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PubMed1999

Orientation of the headgroup of phosphatidylinositol in a model biomembrane as determined by neutron diffraction.

Derivatives of the sodium salt of dimyristoylphosphatidylinositol (DMPI) have been synthesized specifically deuterated in the headgroup. A 50:50 (molar) mixture of DMPI with dimyristoylphosphatidylcholine (DMPC) hydrated to the level of 16 waters/lipid gives a biomembrane-like Lalpha phase at 50 degrees C. Comparison of the neutron diffraction scattering profiles for deuterated and undeuterated membranes allowed the depth of each deuterium (hydrogen) within the bilayer to be determined to +/-0.5 A. This gave the orientation of the inositol ring which lies more-or-less along the bilayer normal projecting directly out into the water. This orientation is similar to that of the sugar residue in glycolipids and confirms previous models for PI. On the assumption that the (P)O-DAG bond is more-or-less parallel to the bilayer normal, it is consistent with a roughly trans, trans, trans, gauche- conformation for the glyceryl-phosphate-inositol link. In the case of DMPI, it is the C4-hydroxy group which is most fully extended into the water layer, but when this is phosphorylated, the inositol ring turns over and tilts so that the C5-hydroxy group is now the one furthest extended into the water layer. Hence, at each stage in the pathway PI --> PI-4P --> PI-4,5-P2, it is the hydroxy position most exposed to the water which undergoes phosphorylation. Whereas the orientation of the inositol ring in DMPI can be seen simply as maximizing its hydration, the tilt of the ring in DMPI-4P cannot be explained in this way. It is suggested that it is due to an electrostatic interaction.

Carbohydrate Conformation↗
PubMed1991

Neutron diffraction studies of the structure of filamentous bacteriophage Pf1. Demonstration that the coat protein consists of a pair of alpha-helices with an intervening, non-helical surface loop.

The structure of filamentous bacteriophage Pf1 has been studied using neutron diffraction from magnetically oriented gels of native and specifically deuterated phage. These methods have been used to determine the positions of the two methionine, two tyrosine and six isoleucine residues of the coat protein. Combined with the positions of the five valine residues previously determined, they represent one third (15 of 46) of the residues of the coat protein. These 15 amino acid residue positions have been used as the basis for constructing a model for the protein consisting of two alpha-helices with an intervening surface loop. The first helix extends from near the amino terminus to Ile12. The second helix extends from Lys20 to at least Met42, and may contain a bend between Ile32 and Val35. The two helices are tilted by about 15 degrees relative to one another, and are positioned in such a way that they appear to be bound end-to-end by main-chain hydrogen bonds. The intervening, non-helical loop, made up of Thr13 to Met19, connects the two helices without disrupting the pattern of main-chain hydrogen bonding, but does not result in a bend in the otherwise continuous helical structure. This model is used to predict the approximate positions of all amino acid residues in the Pf1 protein coat, providing a basis for further understanding of a number of viral properties including the symmetry transitions, the non-isomorphism of heavy-atom derivatives, and the protein-protein and protein-DNA interactions in the virion.

Amino Acid Sequence↗
PubMedDate not supplied

A combined X-ray and neutron diffraction study of selectively deuterated melittin in phospholipid bilayers: effect of pH.

In order to study consequences of protonation of the N-terminus upon the interaction of the bee venom melittin with phospholipid bilayers, analogues of melittin, some of which were specifically deuterated at either Ala-12 or 15, were synthesized. These peptides were incorporated into bilayers of 1,2-dioleoyl-sn-glycero-3-phosphocholine at either low pH (N-terminus protonated) or high pH (N-terminus unprotonated). X-ray and neutron diffraction data were collected from ordered stacks of these bilayers and from peptide-free controls. Phase determination was carried out using the swelling series (X-ray) and isomorphous derivative (neutron) methods. The water distribution between adjacent bilayers in the stacks may be described by a pair of Gaussians whose position and width change with the protonation state of the melittin. Difference Fourier profiles reveal that the melittin largely incorporates into the phospholipid bilayers. Changes in the water, melittin and deuterium label distributions fit a model in which the melittin lies both at the surface and close to the centre of the bilayer, the distribution of peptide between these locations being pH-dependent, with a larger population of surface melittin when the N-terminus is unprotonated.

