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The present study investigates the structure-property relationship of gravity die-cast and rheocast in situ processed 1wt%TiB2/Al-3.5Mg-0.15Sc-0.075Zr composites. The reinforcement was synthesized via the reaction of fluoride salts (K2TiF6 and KBF4) in the melt at 750 °C for an hour. The cooling slope technique was used for rheocasting, wherein the melt (pouring temperature of 700 °C) was allowed to flow over the cooling slope at an angle of 60°. Thereafter, all samples (gravity die cast and rheocast) were aged at 300 °C for 5 h. Microstructural characterization, hardness measurements, tensile tests, and fractography were necessary supplements to this investigation. The results obtained from this investigation infer: (a) The presence of nano-TiB2 particles increases the ductility (15%) of the gravity die-cast specimens; (b) rheocasting increases the strength of the specimen due to transformation from dendritic to equiaxed dendritic morphology and uniform particle distribution (reduced agglomeration). (c) Rheocast and aged specimens show maximum strength and adequate ductility due to the combined effects of structure refinement, reduced agglomeration, and the formation of fine precipitates. [ABSTRACT FROM AUTHOR]

The crystal structure of uralolite, Ca2Be4(PO4)3(OH)3·5H2O, from the spodumene deposit of Weinebene, Carinthia, Austria, has been refined with X-ray single crystal data gathered on a CCD diffractometer. Uralolite is monoclinic, space group P21/n, a = 6.553(1), b = 16.005(3), c = 15.979(3) Å, β = 101.63(1)°, V = 1641.5(5) Å3. While previously only isotropic displacement parameters and no hydrogen atom positions were reported for uralolite, now anisotropic displacement parameters were used for non-hydrogen atoms and hydrogen atoms were located and refined yielding R1 = 0.038 for 3909 observed reflections. Uralolite is built up from corrugated layers [Be4(PO4)3(OH)3]4- parallel to (010), which contain Z-shaped groups of four BeO4 tetrahedra sharing corners via three OH groups and are further crosslinked by PO4 tetrahedra. Two Ca atoms in Ca(Ophosphate)5(H2O)2 coordination and an interstitial water molecule link these layers along [010]. The OH groups and the Ca-bonded H2O molecules are all involved in hydrogen bonds with O···O distances of 2.780(2) − 3.063(2) Å and O-H···O angles of 150(1) − 179(1)° excluding a bifurcated bond. The interstitial water molecule displays a distorted tetrahedral environment of O atoms and accepts and donates each two hydrogen bonds. The crystal structure exhibits a C2/c pseudosymmetry for the [Be4(PO4)3(OH)3]4- layers and the Ca atoms. However, the disposition of the water molecules and an asymmetric hydrogen bond pattern involving OH groups as well as H2O molecules are decisive for the lowering of the symmetry of the structure to the true space group P21/n. [ABSTRACT FROM AUTHOR]

Six Al- and Li-bearing tourmaline crystals from pegmatites were structurally and chemically characterized. These samples can be assigned to elbaite, fluor-elbaite and rossmanite. Quantitative analyses of light elements such as Li, B and H are not always easily accessible. Therefore a method for the calculation of Li and OH would be of a general interest for the Geosciences. In the present work we test whether relatively accurate Li and OH estimations are possible based on the deconvolution of the O–H stretching vibration modes in a Raman spectrum on common (Al, Li)-rich tourmalines. We use the short-range arrangement model in our band interpretation as this model, in contrast to other models, provides the ability to evaluate an additional parameter by analyzing the OH stretching modes that can be used in the formula calculation process, which ultimately leads to the estimation of Li and OH with high accuracy. We also compare microprobe and Raman spectroscopy results, which we combine, with optimized data derived from microprobe and single-crystal structure refinement by using the same crystals. Based on our investigations, where the Raman spectra were recorded on non-oriented crystal sections, we conclude that we produce more accurate estimations, when the effects of the section orientation are considered. Therefore, we also propose a new method to correct the influence of the orientation of the crystal section. [ABSTRACT FROM AUTHOR]

In protein simulation or structure refinement based on values of observable quantities measured in (aqueous) solution, solvent (water) molecules may be explicitly treated, omitted, or represented by a potential of mean-solvation-force term, depending on protein coordinates only, in the force field used. These three approaches are compared for hen egg white lysozyme (HEWL). This 129-residue non-spherical protein contains a variety of secondary-structure elements, and ample experimental data are available: 1630 atom–atom Nuclear Overhauser Enhancement (NOE) upper distance bounds, 213 3 J-couplings and 200 S2 order parameters. These data are used to compare the performance of the three approaches. It is found that a molecular dynamics (MD) simulation in explicit water approximates the experimental data much better than stochastic dynamics (SD) simulation in vacuo without or with a solvent-accessible-surface-area (SASA) implicit-solvation term added to the force field. This is due to the missing energetic and entropic contributions and hydrogen-bonding capacities of the water molecules and the missing dielectric screening effect of this high-permittivity solvent. Omission of explicit water molecules leads to compaction of the protein, an increased internal strain, distortion of exposed loop and turn regions and excessive intra-protein hydrogen bonding. As a consequence, the conformation and dynamics of groups on the surface of the protein, which may play a key role in protein–protein interactions or ligand or substrate binding, may be incorrectly modelled. It is thus recommended to include water molecules explicitly in structure refinement of proteins in aqueous solution based on nuclear magnetic resonance (NMR) or other experimentally measured data. [ABSTRACT FROM AUTHOR]

Isomorphous bismuth substitution for neodymium in the Nd5Mo3O16 + δ compound has been studied by X-ray diffraction. The crystal structure of a single-phase solid solution with the composition Nd4.95Bi0.05Mo3O16 + δ has been refined by the Rietveld method, and the electrical conductivity of the modified molybdate has been measured in the temperature range 300–700°C. [ABSTRACT FROM AUTHOR]

