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PubMed1992

Conformational interconversion in protein crystals.

We present evidence that the structure of carbonmonoxy myoglobin crystals can be altered by lowering the pH. This structural change is monitored by the characteristic Fe-CO Raman modes at 508 and 491 cm-1 and is thought to involve a localized distal pocket transition from a "closed" conformation at pH 7 to a more "open" conformation at pH 4. These changes take place in the crystal without loss of intensity of a conformationally sensitive Raman mode at 252 cm-1 that signals a partial unfolding of the globin structure in solution. Quantitative studies, which monitor the open and closed populations as a function of laser photolysis, demonstrate that the interconversion rates (k+/-) in solution at 298 K are fast compared to the photolysis and CO entry rates (i.e. k+/- much greater than 10(3) s-1), while in frozen samples the interconversion is much slower than the experimental time scale (minutes). Since the open conformation is a minority species at pH 7, rapid exchange in aqueous solution is a necessary condition for this species to play a functional role. In the crystal, the interconversion rates are slowed compared to solution and begin to approach the photolysis rate (i.e. k+/- approximately 10(3) to 10(4) s-1). This indicates that the barriers for conformational exchange are increased in the crystal environment, compared to the solution, apparently due to the packing forces of the surrounding molecules. X-ray and neutron diffraction studies of MbCO crystals at high and low pH are needed to characterize the details of the structural changes and to test the hypothesis that closed and open distal pocket structures are associated with the 508 and 491 cm-1 Fe-CO modes.

Hydrogen-Ion Concentration↗
PubMed1994

The production and X-ray structure determination of perdeuterated Staphylococcal nuclease.

Staphylococcal Nuclease (SNase) has been chosen as a model protein system to evaluate the improvement in neutron diffraction data quality using fully perdeuterated protein. Large quantities of the protein were expressed in Escherichia coli grown in medium containing deuterated amino acids and deuterated water (D2O) and then purified. The mean perdeuteration level of the non-exchangable sites in the protein was found to be 96% by electrospray ionization mass spectrometry. The perdeuterated enzyme was crystallized and its X-ray structure determined. Crystals of perdeuterated SNase have been grown to 1.5 mm3. Crystallization conditions, space group and cell parameters were found to be the same for both native and perdeuterated forms of the protein. Comparison of these two forms of SNase revealed no significant structural differences between them at the atomic resolution of 1.9 A. Data collection using crystals of the perdeuterated protein is scheduled at the Brookhaven High Flux Beam Reactor.

Chromatography, High Pressure Liquid↗
PubMed1994

Correlations between 27Al magic-angle spinning nuclear magnetic resonance spectra and the coordination geometry of framework aluminates.

A range of aluminate sodalites of general formula M8(AlO2)12.X2, where M and X are a divalent cation and anion, respectively, has been synthesised. The structures of these materials, which contain a single aluminum environment, have been refined from powder X-ray or neutron diffraction data and the compounds further characterised using 27Al magic-angle spinning nuclear magnetic resonance (MAS NMR). Correlations between (i) the Al-O-Al bond angles and the 27Al chemical shift and (ii) the quadrupolar coupling constant and the distorted AlO4 tetrahedral geometry have been determined.

Aluminum↗
PubMed2005

Plastic deformation in structural materials, investigated in situ by neutrons and positrons.

During residual stress measurements by neutron diffraction additional information becomes available through the accompanying high-energy prompt capture gamma radiation, which in turn produces positrons within the bulk of the specimen. Plastic deformation will increase the dislocation density within the material. This leads to an increase in the mosaic spread of the diffraction reflections and to changes of the lineshape of the positron annihilation radiation. The correlation between the width of the Bragg reflections and the S-parameter, which describes the shape variation of the annihilation line was investigated as a function of the degree of plastic deformation. The experimental work was performed at the FRG-I research reactor of GKSS.

Journal Article↗
PubMed2005

A structural study of the myristoylated N-terminus of ARF1.

The effect of myristoylation on the 15-amino-acid peptide from the membrane-binding N-terminus of ADP ribosylation factor 1 (ARF1) was studied using neutron diffraction and circular dichroism. A previous study on the non-acylated form indicated that the peptide lies parallel to the membrane, at a shallow depth and in the vicinity of the phosphorylcholine headgroups. It was suggested that the helix does not extend past residue 12, an important consequence for the linking region of the ARF1 protein. In this paper, we show that the result of myristoylation is to increase the helical content reaching the peptide's C-terminus, resulting in the formation of a new hydrophobic face. This increased helicity may augment the entire protein's membrane-binding affinity, indicating that ARF1 effectively has two interdependent membrane-binding motifs.

ADP-Ribosylation Factor 1↗
PubMed2006

A density functional study of (17)O, (14)N and (2)H electric field gradient tensors in the real crystalline structure of alpha-glycine.

