SEARCH · Search PubMed
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
The straightforward solution of the crystal structure of cyclosporin (C(62)H(111)N(11)O(12).H(2)O) by a modified Shake-and-Bake procedure, using experimental neutron diffraction data alone, shows that the positivity of the density function is not a necessary prerequisite for solving the phase problem. The initial applications suggest the intriguing possibility that positivity may actually be a hindrance.
The connectivity-based phasing method has been applied independently to three neutron diffraction data sets obtained from the same crystal of tRNA(Asp)-aspartyl-tRNA synthetase complex but at different concentrations of D(2)O/H(2)O, thus masking different components of the crystal. The obtained low-resolution images correlate perfectly with the solvent level.
Neutron diffraction and spectroscopy were applied to describe the hydration and dynamics of a soluble protein and a natural membrane from extreme halophilic Archaea. The quantitative dependence of protein motions on water activity was clearly illustrated, and it was established that a minimum hydration shell is required for the systems to access their functional resilience, i.e. a dynamics state that allows biological activity.
Bilayers of palmitoyl-oleoylphosphatidylnucleoside derivatives (1-palmitoyl-2-oleoyl-phosphatidyl-adenosine and 1-palmitoyl-2-oleoyl-phosphatidyl-uridine) were synthesized and investigated in the low-water content regime by a combination of neutron diffraction and Fourier transform infrared linear dichroism (LD-FTIR). Attention was focused on the modulation of structural properties operated by the presence of nucleic acid bases (either adenosine or uridine, a purine and a pyrimidine that are complementary in RNA). Base substitution causes major differences in phase behavior of the phospholipids, i.e., water sorption from a controlled humidity atmosphere and smectic periodicity. The profile of scattering length density can be inferred from five diffraction orders for 1-palmitoyl-2-oleoyl-phosphatidyl-uridine lamellar phase. 1-Palmitoyl-2-oleoyl-phosphatidyl-adenosine is characterized by lower and less ready hydration, giving rise to a powder-like sample. A linear dichroism FTIR investigation on the same lamellar phases was undertaken with the purpose of gathering details at the submolecular level on different portions of the molecule. 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers were also investigated with the same technique for the sake of comparison. Besides a confirmation of the diffraction data interpretation, FTIR has provided evidence that the same chemical groups at the bilayer interface (namely the sugar-phosphate) have a different orientation depending on whether the base is a purine or a pyrimidine. A very simple geometrical optimization agrees with this observation. This indicates that a different pattern of base interaction is operating in the two cases and that base substitution acts as a modulator of the phase properties.
Thin stacks of lipid multibilayers supported on rigid silicon and mica substrates are found to exhibit finite-size effects. Using neutron diffraction we find that the repeat spacing (d) of stacks containing up to a few tens of bilayers depends on their thickness (D), with d increasing with decreasing D. Differences in d are larger in the low-temperature Lbeta' phase consisting of rigid bilayers than in the high-temperature Lalpha phase where the bilayers are more flexible. Various scenarios that may be responsible for this counterintuitive observation are discussed.
Terminal mono-oxo complexes of the late transition metal elements have long been considered too unstable to synthesize because of repulsion between the oxygen electrons and the mostly filled metal d orbitals. A platinum(IV)-oxo compound flanked by two polytungstate ligands, K7Na9[O=Pt(H2O)L2], L = [PW9O34(9-)], has now been prepared and isolated at room temperature as air-stable brown crystals. X-ray and neutron diffraction at 30 kelvin revealed a very short [1.720(18) angstrom] Pt-O bond and no evidence of a hydrogen atom at the terminal oxygen, ruling out a better precedented Pt-OH complex. Density functional theory and spectroscopic data account for the stability of the Pt(IV)-oxo unit by electron withdrawal into delocalized orbitals of the polytungstates.