NMR structure calculation using NOE-derived distance restraints requires a considerable number of assignments of both backbone and sidechains resonances, often difficult or impossible to get for large or complex proteins. Pseudocontact shifts (PCSs) also play a well-established role in NMR protein structure calculation, usually to augment existing structural, mostly NOE-derived, information. Existing refinement protocols using PCSs usually either require a sizeable number of sidechain assignments or are complemented by other experimental restraints. Here, we present an automated iterative procedure to perform backbone protein structure refinements requiring only a limited amount of backbone amide PCSs. Already known structural features from a starting homology model, in this case modules of repeat proteins, are framed into a scaffold that is subsequently refined by experimental PCSs. The method produces reliable indicators that can be monitored to judge about the performance. We applied it to a system in which sidechain assignments are hardly possible, designed Armadillo repeat proteins (dArmRPs), and we calculated the solution NMR structure of YM4A, a dArmRP containing four sequence-identical internal modules, obtaining high convergence to a single structure. We suggest that this approach is particularly useful when approximate folds are known from other techniques, such as X-ray crystallography, while avoiding inherent artefacts due to, for instance, crystal packing. [ABSTRACT FROM AUTHOR]

Values of 3J-couplings as obtained from NMR experiments on proteins cannot easily be used to determine protein structure due to the difficulty of accounting for the high sensitivity of intermediate 3J-coupling values (4–8 Hz) to the averaging period that must cover the conformational variability of the torsional angle related to the 3J-coupling, and due to the difficulty of handling the multiple-valued character of the inverse Karplus relation between torsional angle and 3J-coupling. Both problems can be solved by using 3J-coupling time-averaging local-elevation restraining MD simulation. Application to the protein hen egg white lysozyme using 213 backbone and side-chain 3J-coupling restraints shows that a conformational ensemble compatible with the experimental data can be obtained using this technique, and that accounting for averaging and the ability of the algorithm to escape from local minima for the torsional angle induced by the Karplus relation, are essential for a comprehensive use of 3J-coupling data in protein structure determination. [ABSTRACT FROM AUTHOR]

Data integration in structural biology has become a paradigm for the characterization of biomolecular systems, and it is now accepted that combining different techniques can fill the gaps in each other's blind spots. In this frame, one of the combinations, which we have implemented in REFMAC-NMR, is residual dipolar couplings from NMR together with experimental data from X-ray diffraction. The first are exquisitely sensitive to the local details but does not give any information about overall shape, whereas the latter encodes more the information about the overall shape but at the same time tends to miss the local details even at the highest resolutions. Once crystals are obtained, it is often rather easy to obtain a complete X-ray dataset, however it is time-consuming to obtain an exhaustive NMR dataset. Here, we discuss the effect of including a-priori knowledge on the properties of the system to reduce the number of experimental data needed to obtain a more complete picture. We thus introduce a set of new features of REFMAC-NMR that allow for improved handling of RDC data for multidomain proteins and multisubunit biomolecular complexes, and encompasses the use of pseudo-contact shifts as an additional source of NMR-based information. The new feature may either help in improving the refinement, or assist in spotting differences between the crystal and the solution data. We show three different examples where NMR and X-ray data can be reconciled to a unique structural model without invoking mobility. [ABSTRACT FROM AUTHOR]

A protein is commonly visualized as a discrete piecewise linear curve, conventionally characterized in terms of the extrinsically determined Ramachandran angles. However, in addition to the extrinsic geometry, the protein has also two independent intrinsic geometric structures, determined by the peptide planes and the side chains respectively. Here we develop a novel 3D visualization method that instead of the extrinsic geometry utilizes the intrinsic geometry of side chains. We base our approach on a series of orthonormal coordinate frames along the protein side chains in combination with a mapping of the atoms positions onto a unit sphere, for visualization purposes. We develop our methodology in terms of an example, by analyzing the acidity dependence of the presumed myoglobin ligand gate. In the literature, the ligand gate is often asserted to be highly localized at the distal histidine, its functioning being regulated by environmental changes. Thus, we investigate whether any pH dependence can be detected in the orientation of the distal and proximal histidine residues, using existing crystallographic data. We observe no pH dependence, in support of the alternative proposals that the ligand gate is more complex and might even be located elsewhere. Our methodology should help the planning of future myoglobin structure experiments, to identify the ligand gate position and its mechanism. More generally, our methodology is designed to visually depict the spatial orientation of side chain covalent bonds in a protein. As such, it can be eventually advanced into a general visual 3D tool for protein structure analysis for purposes of prediction, validation and refinement. It can serve as a complement to widely used visualization suites such as VMD, Jmol, PyMOL and others. [ABSTRACT FROM AUTHOR]

In-situ single-crystal and powder X-ray diffraction (XRD) experiments were performed on diaspore at high temperatures. The powder XRD experiments showed that the dehydration reaction from diaspore to corundum occurs between 703 and 733 K. The in-situ single-crystal XRD measurements of diaspore could successfully determine the cell parameters, fractional atomic coordinates and anisotropic displacement parameters at high temperatures, i.e., from 295 to 698 K. Temperature variations in the cell parameters indicate that thermal expansion of the a-axis is a little higher than those of the b-axis and the c-axis. However, the axial thermal expansivity is not as anisotropic as was previously suggested. The results of structure refinements indicate that such lattice expansion behavior is the result of thermal expansion of the tunnels through O2-H···O1 hydrogen-bond separation in the diaspore structure. To the best of our knowledge, this is the first time that the thermal expansion of diaspore has been investigated at an atomic level by in-situ single-crystal XRD experiments at high temperatures. [ABSTRACT FROM AUTHOR]