A density functional theory (DFT) study was carried out to calculate (17)O, (14)N and (2)H electric field gradient (EFG) tensors in accurate neutron diffraction structures of alpha-glycine at 288 and 427 K. B3LYP is the used method and 6-311+G(*) and 6-311++G(**) are the basis sets in the calculations of EFG tensors at the sites of (17)O, (14)N and (2)H nuclei in the monomer and the octameric cluster of alpha-glycine at two temperatures. Quadrupole coupling constants and asymmetry parameters are the converted parameters of calculated EFG tensors to experimentally measurable ones. The calculated results of monomer and the target molecule in octameric cluster reveal that hydrogen-bonding interactions play an important role in the crystalline structure of alpha-glycine where the results of the target molecule in octameric cluster are in good agreement with the experiments.

Crystallography↗
PubMed2005

Surface adsorption of zwitterionic surfactants: n-alkyl phosphocholines characterised by surface tensiometry and neutron reflection.

The surface adsorption of n-dodecyl phosphocholine (C12PC) has been characterised by a combined measurement of surface tension and neutron reflectivity. The critical micellar concentration (CMC) was found to be 0.91 mM at 25 degrees C in pure water. At the CMC, the limiting area per molecule (A(cmc)) was found to be 52+/-3 A2 and the surface tension (gamma(cmc)) to be ca. 40.0+/-0.5 mN/m. The parallel study of chain isomer n-hexadecyl phosphocholine (C16PC) showed a decrease of the CMC to 0.012 mM and a drop of gamma(cmc) to 38.1+/-0.5 mN/m. However, A(cmc) for C16PC was found to be 54+/-3 A2, showing that increase in alkyl chain length by four methylene groups has little effect on A(cmc). The almost constant A(cmc) suggested that the limiting area per molecule was determined by the bulky PC head group. It was further found that the surface tension and related key physical parameters did not vary much with temperature, salt addition, solution pH or any combination of these, thus showing that surface adsorption and solution aggregation from PC surfactants is largely similar to the zwitterionic betaine surfactants and is distinctly different from ionic and non-ionic surfactants. The thickness of the adsorbed monolayers measured from both dC12hPC and dC16hPC was found to be 20-22 A at the CMC from neutron reflectivity. Neither A(cmc) nor layer thickness varied with alkyl chain length, indicating that as the alkyl chain length became longer it was further tilted away from the surface normal direction and the layer packing density increased. It was also observed that the thickness of the layer varied little with surfactant concentration, indicating that the average conformational orientation of the alkyl chain remained unchanged against varying surface coverage.

Adsorption↗
PubMed2005

Preferred orientation in filtercakes of kaolinite.

The orientational order parameter of dense colloidal dispersions of plate-like particles as a function of volume fraction is measured using neutron diffraction. This non-invasive experimental approach directly provides the full particle orientation distribution from which the order parameters can be calculated. The orientation parameters are shown to be linked to the solids fractions of the cakes and the macroscopic permeability of the samples. However, this study suggests that, although orientation can be relevant for a given system, other factors can have a stronger influence, for example, the degree of dispersion or colloidal stability of the clay and may be the principle factor that controls permeability. In addition, we report enhanced ordering of these materials under the influence of an external cross-flow field.

Journal Article↗
PubMed2006

Lift-off compensation for improved accuracy in ultrasonic lamb wave velocity measurements using electromagnetic acoustic transducers (EMATs).

The crystalline texture of a sheet metal strongly affects its formability, so having knowledge of this texture is of great industrial relevance. The texture of rolled sheet metals, such as aluminium and steel, may be determined by ultrasonic measurement of the velocity of the zero order symmetric (S(0)) Lamb wave as a function of angle to the rolling direction. Electromagnetic acoustic transducers (EMATs) may perform this measurement without contacting the sample, therefore reducing perturbation to the plate wave system, as they are electromagnetically coupled to the sheet. The EMAT system measurements are non-destructive and may be made in real time, therefore offering advantages over the conventional techniques such as X-ray and neutron diffraction. It has been noticed that in the two EMAT pitch-catch system, the apparent arrival times of the ultrasonic waves change with variation in lift-off (distance between sample and transducer) due to impedance and aperture effects. For precise and accurate texture parameters to be obtained, accurate absolute ultrasonic velocity measurement is required and hence lift-off must be compensated for. This is of particular importance to online inspection systems where constant lift-off may be difficult to maintain. The impedance behaviour of various coil geometries has been investigated as a function of lift-off and frequency and compared to the received ultrasonic signal and the drive current pulse profile. Theoretical models have been used to explain the observed behaviour, and hence a scheme has been proposed for the compensation of lift-off effects in real time.

Journal Article↗
PubMed2000

Hydrogen bonds and proton transfer in general-catalytic transition-state stabilization in enzyme catalysis.