Amino Acid Sequence↗
PubMed1981

The reaction center profile structure derived from neutron diffraction.

Both reaction center protein from the photosynthetic bacteria Rhodopseudomonas sphaeroides and egg phosphatidylcholine can be deuterium labelled; the reaction center protein can be incorporated into the phosphatidylcholine bilayers forming a homogeneous population of unilamellar vesicles. The lipid profile and the reaction center profile within these reconstituted membrane profiles were directly determined to 32 A resolution using lamellar neutron diffraction from oriented membrane multilayers containing either deuterated or protonated reaction centers, and either deuterated or protonated phosphatidylcholine. The 32 A resolution reaction center profile shows that the protein spans the membranes, and has an asymmetric mass distribution along the perpendicular to the membrane plane. These results were combined with previously described X-ray diffraction results in order to extend the resolution of the derived reaction center profile to 9 A.

Bacterial Proteins↗
PubMed1991

Fluid bilayer structure determination by the combined use of x-ray and neutron diffraction. I. Fluid bilayer models and the limits of resolution.

This is the first in a series of papers concerned with methods for the determination of the structures of fluid phospholipid bilayers in the liquid-crystalline (L alpha) phase. The basic approach is the joint refinement of quasimolecular models (King and White, 1986. Biophys. J. 49:1047-1054) using x-ray and neutron diffraction data. We present here (a) the rationale for quasimolecular models, (b) the nature of the resolution problem for thermally disordered bilayers, and (c) an analysis of the resolution of experiments in which Gaussian functions are used to describe the distribution of submolecular components. We show that multilamellar liquid-crystalline bilayers are best described by the convolution of a perfect lattice function with a thermally disordered bilayer unit cell. Lamellar diffraction measurements on such a system generally yield only 5-10 orders of diffraction data from which transbilayer profiles of the unit cell can be constructed. The canonical resolution of these transbilayer profiles, defined as the Bragg spacing divided by the index of the highest recorded diffraction order, is typically 5-10 A. Using simple model calculations, we show that the canonical resolution is a measure of the widths of the distributions of constituents of the unit cell rather than a measure of the spatial separation of the distributions. The widths provide a measure of the thermal motion of the bilayer constituents which can be described by Gaussian functions. The equilibrium positions of the centers of the distributions can be determined with a precision of 0.1-0.5 A based upon typical experimental errors.

Lipid Bilayers↗
PubMed2004

Crystalline, mixed-valence manganese analogue of prussian blue: magnetic, spectroscopic, X-ray and neutron diffraction studies.

The compound of stoichiometry Mn(II)3[Mn(III)(CN)6]2.zH2O (z = 12-16) (1) forms air-stable, transparent red crystals. Low-temperature single crystal optical spectroscopy and single crystal X-ray diffraction provide compelling evidence for N-bonded high-spin manganese(II), and C-bonded low-spin manganese(III) ions arranged in a disordered, face-centered cubic lattice analogous to that of Prussian Blue. X-ray and neutron diffraction show structured diffuse scattering indicative of partially correlated (rather than random) substitutions of [Mn(III)(CN)6] ions by (H2O)6 clusters. Magnetic susceptibility measurements and elastic neutron scattering experiments indicate a ferrimagnetic structure below the critical temperature Tc = 35.5 K.

Journal Article↗
PubMed2002

Structure and dynamics of ND3BF3 in the solid and gas phases: a combined NMR, neutron diffraction, and Ab initio study.

