Three-dimensional Motif Research Articles

Application of numerical modelling in the design of a full-scale heated Tunnel Sealing Experiment

The Tunnel Sealing Experiment (TSX) was a full-scale in situ demonstration of technology for constructing nearly water tight-seals in excavations through crystalline rock deep below the surface of the earth. The experiment has been carried out at Atomic Energy of Canada Limited's (AECL's) Underground Research Laboratory near Lac du Bonnet, Canada, in support of international programs for geologic disposal of radioactive waste. The TSX, with partners from Canada, Japan, France and the United States, was carried under conditions of high pressure (up to 4 MPa) and elevated temperature (up to 85°C). Comparing numerical model predictions with eight years of data collected from approximately 900 sensors was an important component of this experiment. Model of Transport In Fractured/porous Media (MOTIF), a finite element computer program developed by AECL for simulating fully coupled or uncoupled fluid flow, solute transport and heat transport, was used to model both the ambient temperature and heated phases of the TSX. The plan to heat the water in the TSX to 85°C was developed using model predictions and a comparison of simulated results with measurements during heating of the water in the TSX to about 50°C. The three-dimensional MOTIF simulations were conducted in parallel with axisymmetric modelling using Fast Lagrangian Analysis of Continua (FLAC), which computed the heat loss from pipes that carried the heated water through the rock to and from the experiment. The numerical model was initially used to develop a plan for operation of the experiment heaters, and then subsequently used to predict temperatures and hydraulic heads in the TSX bulkhead seals and surrounding rock. Copyright © 2005 John Wiley & Sons, Ltd.

Bis and tris(oxalato)ferrate(iii) complexes as precursors of polynuclear compounds

The preparation and crystal structure of two oxalato-bridged NaI–FeIII compounds, [Na3Fe(ox)3(H2O)4]·H2O (1) and [FeII(phen)3][NaFe(ox)3(H2O)3]·4H2O (5), two mononuclear FeIII complexes AsPh4[Fe(bipy)(ox)2]·H2O (3) and AsPh4[Fe(phen)(ox)2]·H2O (4) and an oxalato-bridged FeIII compound [AsPh4]4[Fe2(ox)5]·5H2O (2) (ox = oxalate dianion, bipy = 2,2′-bipyridine, phen = 1,10-phenantroline and AsPh4+ = tetraphenylarsonium cation) are reported here. The structure of 1 consists of infinite anionic [NaFe(ox)3]2− layers linked trough centrosymmetric [Na4(H2O)8]4+ tetranuclear units yielding a three-dimensional motif. Crystallization water molecules ensure the cohesion of the crystal lattice in 1. The iron environment is distorted octahedral being surrounded by six oxygen atoms of three oxalate groups, with an average iron to oxalate-oxygen bond distance of 2.012(3) A. There are four crystallographically independent sodium atoms, all of which have a highly distorted octahedral environment. Six oxalate-oxygen atoms are bound to Na(1) and Na(2), whereas the other two sodium atoms are surrounded by four water oxygen and two oxalate oxygen atoms [Na(3)] and three water oxygen and three oxalate oxygen atoms [Na(4)]. The structure of compound 2 consists of centrosymmetric dinuclear [Fe2(ox)5]4− anions, AsPh4+ cations and crystallization water molecules. The anionic unit contains two Fe(III) atoms, four bidentate and one bridging oxalato ligands. Each iron atom has a distorted octahedral environment. The structures of 3 and 4 consist of discrete [Fe(AA)(ox)2]− [AA = bipy (3) and phen (4)] anions, tetraphenylarsonium cations and uncoordinated water molecules which are linked by hydrogen bonds. Each iron atom is six-coordinated with two nitrogen atoms from the bidentate AA ligand and four oxalate-oxygen atoms building a distorted octahedral environment. The structure of compound 5 consists of anionic [Fe(ox)3Na(H2O)3]2− chains, tris-chelated low-spin iron(II) [Fe(phen)3]2+ units and lattice water molecules linked to the chains through hydrogen bonds in which the water molecules and oxygen atoms of the oxalate groups are involved. The chains contain Fe3+ and Na+ cations alternatively bridged by oxalate groups, the tris-chelated [Fe(ox)3]3− unit acting as a bidentate ligand through one oxalato group toward a central sodium atom. Magnetic susceptibilty measurements in the temperature range 2.0–290 K for 2 that reveal the occurrence of antiferromagnetic coupling (J = −6.5 cm−1, the Hamiltonian being defined as H = −JS1S2) between the high-spin iron(III) ions across the oxalato bridge.

