Protein structure refinement algorithms

Protein structure prediction has remained a major challenge in structural biology for more than half a century. Accelerated and cost efficient sequencing technologies have allowed researchers to sequence new organisms and discover new protein sequences. Novel protein structure prediction technologies will allow researchers to study the structure of proteins and to determine their roles in the underlying biology processes and develop novel therapeutics.

Difficulty of the problem stems from two folds: (a) describing the energy landscape that corresponds to the protein structure, commonly referred to as force field problem; and (b) sampling of the energy landscape, trying to find the lowest energy configuration that is hypothesized to be the native state of the structure in solution. The two problems are interweaved and they have to be solved simultaneously. This thesis is composed of three major contributions. In the first chapter we describe a novel high-resolution protein structure refinement algorithm called GRID. In the second chapter we present REMCGRID, an algorithm for generation of low energy decoy sets. In the third chapter, we present a machine learning approach to ranking decoys by incorporating coarse-grain features of protein structures.

Liquid alumina: detailed atomic coordination determined from neutron diffraction data using empirical potential structure refinement

Greaves, George; Jenkins, T.E.; Landron, C.; Hennet, L., (2001) 'Liquid alumina: detailed atomic coordination determined from neutron diffraction data using empirical potential structure refinement', Physical Review Letters 86 pp.4839-4842 RAE2008

A detailed single chain model for molten poly(tetrafluoroethylene) from a novel structure refinement technique on neutron scattering data

We present a new methodology that couples neutron diffraction experiments over a wide Q range with single chain modelling in order to explore, in a quantitative manner, the intrachain organization of non-crystalline polymers. The technique is based on the assignment of parameters describing the chemical, geometric and conformational characteristics of the polymeric chain, and on the variation of these parameters to minimize the difference between the predicted and experimental diffraction patterns. The method is successfully applied to the study of molten poly(tetrafluoroethylene) at two different temperatures, and provides unambiguous information on the configuration of the chain and its degree of flexibility. From analysis of the experimental data a model is derived with CC and CF bond lengths of 1.58 and 1.36 Å, respectively, a backbone valence angle of 110° and a torsional angle distribution which is characterized by four isometric states, namely a split trans state at ± 18°, giving rise to a helical chain conformation, and two gauche states at ± 112°. The probability of trans conformers is 0.86 at T = 350°C, which decreases slightly to 0.84 at T = 400°C. Correspondingly, the chain segments are characterized by long all-trans sequences with random changes in sign, rather anisotropic in nature, which give rise to a rather stiff chain. We compare the results of this quantitative analysis of the experimental scattering data with the theoretical predictions of both force fields and molecular orbital conformation energy calculations.

Crystal structure refinement of Co-doped lanthanum chromites

Results of crystal structure refinements and phase quantification for samples of Co-doped lanthanum chromites with nominal composition LaCr(1-x)Co(x)O(3), for x=0.00, 0.10, 0.20, and 0.30, prepared by combustion synthesis are presented. The resulting powders were characterized by scanning electron microscopy and X-ray diffraction (XRD). The XRD patterns were obtained with Cu K alpha radiation for non-doped lanthanum chromite sample and additionally with Cr K alpha radiation for Co-doped lanthanum chromites samples, in order to enhance the signal from scattering. Rietveld analysis of XRD data showed that the studied samples presented the lanthanum chromite with an orthorhombic structure (Pnma), except for the composition with x=0.30, in which the space group was found to be R (3) over barc. (C) 2008 International Centre for Diffraction Data.

Hyalotekite, (Ba,Pb,K)(4)(Ca,Y)(2)Si-8(B,Be)(2)(Si,B)(2)O28F, a Tectosilicate Related to Scapolite: New Structure Refinement, Phase Transitions and a Short-Range Ordered 3B Superstructure