The decrease in D-->A bond lengths, previously reported for some Lewis acid/base complexes, in going from the gas to the solid phases is investigated by obtaining an accurate crystal structure of solid ND(3)BF(3) by powder neutron diffraction. The B-N internuclear distance is 1.554(3) A, 0.118 A shorter than the most recent gas-phase microwave value and 0.121 A shorter than the single molecule geometry optimized (1.672 A, CISD/6-311++G(d,p)) bond length. The crystal structure also shows N-D.F-B hydrogen bonds. The effects of this change in structure and of intermolecular hydrogen-bonding on nuclear magnetic shielding (i.e., chemical shifts) and the nuclear quadrupolar coupling constants (QCC) are investigated by ab initio molecular orbital and density functional theory calculations. These calculations show that the nitrogen ((15)N and (14)N) and boron ((11)B and (10)B) chemical shifts should be rather insensitive to changes in r(BN) and that the concomitant changes in molecular structure. Calculations on hydrogen-bonded clusters, based on the crystal structure, indicate that H-bonding should also have very little effect on the chemical shifts. On the other hand, the (11)B and (14)N QCCs show large changes because of both effects. An analysis of the (10)B[(19)F] line shape in solid ND(3)(10)BF(3) yields a (11)B QCC of +/-0.130 MHz. This is reasonably close an earlier value of +/-0.080 MHz and the value of +/-0.050 MHz calculated for a [NH(3)BF(3)](4) cluster. The gas-phase value is 1.20 MHz. Temperature-dependent deuterium T(1) measurements yield an activation energy for rotation of the ND(3) group in solid ND(3)BF(3) of 9.5 +/- 0.1 kJ/mol. Simulations of the temperature-dependent T(1) anisotropy gave an E(a) of 9.5 +/- 0.2 kJ/mol and a preexponential factor, A, of 3.0 +/- 0.1 x 10(12) s(-)(1). Our calculated value for a [NH(3)BF(3)](4) cluster is 16.4 kJ/mol. Both are much higher than the previous value of 3.9 kJ/mol, from solid-state proton T(1) measurements.

Journal Article↗
PubMed2005

Propene adsorption sites in zeolite ITQ-12: a combined synchrotron X-ray and neutron diffraction study.

The adsorption site of propene in the small-pore, pure silica zeolite [Si24O48]-ITW-ITQ-12 has been characterized via Rietveld refinement of the crystal structure of propene-loaded ITQ-12 on the basis of synchrotron X-ray and neutron diffraction data taken at 298 K. The structure can be described with a monoclinic unit cell having Cm symmetry and unit cell parameters a = 10.436 angstroms, b = 15.018 angstroms, c = 8.855 angstroms, beta = 105.74 degrees, and volume = 1335.9 angstroms3. Four-fold disordered adsorption sites that are nearly equivalent relative to the cage's 2/m pseudosymmetry are located near the center of each ellipsoidally shaped [4(4)5(4)6(4)8(4)] cage. At this site, the adsorbed propene molecule lies on a plane close and approximately parallel to the equatorial plane of the cage and is aligned with its methylene group pointing toward the pore's eight-ring window. The refined propene concentration, 1.8 per unit cell content, is close to one propene molecule per [4(4)5(4)6(4)8(4)] cage and the amount observed in adsorption experiments at 298 K and 1 atm propene partial pressure.

Journal Article↗
PubMed1983

The determination of the separate Ca2+ pump protein and phospholipid profile structures within reconstituted sarcoplasmic reticulum membranes via X-ray and neutron diffraction.

We have previously compared the electron density profiles for several highly-functional reconstituted sarcoplasmic reticulum membranes with that for the isolated sarcoplasmic reticulum membrane (Herbette, L., Scarpa, A., Blasie, J.K., Wang, C.T., Saito, A. and Fleischer, S. (1981) Biophys. J. 36, 47-72). In this paper, we compare the separate calcium pump protein profile within these reconstituted sarcoplasmic reticulum membranes, as derived by X-ray and neutron diffraction methods, with that within isolated sarcoplasmic reticulum membranes. In addition, the time-average perturbation of the lipid bilayer by the incorporated calcium pump protein within these reconstituted sarcoplasmic reticulum membranes has been determined in some detail.

Animals↗
PubMed1980

Neutron diffraction identifies His 57 as the catalytic base in trypsin.

The mechanism of action of trypsin and other serine proteases has been widely debated, particularly with regard to the identification of the group at the active site which functions as the chemical base during the catalytic process. Attempts to resolve this question by a number of indirect techniques, including NMR, isotope exchange, difference IR and quantum mechanical calculations, have resulted in different identifications of this group. Neutron diffraction, because of its ability to locate hydrogen atoms experimentally, offers the most direct way of resolving this issue. Results are presented here from a 2.2-A neutron data set for bovine trypsin covalently inhibited by a transition-state analogue, the monoisopropylphosphoryl (MIP) group. His 57 is clearly identified as the base in the catalytic process.