Characterisation of the 3D waviness and roughness motifs

The surface summits and their waviness envelope constitute the boundary surface of contact area during the tribological life of solids. The form, scale and orientation of the three-dimensional motifs play an important role on flatness behaviour of engineered surfaces, contact mechanics, adherence, friction, lubrication and leakage problems. The basic idea of this work considers that the three-dimensional motifs of the surface are a key elements of surface topography in regard to different field of tribology. The 2D motif is defined as the part of profile which associates tow peaks separated a deep valley (pit). The extension of the 2D motif definition to the 3D morphology needs the simultaneous assessment of waviness and roughness. The approach developed in this work is based on a geomorphologic definition of 3D motif. The approach is improved by a new algorithm of waviness envelope construction and a morphologic filter using the waviness envelope as a low-frequency surface of filtering.

Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns.

Release 2.0.1 of the Structural Classification of RNA (SCOR) database, http://scor.lbl.gov, contains a classification of the internal and hairpin loops in a comprehensive collection of 497 NMR and X-ray RNA structures. This report discusses findings of the classification that have not been reported previously. The SCOR database contains multiple examples of a newly described RNA motif, the extruded helical single strand. Internal loop base triples are classified in SCOR according to their three-dimensional context. These internal loop triples contain several examples of a frequently found motif, the minor groove AGC triple. SCOR also presents the predominant and alternate conformations of hairpin loops, as shown in the most well represented tetraloops, with consensus sequences GNRA, UNCG and ANYA. The ubiquity of the GNRA hairpin turn motif is illustrated by its presence in complex internal loops.

Multidimensional signatures in antimicrobial peptides.

Conventional analyses distinguish between antimicrobial peptides by differences in amino acid sequence. Yet structural paradigms common to broader classes of these molecules have not been established. The current analyses examined the potential conservation of structural themes in antimicrobial peptides from evolutionarily diverse organisms. Using proteomics, an antimicrobial peptide signature was discovered to integrate stereospecific sequence patterns and a hallmark three-dimensional motif. This striking multidimensional signature is conserved among disulfide-containing antimicrobial peptides spanning biological kingdoms, and it transcends motifs previously limited to defined peptide subclasses. Experimental data validating this model enabled the identification of previously unrecognized antimicrobial activity in peptides of known identity. The multidimensional signature model provides a unifying structural theme in broad classes of antimicrobial peptides, will facilitate discovery of antimicrobial peptides as yet unknown, and offers insights into the evolution of molecular determinants in these and related host defense effector molecules.

Fast 3D motif search of EM density maps using a locally normalized cross-correlation function

Three-dimensional motif search is becoming increasingly important both in the search for molecular signatures within a tomographic reconstruction, at low resolution, and in the search for atomic structures within high-resolution cryo-EM maps of macromolecular complexes. The present work describes the implementation of a fast local correlation algorithm suitable for template matching in the SPIDER environment. Two examples are given, one in each of the areas of application: (i) within a 7.8 Å single-particle reconstruction of the Escherichia coli ribosome, four proteins and one RNA structure were located with high accuracy; (ii) within a cryo-tomogram of sarcoplasmic reticulum vesicles, ryanodine receptors were located in positions that agreed with expert knowledge.