BACKGROUND: Soluble Alzheimer's Abeta oligomers autoinsert into neuronal cell membranes, contributing to the pathology of Alzheimer's Disease (AD), and elevated serum cholesterol is a risk factor for AD, but the reason is unknown. We investigated potential connections between these two observations at the membrane level by testing the hypothesis that Abeta(1-42) relocates membrane cholesterol. RESULTS: Oligomers of Abeta(1-42), but not the monomeric peptide, inserted into cholesterol-containing phosphatidylcholine monolayers with an anomalously low molecular insertion area, suggesting concurrent lipid rearrangement. Membrane neutron diffraction, including isomorphous replacement of specific lipid hydrogens with highly-scattering deuterium, showed that Abeta(1-42) insertion was accompanied by outward displacement of membrane cholesterol, towards the polar surfaces of the bilayer. Changes in the generalised polarisation of laurdan confirmed that the structural changes were associated with a functional alteration in membrane lipid order. CONCLUSION: Cholesterol is known to regulate membrane lipid order, and this can affect a wide range of membrane mechanisms, including intercellular signalling. Previously unrecognised Abeta-dependent rearrangement of the membrane sterol could have an important role in AD.
We present four experimental physical methods--X-ray and neutron diffraction, nuclear magnetic resonance spectroscopy, mass spectrometry and calorimetry--and two computational methods--molecular dynamics simulations and electrostatics calculations--which are general and widely applicable in the study of protein structure, dynamics and binding. These methods are useful tools for biologists that lead to structure-function, dynamics-function and binding-function correlations, in efforts to understand biomolecular function. Standard and emerging technologies within these methods are discussed and representative examples of applications in immunology are presented, from antigen-antibody, complement and MHC-T-cell receptor research. The examples demonstrate the power of the reviewed methods in immunological studies at the molecular level.
The physiological relationship between brain cholesterol content and the action of amyloid beta (Abeta) peptide in Alzheimer's disease (AD) is a highly controversially discussed topic. Evidences for modulations of the Abeta/membrane interaction induced by plasma membrane cholesterol have already been observed. We have recently reported that Abeta(25-35) is capable of inserting in lipid membranes and perturbing their structure. Applying neutron diffraction and selective deuteration, we now demonstrate that cholesterol alters, at the molecular level, the capability of Abeta(25-35) to penetrate into the lipid bilayers; in particular, a molar weight content of 20% of cholesterol hinders the intercalation of monomeric Abeta(25-35) completely. At very low cholesterol content (about 1% molar weight) the location of the C-terminal part of Abeta(25-35) has been unequivocally established in the hydrocarbon region of the membrane, in agreement with our previous results on pure phospholipids membrane. These results link a structural property to a physiological and functional behavior and point to a therapeutical approach to prevent the AD by modulation of membrane properties.
Neutron diffraction measurements and theoretical calculations of the structure factor S(k) of liquid Kr are extended to small k values (k<4 nm(-1)). The results show that many-body interaction contributions have an increasing effect on S(k) as k-->0, reaching at least 40% of the measured intensity. Both the phase diagram and the low-k structural data of dense Kr turn out to be closely reproduced by the hierarchical reference theory if additional many-body forces are taken into account by an augmented strength of the Axilrod-Teller triple-dipole potential. The experimental density derivative of S(k) is also used for a very sensitive test of the theories and interaction models considered here.
The addition of hydrogen atoms to models or experimental structures of proteins that contain only non-hydrogen atoms is a common step in crystallographic structure refinement, in theoretical studies of proteins, and in protein structure prediction. Accurate prediction of the hydrogen positions is essential, since they constitute around half of the atoms in proteins and hence contribute significantly to their energetics. Many computational tools exist for predicting hydrogen positions, although to date no quantitative comparison has been made of their accuracy or efficiency. Here we take advantage of the recent increase in ultra-high-resolution X-ray crystal structures (< 0.9 A resolution), as well as of a number of relatively high-resolution neutron diffraction structures (< 1.8 A resolution), to compare the quality of the predictions generated by a large set of commonly used methods. These include CHARMM, CNS, GROMACS, MCCE, MolProbity, WHAT IF, and X-PLOR. The hydrogen atoms that lack a rotational degree of freedom are mostly, but not always, accurately predicted. For hydrogens with a rotational degree of freedom, all the methods give much less accurate predictions. The predictions for the hydroxyl hydrogens are analyzed in detail, particularly those buried within the protein, and some explanation is provided for the errors observed. The results provide a means to make informed decisions regarding the choice and implementation of methodologies for placing hydrogens on structures of proteins. They also point to shortcomings in current force fields and suggest the need for improved descriptions of hydrogen bonding energetics.
