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PubMed2003

Membrane insertion of a lipidated ras peptide studied by FTIR, solid-state NMR, and neutron diffraction spectroscopy.

Membrane binding of a doubly lipid modified heptapeptide from the C-terminus of the human N-ras protein was studied by Fourier transform infrared, solid-state NMR, and neutron diffraction spectroscopy. The 16:0 peptide chains insert well into the 1,2-dimyristoyl-sn-glycero-3-phosphocholine phospholipid matrix. This is indicated by a common main phase transition temperature of 21.5 degrees C for both the lipid and peptide chains as revealed by FTIR measurements. Further, (2)H NMR reveals that peptide and lipid chains have approximately the same chain length in the liquid crystalline state. This is achieved by a much lower order parameter of the 16:0 peptide chains compared to the 14:0 phospholipid chains. Finally, proton/deuterium contrast variation of neutron diffraction experiments indicates that peptide chains are localized in the membrane interior analogous to the phospholipid chains. In agreement with this model of peptide chain insertion, the peptide part is localized at the lipid-water interface of the membrane. This is revealed by (1)H nuclear Overhauser enhancement spectra recorded under magic angle spinning conditions. Quantitative cross-peak analysis allows the examination of the average location of the peptide backbone and side chains with respect to the membrane. While the backbone shows the strongest cross-relaxation rates with the phospholipid glycerol, the hydrophobic side chains of the peptide insert deeper into the membrane interior. This is supported by neutron diffraction experiments that reveal a peptide distribution in the lipid-water interface of the membrane. Concurring with these experimental findings, the amide protons of the peptide show strong water exchange as seen in NMR and FTIR measurements. No indications for a hydrogen-bonded secondary structure of the peptide backbone are found. Therefore, membrane binding of the C-terminus of the N-ras protein is mainly due to lipid chain insertion but also supported by interactions between hydrophobic side chains and the lipid membrane. The peptide assumes a mobile and disordered conformation in the membrane. Since the C-terminus of the soluble part of the ras protein is also disordered, we hypothesize that our model for membrane binding of the ras peptide realistically describes the membrane binding of the lipidated C-terminus of the active ras protein.

Dimyristoylphosphatidylcholine↗

PubMed2000

X-ray and neutron diffraction studies of crystallinity in hydroxyapatite coatings.

To standardize industrial implant production and make comparisons between different experimental results, we have to be able to quantify the crystallinity of hydroxyapatite. Methods of measuring crystallinity ratio were developed for various HA samples before and after plasma spraying. The first series of methods uses X-ray diffraction. The advantage of these methods is that X-ray diffraction equipment is used widely in science and industry. In the second series, a neutron diffraction method is developed and the results recorded are similar to those obtained by the modified X-ray diffraction methods. The advantage of neutron diffraction is the ability to obtain measurements deep inside a component. It is a nondestructive method, owing to the very low absorption of neutrons in most materials.

Biocompatible Materials↗

PubMed1990

Water molecules and exchangeable hydrogen ions at the active centre of bacteriorhodopsin localized by neutron diffraction. Elements of the proton pathway?

Neutron diffraction is used to localize water molecules and/or exchangeable hydrogen ions in the purple membrane by H2O/2H2O exchange experiments at different values of relative humidity. At 100% relative humidity, differences in the hydration between protein and lipid areas are observed, accounting for an excess amount of about 100 molecules of water in the lipid domains per unit cell. A pronounced isotope effect was observed, reproducibly showing an increase in the lamellar spacing from 60 A in 2H2O to 68 A in H2O. At 15% relative humidity, the positions of exchangeable protons became visible. A dominant difference density peak corresponding to 11 +/- 2 exchangeable protons was detected in the central part of the projected structure of bacteriorhodopsin at the Schiff's base end of the chromophore. A difference density map obtained from data on purple membrane films at 15% relative humidity in 2H2O, and the same sample after complete drying in vacuum, revealed that about eight of these protons belong to four water molecules. This is direct evidence for tightly bound water molecules close to the chromophore binding site of bacteriorhodopsin, which could participate in the active steps of H+ translocation as well as in the proton pathway across this membrane protein.

Bacteriorhodopsins↗

PubMed2002

Anomalous spin-density distribution on oxygen and Ru in Ca(1.5)Sr(0.5)RuO(4): polarized neutron diffraction study.