Synthesis and characterization of new coordination polymers generated from oxadiazole-containing ligand and inorganic M(ii) [M = Cu(ii), Co(ii)] salts

The coordination chemistry of the oxadiazole-containing ligand 2,5-bis(4-pyridyl)-1,3,4-oxadiazole (L5) with inorganic Cu(II) and Co(II) salts has been investigated. Three new coordination polymers (1–3) and one H-bonded polymer (4) were prepared by solution reactions. [Cu(L5)(H2O)(SO4)]·2(H2O) (1) adopts a novel chiral three-dimensional motif with rhombus channels (ca. 6.04 × 14.09 Å). [Co(L5)(CH3OH)2(SO4)](CH3OH)(H2O)3.5 (2) features a novel two-dimensional network. [Cu(L5)2(H2O)2](L5)2(ClO4)2(CH3OH)(H2O) (3) features a two-dimensional rhombus-grid-type layer with inner grid cavity dimensions of 13.22 × 13.22 Å2. Compound 4, however, is a molecular complex that is bound together by strong N⋯H–O and O⋯H–O hydrogen bonds into a three-dimensional H-bonded network.

A Zwitterionic Viologen Disulfonate—Hydroquinone Charge‐Transfer Crystal: 2,2′‐(4,4′‐Bipyridinium‐1,1′‐diyl)di(ethanesulfonate)—Hydroquinone (1/2).

AbstractFor Abstract see ChemInform Abstract in Full Text.

A zwitterionic viologen disulfonate-hydroquinone charge-transfer crystal: 2,2'-(4,4'-bipyridinium-1,1'-diyl)di(ethanesulfonate)-hydroquinone (1/2).

The structure of the title compound, C(14)H(16)N(2)O(6)S(2).2C(6)H(6)O(2), consists of 2,2'-(4,4'-bipyridinium-1,1'-diyl)di(ethanesulfonate) molecules (with crystallographically imposed twofold symmetry) that are hydrogen bonded to each other, as well as to hydroquinone molecules, in a complex three-dimensional motif. The orange color of the crystals is indicative of the donor-acceptor interaction between the electron-rich hydroquinone pi-donor and the electron-deficient bipyridinium pi-acceptor. The dihedral angle between the bipyridyl planes is 38.31 (11) degrees. The distance from the centroid of one of the hydroquinone molecules to the center of the bipyridinium group is 3.653 (3) A, which is within the range typically observed for molecular complexes exhibiting charge-transfer characteristics.

The non-Watson-Crick base pairs and their associated isostericity matrices.

RNA molecules exhibit complex structures in which a large fraction of the bases engage in non-Watson-Crick base pairing, forming motifs that mediate long-range RNA-RNA interactions and create binding sites for proteins and small molecule ligands. The rapidly growing number of three-dimensional RNA structures at atomic resolution requires that databases contain the annotation of such base pairs. An unambiguous and descriptive nomenclature was proposed recently in which RNA base pairs were classified by the base edges participating in the interaction (Watson-Crick, Hoogsteen/CH or sugar edge) and the orientation of the glycosidic bonds relative to the hydrogen bonds (cis or trans). Twelve basic geometric families were identified and all 12 have been observed in crystal structures. For each base pairing family, we present here the 4 x 4 'isostericity matrices' summarizing the geometric relationships between the 16 pairwise combinations of the four standard bases, A, C, G and U. Whenever available, a representative example of each observed base pair from X-ray crystal structures (3.0 A resolution or better) is provided or, otherwise, theoretically plausible models. This format makes apparent the recurrent geometric patterns that are observed and helps identify isosteric pairs that co-vary or interchange in sequences of homologous molecules while maintaining conserved three-dimensional motifs.

SCOR: a Structural Classification of RNA database.

The Structural Classification of RNA (SCOR) database provides a survey of the three-dimensional motifs contained in 259 NMR and X-ray RNA structures. In one classification, the structures are grouped according to function. The RNA motifs, including internal and external loops, are also organized in a hierarchical classification. The 259 database entries contain 223 internal and 203 external loops; 52 entries consist of fully complementary duplexes. A classification of the well-characterized tertiary interactions found in the larger RNA structures is also included along with examples. The SCOR database is accessible at http://scor.lbl.gov.

Greek Origami: A Sculpture Exploring the Golden Ratio

The author created a sculpture using a rigorous mathematical procedure informed by aesthetic decisions. The form is based on the relationships found in the golden triangle and its spiral folded into three dimensions. In creating the form, the author discovered a three-dimensional motif (the “golden gnomonoid”) with interesting mathematical properties and sculptural ramifications.