A combination of neutron diffraction augmented with isotopic substitution and computer modeling using empirical potential structure refinement has been used to extract detailed structural information for L-glutamic acid dissolved in 2 M NaOH solution. This work shows that the tetrahedral hydrogen bonding network in water is severely disrupted by the addition of glutamic acid and NaOH, with the number of water-water hydrogen bonds being reduced from 1.8 bonds per water molecule in pure water to 1.4 bonds per water molecule in the present solution. In the glutamic acid molecule, each carboxylate oxygen atom forms an average of three hydrogen bonds with the surrounding water solvent with one of these hydrogens being shared between the two oxygen atoms on each carboxylate group, while each amine hydrogen forms a single hydrogen bond with the surrounding water solvent. Additionally, the average conformation of the glutamic acid molecules in these solutions is extracted.
Crystals of a human (Sea) Bence-Jones dimer were produced in a capillary by vapor diffusion under microgravity conditions in the 9 day US Space Shuttle Mission STS-95. In comparison to ground-based experiments, nucleation was facile and spontaneous in space. Appearance of a very large (8 x 1.6 x 1.0 mm) crystal in a short time period is a strong endorsement for the use of microgravity to produce crystals sufficiently large for neutron diffraction studies. The Sea dimer crystallized in the orthorhombic space group P2(1)2(1)2(1), with a = 48.9 A, b = 85.2 A, and c = 114.0 A. The crystals grown in microgravity exhibited significantly lower mosaicities than those of ground-based crystals and the X-ray diffraction data had a lower overall B factor. Three-dimensional structures determined by X-ray analysis at two temperatures (100 and 293 K) were indistinguishable from those obtained from ground-based crystals. However, both the crystallographic R factor and the free R factor were slightly lower in the models derived from crystals produced in microgravity. The major difference between the two crystal growth systems is a lack of convection and sedimentation in a microgravity environment. This environment resulted in the growth of much larger, higher-quality crystals of the Sea Bence-Jones protein. Structurally, heretofore unrecognized grooves on the external surfaces of the Sea and other immunoglobulin-derived fragments are regular features and may offer supplementary binding regions for super antigens and other elongated ligands in the bloodstream and perivascular tissues.
The presence of ions in water provides a rich and varied environment in which many natural processes occur with important consequences in biology, geology and chemistry. This article will focus on the structural properties of ions in water and it will be shown how the 'difference' methods of neutron diffraction with isotopic substitution (NDIS) and anomalous X-ray diffraction (AXD) can be used to obtain direct information regarding the radial pair distribution functions of many cations and anions in solution. This information can subsequently be used to calculate coordination numbers and to determine ion-water conformation in great detail. As well as enabling comparisons to be made amongst ions in particular groups in the periodic table, such information can also be contrasted with results provided by molecular dynamics (MD) simulation techniques. To illustrate the power of these 'difference' methods, reference will be made to the alkali group of ions, all of which have been successfully investigated by the above methods, with the exception of the radioactive element francium. Additional comments will be made on how NDIS measurements are currently being combined with MD simulations to determine the structure around complex ions and molecules, many of which are common in biological systems.
Neutron diffraction augmented with hydrogen isotope substitution has been used to examine the water structure around the acetylcholine molecular ion in aqueous solution. It is shown that the nearest-neighbor water molecules in the region around the trimethylammonium headgroup are located either in a ring around the central nitrogen atom or between the carbon atoms, forming a sheath around the onium group. Moreover the water molecules in this cavity do not bond to the onium group but rather form hydrogen bonds with water molecules in the surrounding aqueous environment. Given that in the bound state the onium headgroup must be completely desolvated, the absence of bonding between the onium headgroup and the surrounding water solvent may be selectively favorable to acetylcholine-binding in the receptor site. Away from the headgroup, pronounced hydrogen-bonding of water to the carbonyl oxygen is observed, but not to the ether oxygen in the acetylcholine chain.