Hyalotekite, a framework silicate of composition (Ba,Pb,K)(4)(Ca,Y)(2)Si-8(B,Be)(2) (Si,B)(2)O28F, is found in relatively high-temperature(greater than or equal to 500 degrees C) Mn skarns at Langban, Sweden, and peralkaline pegmatites at Dara-i-Pioz, Tajikistan. A new paragenesis at Dara-i-Pioz is pegmatite consisting of the Ba borosilicates leucosphenite and tienshanite, as well as caesium kupletskite, aegirine, pyrochlore, microcline and quartz. Hyalotekite has been partially replaced by barylite and danburite. This hyalotekite contains 1.29-1.78 wt.% Y2O3, equivalent to 0.172-0.238 Y pfu or 8-11% Y on the Ca site; its Pb/(Pb+Ba) ratio ranges 0.36-0.44. Electron microprobe F contents of Langban and Dara-i-Pioz hyalotekite range 1.04-1.45 wt.%, consistent with full occupancy of the F site. A new refinement of the structure factor data used in the original structural determination of a Langban hyalotekite resulted in a structural formula, (Pb1.96Ba1.86K0.18)Ca-2(B1.76Be0.24)(Si1.56B0.44)Si8O28F, consistent with chemical data and all cations with positive-definite thermal parameters, although with a slight excess of positive charge (+57.14 as opposed to the ideal +57.00). An unusual feature of the hyalotekite framework is that 4 of 28 oxygens are non-bridging; by merging these 4 oxygens into two, the framework topology of scapolite is obtained. The triclinic symmetry of hyalotekite observed at room temperature is obtained from a hypothetical tetragonal parent structure via a sequence of displacive phase transitions. Some of these transitions are associated with cation ordering, either Pb-Ba ordering in the large cation sites, or B-Be and Si-B ordering on tetrahedral sites. Others are largely displacive but affect the coordination of the large cations (Pb, Ba, K, Ca). High-resolution electron microscopy suggests that the undulatory extinction characteristic of hyalotekite is due to a fine mosaic microstructure. This suggests that at least one of these transitions occurs in nature during cooling, and that it is first order with a large volume change. A diffuse superstructure observed by electron diffraction implies the existence of a further stage of short-range cation ordering which probably involves both (Pb,K)-Ba and (BeSi,BB)-BSi.

New methods of structure refinement for macromolecular structure determination by NMR

Recent advances in multidimensional NMR methodology have permitted solution structures of proteins in excess of 250 residues to be solved. In this paper, we discuss several methods of structure refinement that promise to increase the accuracy of macromolecular structures determined by NMR. These methods include the use of a conformational database potential and direct refinement against three-bond coupling constants, secondary 13C shifts, 1H shifts, T1/T2 ratios, and residual dipolar couplings. The latter two measurements provide long range restraints that are not accessible by other solution NMR parameters.

The crystal structure of eulytite Pb3BiV3O12

The crystal structure of Pb3BiV3O12 was solved using single-crystal X-ray diffraction technique. The compound crystallizes in the cubic system View the MathML source (No. 220) with eulytite structure with a = 10.7490(7) Å, V = 1241.95(14) Å3 and Z = 4. The final R1 value of 0.0198 (wR2=0.0384) was achieved for 359 independent reflections during the structure refinement. The Pb2+ and Bi3+ cations occupy the special position (16c) while the oxygen anions occupy the general position (48e) in the crystal structure. Unlike many other eulytite compounds, all the crystallographic positions are fully occupied. The structure consists of edge-shared Pb/Bi octahedra linked at the corners to independent [VO4]3− tetrahedra units, generating a eulytite-type network in the crystal lattice.

Synthesis, Structure, Negative Thermal Expansion, and Photocatalytic Property of Mo Doped ZrV(2)O(7)

A new series of compounds identified in the phase diagram of ZrO(2)-V(2)O(8)-MoO(3) have been synthesized via the solution combustion method. Single crystals of one of the compounds in the series, ZrV(1.50)Mo(0.50)O(7.25), were grown by the melt-cool technique from the starting materials with double the MoO(3) quantity. The room temperature average crystal structure of the grown crystals was solved using the single crystal X-ray diffraction technique. The crystals belong to the cubic crystal system, space group Pa (3) over bar (No. 205) with a = 8.8969 (4) angstrom, V = 704.24 (6) angstrom(3), and Z = 4. The final R(1) value of 0.0213 was achieved for 288 independent reflections during the structure refinement. The Zr(4+) occupies the special position (4a) whereas V(5+) and Mo(6+) occupy two unique (8c) Wyckoff positions. Two fully occupied O atoms, (24d) and (4b), one partially occupied 0 atom (8c) have been identified for this molybdovanadate, which is a unique feature for these crystals. The structure is related to both ZrV(2)O(7) and cubic ZrMo(2)O(8). The temperature dependent single crystal studies show negative thermal expansion above 370 K. The compounds have been characterized by powder X-ray diffraction, solid-state UV-vis diffuse reflectance spectra, scanning electron microscopy (SEM), and transmission electron microscopy (TEM). The photocatalytic activity of these compounds has been investigated for the degradation of various dyes, and these compounds show specificity toward the degradation of non-azoic dyes.

Hydrothermal synthesis and structure of a neutral open-framework zincophosphate

A neutral open-frame work zincophosphate has been hydrothermally synthesized: structure refinement shows that it is composed of Zn4O12 tetramers and infinite Zn-O-Zn chains that are linked by PO4 groups forming one-dimensional 16-membered ring channels along b direction.