Amino Acid Sequence↗
PubMed2002

Electron distribution and molecular motion in crystalline benzene: an accurate experimental study combining CCD X-ray data on C6H6 with multitemperature neutron-diffraction results on C6D6.

The electronic properties of the benzene molecule, for example its quadrupole moment and the electric field gradients (EFG's) at the H nuclei, are of fundamental importance in theoretical and experimental chemistry. With this in mind, single-crystal X-ray diffraction data on C(6)H(6) were collected with a charge-coupled device detector at T approximately 110 K. As accurate modelling of the thermal motion in the crystal was regarded as vital, especially for the hydrogen atoms, anisotropic-displacement parameters (ADP's) for the C and H atoms in C(6)H(6) were derived in a straightforward fashion from analysis of the temperature dependence of ADP's for the C and D atoms in C(6)D(6) at 15 K and 123 K obtained by neutron diffraction. Agreement between C-atom ADP's derived from thermal-motion analysis of neutron data and those obtained from multipole refinement by using the X-ray data is extraordinarily good; this gives confidence in the modelling of vibrational motion for the H atoms. The molecular quadrupole moment derived from the total charge density of the molecule in the crystal is (-29.7+/-2.4)x10(-40) C m(2), in excellent agreement with measurements made in the gas phase and in solution. The average deuterium nuclear quadrupole coupling constant (DQCC) derived from EFG tensors at H atoms is 182+/-17 kHz, also in excellent agreement with independent measurements. The strategy employed in this work may be of more general applicability for future accurate electron density studies.

Benzene↗
PubMed2004

Modeling the structure of amorphous MoS3: a neutron diffraction and reverse Monte Carlo study.

A model for the structure of amorphous molybdenum trisulfide, a-MoS3, has been created using reverse Monte Carlo methods. This model, which consists of chains of MoS6 units sharing three sulfurs with each of its two neighbors and forming alternate long, nonbonded, and short, bonded, Mo-Mo separations, is a good fit to the neutron diffraction data and is chemically and physically realistic. The paper identifies the limitations of previous models based on Mo3 triangular clusters in accounting for the available experimental data.

Journal Article↗
PubMed2001

Lu2SiO5 by single-crystal X-ray and neutron diffraction.

The structure of dilutetium silicon pentaoxide, Lu2SiO5, has isolated ionic SiO4 tetrahedral units and non-Si-bonded O atoms in distorted OLu4 tetrahedra. The OLu4 tetrahedra form edge-sharing infinite chains and double O2Lu6 tetrahedra along the c axis. The edge-sharing chains are connected to the O2Lu6 double tetrahedra by isolated SiO4 units. The structure has been determined by neutron diffraction.

Crystallography, X-Ray↗
PubMed1994

Light-induced isomerization causes an increase in the chromophore tilt in the M intermediate of bacteriorhodopsin: a neutron diffraction study.

Bacteriorhodopsin (BR) was regenerated with two selectively deuterated retinals, one with 11 deuterons in the beta-ionone ring (D11) and the other with 5 deuterons (D5) at the end of the polyene chain closest to the Schiff base at carbon atoms C-14, C-15, and C-20. Both label positions (centers of deuteration) were obtained from difference Fourier maps of projections onto the plane of the membrane by neutron diffraction at 90 K, both in the light-adapted ground-state BR568 and in the photocycle intermediate M412. To retard the decay of M412, purple membrane films were soaked in 0.1 M or 1 M guanidine hydrochloride at pH 9.6. M412 was produced by illuminating oriented membrane films at physiological temperature (278 K), followed by rapid cooling to 90 K in the absence of light. The results show that in the projected structure the ring position is unaltered during the transition from BR568 to M412, whereas the position of the D5 label shifts by 1.4 +/- 0.9 A toward the ring. The shortened interlabel distance in the projected structure for the M412 state implies that as a result of the all-trans/13-cis isomerization, the C-5 to C-13 part of the polyene chain tilts out of the plane of the membrane toward the cytoplasm by about 11 degrees +/- 6 degrees. Pairwise comparison of data sets with the same retinal for the two photocycle states M412 and BR568 leads to four difference-density maps for the protein, which are in agreement with previous work. They show changes in the protein density near helices G and F.