The binding of paramagnetic metal ions to proteins produces a number of different effects on the NMR spectra of the system. In particular, when the magnetic susceptibility of the metal ion is anisotropic, pseudocontact shifts (PCSs) arise and can be easily measured. They constitute very useful restraints for the solution structure determination of metal-binding proteins. In this context, there has been great interest in the use of lanthanide(III) ions to induce PCSs in diamagnetic proteins, e.g. through the replacement native calcium(II) ions. By preparing multiple samples in each of which a different ion of the lanthanide series is introduced, it is possible to obtain multiple independent PCS datasets that can be used synergistically to generate protein structure ensembles (typically called bundles). For typical NMR-based determination of protein structure, it is necessary to perform an energetic refinement of such initial bundles to obtain final structures whose geometric quality is suitable for deposition in the PDB. This can be conveniently done by using restrained molecular dynamics simulations (rMD) in explicit solvent. However, there are no available protocols for rMD using multiple PCS datasets as part of the restraints. In this work, we extended the PCS module of the AMBER MD package to handle multiple datasets and tuned a previously developed protocol for NMR structure refinement to achieve consistent convergence with PCS restraints. Test calculations with real experimental data show that this new implementation delivers the expected improvement of protein geometry, resulting in final structures that are of suitable quality for deposition. Furthermore, we observe that also initial structures generated only with traditional restraints can be successfully refined using traditional and PCS restraints simultaneously. [ABSTRACT FROM AUTHOR]

Hexagonal A-Mg-Si with A = Sr and Ba Zintl phases are promising candidates for p-type magnesium silicides usable with n-MgSi under 900 K. We synthesized p-type A-Mg-Si Zintl phases by the spark plasma synthesis procedure. MgSi and MgA powders were mixed at the ratio of 1− x/ x with x = 0.3-0.4. Two-step synthesis was performed at 850 K for 20 min and 1100 K for 20 min under uniaxial pressure at 30 MPa. Sintered pellets exhibited a stable p-type thermoelectric property. These pellets consisted of several unknown phases. We found two semiconductor phases, namely AMgSi and AMgSi. The crystal structures of the 2/4/3- and 2/12/7-phases were $$ P\bar{6}2m$$ (No. 189)- and $$ P6_{3} /m$$ (No. 176)-types, respectively. SrMgSi, BaMgSi and SrMgSi phases are newly found and characterized by a single crystal diffraction study. Previously found SrMgSi single phase polycrystalline 30φ × 10 mm pellets were successfully synthesized. The thermoelectric performance of the SrMgSi single phase sample was tested. The pellets exhibit p-type behavior from room temperature to 700 K. The thermal conductivity, κ, was almost constant at 1.1 W/mK from 350 K to 700 K. [ABSTRACT FROM AUTHOR]

Deriving molecular structure from $$^3J$$ -couplings obtained from NMR experiments is a challenge due to (1) the uncertainty in the Karplus relation $$^3J(\theta )$$ connecting a $$^3J$$ -coupling value to a torsional angle $$\theta $$ , (2) the need to account for the averaging inherent to the measurement of $$^3J$$ -couplings, and (3) the sampling road blocks that may emerge due to the multiple-valuedness of the inverse function $$\theta (^3J)$$ of the function $$^3J(\theta )$$ . Ways to properly handle these issues in structure refinement of biomolecules are discussed and illustrated using the protein hen egg white lysozyme as example. [ABSTRACT FROM AUTHOR]

A method is described that allows experimental $$S^2$$ order parameters to be enforced as a time-averaged quantity in molecular dynamics simulations. The two parameters that characterize time-averaged restraining, the memory relaxation time and the weight of the restraining potential energy term in the potential energy function used in the simulation, are systematically investigated based on two model systems, a vector with one end restrained in space and a pentapeptide. For the latter it is shown that the backbone N-H order parameter of individual residues can be enforced such that the spatial fluctuations of quantities depending on atomic coordinates are not significantly perturbed. The applicability to realistic systems is illustrated for the B3 domain of protein G in aqueous solution. [ABSTRACT FROM AUTHOR]

The behavior of a natural topaz, AlSiO(OHF), has been investigated by means of in situ single-crystal synchrotron X-ray diffraction up to 45 GPa. No phase transition or change in the compressional regime has been observed within the pressure-range investigated. The compressional behavior was described with a third-order Birch-Murnaghan equation of state (III-BM-EoS). The III-BM-EoS parameters, simultaneously refined using the data weighted by the uncertainties in P and V, are as follows: K = 158(4) GPa and K ′ = 3.3(3). The confidence ellipse at 68.3 % (Δχ = 2.30, 1σ) was calculated starting from the variance-covariance matrix of K and K′ obtained from the III-BM-EoS least-square procedure. The ellipse is elongated with a negative slope, indicating a negative correlation of the parameters K and K ′, with K = 158 ± 6 GPa and K ′ = 3.3 ± 4. A linearized III-BM-EoS was used to obtain the axial-EoS parameters (at room- P), yielding: K( a) = 146(5) GPa [ β = 1/(3 K( a)) = 0.00228(6) GPa] and K′( a) = 4.6(3) for the a-axis; K( b) = 220(4) GPa [ β = 0.00152(4) GPa] and K′( b) = 2.6(3) for the b-axis; K( c) = 132(4) GPa [ β = 0.00252(7) GPa] and K′( c) = 3.3(3) for the c-axis. The elastic anisotropy of topaz at room- P can be expressed as: K( a): K( b): K( c) = 1.10:1.67:1.00 ( β: β: β = 1.50:1.00:1.66). A series of structure refinements have been performed based on the intensity data collected at high pressure, showing that the P-induced structure evolution at the atomic scale is mainly represented by polyhedral compression along with inter-polyhedral tilting. A comparative analysis of the elastic behavior and P/ T-stability of topaz polymorphs and 'phase egg' (i.e., AlSiOOH) is carried out. [ABSTRACT FROM AUTHOR]

Three natural minerals of ettringite group were investigated by TG to refine their chemical composition. Two samples are ettringite CaMgSrAlCr(SO)(OH)·23.7HO and bentorite CaMgCrAlSi(SO)·(CO)(OH)·19.4HO, but the third one CaNaAlSi(SO)·(CrO)·(CO)(OH)·15.8HO has found to be a solid solution among ettringite, thaumasite, and chromate-ettringite, not registered yet as a new mineral species. Similar phase is well known in concrete formed with Cr admixture, but is found for the first time as a natural compound. X-ray single-crystal investigation allowed us to refine the structure and support substitution (SO) ↔ (CrO) in natural minerals of ettringite group. [ABSTRACT FROM AUTHOR]