Structure of Ionic Liquid-Benzene Mixtures

Neutron diffraction has been used to investigate the structure of liquid mixtures of 1,3-dimethylimidazolium hexafluorophosphate with benzene. Two concentrations of benzene were investigated, namely, 33 mol % and 67 mol %, and show similar structures in each case. The presence of benzene significantly alters the ionic liquid structure, in particular, in the cation-cation interactions, in agreement with the single-crystal structure described recently (Holbrey, J. D.; Reichert, W. M.; Nieuwenhuyzen, M.; Sheppard, O.; Hardacre, C.; Rogers, R. D. Chem. Commun. 2003, 476). In each case, the data was analyzed using an empirical potential structure refinement process.

Liquid structure of the ionic liquid, 1-methyl-4-cyanopyridinium bis{(trifluoromethyl)sulfonyl}imide determined from neutron scattering and molecular dynamics simulations

The liquid structure of 1-methyl-4-cyanopyridinium bis {(trifluoromethyl)sulfonyl}imide, a prototypical ionic liquid containing an electron-withdrawing group on the cation, has been investigated at 368 K. Experimental neutron scattering combined with empirical potential structure refinement analysis of the data and classical molecular dynamics simulations have been used to probe the liquid structure in detail. Both techniques generated highly consistent results that provide valuable validation of the force fields and refinement approaches. A significant degree of apparent charge ordering is found in the liquid structure, although the nonspherical shape of the ions results in interpenetration of cations into the first shell of adjacent cations, with much shorter closest contact distances than the averaged center-of-mass cation-cation and cation-anion separations.

Liquid structure of 1, 3-dimethylimidazolium salts

The structure of liquid 1, 3-dimethylimidazolium hexafluorophosphate is described in detail and compared with the structure of 1, 3-dimethylimidazolium chloride. In each case, the data were obtained from neutron diffraction experiments and analysed using an empirical potential structure refinement process. Overall, the structures are similar; however, significant differences arise from the variation in anion size.

New ruthenium(II) complexes of functionalized monoanionic aryldiamine N,C,N'-terdentate ligands: Syntheses of [Ru-II{2,6-(Me(2)NCH(2))(2)-4-R-C6H2}(terpy)]Cl+(-); X-ray structure of a dimeric organolithium compound,[Li{2,6-(Me(2)NCH(2))(2)-4-Ph-C6H2}](2)

The new anionic functionalized aryldiamine ligands [2,6-(Me(2)NCH(2))(2)-4-R-C6H2](-) (R = Me(3)SiC=C, C6H5, Me(3)Si), formally derived from [2,6-(Me(2)NCH(2))(2)C6H3](-), have been prepared as their lithium compounds. The compound [Li{2,6-(Me(2)NCH(2))(2)-4-Ph-C6H2}](2) crystallizes in the monoclinic space group C2/c (no. 15) with a = 13.1225(5), b = 13.5844(7), c = 15.9859(12) Angstrom, beta = 105.329(5)degrees, V = 3264.0(3)Angstrom(3), Z = 4. The structure refinement converged to R(1) = 0.0374 for 2037 observed reflections [F-o>4 sigma(F-o)] and wR(2) = 0.0922 for 2560 unique data. The organolithium compounds have been used in transmetalation reactions to give the corresponding functionalized organoruthenium(II) complexes [Ru-II{2,6-(Me(2)NCH(2))(2)-4-R-C6H2}(terpy)]Cl-+(-) (terpy = 2,2';6',2 ''-terpyridine). The Ru-II species with R = HC = C has also been synthesized.

Structure of molten 1,3-dimethylimidazolium chloride using neutron diffraction

The model room temperature ionic liquid, 1,3-dimethylimidazolium chloride, has been studied by neutron diffraction for the first time. The diffraction data are used to derive a structural model of this liquid using Empirical Potential Structure Refinement. The model obtained indicates that significant charge ordering is present in the liquid salt and that the local order in this liquid closely resembles that found in the solid state. As in the crystal structure, hydrogen-bonding interactions between the ring hydrogens and the chloride dominate the structure. The model is compared with the data reported previously for both simple alkyl substituted imidazolium halides and binary mixtures with AlCl3. (C) 2003 American Institute of Physics.

The solution structure of 1:2 phenol/N-methylpyridinium bis{(trifluoromethyl)sulfonyl}imide liquid mixtures

Neutron diffraction has been used to investigate the liquid structure of a 1:2 solution of phenol in the ionic liquid N-methylpyridinium bis{(trifluoromethyl)sulfonyl}imide at 60 ◦C, using the empirical potential structure refinement (EPSR) process to model the data obtained from the SANDALS diffractometer at ISIS. Addition of phenol results in suppression of the melting point of the pyridinium salt and formation of a room temperature solution with aromatic phenol–cation and phenol-OH to anion hydrogen-bonding interactions.