By means of polarized neutron diffraction in a magnetic field of 7.0 T at 1.6 K an anomalously large magnetization density is observed on the in-plane oxygen in Ca(1.5)Sr(0.5)RuO(4). Field-induced moments of different ions are determined by refinement on the flipping ratios, yielding micro(Ru)=0.346(11)micro(B), micro(O1)=0.076(6)micro(B), and micro(O2)=0.009(6)micro(B). The moment on the oxygen arises from the strong hybridization between the Ru-4d and O-2p orbitals. The maximum entropy magnetization density reconstruction reveals a strongly anisotropic density at the Ru site, consistent with the distribution of the xy (t(2g) band) d orbitals.

Journal Article↗

PubMed1983

Neutron diffraction of chromatin in interphase nuclei and metaphase chromosomes.

We have used neutron diffraction to study chromatin structure in interphase nuclei and metaphase chromosomes as a function of decreasing ion concentration. Aliquots of a suspension of rat liver nuclei prepared in a polyamine-free buffer were washed in buffers of 1/3, 1/6 and 1/12 if the original concentration of monovalent and divalent cations (40 mM KCl; 20 mM NaCl; 1.2 mM MgCl2). After the first dilution step (1/1 to 1/3), only small changes occurred in the diffraction pattern. They can be interpreted by a loosening of the original structure, i.e. by the formation of isolated buffer-filled spaces with an overall size of the order of 35-45 nm. Drastic changes in the diffraction pattern were observed, however, when the nuclei were washed in the more diluted buffers (1/6 and 1/12). The profiles of the distances distribution functions indicate the formation of supranucleosomal particles with an overall diameter of 40-50 nm. The compact chromatin structure disassembled directly into these fundamental structural units. Structural transformations in the Chinese hamster ovary metaphase chromosomes were induced by diminishing the Ca2+ ion concentration of the buffer from originally 3.0 mM to 0.3 mM and/or by increasing the pH value of the buffer from originally 7.0 up to 8.0. The neutron diffraction patterns remained essentially unchanged during these treatments, i.e. the decondensation of the chromosomes as observed in the light microscope is not accompanied by disassembly at the ultrastructural level between 2 nm and 150 nm.

Animals↗

PubMed1983

Absolute configuration of a chiral CHD group via neutron diffraction: confirmation of the absolute stereochemistry of the enzymatic formation of malic acid.

Neutron diffraction has been used to monitor the absolute stereochemistry of an enzymatic reaction. (-)(2S)malic-3-d acid was prepared by the action of fumarase on fumaric acid in D2O. After a large number of cations were screened, it was found that (+)(R) alpha-phenylethylamine forms the large crystals necessary for a neutron diffraction analysis. The subsequent structure determination showed that (+)(R) alpha-phenylethylammonium (-)(2S)malate-3-d has an absolute configuration of R at the CHD site (i.e., the C3 carbon of malate). This result confirms the absolute stereochemistry of fumarate-to-malate transformation as catalyzed by the enzyme fumarase.

Malates↗

PubMed2003

Recent results from the in situ study of hydrothermal crystallisations using time-resolved X-ray and neutron diffraction methods.

We present new time-resolved powder diffraction data measured in situ during the hydrothermal crystallisation of two families of crystalline inorganic materials. In the first study, we have used time-resolved energy-dispersive X-ray diffraction (EDXRD) to follow the formation of zeolitic zinc phosphates from amine phosphates and zinc oxide in acidic solutions at 60-150 degrees C. The advantage of this method is the ability to penetrate a laboratory-sized reaction vessel and to measure data in short (< 1 min) time intervals. Integration of the Bragg peak intensities during the crystallisation of the product allows accurate crystallisation curves to be produced. In addition, in a number of cases, we observe the formation of transient crystalline intermediate phases which can be identified by use of a new three-element detector that allows a large amount of diffraction data to be measured during the experiment. We are thus able to show that three-dimensional zinc phosphate architectures often form via low-dimensional chain and layered phases, which is consistent with a recent aufbau model proposed for their formation. In the second study, we focus on the hydrothermal formation of ferroelectric barium titanate from TiO2 and barium salts in alkaline solution using time-resolved neutron diffraction. Although the time resolution of the neutron diffraction experiment is lower than the EDXRD experiment (data are measured in intervals of 5 min), we are able to penetrate reaction mixtures that are highly absorbing towards X-rays, and thus can measure data in a large volume reaction cell. Neutron diffraction data were collected on one of the highest-flux/highest detector-coverage diffractometers currently available; the GEM diffractometer at ISIS, UK. These experiments reveal that BaTiO3 crystallises after a large amount of TiO2 has been consumed; this implies that a dissolution crystallisation mechanism predominates. Additional mechanistic information is inferred by the observation of transient crystalline phases under certain reaction conditions.

