the lipid bilayer. The model in which the hydrophobic domain of the protein is distributed across the bilayer agreed most closely with the data.

Animals↗
PubMed1983

Structure and thermotropic properties of 1,3-dipalmitoyl-glycero-2-phosphocholine.

The structure and thermotropic properties of hydrated 1,3-dipalmitoyl-glycero-2-phosphocholine (beta-DPPC) have been studied by X-ray diffraction and differential scanning calorimetry. After prolonged storage at -3 degrees C, differential scanning calorimetry heating scans exhibit endothermic transitions at 27 degrees C and 37 degrees C, with transition enthalpies, delta H = 9.1 and 10.5 kcal/mol beta-DPPC, respectively (1 cal = 4.184 J). Upon cooling, the high temperature transition is completely reversible, whereas the low temperature transition is not. Prolonged incubation of hydrated beta-DPPC at low temperatures is necessary in order to regain the full enthalpy of the low temperature transition, indicating metastability of the low temperature form. X-ray diffraction studies indicate three different lamellar phases upon heating equilibrated beta-DPPC from -3 degrees C: (1) below 18 degrees C, a hydrated (14 mol water/mol beta-DPPC) "crystalline" bilayer phase, Lc, with an ordered hydrocarbon chain-packing mode and a bilayer periodicity d = 58 A; (2) between 30 degrees C and 35 degrees C, a hydrated (22 mol water/mol beta-DPPC) gel phase, L beta, with hexagonal chain-packing and d = 47 A; hydrocarbon chain interdigitation in this phase is suggested by the small bilayer periodicity, a sharp, symmetric wide-angle reflection at 1/4.2 A-1, an area per mol beta-DPPC at the interface of approximately 80 A2, electron density profiles and structure factor calculations using strip electron density models; (3) above 37 degrees C, a highly hydrated (48 mol water/mol beta-DPPC) liquid crystalline bilayer phase, L alpha, with d = 65 A. Previous nuclear magnetic resonance and neutron diffraction studies have suggested that in beta-DPPC the glycerol backbone adopts an orientation parallel to the bilayer surface, in contrast to its usual perpendicular orientation in alpha-DPPC. This conformation presumably results in an increased intramolecular chain separation, with consequent changes in the molecular packing, hydration and thermotropic behavior of beta-DPPC, compared to its positional isomer alpha-DPPC.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed1991

Membrane-mediated assembly of filamentous bacteriophage Pf1 coat protein.

Filamentous bacteriophage Pf1 assembles by a membrane-mediated process during which the viral DNA is secreted through the membrane while being encapsulated by the major coat protein. Neutron diffraction studies showed that in the virus most of the coat protein consists of two alpha-helical segments arranged end-to-end with an intervening mobile surface loop. Nuclear magnetic resonance studies of the coat protein in the membrane-bound form have shown that the secondary structure is essentially identical to that in the intact virus. A comparison indicates that during membrane-mediated viral assembly, while the secondary structure of the coat protein is largely conserved, its tertiary structure changes substantially.

Bacteriophages↗
PubMedDate not supplied

An evaluation of NMR cryoporometry, density measurement and neutron scattering methods of pore characterisation.

Sol-gel silicas with nominal pore diameters ranging from 25A to 500A were studied by NMR cryoporometry, and by neutron diffraction and small angle scattering from dry silicas over the Q range 8. 10(-4)A(-1) < or = Q < or = 17A(-1). Density and imbibation experiments were also performed. Geometric models of porous systems were constructed and were studied by both analytic techniques and Monte-Carlo integration. These models, combined with the information from the above measurements, enabled the calculation of the fully density corrected solid-solid density correlation functions G(r) for the sol-gel silicas, deduction of the (voidless) silica matrix density, measurement of the silica fraction in the grain and of the packing fraction of the silica grains and an estimation of the water equivalent residual hydrogen on the dried silica surface. In addition, the pore diameter D, pore diameter to lattice spacing ratio D/a, and pore and lattice variance sigma could also be measured. While the NMR cryoporometry pore diameter measurements for the sol-gel silicas show excellent co-linearity with the nominal pore diameters as measured by gas adsorption, and the calculated pore diameters from the measured neutron scattering show surprisingly good agreement with these measurements at large pore diameters, there is a divergence between the calibrations for pore diameters below about 100A.

Magnetic Resonance Spectroscopy↗
PubMed1983

Fibrinogen and fibrin structure and fibrin formation measured by using magnetic orientation.

Accurate birefringence measurements show that fibrinogen orients to a small degree in high magnetic fields. This effect can be explained as due to the molecule having about 30% (by weight) alpha-helix oriented relatively parallel to the long axis. Birefringence measurements on fully oriented fibrin suggest that aligned alpha-helical content is less than that estimated for fibrinogen. But because of limitations in the analysis this difference must be viewed with caution. Highly oriented fibrin results when polymerization takes place slowly in a strong magnetic field. Low-angle neutron diffraction patterns from oriented fibrin made in the presence of EDTA, made in the presence of calcium, or stabilized with factor XIIIa are very similar, showing that the packing of the molecules within the fibers is the same or very similar in these different preparations. The induced magnetic birefringence was used to follow fibrin formation under conditions in which thrombin was rate limiting. The fiber network formed by approximately the gelation point constitutes a kind of matrix or frame that is largely built upon during the remaining approximately 85% of the reaction. After gelation the reaction is pseudo-first order.

Animals↗