A neutron diffraction study has been carried out at 1.6 A resolution on a mutant rubredoxin from Pyrococcus furiosus using the BIX-3 single-crystal diffractometer at the JRR-3 reactor of the Japan Atomic Energy Research Institute. In order to study the unusual thermostability of rubredoxin from P. furiosus (an organism that grows optimally at 373 K), the hydrogen-bonding patterns were compared between the wild-type protein and a 'triple-mutant' variant. In this mutant protein, three residues were changed (Trp3-->Tyr3, Ile23-->Val23, Leu32-->Ile32) so that they are identical to those in a mesophilic rubredoxin from Clostridium pasteurianum. In the present study, some minor changes were found between the wild-type and mutant proteins in the hydrogen-bonding patterns of the Trp3/Tyr3 region. In this investigation, the H/D-exchange ratios in the protein were also studied. Because the target protein was soaked in D2O during the crystallization procedure, most of the N-H and O-H bonds have become deuterated, while essentially all of the C-H bonds have not. In particular, the H/D-exchange pattern of the N-H amide bonds of the protein backbone is of interest because it may contain some indirect information about the mechanism of unfolding of this small protein. The results are in broad agreement with those from solution NMR studies, which suggest that the backbone amide bonds near the four Cys residues of the FeS4 redox center are most resistant to H/D exchange. Finally, the detailed geometries of the water molecules of hydration around the rubredoxin molecule are also reported. The 1.6 A resolution of the present neutron structure determination has revealed a more detailed picture than previously available of some portions of the water structure, including ordered and disordered O-D bonds. Crystallographic details: space group P2(1)2(1)2(1) (orthorhombic), unit-cell parameters a = 34.48, b = 35.70, c = 43.16 A; final agreement factors R = 0.196 and Rfree = 0.230 for 19,384 observed and 6548 unique neutron reflections collected at room temperature; crystal size 4 mm3; a total of 423 non-H atoms, 290 H atoms and 88 D atoms were located in this study.
Using neutron diffraction and a specially constructed high pressure cell suitable for aligned multibilayer systems, we have studied, as a function of pressure, the much observed anomalous swelling regime in dimyristoyl- and dilauroyl-phosphatidylcholine bilayers, DMPC and DLPC, respectively. We have also reanalyzed data from a number of previously published experiments and have arrived at the following conclusions. (a). The power law behavior describing anomalous swelling is preserved in all PC bilayers up to a hydrostatic pressure of 240 MPa. (b). As a function of increasing pressure there is a concomitant decrease in the anomalous swelling of DMPC bilayers. (c). For PC lipids with hydrocarbon chains >or=13 carbons the theoretical unbinding transition temperature T small star, filled is coupled to the main gel-to-liquid crystalline transition temperature T(M). (d). DLPC is intrinsically different from the other lipids studied in that its T small star, filled is not coupled to T(M). (e). For DLPC bilayers we predict a hydrostatic pressure (>290 MPa) where unbinding may occur.
The structure of water and the nature of ionic hydration is explored in aqueous solutions of potassium fluoride, chloride, bromide and iodide over a range of concentrations up to 4.8 ion pairs per 100 water molecules, using the combined techniques of neutron diffraction with hydrogen isotope substitution. The diffraction data are interpreted using the method of empirical potential structure refinement, which attempts to build a three-dimensional model of the scattering system consistent with the diffraction data. The water structure is strongly perturbed in the first hydration shells of both anion and cation, but is found to be only mildly perturbed outside of this region, with the largest effects occurring with the smallest anion and highest concentrations. For the potassium ion there are strong orientational correlations in the first hydration shell, with the water molecules lying with their dipole moments pointing almost directly away from the cation on average, but with an angular spread of approximately +/-60 degrees which is mildly dependent on the anion type present. For all the anions the water molecules in the first shell are strongly oriented with one O-H vector pointing directly towards the anion on average, with an angular spread of approximately +/-10 degrees for F(-), increasing to approximately +/-22 degrees for I(-). For both anions and cations the second hydration shell is much more disordered than the first, but there is a weak pattern of orientational correlation which becomes more pronounced with the larger anions. There is some evidence that the fluoride ion structures water significantly in its first hydration shell, but not beyond. The findings throw further light on recent findings that the orientational relaxation time for water outside the first shell of dissolved ions is the same as in the bulk liquid.