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At least 19 recordsLinked to original sources

PubMed1998

Structure and hydration of the M-state of the bacteriorhodopsin mutant D96N studied by neutron diffraction.

Neutron diffraction from oriented purple membrane fragments at various hydration levels, coupled with H2O/2H2O exchange, was used to compare the structure and hydration of the light-adapted initial state (B-state) and the M photointermediate of bacteriorhodopsin mutant D96N. Diffraction patterns were recorded at 86%, 75% and 57% relative humidity (r.h.). Structural changes observed at 86% and 75% r.h. are absent at 57% r.h., showing that they are uncoupled from the deprotonation of the Schiff base during formation of the M-state. In a current model, the M-state consists of two substates, M1 and M2. Our data suggest that the state trapped at 57% r.h. is M1 and that M2 is trapped at the higher r.h. values. The observed structural changes are, therefore, associated with the M1-->M2 transition, which can only take place at higher r.h. The difference Fourier projections of exchangeable hydrogen atoms and water molecules in the membrane plane are very similar for the B and M-states at 75% and 86% r.h. This shows that contrary to certain models, the structural changes in the M-state are not correlated with major hydration changes in the proton channel projection.

Asparagine↗

PubMed2002

Structures of high and low density amorphous ice by neutron diffraction.

Neutron diffraction with isotope substitution is used to determine the structures of high (HDA) and low (LDA) density amorphous ice. Both "phases" are fully hydrogen bonded, tetrahedral networks, with local order similarities between LDA and ice Ih, and HDA and liquid water. Moving from HDA, through liquid water and LDA to ice Ih, the second shell radial order increases at the expense of spatial order. This is linked to a fifth first neighbor "interstitial" that restricts the orientations of first shell waters. This "lynch pin" molecule which keeps the HDA structure intact has implications for the nature of the HDA-LDA transition that bear on the current metastable water debate.

Journal Article↗

PubMed1994

Location of diphenyl-hexatriene and trimethylammonium-diphenyl-hexatriene in dipalmitoylphosphatidylcholine bilayers by neutron diffraction.

Neutron scattering experiments have been performed on oriented dipalmitoylphosphatidylcholine (DPPC) bilayers containing diphenylhexatriene (DPH) or its trimethylammonium analog (TMA-DPH). DPH and TMA-DPH were either protonated or deuterated in one of the phenyl rings which afforded by using proton-deuterium contrast methods the location of these fluorescent probes in the model membrane. Both probes exhibit bimodal distributions in DPPC. The position, population and orientation in the two sites vary depending upon the physical state of the bilayer (gel or fluid) and the presence or absence of the TMA group. In gel (L beta') phase lipids DPH is located close and parallel to the bilayer surface (site I) and near the bilayer center, oriented at approximately 30 degrees with respect to the normal to the surface (site II). On going to the fluid (L alpha) phase, a distribution of orientations around the parallel to the surface is only observed for site II. Orientation of DPH in site I is unchanged. In the gel phase TMA-DPH is found in a position close and parallel to the bilayer surface (site I) and in a position (site II) oriented at an angle of approximately 25 degrees with respect to the bilayer normal, with the trimethylammonium group anchored in the head group domain. On going to the fluid phase there is a change in molecular orientation of each of the sites. In site I the molecule penetrates deeper in the bilayer and adopts a approximately 20 degrees tilt with respect to the surface, with an orientational distribution of +/- 10 degrees. In site II the molecule becomes perpendicular to the membrane surface. Changes in population of sites, both with DPH and TMA-DPH, are observed on going from low to high temperatures. They are however difficult to quantitate due to experimental conditions. The H2O-2H2O exchange experiments afforded an estimate of the water layer thickness as well as the maximum penetration of water into the interior of the bilayer.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2002

Beyond Bragg scattering: the structure of AgCN determined from total neutron diffraction.

Total neutron diffraction has yielded accurate bond lengths, Ag-C = Ag-N = 2.06 A and C-N = 1.16 A, for the disordered crystalline solid AgCN. This information cannot be obtained from analysis of Bragg scattering studies, because the (-Ag-CN-)(n) chains are randomly displaced along the chain axis relative to each other by a root-mean-square displacement of 0.24 A at 10 K. These results show the power of total neutron diffraction for determining structure in disordered systems.