Scandium substitution in the diopside structure was studied by single-crystal X-ray diffraction on a series of synthetic diopside samples. These diopsides were doped with increasing amounts of Sc through a coupled substitution involving (Sc)[](B)(Mg)(Ca)(Si) exchange, whereby charge compensation is achieved by vacancies at the M2 sites and B at the tetrahedral sites. The substitution of scandium for magnesium at the M1 site results in an increase in volume and distortion of the M1O polyhedron. The accompanying creation of vacancies at the M2 sites causes an increase in the M2 polyhedral volume. The modifications of the M1 and M2 polyhedra result in an increase of the polyhedral strip along the b lattice direction and a straightening of the tetrahedral chain. The geometrical modification of the M1 polyhedron due to scandium incorporation is comparable to those observed when similar amounts of Ti/Ti substitute for Mg in the diopside structure, suggesting a structural control on the solubility of Sc and Ti in diopside that may influence the extent of the solid solutions between the Sc and Ti end-members. [ABSTRACT FROM AUTHOR]

The crystal structure of gearksutite, Ca and Al hydrofluoride CaAlF(OH) · HO, was refined using the Rietveld method with power diffraction data. The thermal stability of its crystal structure was studied for the first time using high-temperature XRD. Thermal XRD study of the mineral in the temperature range from 25 to 300°C revealed its stability to temperatures of 300-310°C. The mineral began to decay at temperatures greater than 300°C. The increase in the unit-cell parameters was established and the coefficients of thermal expansion were calculated. [ABSTRACT FROM AUTHOR]

Deriving structural information about a protein from NMR experimental data is still a non-trivial challenge to computational biochemistry. This is because of the low ratio of the number of independent observables to the number of molecular degrees of freedom, the approximations involved in the different relationships between particular observable quantities and molecular conformation, and the averaged character of the experimental data. For example, protein J-coupling data are seldom used for structure refinement because of the multiple-valuedness and limited accuracy of the Karplus relationship linking a J-coupling to a torsional angle. Moreover, sampling of the large conformational space is still problematic. Using the 99-residue protein plastocyanin as an example we investigated whether use of a thermodynamically calibrated force field, inclusion of solvent degrees of freedom, and application of adaptive local-elevation sampling that accounts for conformational averaging produces a more realistic representation of the ensemble of protein conformations than standard single-structure refinement in a non-explicit solvent using restraints that do not account for averaging and are partly based on non-observed data. Yielding better agreement with observed experimental data, the protein conformational ensemble is less restricted than when using standard single-structure refinement techniques, which are likely to yield a picture of the protein which is too rigid. [ABSTRACT FROM AUTHOR]

Structural knowledge about proteins is mainly derived from values of observables, measurable in NMR spectroscopic or X-ray diffraction experiments, i.e. absorbed or scattered intensities, through theoretically derived relationships between structural quantities such as atom positions or torsional angles on the one hand and observable quantities such as squared structure factor amplitudes, NOE intensities or J-coupling constants on the other. The standardly used relation connecting J-couplings to torsional angles is the Karplus relation, which is used in protein structure refinement as well as in the evaluation of simulated properties of proteins. The accuracy of the simple and generalised Karplus relations is investigated using side-chain structural and J-coupling data for three different proteins, Plastocyanin, Lysozyme, and FKBP, for which such data are available. The results show that the widely used Karplus relations are only a rough estimate for the relation between J-couplings and the corresponding χ-angle in proteins. [ABSTRACT FROM AUTHOR]

For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simulation. The methodology and some implementation details of the computation of NMR NOE data, J-couplings and residual dipolar couplings, X-ray scattering intensities from crystals and solutions and neutron scattering intensities used in GROMOS is described and refinement strategies and concepts are discussed using example applications. The GROMOS software allows structure refinement combining different types of experimental data with different types of restraining functions, while using a variety of methods to enhance conformational searching and sampling and the thermodynamically calibrated GROMOS force field for biomolecular simulation. [ABSTRACT FROM AUTHOR]

The crystal structure and the formation conditions of crystals of the LiFe5O8 ordered phase obtained from the solution-melt of the Bi2O3-Fe2O3-B2O3-LiCl quadruple system are refined. The crystals are black, octahedral, of cubic symmetry (space group P4332). Unit cell parameters: a = 8.3339(1) Å, V = 578.82(1) Å3, Z = 4, d calc = 4.753 g/cm3. From 6046 of the collected array I hkl 358 are independent ( R int = 0.0321). As a result of anisotropic refinement of structural parameters, R 1 factor is found to be 0.0186 ( wR 2 = 0.0467). Lithium atoms are in octahedral environment, Li-O is 2.109(1) Å; iron atoms are of two types: in octahedra with Fe-O (by two) distances of 1.9586(9) Å, 2.0152(9) Å, and 2.0652(10) Å and tetrahedra with Fe-O (three) 1.8848(10) Å and 1.914(2) Å. The structure is of inverted spinel type. [ABSTRACT FROM AUTHOR]

The use of time-dependent restraints in molecular simulation in order to generate a conformational ensemble for molecules that is in accordance with measured ensemble averages for particular observable quantities is investigated. Using a model system consisting of liquid butane and the cyclic peptide antamanide the reproduction of particular average 3 J-coupling constant values in a molecular dynamics simulation is analysed. It is shown that the multiple-valuedness and the sizeable gradients of the Karplus curve relating 3 J-coupling constants measured in NMR experiments to the corresponding torsional-angle values cause severe problems when trying to restrain a 3 J-coupling constant to a value close to the extrema of the Karplus curve. The introduction of a factor oscillating with time into the restraining penalty function alleviates this problem and enhances the restrained conformational sampling. [ABSTRACT FROM AUTHOR]