Bacteriorhodopsins↗
PubMed1996

Neutron diffraction studies of amphipathic helices in phospholipid bilayers.

The structural feature which is thought to facilitate the interaction of many peptides with phospholipid bilayers is the ability to fold into an amphipathic helix. In most cases the exact location and orientation of this helix with respect to the membrane is not known, and may vary with factors such as pH and phospholipid content of the bilayer. The growing interest in this area is stimulated by indications that similar interactions can contribute to the binding of certain hormones to their cell-surface receptors. We have been using the techniques of neutron diffraction from stacked phospholipid bilayers in an attempt to investigate this phenomenon with a number of membrane-active peptides. Here we report some of our findings with three of these: the bee venom melittin; the hormone calcitonin; and a synthetic peptide representing the ion channel fragment of influenza A M2 protein.

Amino Acid Sequence↗
PubMed2006

Competing magnetic interactions in Na10Co4O10, studied by neutron diffraction.

Na(10)Co(4)O(10) was investigated by neutron powder diffraction at 230, 70, and 4 K. The crystal structure, determined previously by X-ray diffraction on single crystals, was confirmed. Na(10)Co(4)O(10) orders magnetically below 37 K. All observed magnetic reflections could be indexed by integers (hkl) with respect to the chemical unit cell and the magnetic propagation vector q=0. The refinement was performed in the Shubnikov space group C2/c and indicated a collinear antiferromagnetic spin structure. The determined spin arrangement is consistent with the magnetic intratetramer interactions suggested previously from the analysis of magnetic susceptibility data: the magnetic moments of the central Co(III) ions of the Co(4)O(10) tetramer lie parallel to each other and couple in an antiparallel fashion to the terminal Co(II) moments. The Rietveld analysis shows that the net moments of 0.64 mu(B) per tetramer form ferromagnetic layers parallel to the ab plane. Adjacent layers are coupled antiferromagnetically along c. The spins are aligned in the ac plane along the line connecting adjacent Co(II) and Co(III) ions of the tetramer. We have determined unusually low values for the ordered magnetic moments of 2.43(5) mu(B) and 2.11(6) mu(B) for Co(III) and Co(II), respectively. The occurrence of spontaneous magnetization below 37 K indicates a slight canting of 2.2 degrees of the antiferromagnetic structure. A representation analysis shows that a weak ferromagnetic component along b is compatible with the determined antiferromagnetic structure.

Journal Article↗
PubMed2004

Electronic interaction in an outer-sphere mixed-valence double salt: a polarized neutron diffraction study of K(3)(MnO(4))(2).

The mixed-valence double salt K(3)(MnO(4))(2) crystallizes in space group P2(1)/m with Z = 2. The manganese centers Mn1 and Mn2 constitute discrete "permanganate", [Mn(VII)O(4)](-), and "manganate", [Mn(VI)O(4)](2-), ions, respectively. There is a spin-ordering transition to an antiferromagnetic state at ca. T = 5 K. The spin-density distribution in the paramagnetic phase at T = 10 K has been determined by polarized neutron diffraction, confirming that unpaired spin is largely confined to the nominal manganate ion Mn2. Through use of both Fourier refinement and maximum entropy methods, the spin on Mn1 is estimated as 1.75 +/- 1% of one unpaired electron with an upper limit of 2.5%.

Journal Article↗
PubMed1988

Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison.

A method for the prediction of hydrogen positions in proteins is presented. The method is based on the knowledge of the heavy atom positions obtained, for instance, from X-ray crystallography. It employs an energy minimization limited to the environment of the hydrogen atoms bound to a common heavy atom or to a single water molecule. The method is not restricted to proteins and can be applied without modification to nonpolar hydrogens and to nucleic acids. The method has been applied to the neutron diffraction structures of trypsin, ribonuclease A, and bovine pancreatic trypsin inhibitor. A comparison of the constructed and the observed hydrogen positions shows few deviations except in situations in which several energetically similar conformations are possible. Analysis of the potential energy of rotation of Lys amino and Ser, Thr, Tyr hydroxyl groups reveals that the conformations of lowest intrinsic torsion energies are statistically favored in both the crystal and the constructed structures.

Hydrogen↗