The question of the nature of the proton bridge involved in general acid-base catalysis in both enzymic and non-enzymic systems is considered in the light of long-known but insufficiently appreciated work of Jencks and his coworkers and of more recent results from neutron-diffraction crystallography and NMR spectroscopic studies, as well as results from isotope-effect investigations. These lines of inquiry lead toward the view that the bridging proton, when between electronegative atoms, is in a stable potential at the transition state, not participating strongly in the reaction-coordinate motion. Furthermore they suggest that bond order is well-conserved at unity for bridging protons, and give rough estimates of the degree to which the proton will respond to structural changes in its bonding partners. Thus if a center involved in general-catalytic bridging becomes more basic, the proton is expected to move toward it while maintaining a unit total bond order. For a unit increase in the pK of a bridging partner, the other partner is expected to acquire about 0.06 units of negative charge. The implications are considered for charge distribution in enzymic transition states as the basicity of catalytic residues changes in the course of molecular evolution or during progress along a catalytic pathway.

Catalysis↗
PubMed2000

Water and bacteriorhodopsin: structure, dynamics, and function.

A wealth of information has been gathered during the past decades that water molecules do play an important role in the structure, dynamics, and function of bacteriorhodopsin (bR) and purple membrane. Light-induced structural alterations in bR as detected by X-ray and neutron diffraction at low and high resolution are discussed in relationship to the mechanism of proton pumping. The analysis of high resolution intermediate structures revealed photon-induced rearrangements of water molecules and hydrogen bonds concomitant with conformational changes in the chromophore and the protein. These observations led to an understanding of key features of the pumping mechanism, especially the vectoriality and the different modes of proton translocation in the proton release and uptake domain of bR. In addition, water molecules influence the function of bR via equilibrium fluctuations, which must occur with adequate amplitude so that energy barriers between conformational states can be overcome.

Bacteriorhodopsins↗
PubMed2000

Crystallization of antimicrobial pores in membranes: magainin and protegrin.

Membrane pores spontaneously formed by antimicrobial peptides in membranes were crystallized for the first time by manipulating the sample hydration and temperature. Neutron diffraction shows that magainins and protegrins form stable pores in fully hydrated fluid membranes. At lower hydration levels or low temperature, the membrane multilayers crystallize. In one crystalline phase, the pores in each bilayer arrange in a regular hexagonal array and the bilayers are stacked into a hexagonal ABC lattice, corresponding to the cubic close-packed structure of spheres. In another crystalline phase, the bilayers are modulated into the rippled multilamellae, corresponding to a 2D monoclinic lattice. The phase diagrams are described. Crystallization of the membrane pores provides possibilities for diffraction studies that might provide useful information on the pore structures.

Amino Acid Sequence↗
PubMed2001

Geometrical properties of gel and fluid clusters in DMPC/DSPC bilayers: Monte Carlo simulation approach using a two-state model.

In this paper the geometrical properties of gel and fluid clusters of equimolar dimyristoylphosphatidylcholine/distearoylphosphatidylcholine (DMPC/DSPC) lipid bilayers are calculated by using an Ising-type model (Sugar, I. P., T. E. Thompson, and R. L. Biltonen. 1999. Biophys. J. 76:2099-2110). The model is able to predict the following properties in agreement with the respective experimental data: the excess heat capacity curves, fluorescence recovery after photobleaching (FRAP) threshold temperatures at different mixing ratios, the most frequent center-to-center distance between DSPC clusters, and the fractal dimension of gel clusters. In agreement with the neutron diffraction and fluorescence microscopy data, the simulations show that below the percolation threshold temperature of gel clusters many nanometer-size gel clusters co-exist with one large gel cluster of size comparable with the membrane surface area. With increasing temperature the calculated effective fractal dimension and capacity dimension of gel and fluid clusters decrease and increase, respectively, within the (0, 2) interval. In the region of the gel-to-fluid transition the following geometrical properties are independent from the temperature and the state of the cluster: 1) the cluster perimeter linearly increases with the number of cluster arms at a rate of 8.2 nm/arm; 2) the average number of inner islands in a cluster increases with increasing cluster size, S, according to a power function of 0.00427 x S(1.3); 3) the following exponential function describes the average size of an inner island versus the size of the host cluster, S: 1 + 1.09(1 - e(-0.0072xS)). By means of the equations describing the average geometry of the clusters the process of the association of clusters is investigated.

Cluster Analysis↗
PubMed1983

Dehydration of cytosine monohydrate at physiological temperatures.

Neutron diffraction, thermogravimetric, and mass spectrographic measurements have been used to show that cytosine monohydrate loses its water of hydration at physiological temperatures (approximately equal to 37 degrees C) and converts to cytosine. The "activation energy" for the dehydration process has been determined from isothermal weight curves and is 27.1 +/- 0.6 kcal . mol-1. It is suggested that pyrimidine dehydration may be involved in structural changes in DNA.