15N–1H residual dipolar couplings (RDC) have been used as additional restraints to refine the solution structure of the ribotoxin α-sarcin. The RDC values were obtained by partial alignment of α-sarcin in the binary mixture of n-dodecyl hexa(ethylene glycol)/hexanol. A total of 131 RDCs were measured and 106 were introduced in the final steps of the calculation protocol following the main calculation based on nuclear Overhauser enhancements and torsion angle restraints. A homogeneous family of 81 conformers was obtained. The resulting average pairwise root-mean-square deviation corresponding to the superposition of the 20 best structures is 0.69±0.12 Å for the backbone and 1.29±0.14 Å for all heavy atoms. The new structural features derived from the refined structure, compared with the non-refined structure of α-sarcin, consist of new hydrogen bonds and a better definition of the backbone conformation. In particular, the loop segment spanning Gly 60 to Lys 70 shows a single conformation, corresponding to the most populated family of conformers observed in the unrefined structure. The information derived from the analysis of the refined structure and the comparison with the homologous protein restrictocin could help in establishing further structure–function relationships concerning α-sarcin which can be reasonably extrapolated to other members of the ribotoxin family. [ABSTRACT FROM AUTHOR]

For biomolecular NMR structures typically only a poor correspondence is observed between statistics derived from the experimental input data and structural quality indicators obtained from the structure ensembles. Here, we investigate the relationship between the amount of available NMR data and structure quality. By generating datasets with a predetermined information content and evaluating the quality of the resulting structure ensembles we show that there is, in contrast to previous findings, a linear relation between the information contained in experimental data and structural quality. From this relation, a new quality parameter is derived that provides direct insight, on a per-residue basis, into the extent to which structural quality is governed by the experimental input data. [ABSTRACT FROM AUTHOR]

Determining an accurate initial native-like protein fold is one of the most important and time-consuming steps ofde novoNMR structure determination. Here we demonstrate that high-quality native-like models can be rapidly generated from initial structures obtained using limited NOE assignments, through replica exchange molecular dynamics refinement with a generalized Born implicit solvent (REX/GB). Conventional structure calculations using an initial sparse NOE set were unable to identify a unique topology for the zinc-bound C-terminal domain ofE. colichaperone Hsp33, due to a lack of unambiguous long range NOEs. An accurate overall topology was eventually obtained through laborious hand identification of long range NOEs. However we were able to obtain high-quality models with backbone RMSD values of about 2 Å with respect to the final structures, using REX/GB refinement with the original limited set of initial NOE restraints. These models could then be used to make further assignments of ambiguous NOEs and thereby speed up the structure determination process. The ability to calculate accurate starting structures from the limited unambiguous NOE set available at the beginning of a structure calculation offers the potential of a much more rapid and automated process for NMR structure determination. [ABSTRACT FROM AUTHOR]

The interaction of manganese(II) with diphenylthiocarbazide in ethanol solutions with various concentrations has been investigated. The structure and composition of the products have been determined. Structure refinement was performed for diphenylcarbazide and dehydrodithizone. [ABSTRACT FROM AUTHOR]

We have examined how the hydrogen bond geometry in three different proteins is affected when structural restraints based on measurements of residual dipolar couplings are included in the structure calculations. The study shows, that including restraints based solely on 1HN-15N residual dipolar couplings has pronounced impact on the backbone rmsd and Ramachandran plot but does not improve the hydrogen bond geometry. In the case of chymotrypsin inhibitor 2 the addition of 13CO-13Cα and 15N-13CO one bond dipolar couplings as restraints in the structure calculations improved the hydrogen bond geometry to a quality comparable to that obtained in the 1.8 Å resolution X-ray structure of this protein. A systematic restraint study was performed, in which four types of restraints, residual dipolar couplings, hydrogen bonds, TALOS angles and NOEs, were allowed in two states. This study revealed the importance of using several types of residual dipolar couplings to get good hydrogen bond geometry. The study also showed that using a small set of NOEs derived only from the amide protons, together with a full set of residual dipolar couplings resulted in structures of very high quality. When reducing the NOE set, it is mainly the side-chain to side-chain NOEs that are removed. Despite of this the effect on the side-chain packing is very small when a reduced NOE set is used, which implies that the over all fold of a protein structure is mainly determined by correct folding of the backbone. [ABSTRACT FROM AUTHOR]

Biomolecular structures provide the basis for many studies in research areas such as structure-based drug design and homology modeling. In order to use molecular coordinates it is important that they are reliable in terms of accurate description of the experimental data and in terms of the overall and local geometry. Besides these primary quality criteria an indication is needed for the uncertainty in the atomic coordinates that may arise from the dynamic behavior of the considered molecules as well as from experimental- and computational procedures. In contrast to the crystallographic B-factor, a good measure for the uncertainty in NMR-derived atomic coordinates is still not available. It has become clear in recent years that the widely used atomic Root Mean Square Deviation (RMSD), which is a measure for the precision of the data, overestimates the accuracy of NMR structure ensembles and therefore is a problematic measure for the uncertainty in the atomic coordinates. In this study we report a method that yields a more realistic estimate of the uncertainty in the atomic coordinates by maximizing the RMSD of an ensemble of structures, while maintaining the accordance with the experimentally derived data. The results indicate that the RMSD of most NMR structure ensembles can be significantly increased compromising neither geometric quality nor NMR data. This maximized RMSD therefore seems a better estimate of the true uncertainty in the atomic coordinates. [ABSTRACT FROM AUTHOR]

The crystal structures of an elbaite, Na0.591Ca0.118 (Al1.395Fe0.007Mn0.390Li1.208)Al6(Si5.986Al0.014O18(BO3)(OH)4, a=15.866(2), c=7.113(1) Å, V=1550.4(6) Å3, R3m, Z=3, and a schorl, Na0.659Ca0.081 (Al0.245Fe1.680Mn0.013Ti0.078Mg0.860Li0.122)Al6(Si5.901Al0.099)O18(BO3)(OH)4, a=15.985(2), c=7.178(1) Å, V=1588.4(6) Å3, R3m, Z=3, have been refined by single-crystal and Rietveld methods to R indices of 2.0/5.9 and 1.7/6.5%, respectively. Half-normal probability analysis of the two sets of results shows that the Rietveld method produces site-scattering values and atomic positions that are accurate. This indicates that the Rietveld method should be a useful technique for the characterization of run products in tourmaline-systhesis experiments as well as synthetic ones having complicated crystal structures. [ABSTRACT FROM AUTHOR]