Journal Article↗

PubMed1979

Stress distribution in the scapula studied by neutron diffraction.

High intensity neutron beams provide a method of measuring the preferred orientation of apatite crystals in bulk samples of bone. Measurements at seven different sites on the scapula show that the c axes of the crystals lie preferentially along the directions of pull of the attached muscles. The highest orientation is found at positions under the influence of only a single group of muscles, such as M. teres major or M. infraspinatus. In intermediate regions a multiple distribution of crystals is found, able to withstand stresses in more than one direction. The technique provides a method of assessing the distribution of stress in bones.

Animals↗

PubMed2000

Direct observation of deuterium migration in crystalline-state reaction by single-crystal neutron diffraction. II. 3-1 photoisomerization of a cobal-oxime complex

Single crystal neutron diffraction analysis of photo-exposed (3-cyanopropyl-d2(alpha,alpha))-[(R)-1-phenylethylamine-d11]bis(dimethylglyoximato-d14)cobalt(III) was carried out in order to clarify the mechanism of the crystalline-state photoisomerization of the 3-cyanopropyl group bonded to the Co atom in some cobaloxime complexes. Before irradiation the two H atoms bonded to the C1 atom of the 3-cyanopropyl group were exchanged with the D atoms such as --CH2CH2CD2CN. On exposure to a xenon lamp, the cell dimensions of the crystal were gradually changed. After 7 d exposure the change became insignificantly small. The structure was analyzed by neutron diffraction. The 3-cyanopropyl group was transformed to the 1-cyanopropyl group such as --CD(CN)C(H1/2,D1/2)2CH3 with retention of the single-crystal form. This indicates that one of the D atoms bonded to C1 migrates to either position bonded to C2. The other atoms of the complex remained unchanged. These results indicate that photoisomerization proceeded in two steps: the 3-cyanopropyl group was isomerized to the 2-cyanopropyl group in the first place and then the 2-cyanopropyl group was transformed to the 1-cyanopropyl group. Moreover, it was made clear that the second-step isomerization was irreversible, since one of the D atoms was retained. The disordered structure at C2 is estimated to be caused by the interconversion between the 1-cyanopropyl group produced and its dehydrogenated olefin after the photoisomerization.

Journal Article↗

PubMed2003

Hydration structures in proteins and neutron diffraction experiment on dissimilatory sul te reductase D (DsrD).

Neutron crystallography can provide a substantial amount of information about the hydration of proteins. The hydration patterns of three proteins, whose structures have been solved at 1.5 or 1.6 A resolution using our BIX-type diffractometers, show interesting features. The water molecules adopt a variety of shapes in the neutron Fourier maps, revealing details of intermolecular hydrogen-bond formation and dynamics of hydration. In addition, the neutron diffraction study of a DNA-binding protein, dissimilatory sulfite reductase D (DsrD) is briefly described, and some preliminary results are presented. This topic is of interest because it is well known that hydrogen bonds play important roles in DNA-protein recognition.

Binding Sites↗

PubMed2001

Long-range magnetic order in Mn[N(CN)2]2(pyz) (pyz = pyrazine). Susceptibility, magnetization, specific heat, and neutron diffraction measurements and electronic structure calculations.