Chemical Phenomena↗
PubMed1989

Relations for lipid bilayers. Connection of electron density profiles to other structural quantities.

Three relations are derived that connect low angle diffraction/scattering results obtained from lipid bilayers to other structural quantities of interest. The first relates the area along the surface of the bilayer, the measured specific volume, and the zeroth order structure factor, F(0). The second relates the size of the trough in the center of the electron density profile, the volume of the terminal methyl groups, and the volume of the methylene groups in the fatty acid chains. The third relates the size of the headgroup electron density peak, the volume of the headgroup, and the volumes of water and hydrocarbon in the headgroup region. These relations, which are easily modified for neutron diffraction, are useful for obtaining structural quantities from electron density profiles obtained by fitting model profiles to measured low angle x-ray intensities.

Lipid Bilayers↗
PubMed1991

Compression of lipid membranes as observed at varying membrane positions.

We have measured the microscopic isothermal compressibility of dioleoyl- and dimyristyl-phosphatidylcholine multilayers and bilayers as a function of membrane depth by the pressure dependence of the polarization of a series of anthroyloxy fatty acids. In both systems, within experimental error, the compressibility did not change with membrane depth. The magnitudes of the compressibilities matched those of organic solids and those reported for dipalmitoylphosphatidylcholine multilayers from neutron diffraction measurements (Braganza, L. F., and D. L. Worcester. 1986. Biochemistry, 25:7484-7488). The bilayer compressibility decreased with temperature and this decrease was similar with membrane depth consistent with the isotropic thermal expansion of membranes previously observed (Scarlata, S. 1989. Biophys. J. 55:1215-1223). The vertical compressibility in the z direction is much lower than the horizontal (xy planes) for probes that lie parallel to the hydrocarbon chains which is consistent with an increase in bilayer thickness. The compressibility for probes that lie perpendicular to the hydrocarbon chains is more isotropic due to their limited spatial access to the z plane.

Biophysical Phenomena↗
PubMed1994

The distal residue-CO interaction in carbonmonoxy myoglobins: a molecular dynamics study of two distal histidine tautomers.

Four independent 90 ps molecular dynamics simulations of sperm-whale wild-type carbonmonoxy myoglobin (MbCO) have been calculated using a new AMBER force field for the haem prosthetic group. Two trajectories have the distal 64N delta nitrogen protonated, and two have the 64N epsilon nitrogen protonated; all water molecules within 16 A of the carbonyl O are included. In three trajectories, the distal residue remains part of the haem pocket, with the protonated distal nitrogen pointing into the active site. This is in contrast with the neutron diffraction crystal structure, but is consistent with the solution phase CO stretching frequencies (upsilon CO) of MbCO and various of its mutants. There are significant differences in the "closed" pocket structures found for each tautomer: the 64N epsilon H trajectories both show stable distal-CO interactions, whereas the 64N delta H tautomer) has a weaker interaction resulting in a more mobile distal side chain. One trajectory (a 64N delta H tautomer) has the distal histidine moving out into the "solvent", leaving the pocket in an "open" structure, with a large unhindered entrance to the active site. These trajectories suggest that the three upsilon CO frequencies observed for wild-type MbCO in solution, rather than representing significantly different Fe-C-O geometries as such, arise from three different haem pocket structures, each with different electric fields at the ligand. Each pocket structure corresponds to a different distal histidine conformer: the A3 band to the 64N epsilon H tautomer, the A1,2 band to the 64N delta H tautomer, and the A0 band to the absence of any significant interaction with the distal side chain.

Animals↗
PubMed1995

Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer.

We report a constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal (L alpha) phase bilayer of dipalmitoylphosphatidylcholine at 50 degrees C and 28 water molecules/lipid. We have shown that the bilayer is stable throughout the 1550-ps simulation and have demonstrated convergence of the system dimensions. Several important aspects of the bilayer structure have been investigated and compared favorably with experimental results. For example, the average positions of specific carbon atoms along the bilayer normal agree well with neutron diffraction data, and the electron density profile is in accord with x-ray diffraction results. The hydrocarbon chain deuterium order parameters agree reasonably well with NMR results for the middles of the chains, but the simulation predicts too much order at the chain ends. In spite of the deviations in the order parameters, the hydrocarbon chain packing density appears to be essentially correct, inasmuch as the area/lipid and bilayer thickness are in agreement with the most refined experimental estimates. The deuterium order parameters for the glycerol and choline groups, as well as the phosphorus chemical shift anisotropy, are in qualitative agreement with those extracted from NMR measurements.

1,2-Dipalmitoylphosphatidylcholine↗