The inclusion of explicit solvent water in molecular dynamics refinement of NMR structures ought to provide the most physically meaningful accounting for the effects of solvent on structure, but is computationally expensive. In order to evaluate the validity of commonly used vacuum refinements and of recently developed continuum solvent model methods, we have used three different methods to refine a set of NMR solution structures of a medium sized protein, Escherichia coli glutaredoxin 2, from starting structures calculated using the program DYANA. The three different refinement protocols used molecular dynamics simulated annealing with the program AMBER in vacuum (VAC), including a generalized Born (GB) solvent model, and a full calculation including explicit solvent water (WAT). The structures obtained using the three methods of refinements were very similar, a reflection of their generally well-determined nature. However, the structures refined with the generalized Born model were more similar to those from explicit water refinement than those refined in vacuum. Significant improvement was seen in the percentage of backbone dihedral angles in the most favored regions of φ,ψ space and in hydrogen bond pattern for structures refined with the GB and WAT models, compared with the structures refined in vacuum. The explicit water calculation took an average of 200 h of CPU time per structure on an SGI cluster, compared to 15–90 h for the GB calculation (depending on the parameters used) and 2 h for the vacuum calculation. The generalized Born solvent model proved to be an excellent compromise between the vacuum and explicit water refinements, giving results comparable to those of the explicit water calculation. Some improvement for φ and ψ angle distribution and hydrogen bond pattern can also be achieved by energy minimizing the vacuum structures with the GB model, which takes a much shorter time than MD simulations with the GB model. [ABSTRACT FROM AUTHOR]

Biomolecular structures provide the basis for many studies in several research areas such as homology modelling, structure-based drug design and functional genomics. It is an important prerequisite that the structure is reliable in terms of accurate description of the experimental data, and in terms of good quality of local- and overall geometry. Recent surveys indicate that structures solved by NMR-spectroscopy normally are of lower precision than high-resolution X-ray structures. Here, we present a refinement protocol that improves the quality of protein structures determined by NMR-spectroscopy to the level of those determined by high resolution X-ray crystallography in terms of local geometry. The protocol was tested on experimental data of the proteins IL4 and Ubiquitin and on simulated data of the protein Crambin. In almost all aspects, the protocol yielded better results in terms of accuracy and precision. Independent validation of the results for Ubiquitin, using residual dipolar couplings, indicates that the ensemble of NMR structure is substantially improved by the protocol. [ABSTRACT FROM AUTHOR]

The relative importance of paramagnetism-based constraints (i.e. pseudocontact shifts, residual dipolar couplings and nuclear relaxation enhancements) with respect to classical constraints in solution structure determinations of paramagnetic metalloproteins has been addressed. The protein selected for the study is a calcium binding protein, calbindin D9k, in which one of the two calcium ions is substituted with cerium(III). From 1823 NOEs, 191 dihedral angles, 15 hydrogen bonds, 769 pseudocontact shifts, 64 orientational constraints, 26 longitudinal relaxation rates, plus 969 pseudocontact shifts from other lanthanides, a final family with backbone r.m.s.d. from the average of 0.25 Å was obtained. Then, several families of structures were generated either by removing subsets of paramagnetism-based constraints or by removing increasing numbers of NOEs. The results show the relative importance of the various paramagnetism-based constraints and their good complementarity with the diamagnetic ones. Although a resolved structure cannot be obtained with paramagnetism-based constraints only, it is shown that a reasonably well resolved backbone fold can be safely obtained by retaining as few as 29 randomly chosen long-range NOEs using the standard version of the program PSEUDYANA. [ABSTRACT FROM AUTHOR]

One important problem when calculating structures of biomolecules from NMR data is distinguishing converged structures from outlier structures. This paper describes how Principal Components Analysis (PCA) has the potential to classify calculated structures automatically, according to correlated structural variation across the population. PCA analysis has the additional advantage that it highlights regions of proteins which are varying across the population. To apply PCA, protein structures have to be reduced in complexity and this paper describes two different representations of protein structures which achieve this. The calculated structures of a 28 amino acid peptide are used to demonstrate the methods. The two different representations of protein structure are shown to give equivalent results, and correct results are obtained even though the ensemble of structures used as an example contains two different protein conformations. The PCA analysis also correctly identifies the structural differences between the two conformations. [ABSTRACT FROM AUTHOR]

Natural barbosalite Fe2+Fe3+ 2 (PO4)2(OH)2 from Bull Moose Mine, South Dakota, U.S.A., having ideal composition, was investigated with single crystal X-ray diffraction techniques, Mössbauer spectroscopy and SQUID magnetometry to redetermine crystal structure, valence state of iron and evolution of 57Fe Mössbauer parameter and to propose the magnetic structure at low temperatures. At 298 K the title compound is monoclinic, space group P21/n, a o = 7.3294(16) Å, b o = 7.4921(17) Å, c o = 7.4148 (18) Å, β = 118.43(3)°, Z = 2. No crystallographic phase transition was observed between 298 K and 110 K. Slight discontinuities in the temperature dependence of lattice parameters and bond angles in the range between 150 K and 180 K are ascribed to the magnetic phase transition of the title compound. At 298 K the Mössbauer spectrum of the barbosalite shows two paramagnetic components, typical for Fe2+ and Fe3+ in octahedral coordination; the area ratio Fe3+/Fe2+ is exactly two, corresponding to the ideal value. Both the Fe2+ and the Fe3+ sublattice order magnetically below 173 K and exhibit a fully developed magnetic pattern at 160 K. The electric field gradient at the Fe2+ site is distorted from axial symmetry with the direction of the magnetic field nearly perpendicular to Vzz, the main component of the electric field gradient. The temperature dependent magnetic susceptibility exhibits strong antiferromagnetic ordering within the corner-sharing Fe3+-chains parallel to [101], whereas ferromagnetic coupling is assumed within the face-sharing [1 1 0] and [−1 1 0] Fe3+-Fe2+-Fe3+ trimer, connecting the Fe3+-chains to each other. [ABSTRACT FROM AUTHOR]