Journal Article↗

PubMed1996

High-level expression and deuteration of sperm whale myoglobin. A study of its solvent structure by X-ray and neutron diffraction methods.

Neutron diffraction has become one of the best ways to study light atoms, such as hydrogens. Hydrogen however has a negative coherent scattering factor, and a large incoherent scattering factor, while deuterium has virtually no incoherent scattering, but a large positive coherent scattering factor. Beside causing high background due to its incoherent scattering, the negative coherent scattering of hydrogen tends to cancel out the positive contribution from other atoms in a neutron density map. Therefore a fully deuterated sample will yield better diffraction data with stronger density in the hydrogen position. On this basis, a sperm whale myoglobin gene modified to include part of the A c11 protein gene has been cloned into the T7 expression system. Milligram amounts of fully deuterated holo-myoglobin have been obtained and used for crystallization. The synthetic sperm whale myoglobin crystallized in P2(1) space group isomorphous with the native protein crystal. A complete X-ray diffraction dataset at 1.5A has been collected. This X-ray dataset, and a neutron data set collected previously on a protonated carbon-monoxymyoglobin crystal have been used for solvent structure studies. Both X-ray and neutron data have shown that there are ordered hydration layers around the protein surface. Solvent shell analysis on the neutron data further has shown that the first hydration layer behaves differently around polar and apolar regions of the protein surface. Finally, the structure of per-deuterated myoglobin has been refined using all reflections to a R factor of 17%.

Animals↗

PubMed1994

Structure of suberic acid at 18.4, 75 and 123 K from neutron diffraction data.

Neutron diffraction data for suberic acid [HOOC(CH2)6COOH] were collected at 18.4, 75 and 123 K using a twinned crystal. The neutron data reduction included derivation of a complete set of corrected intensities, as if from a single crystal. This was followed by full-matrix structure refinement in the usual way. The molecule has an almost fully extended conformation with the hydrocarbon chains packed in an orthorhombic mode. Molecules form infinite hydrogen-bonded chains with crystallographic inversion centers occuring at the center and at the ends of each molecule. We suggest that at the twin boundary the hydrogen bonding is different, involving only the hydroxyl groups as both donors and acceptors. Accurate bond lengths have been obtained with corrections for thermal vibration (harmonic for C--C, C--O; harmonic and anharmonic for C--H). Values at the three temperatures agree well in terms of their e.s.d.'s (0.001 A for C--C and C--O and 0.005 A for C--H). Similar agreement is obtained for the corrected bond angles (e.s.d.'s 0.1 degrees for C--C--C, 0.2 degrees for H--C--H). For the methylene groups, the observed m.s. displacement parameters at each temperature are significantly greater at the middle of the molecule than at the ends. This indicates that the molecular backbone is vibrating internally. The thermal vibrations of the molecule have been analysed in terms of a simple segmented body model.

Caprylates↗

PubMed1989

Structural changes in bacteriorhodopsin during proton translocation revealed by neutron diffraction.

A neutron diffraction study of spectroscopic states for the light-energized proton pump bacteriorhodopsin (BR) is presented. The photocycle states BR-568 and M were generated at temperatures above 4 degrees C and were measured after trapping at--180 degrees C. In the BR-568 to M-state transition, which is known to be a key step in transmembrane proton pumping, reversible structural changes of the protein were detected. These structural alterations occur in the neighborhood of the cyclohexene ring and at the Schiff's base end of the chromophore retinal. They are interpreted as a 1-2 degree tilt of three or four of the transmembrane alpha-helices or as positional changes of four or five amino acids. The structural changes observed are inherent in the transport mechanism of bacteriorhodopsin.

Bacteriorhodopsins↗

PubMed1998

Interaction of substance P with phospholipid bilayers: A neutron diffraction study.

Neutron diffraction has been used to study the membrane-bound structure of substance P (SP), a member of the tachykinin family of neuropeptides. The depth of penetration of its C-terminus in zwitterionic and anionic phospholipid bilayers was probed by specific deuteration of leucine 10, the penultimate amino acid residue. The results show that the interaction of SP with bilayers, composed of either dioleoylphosphatidylcholine (DOPC), or a 50:50 mixture of DOPC and the anionic phospholipid dioleoylphosphatidylglycerol (DOPG), takes place at two locations. One requires insertion of the peptide into the hydrophobic region of the bilayer, the other is much more peripheral. The penetration of the peptide into the hydrophobic region of the bilayer is reflected in a marked difference in the water distribution profiles. SP is seen to insert into DOPC bilayers, but a larger proportion of the peptide is found at the surface when compared to the anionic bilayers. The positions of the two label populations show only minor differences between the two types of bilayer.