Using dc magnetization, ac susceptibility, specific heat, and neutron diffraction, we have studied the magnetic properties of Mn[N(CN)2]2(pyz) (pyz = pyrazine) in detail. The material crystallizes in the monoclinic space group P2(1)/n with a = 7.3248(2), b = 16.7369(4), and c = 8.7905 (2) A, beta = 89.596 (2) degrees, V = 1077.65(7) A(3), and Z = 4, as determined by Rietveld refinement of neutron powder diffraction data at 1.35 K. The 5 K neutron powder diffraction data reflect very little variation in the crystal structure. Interpenetrating ReO3-like networks are formed from axially elongated Mn(2+) octahedra and edges made up of mu-bonded [N(CN)2](-) anions and neutral pyz ligands. A three-dimensional antiferromagnetic ordering occurs below T(N) = 2.53(2) K. The magnetic unit cell is double the nuclear one along the a- and c-axes, giving the (1/2, 0, 1/2) superstructure. The crystallographic and antiferromagnetic structures are commensurate and consist of collinear Mn(2+) moments, each with a magnitude of 4.15(6) mu(B) aligned parallel to the a-direction (Mn-pyz-Mn chains). Electronic structure calculations indicate that the exchange interaction is much stronger along the Mn-pyz-Mn chain axis than along the Mn-NCNCN-Mn axes by a factor of approximately 40, giving rise to a predominantly one-dimensional magnetic system. Thus, the variable-temperature magnetic susceptibility data are well described by a Heisenberg antiferromagnetic chain model, giving g = 2.01(1) and J/k(B) = -0.27(1) K. Owing to single-ion anisotropy of the Mn(2+) ion, field-induced phenomena ascribed to spin-flop and paramagnetic transitions are observed at 0.43 and 2.83 T, respectively.

Journal Article↗

PubMed1986

Determining bilayer hydrocarbon thickness from neutron diffraction measurements using strip-function models.

Neutron diffraction methods provide information about the distribution of matter in biological and model membrane systems. The information is derived from plots (profiles) of scattering length density along an axis normal to the membrane plane. Without the use of specific deuteration, the generally low resolution of the profiles limits their interpretation in terms of specific chemical constituents (e.g., lipid headgroup, lipid hydrocarbon, protein, and water). A fundamental and useful structural assignment to make is the boundary between the headgroup and hydrocarbon regions of bilayers. We demonstrate here that strip-function model representations of neutron scattering length density profiles of bilayers are sufficient to determine accurately the position of the headgroup-hydrocarbon boundary. The resulting hydrocarbon thickness of the bilayer is useful for determining the area per lipid molecule and consequently the molecular packing arrangements of the membrane constituents. We analyze data obtained from dioleoylphosphatidylcholine (DOPC) bilayers at 66% RH using standard Fourier profile analyses and from DOPC deuterated specifically at the C-2 carbon of the acyl chains using difference Fourier analysis. We demonstrate that strip-function models accurately define the positions of the C-2 carbons and thus the hydrocarbon thickness (dhc) of the bilayer. We then show, using quasi-molecular models, that the strip-model analysis probably provides an accurate measure of dhc because of the exceptionally high scattering length density difference between the carbonyl and methylene groups.

Deuterium↗

PubMed1976

Neutron diffraction studies of biological membranes and membrane components.

In this paper the methods and techniques of neutron diffraction studies of biological membranes and membrane components have been described and demonstrated. Foremost among these are the methods of deuterium exchange and deuterium labeling, since they can directly provide locations of membrane components. In addition, the methods of contrast variation with H2O-D2O mixtures, swelling, direct scaling of data from deuterium-labeled structures, and magnetic orientation have provided useful information in neutron diffraction analyses of membrane structures. Although this field is only in its infancy, it clearly has very encouraging prospects.

Cell Membrane↗

PubMed2003

Neutron diffraction studies on rubredoxin from Pyrococcus furiosus.

Single-crystal neutron diffraction data up to a resolution of 1.5 A have been collected at room temperature on two forms of rubredoxin using the BIX-3 diffractometer at the JRR-3 reactor of the Japan Atomic Energy Research Institute (JAERI). Rubredoxin is a small iron-sulfur redox protein with 53 amino acid residues, and the source of this particular protein is the hyperthermophile Pyrococcus furiosus, a microorganism that normally lives at temperatures near that of boiling water. Data were collected on crystals of the wild-type protein and on a mutant in which three of the residues have been replaced. In this paper we will be describing several sets of results arising from these high-resolution neutron structure determinations: (a) the H/D exchange pattern of the N-H bonds of the main backbone, which give information about which regions of the molecule are more exposed to solvent; (b) the orientations of some of the O-D bonds in the protein, information which is often not obtainable from X-ray results; (c) the structure and appearance of water molecules in the protein crystals; and (d) some structural features which may help rationalize the remarkable thermal stability of the wild-type protein from this intriguing microorganism

Binding Sites↗

PubMed1989

Tertiary structure of bacteriorhodopsin. Positions and orientations of helices A and B in the structural map determined by neutron diffraction.