A new algorithm is presented for determination of structural conformers and their populations based on NMR data. Restrained Metropolis Monte Carlo simulations or restrained energy minimizations are performed for several copies of a molecule simultaneously. The calculations are restrained with dipolar relaxation rates derived from measured NOE intensities via complete relaxation matrix analysis. The novel feature of the algorithm is that the weights of individual conformers are determined in every refinement step, by the quadratic programming algorithm, in such a way that the restraint energy is minimized. Its design ensures that the calculated populations of the individual conformers are based only on experimental restraints. Presence of internally inconsistent restraints is the driving force for determination of distinct multiple conformers. The method is applied to various simulated test systems. Conformational calculations on nucleic acids are carried out using generalized helical parameters with the program DNAminiCarlo. From different mixtures of A- and B-DNA, minor fractions as low as 10% could be determined with restrained energy minimization. For B-DNA with three local conformers (C2′-endo, O4′-exo, C3′-endo), the minor O4′-exo conformer could not be reliably determined using NOE data typically measured for DNA. The other two conformers, C2′-endo and C3′-endo, could be reproduced by Metropolis Monte Carlo simulated annealing. The behavior of the algorithm in various situations is analyzed, and a number of refinement protocols are discussed. Prior to application of this algorithm to each experimental system, it is suggested that the presence of internal inconsistencies in experimental data be ascertained. In addition, because the performance of the algorithm depends on the type of conformers involved and experimental data available, it is advisable to carry out test calculations with simulated data modeling each experimental system studied. [ABSTRACT FROM AUTHOR]

Cross-correlated relaxation rates involving the Cα-Hα dipolar interaction and the carbonyl (C′) chemical shift anisotropy (CSA) have been measured using two complementary 3D experiments. We show that the protein backbone angle ψ can be directly refined against such cross-correlated relaxation rates (ΓHα Cα,C′) and the three-bond H/D isotope effect on the Cα chemical shifts (3ΔCα(ND)). By simultaneously using both experimental parameters as restraints during NMR structure calculations, a unique value for the backbone angle ψ is defined. We have applied the new refinement method to the α-Spectrin SH3 domain (a β-sheet protein) and to the Sgs1p HRDC domain (an α-helical protein) and show that the quality of the NMR structures is substantially improved, judging from the atomic coordinate precision and the Ramachandran map. In addition, the ψ-refined NMR structures of the SH3 domain deviate less from the 1.8 Å crystal structure, suggesting an improved accuracy. The proposed refinement method can be used to significantly improve the quality of NMR structures and will be applicable to larger proteins. [ABSTRACT FROM AUTHOR]

The main limitation in NMR-determined structures of nucleic acids and their complexes with proteins derives from the elongated, non-globular nature of physiologically important DNA and RNA molecules. Since it is generally not possible to obtain long-range distance constraints between distinct regions of the structure, long-range properties such as bending or kinking at sites of protein recognition cannot be determined accurately nor precisely. Here we show that use of residual dipolar couplings in the refinement of the structure of a protein–RNA complex improves the definition of the long-range properties of the RNA. These features are often an important aspect of molecular recognition and biological function; therefore, their improved definition is of significant value in RNA structural biology. [ABSTRACT FROM AUTHOR]

The NMR structure of the peptide deformylase (PDF) (1–150) from Escherichia coli, which is an essential enzyme that removes the formyl group from nascent polypeptides and represents a potential target for drug discovery, was determined using 15N/13C doubly labeled protein. Nearly completely automated assignment routines were employed to assign three-dimensional triple resonance, 15N-resolved and 13C-resolved NOESY spectra using the program GARANT. This assignment strategy, demonstrated on a 17 kDa protein, is a significant advance in the automation of NMR data assignment and structure determination that will accelerate future work. A total of 2302 conformational constraints were collected as input for the distance geometry program DYANA. After restrained energy minimization with the program X-PLOR the 20 best conformers characterize a high quality structure with an average of 0.43 Å for the root-mean-square deviation calculated from the backbone atoms N, Cα and C′, and 0.81 Å for all heavy atoms of the individual conformers relative to the mean coordinates for residues 1 to 150. The globular fold of PDF contains two α-helices comprising residues 25–40, 125–138, six β-strands 57–60, 70–77, 85–88, 98–101, 105–111, 117–123 and one 310 helix comprising residues 49–51. The C-terminal helix contains the HEXXH motif positioning a zinc ligand in a similar fashion to other metalloproteases, with the third ligand being cysteine and the fourth presumably a water. The three-dimensional structure of PDF affords insight into the substrate recognition and specificity for N-formylated over N-acetylated substrates and is compared to other PDF structures. [ABSTRACT FROM AUTHOR]

We have constructed an extensive database of 13C Cα and Cβ chemical shifts in proteins of solution, for proteins of which a high-resolution crystal structure exists, and for which the crystal structure has been shown to be essentially identical to the solution structure. There is no systematic effect of temperature, reference compound, or pH on reported shifts, but there appear to be differences in reported shifts arising from referencing differences of up to 4.2 ppm. The major factor affecting chemical shifts is the backbone geometry, which causes differences of ca. 4 ppm between typical α- helix and β-sheet geometries for Cα, and of ca. 2 ppm for Cβ. The side-chain dihedral angle χ1 has an effect of up to 0.5 ppm on the Cα shift, particularly for amino acids with branched side-chains at Cβ. Hydrogen bonding to main-chain atoms has an effect of up to 0.9 ppm, which depends on the main- chain conformation. The sequence of the protein and ring-current shifts from aromatic rings have an insignificant effect (except for residues following proline). There are significant differences between different amino acid types in the backbone geometry dependence; the amino acids can be grouped together into five different groups with different φ,ψ shielding surfaces. The overall fit of individual residues to a single non-residue-specific surface, incorporating the effects of hydrogen bonding and χ1 angle, is 0.96 ppm for both Cα and Cβ. The results from this study are broadly similar to those from ab initio studies, but there are some differences which could merit further attention. [ABSTRACT FROM AUTHOR]