Deuterium Oxide↗

PubMed2000

Real-time swelling-series method improves the accuracy of lamellar neutron-diffraction data.

Neutron-diffraction data were collected from stacked bilayers of 1, 2-dioleoyl-sn-glycero-phosphocholine under conditions of increasing relative humidity at both 0 and 8.06% (2)H(2)O. Over the period of data collection, the d-repeat of both swelling-series samples increased. Each family of structure factors, representing each of the five orders of diffraction, are shown to lie on smooth curves, allowing structure factors of intermediate d-repeat to be determined. In the case of the 8.06% (2)H(2)O data, but not the 0% (2)H(2)O data, all observed structure factors lie on a single continuous transform. 8.06% (2)H(2)O has a net neutron-scattering density of zero; its use in neutron-diffraction experiments presents a novel application of the so-called 'minus fluid' approach, without mathematical manipulation. The data are used to demonstrate the increased accuracy inherent in this real-time swelling-series approach. A quantitative analysis of errors caused by differences in d--repeat in difference subtractions is presented.

Crystallography↗

PubMed1990

Light- and dark-adapted bacteriorhodopsin, a time-resolved neutron diffraction study.

Recently, neutron diffraction experiments have revealed well-resolved and reversible changes in the protein conformation of bacteriorhodopsin (BR) between the light-adapted ground state and the M-intermediate of the proton pumping photocycle (Dencher, Dresselhaus, Zaccai and Büldt (1989) Proc. Natl. Acad. Sci. USA 86, 7876-7879). These changes are triggered by the light-induced isomerization of the chromophore retinal from the all-trans to the 13-cis configuration. Dark-adapted purple membranes contain a mixture of two pigment species with either the all-trans- or 13-cis-retinal isomer as chromophore. Employing a time-resolved neutron diffraction technique, no changes in protein conformation in the resolution regime of up to 7 A are observed during the transition between the two ground-state species 13-cis-BR and all-trans-BR. This is in line with the fact that the conversion of all-trans BR to 13-cis-BR involves an additional isomerization about the C15 = N Schiff's base bond, which in contrast to M formation minimizes retinal displacement and keeps the Schiff's base in the original protein environment. Furthermore, there is no indication for large-scale redistribution of water molecules in the purple membrane during light-dark adaptation.

Bacteriorhodopsins↗

PubMed1991

Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. I. Scaling of neutron data and the distributions of double bonds and water.

We described in two previous papers a method for the joint refinement of the structure of fluid bilayers using neutron and x-ray diffraction data (Wiener, M. C., and S. H. White 1991a, b. Biophys. J. 59: 162-173 and 174-185). An essential part of the method is the appropriate scaling of the diffraction data. Here we describe the scaling of the neutron data and the determination of the transbilayer distribution of double bonds in liquid-crystalline (L alpha phase) phospholipid bilayers of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). The distribution was determined by neutron diffraction of oriented multilayers (66% RH) of DOPC specifically deuterated at the 9- and 10-position of both acyl chains. The double-bond distribution is described accurately by a pair of Gaussian functions each located at a position Zcc = 7.88 +/- 0.09 A from the bilayer center with 1/e-halfwidths of Acc = 4.29 +/- 0.16 A. Previously, we determined the transbilayer distribution of bromine atoms in a specifically halogenated lipid, 1-oleoyl-2-9,10-dibromostearoyl-sn-glycero-3-phosphocholine (OBPC), and showed it to be an isomorphous replacement for DOPC (Wiener, M. C., and S. H. White, 1991c. Biochemistry. In press). A comparison of the double-bond and bromine profiles indicates that the positions of the centers of the deuterated double bond and the brominated methylene Gaussian distributions are equal within experimental error and that each label undergoes similar average thermal motions with respect to the bilayer normal. The observation that the average position of a label on both acyl chains (the deuterated double bonds) is similar to the average position of a label on the 2-chain alone (the brominated methylenes) indicates that the maximum separation along the bilayer normal between the double bonds of the acyl chains is 1 A or less. The fully-resolved transbilayer water distribution, previously determined at lower resolution (Jacobs, R. E., and S. H. White. 1989. Biochemistry. 28:3421-3437), was obtained from the analysis of neutron diffraction data of DOPC hydrated with a D20/H20 mixture. The water distribution is described accurately by a pair of Gaussian functions each located at a position Zw = 22.51 +/- 0.77 A from the bilayer center with 1/e-half widths of Aw = 4.63 +/- 0.48A. We present the relative absolute neutron and x-ray structure factors of DOPC at 66% RH that will be used to solve the complete structure of DOPC which will be presented in a later paper of this series.