Geometric nomenclature and classification of RNA base pairs.

Non-Watson-Crick base pairs mediate specific interactions responsible for RNA-RNA self-assembly and RNA-protein recognition. An unambiguous and descriptive nomenclature with well-defined and nonoverlapping parameters is needed to communicate concisely structural information about RNA base pairs. The definitions should reflect underlying molecular structures and interactions and, thus, facilitate automated annotation, classification, and comparison of new RNA structures. We propose a classification based on the observation that the planar edge-to-edge, hydrogen-bonding interactions between RNA bases involve one of three distinct edges: the Watson-Crick edge, the Hoogsteen edge, and the Sugar edge (which includes the 2'-OH and which has also been referred to as the Shallow-groove edge). Bases can interact in either of two orientations with respect to the glycosidic bonds, cis or trans relative to the hydrogen bonds. This gives rise to 12 basic geometric types with at least two H bonds connecting the bases. For each geometric type, the relative orientations of the strands can be easily deduced. High-resolution examples of 11 of the 12 geometries are presently available. Bifurcated pairs, in which a single exocyclic carbonyl or amino group of one base directly contacts the edge of a second base, and water-inserted pairs, in which single functional groups on each base interact directly, are intermediate between two of the standard geometries. The nomenclature facilitates the recognition of isosteric relationships among base pairs within each geometry, and thus facilitates the recognition of recurrent three-dimensional motifs from comparison of homologous sequences. Graphical conventions are proposed for displaying non-Watson-Crick interactions on a secondary structure diagram. The utility of the classification in homology modeling of RNA tertiary motifs is illustrated.

Three-dimensional view of the surface motif associated with the P-loop structure: cis and trans cases of convergent evolution

Here we identify the determinants of the nucleotide-binding ability associated with the P-loop-containing proteins, inferring their functional importance from their structural convergence to a unique three-dimensional (3D) motif. (1) A new surface 3D pattern is identified for the P-loop nucleotide-binding region, which is more selective than the corresponding sequence pattern; (2) the signature displays one residue that we propose is the determinant for the guanine-binding ability (the residues aligned to ras D119; this residue is known to be important only in the G-proteins, we extend the prediction to all the other P-loop-containing proteins); and (3) two cases of convergent evolution at the molecular level are highlighted in the analysis of the active site: the positive charge aligned to ras K117 and the arginine residues aligned to the GAP arginine finger.The analysis of the residues conserved on protein surfaces allows one to identify new functional or evolutionary relationships among protein structures that would not be detectable by conventional sequence or structure comparison methods.

Rational drug design and high-throughput techniques for RNA targets.

RNA molecules are the only known molecules which possess the double property of being depository of genetic information, like DNA, and of displaying catalytic activities, like protein enzymes. RNA molecules intervene in all steps of gene expression and in many other biological activities. Like proteins, RNAs achieve those biological functions by adopting intricate three-dimensional folds and architectures. Further, as in protein sequences, RNA sequences contain signatures specific for three-dimensional motifs which participate in recognition and binding. In regulatory pathways, RNA molecules exist in equilibria between transient structures differentially stabilized by effectors such as proteins or cofactors. Therefore, RNA molecules display their potential as drug targets on different levels, namely in three-dimensional folds, in structural equilibria and in RNA-protein interfaces. Several examples will be described together with the already available techniques for combinatorial synthesis and high-throughput screening of potential drug and target RNA molecules.