Positions and rotations of two helices in the tertiary structure of bacteriorhodopsin have been studied by neutron diffraction using reconstituted, hybrid purple membrane samples. Purple membrane was biosynthetically 2H-labeled at non-exchangeable hydrogen positions of leucine and tryptophan residues. Two chymotryptic fragments were purified, encompassing either the first two or the last five of the seven putative transmembrane segments identified in the amino acid sequence of bacteriorhodopsin. The 2H-labeled fragments, diluted to variable extents with the identical, unlabeled fragment, were mixed with their unlabeled counterpart; bacteriorhodopsin was then renatured and reconstituted. The crystalline purple membrane samples thus obtained contained hybrid bacteriorhodopsin molecules in which certain transmembrane segments had been selectively 2H-labeled to various degrees. Neutron diffraction powder patterns were recorded and analyzed both by calculating difference Fourier maps and by model building. The two analyses yielded consistent results. The first and second transmembrane segments in the sequence correspond to helices 1 and 7 of the three-dimensional structure, respectively. Rotational orientations of these two helices were identified using best fits to the observed diffraction intensities. The data also put restrictions on the position of the third transmembrane segment. These observations are discussed in the context of folding models for bacteriorhodopsin, the environment of the retinal Schiff base, and site-directed mutagenesis experiments.

Amino Acid Sequence↗

PubMed1985

Neutron diffraction studies of collagen in fully mineralized bone.

Neutron diffraction measurements have been made of the equatorial and meridional spacings of collagen in fully mineralized mature bovine bone and demineralized bone collagen, in both wet and dry conditions. The collagen equatorial spacing in wet mineralized bovine bone is 1.24 nm, substantially lower than the 1.53 nm value observed in wet demineralized bovine bone collagen. Corresponding spacings for dry bone and demineralized bone collagen are 1.16 nm and 1.12 nm, respectively. The collagen meridional long spacing in mineralized bovine bone is 63.6 nm wet and 63.4 nm dry. These data indicate that collagen in fully mineralized bovine bone is considerably more closely packed than had been assumed previously, with a packing density similar to that of the relatively crystalline collagens such as wet rat tail tendon. The data also suggest that less space is available for mineral within the collagen fibrils in bovine bone than had previously been assumed, and that the major portion of the mineral in this bone must be located outside the fibrils.

Achilles Tendon↗

PubMed2003

A neutron diffraction study of xylitol: derivation of mean square internal vibrations for H atoms from a rigid-body description.

A neutron diffraction study of xylitol (C(5)O(5)H(12)) is presented. The nuclear anisotropic displacement parameters have been analysed showing that the carbon-oxygen skeleton conforms to a rigid-body (TLS) description. Applying this TLS model to the xylitol H atoms allows characterization of the internal molecular displacements of the H nuclei, assuming that the observed H nuclear mean-square displacements are a sum of the internal displacements and rigid-body displacements. These internal molecular displacements are very similar for chemically equivalent H atoms and in good agreement with the values obtained by other methods. In all cases the smallest eigenvector of the residual mean-square displacement tensor is almost parallel to the X-H bond. The use of ab initio calculations to obtain the internal vibrations in xylitol is discouraging. Another 12 structures extracted from the literature which have been investigated by neutron diffraction were subjected to a similar analysis. The results for the nine compounds investigated at low temperature conform to the results from xylitol and provide estimates of the internal vibrations of H atoms in a range of chemical environments.

Journal Article↗

PubMed1976

Neutron diffraction studies of retinal rod outer segment membranes.

Neutron diffraction measurements on isolated retinal rod outer segments show that most of the visual pigment protein, rhodopsin, is embedded in the hydrophobic core of the disk membrane. A very slight outward shift of protein at the cytoplasmic side of the membrane is associated with pigment bleaching.

Animals↗