Lipid Bilayers↗

PubMed2001

Tetrachlorobis(N1-phenylacetamidino-kappaN2)rhenium(IV) at 11 K by X-ray diffraction and at 20 K by neutron diffraction.

The crystal structure of the title compound, [ReCl(4)(C(8)H(10)N(2))(2)], has been determined by X-ray diffraction at 11 K and by neutron diffraction at 20 K. The accurate and extensive data sets lead to more precise determinations than are available from earlier work. The agreement in atomic positional and displacement parameters at these very low temperatures is good. The results will facilitate re-examination of the magnetic structure of the complex. The Re atom lies on a special position and the molecule has twofold crystallographic symmetry.

Journal Article↗

PubMed1990

Neutron diffraction from cannabinoids in phospholipid membranes.

Neutron diffraction measurements have been utilized to study the effects of delta 9-tetrahydrocannabinol (delta 9-THC) and delta 8-tetrahydrocannabinol (delta 8-THC) incorporated in phospholipid membranes of dipalmitoylphosphatidylcholine (DPPC). Low-angle diffraction indicated that these cannabinoids induce increases in interlamellar spacing similar to those produced by cholesterol. Wide-angle diffraction indicated significant differences in how the intralamellar structure is affected by the inclusion of either cannabinoids or cholesterol. Similar weight percentages of cholesterol and cannabinoids in membranes yielded different thermal analysis profiles but the profiles for membranes with either delta 8 or delta 9-THC were similar. Since the neutron diffraction results for inclusions of delta 8 and delta 9-THC were also similar, this suggests that the difference in psychoactivity of delta 8 and delta 9-THC is probably due to interactions with membrane proteins rather than with phospholipids.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed1985

Study of ethanol-lysozyme interactions using neutron diffraction.

Single-crystal neutron diffraction has been used to observe the interactions between deuterated ethanol (CD3CD2OH) and lysozyme in triclinic crystals of hen egg white lysozyme soaked in 25% (v/v) ethanol solutions. A total of 6047 observed reflections to a resolution of 2 A were used, and 13 possible ethanol sites were identified. The three highest occupied sites are close to locations for bromoethanol found in an earlier study by Yonath et al. [Yonath, A., Podjarny, A., Honig, B., Traub, W., Sielecki, A., Herzberg, O., & Moult, J. (1978) Biophys. Struct. Mech. 4, 27-36]. Structure refinements including a model for the flat solvent lead to a final crystallographic agreement factor of 0.097. Comparison with earlier neutron studies on triclinic lysozyme showed that neither the molecular structure nor the thermal motions were affected significantly by the ethanol. A detailed analysis of the ethanol-lysozyme contacts showed 61% of these to be with hydrophobic sites, in agreement with the dominant hydrophobic nature of ethanol. This, together with the fact that the molecular structure of lysozyme is not perturbed, suggests a model for denaturation of lysozyme by alcohol, which proceeds via a dehydration of the protein at high alcohol concentration.

Animals↗

PubMed1995

Hexamethylenetetramine: extinction and thermal vibrations from neutron diffraction at six temperatures.

Neutron diffraction data have been collected for hexamethylenetetramine (HMT) at 15, 50, 80, 120, 160 and 200K using a single crystal (mass 8.1 mg). The structure refinement at each temperature included two extinction parameters and third-order thermal parameters for the H nuclei. Extinction effects are very severe with extinction factors as small as 0.2Fkin2 for three reflections (800, 110 and 440). Application of the Sabine extinction theory indicates that the crystal domain size decreases from 115 microns at 200 K to 85 microns at 15 K. The half-width in the mosaic spread (7" of arc) is almost independent of temperature. An extinction model without phase correlations between mosaic blocks gives a slightly better fit to the diffraction data. The nuclear mean square thermal displacements have been analysed assuming no coupling between the external (rigid body) and internal vibrations. This gives mean square displacements for rigid-body vibration in which zero-point vibrational effects are apparent. The methylene H nuclei have internal vibrations approximately independent of temperature. At 200 K, the H nuclear vibrations have a small anharmonic component, but at temperatures below 160 K this becomes insignificant in terms of the experimental error.