Protein-Assisted Pericyclic Reactions: An Alternate Hypothesis for the Action of Quantal Receptors

The rules for allowable pericyclic reactions indicate that the photoisomerizations of retinals in rhodopsins can be formally analogous to thermally promoted Diels-Alder condensations of monoenes with retinols. With little change in the seven-transmembrane helical environment these latter reactions could mimic the retinal isomerization while providing highly sensitive chemical reception. In this way archaic progenitors of G-protein-coupled chemical quantal receptors such as those for pheromones might have been evolutionarily plagiarized from the photon quantal receptor, rhodopsin, or vice versa. We investigated whether the known structure of bacteriorhodopsin exhibited any similarity in its active site with those of the two known antibody catalysts of Diels-Alder reactions and that of the photoactive yellow protein. A remarkable three-dimensional motif of aromatic side chains emerged in all four proteins despite the drastic differences in backbone structure. Molecular orbital calculations supported the possibility of transient pericyclic reactions as part of the isomerization-signal transduction mechanisms in both bacteriorhodopsin and the photoactive yellow protein. It appears that reactions in all four of the proteins investigated may be biological analogs of the organic chemists’ chiral auxiliary-aided Diels-Alder reactions. Thus the light receptor and the chemical receptor subfamilies of the heptahelical receptor family may have been unified at one time by underlying pericyclic chemistry.

Functional analysis of the Escherichia coli genome for members of the α/ β hydrolase family

Database-searching methods based on sequence similarity have become the most commonly used tools for characterizing newly sequenced proteins. Due to the often underestimated functional diversity in protein families and superfamilies, however, it is difficult to make the characterization specific and accurate. In this work, we have extended a method for active-site identification from predicted protein structures. The structural conservation and variation of the active sites of the alpha/beta hydrolases with known structures were studied. The similarities were incorporated into a three-dimensional motif that specifies essential requirements for the enzymatic functions. A threading algorithm was used to align 651 Escherichia coli open reading frames (ORFs) to one of the members of the alpha/beta hydrolase fold family. These ORFs were then screened according to our three-dimensional motif and with an extra requirement that demands conservation of the key active-site residues among the proteins that bear significant sequence similarity to the ORFs. 17 ORFs from E. coli were predicted to have hydrolase activity and their putative active-site residues were identified. Most were in agreement with the experiments and results of other database-searching methods. The study further suggests that YHET_ECOLI, a hypothetical protein classified as a member of the UPF0017 family (an uncharacterized protein family), bears all the hallmarks of the alpha/beta hydrolase family. The novel feature of our method is that it uses three-dimensional structural information for function prediction. The results demonstrate the importance and necessity of such a method to fill the gap between sequence alignment and function prediction; furthermore, the method provides a way to verify the structure predictions, which enables an expansion of the applicable scope of the threading algorithms.

Construction of a Crystalline Tetramer and Infinite Network through the Dual Use of Au(I)···Au(I) and π-π Interactions

Abstract SC6H5 was substituted for Cl in AuCl(PPh3) and (AuCl)2(trans-Ph2PCH=CHPPh2) by reacting with Sn(SC6H5)(n-Bu)3 in refluxing THF. Both products exhibit new three-dimensional motifs which are created by Au···Au interaction and π-π interaction between phenyl rings in crystals.

Spectral and 3D motifs identification of anisotropic topographical components. Analysis and filtering of anisotropic patterns by morphological rose approach

In this paper we show two new developments in the three-dimensional characterisation of rough surfaces. The basic idea is to consider roughness as a combination of components defined by the roughness amplitude, wave length, local and overall direction of various components. The anisotropic topography is dealt with in two ways: • - the anisotropy between form, waviness and roughness; • - the local anisotropy of three-dimensional motifs. The directional parameter is used both to identify and separate the anisotropic components by appropriate anisotopic filtering and by a complete characterisation of surface motifs. This allows the decomposition of the topography into local motifs with a representation similar to the two-dimensional Fourier transform, where the direction represents the topographic phase in the form of a morphological rose.

X-ray structural study of 2-amino-5,5-dimethoxy-3-cyano-4-dicyanomethylene-4,5-dihydropyrrole and its sodium salt

According to the XSA data, a conjugation system in which both endo- and exocyclic bonds are included is realized in the molecule of 2-amino-5,5-dimethoxy-3-cyano-4-dicyanomethylene-4,5-dihydropyrrole and the anion of its sodium salt due to the planar structure, and this is reflected in their unusual length. Due to the developed system of intermolecular hydrogen bonds, the molecules in the crystals are joined in infinite three-dimensional motifs.