The space in the unit cell of a metmyoglobin crystal not occupied by myoglobin atoms was filled with water using Monte Carlo calculations. Independent calculations with different amounts of water have been performed. Structure factors were calculated using the water coordinates thus obtained and the known coordinates of the myoglobin atoms. A comparison with experimental structure factors showed that both the low and the high resolution regime could be well reproduced with 814 Monte Carlo water molecules per unit cell with a B-value of 50 Å. The Monte Carlo water molecules yield a smaller standard R-value (0.166) than using a homogeneous electron density for the simulation of the crystal water (R = 0.212). A reciprocal space refinement of the water and the protein coordinates has been performed. Monte Carlo calculations can be used to obtain information for crystallographically invisible parts of the unit cell and yield better coordinates for the visible part in the refinement. [ABSTRACT FROM AUTHOR]

In the absence of a high resolution crystal structure for the ribosome, numerous research groups are carrying out low resolution structural studies using neutron diffraction, electron microscopy, fluorescence energy transfer, chemical crosslinking, chemical footprinting studies, and other methods. We have developed a computer-based refinement method for incorporating these data into low resolution three-dimensional models. The method is based on a molecular mechanics approach, with proteins represented by spherical particles of suitable diameter and the ribosomal RNA represented by a string of spherical pseudoatoms, one for each nucleotide. Experimental data are used to derive constraints that are introduced through a special force field (potential function). Models are refined by simulated annealing. Since every term in the force field is quadratic, any model that satisfies all of the input data has an energy of zero; higher energies indicate residual unsatisfied constraints. The residual energy provides a quantitative statement of model quality and can be used to identify conflicts in the experimental data. The method has been applied to the refinement of a low resolution model for the 30S subunit (the small subunit) of the E. coli ribosome. Since this is a very underdetermined system, the range of acceptable models has also been explored. This provides an estimate of the resolution of the structure, which is about 15 Å overall, with the uncertainty in position of individual nucleotides ranging from about 5 Å to 50 Å. [ABSTRACT FROM AUTHOR]

Introducing experimental values as restraints into molecular dynamics (MD) simulations to bias the values of particular molecular properties, such as nuclear Overhauser effect intensities or distances, 3J coupling constants, chemical shifts or crystallographic structure factors, towards experimental values is a widely used structure refinement method. To account for the averaging of experimentally derived quantities inherent in the experimental techniques, time-averaging restraining methods may be used. In the case of structure refinement using 3J coupling constants from NMR experiments, time-averaging methods previously proposed can suffer from large artificially induced structural fluctuations. A modified time-averaged restraining potential energy function is proposed which overcomes this problem. The different possible approaches are compared using stochastic dynamics simulations of antamanide, a cyclic peptide of ten residues. [ABSTRACT FROM AUTHOR]

The program DYANA, for calculation of solution structures of biomolecules with an algorithm based on simulated annealing by torsion angle dynamics, has been supplemented with a new routine, PSEUDYANA, that enables efficient use of pseudocontact shifts as additional constraints in structure calculations of paramagnetic metalloproteins. PSEUDYANA can determine the location of the metal ion inside the protein frame and allows to define a single tensor of magnetic susceptibility from a family of conformers. As an illustration, a PSEUDYANA structure calculation is provided for a metal-undecapeptide complex, where simulated pseudocontact shifts but no NOE restraints are used as conformational constraints. [ABSTRACT FROM AUTHOR]

The three-dimensional solution structures of proteins determinedwith NMR-derived constraints are almost always calculated in vacuo. Thesolution structure of (Ca2+)_2-calbindinD9k has been redetermined by new restrained molecular dynamics(MD) calculations that include Ca2+ ions and explicit solventmolecules. Four parallel sets of MD refinements were run to provide accuratecomparisons of structures produced in vacuo, in vacuo withCa2+ ions, and with two different protocols in a solvent bathwith Ca2+ ions. The structural ensembles were analyzed interms of structural definition, molecular energies, packing density,solvent-accessible surface, hydrogen bonds, and the coordination of calciumions in the two binding loops. Refinement including Ca2+ ionsand explicit solvent results in significant improvements in the precisionand accuracy of the structure, particularly in the binding loops. Theseresults are consistent with results previously obtained in free MDsimulations of proteins in solution and show that the rMD refinedNMR-derived solution structures of proteins, especially metalloproteins, canbe significantly improved by these strategies. [ABSTRACT FROM AUTHOR]

The solution structures of staphylococcal nuclease (nuclease) H124L and itsternary complex, (nuclease-H124L)•pdTp•Ca2+, were determinedby ab initio dynamic simulated annealing using 1925 NOE, 119 φ, 20χ1 and 112 hydrogen bond constraints for the free protein,and 2003 NOE, 118 φ, 20 χ1 and 114 hydrogen bondconstraints for the ternary complex. In both cases, the final structuresdisplay only small deviations from idealized covalent geometry. In structuredregions, the overall root-mean-square deviations from mean atomic coordinatesare 0.46 (±0.05) Å and 0.41 (±0.05) Å for thebackbone heavy atoms of nuclease and its ternary complex, respectively. Thebackbone conformations of residues in the loop formed byArg81–Gly86, which is adjacent to the activesite, are more precisely defined in the ternary complex than in unligatednuclease. Also, the protein side chains that show NOEs and evidence forhydrogen bonds to pdTp (Arg35, Lys84,Tyr85, Arg87, Tyr113, andTyr115) are better defined in the ternary complex. As has beenobserved previously in the X-ray structures of nuclease-WT, the binding ofpdTp causes the backbone of Tyr113 to change from an extendedto a left-handed α-helical conformation. The NMR structures reportedhere were compared with available X-ray structures: nuclease-H124L [Truckseset al. (1996) Protein Sci., 5, 1907–1916] and the ternary complex ofwild-type staphylococcal nuclease [Loll and Lattman (1989) Proteins Struct.Funct. Genet., 5, 183–201]. Overall, the solution structures ofnuclease-H124L are consistent with these crystal structures, but smalldifferences were observed between the structures in the solution and crystalenvironments. These included differences in the conformations of certain sidechains, a reduction in the extent of helix 1 in solution, and many fewerhydrogen bonds involving side chains in solution. [ABSTRACT FROM AUTHOR]