Crystallization↗

PubMed1991

Neutron diffraction study of carbonmonoxymyoglobin.

Neutron diffraction data from a crystal of carbonmonoxymyoglobin were refined by PROLSQ, a modern restrained least-squares procedure in reciprocal space, in conjunction with a solvent analysis technique, to a final R-factor of 11.3%. The ligand CO occupies two sites and its binding conformations are distorted from the linear conformation. The N epsilon atom of the distal histidine residue is deprotonated (not deuterated), and a water molecule is bound to the N delta atom of the distal histidine. The side-chain of Lys56 (D6) exists in two alternative charge-binding sites. His24 (B5) and His119 (GH1) share a hydrogen atom. His12 (A10) and His36 (C1) are deprotonated. The deprotonated imidazole ring of His12 (A10) may act as a hydrogen-bond acceptor. The heme group is planar within 0.09 A root-mean-square (r.m.s.) deviation from planarity. The solvent environments for the two propionic acid groups are different. The side-chain of Arg45 (CD3) forms hydrogen bonds with the side-chain of Asp60 (E3) and one of the two propionic acid groups. An average N-2H . . . O angle in helical regions is 147 (+/- 11) degrees. Eleven main-chain amide hydrogen atoms from hydrophobic residues do not exchange with deuterium. The overall atomic occupancy factors for the main-chain and side-chain atoms are quite uniform, at 0.97 (+/- 0.07) and 0.93 (+/- 0.10), respectively, as shown by an occupancy analysis made at the end of the refinement procedure.

Amino Acid Sequence↗

PubMed2002

Two-dimensional water and ice layers: neutron diffraction studies at 278, 263, and 20 k.

Neutron diffraction elucidates the structures of two-dimensional (2D) water layers (278 K) or 2D ice layers confined in an organic slit-shaped nanospace. The two-dimensional ice phases reported here consist of individual eight-membered rings or folded-chain segments (263 K) and condensed twelve-membered irregular rings (20 K). This is quite different from bulk or other 2D ice structures; the latter usually form hexagonal honeycomb lattices. Both low-temperature structures typically feature water molecules which are surrounded by two or three other water molecules. Neutron diffraction and thermochemical studies indicate a liquid-solid-phase transition around 277 K for two-dimensional D2O layers. A further solid-solid-phase transition occurs between 263 and 20 K.

Chelating Agents↗

PubMed1994

Rotational orientation of transmembrane alpha-helices in bacteriorhodopsin. A neutron diffraction study.

The rotational orientation of the seven transmembrane alpha-helices (A-G) in bacteriorhodopsin has been investigated by neutron diffraction. The current model of bacteriorhodopsin is based on an electron density map obtained by high-resolution electron microscopy (EM). Assigning helix rotational positions in the EM model depended on fitting large side-chains, mainly aromatic residues, into bulges in the electron density map. For helix D, which contains no aromatic residues, the EM map is more difficult to interpret. For helices A and B, whose position and orientation had been determined previously by neutron diffraction, the positions defined by EM agree within experimental error with these earlier conclusions. The orientation of all seven helices has been examined by using neutron diffraction on bacteriorhodopsin samples with specifically deuterated valine, leucine and tryptophan residues. Experimental peak intensities were compared to those predicted for an extensive set of structural models. The models were generated by (1) rotating all helices around their axis; (2) moving deuterated residues in the extramembrane loops about their probable positions and changing the weight of their contribution to the neutron diffraction pattern; (3) allowing deuterated side-chains to change their conformation. The analysis confirmed exactly the positions previously determined for helices A and B. For an optimal fit to the data to be obtained, the other five helices, including helix D, must lie either at or within 20 degrees of their position in the current EM model. The complementarity of medium-resolution EM, neutron diffraction and model building for the structural study of integral membrane proteins is discussed.

Bacteriorhodopsins↗