Basic Structural Motif Research Articles

Unexpected isostructurality by permutation of classical and “weak” hydrogen bonds

The compounds 2-chloromethylpyridinium chloride and 3-bromomethylpyridinium bromide are essentially isostructural despite their different substitution loci; the basic structural motif in both cases is a hydrogen-bonded dimer, but the positions of the classical and weak hydrogen bonds are interchanged.

Synthesis and structural study of two new heparin-like hexasaccharides.

Two new heparin-like hexasaccharides, 5 and 6, have been synthesised using a convergent block strategy and their solution conformations have been determined by NMR spectroscopy and molecular modelling. Both hexasaccharides contain the basic structural motif of the regular region of heparin but with negative charge distributions which have been designed to get insight into the mechanism of fibroblast growth factors (FGFs) activation.

Mutational switching of a yeast tRNA synthetase into a mammalian-like synthetase cytokine.

Aminoacyl-tRNA synthetases catalyze the attachment of amino acids to their cognate tRNAs. A link was recently established between protein biosynthesis and cytokine signal transduction. Human tyrosyl-tRNA synthetase can be split into two fragments, each of which has a distinct cytokine function. This activity is specific to the human enzyme. It is absent in the enzymes from lower organisms such as bacteria and yeast. Here, yeast tyrosyl-tRNA synthetase (TyrRS), which lacks cytokine activity, was used as a model to explore how a human tyrosyl-tRNA synthetase during evolution acquired novel functions beyond aminoacylation. We found that a rationally designed mutant yeast TyrRS(ELR) gained cytokine function. The mutant yeast enzyme gained this function without sacrifice of aminoacylation activity. Therefore, relatively simple alteration of a basic structural motif imparts cytokine activity to a tRNA synthetase while preserving its canonical function. Further work established that mutational switching of a yeast protein to a mammalian-like cytokine was specific to this synthetase and not to just any yeast ortholog of a mammalian cytokine.

Characterization of a planar cyclic form of water hexamer in an organic supramolecular complex: an unusual self-assembly of bimesityl-3,3'-dicarboxylic acid.

Trapped water: Six molecules of water are trapped in the crystal lattice of an organic supramolecular complex with bimesityl-3,3′-dicarboxylic acid in the form of a planar cyclic “ring”, which is the basic structural motif of Ice II. The water molecules of the hexamer (see picture) are associated in the crystal lattice by eighteen OH⋅⋅⋅O hydrogen bonds.

The activation of fibroblast growth factors by heparin: Synthesis and structural study of rationally modified heparin-like oligosaccharides

Heparin-like hexasaccharide 3 and octasaccharide 4 have been synthesized using a convergent block strategy and their solution conformations have been determined by NMR spectroscopy. Both oligosaccharides contain the basic structural motif of the regular region of heparin but have been constructed as to display negatively charged sulfate groups only on one side of their solution helical structures. This charge distribution along the saccharide chain has been designed to get insight into the proposed mechanism for fibroblast growth factors (FGFs) activation that involves heparin-induced FGF dimerization.Key words: heparin oligosaccharides, synthesis design, conformational analysis, FGF activation.

Ruthenium Alkylidenes: Modulation of a New Class of Catalysts for Controlled Radical Polymerization of Vinyl Monomers

Air-stable and readily available ruthenium benzylidene complexes of the general type [RuCl2(=CHPh)(L)(L')] (L, L' = PCy3 and/or N-heterocyclic carbene) constitute a new class of catalyst precursors for atom-transfer radical polymerization (ATRP) of methyl methacrylate and styrene, and provide an unprecedented example for the involvement of ruthenium alkylidenes in radical reactions. They promote the polymerization of various monomers with good to excellent yields, and in a controlled way with methyl methacrylate and styrene. Variations of their basic structural motif provide insights into the essential parameters responsible for catalytic activity. The ligands L (PCy3 and/or N-heterocyclic carbene) turned out to play a particularly important role in determining the rate of the polymerizations. A similarly pronounced influence is exerted by the substituents on the N-heterocyclic carbene. Our results indicate that the catalysts decompose quickly under ATRP conditions, and polymerizations are mediated by both [RuCl2(=CHPh)(L)(L')] complexes and ruthenium species bereft of the benzylidene moiety, through a pathway in which both tricyclohexylphosphane and/or N-heterocyclic carbene ligands remain bound to the metal center. Polymerization of n-butyl acrylate and vinyl acetate is not controlled and most probably takes place through a redox-initiated free-radical process.

Synthesis and Structure of 1-D-6-O-(2-Amino-2-deoxy-α- and -β-D-gluco- and -galactopyranosyl)-3-O-methyl-D-chiro-inositol

A convenient preparative synthesis of 1-D-6-O-(2-amino-2-deoxy-α-D-glucopyranosyl)-3-O-methyl-chiro-inositol (Ia), 1D-6-O-(2-amino-2-deoxy-β-D-glucopyranosyl)-3-O-methylchiro-inositol (Ib), 1-D-6-O-(2-amino-2-deoxy-α-D-galactopyranosyl)-3-O-methyl-chiro-inositol (IIa), and 1-D-6-O-(2-amino-2-deoxy-β-D-galactopyranosyl)-3-O-methyl-chiro-inositol (IIb) from 3-O-methyl-D-chiro-inositol (pinitol) as starting material is reported. These compounds contain some of the basic structural motifs proposed for insulin mediators. The three-dimensional structures of these compounds have been determined by NMR spectroscopy and molecular dynamics simulations.

BINOL Compounds of Group 13

The reaction of GaMe3 with 1 equiv of (S)-BINOL ((S)-(−)-2,2‘-dihydroxy-1,1‘-binaphthyl) in toluene at reflux conditions gave after recrystallization from THF the chiral organogallium alkoxide [(THF)MeGa((S)-BINOLate)]2 (1). In contrast treatment of PhCH2InCl2 with 1 equiv of Li2((S)-BINOLate) in THF at reflux and recrystallization from DME led not to the desired organoindium alkoxide but to [{(DME)Li}3{In((S)-BINOLate)3}]·2DME (2·2DME). The similar salt [{(DME)Li}3{In((S)-BINOLate)3}]·0.75THF (2·0.75THF) was obtained by direct synthesis of InCl3 with 3 equiv of Li2((S)-BINOLate) in THF at 65 °C and recrystallization from DME. The compounds 1 and 2 are readily soluble only in donor solvents, while the potassium derivative [{(toluene)2K}3{In((S)-BINOLate)3}]·2toluene (3·2toluene), obtained in the reaction of InCl3 with 3 equiv of K2((S)-BINOLate) in toluene, is very soluble in toluene and n-hexane. 1−3 have been characterized by their NMR, IR, and MS spectra as well as by X-ray analyses. Compound 1 is dimeric with a Ga2O2 four-membered ring. 2 consists of a tetranuclear InO6Li3 skeleton in which every Li+ ion is coordinated by one additional DME ligand. The basic structural motif in 3, an InO6K3 core, is comparable to the skeleton in 2. However, the coordinated toluene molecules of every K+ ion in 3 are bound by mainly electrostatic metal−π-electron interactions.

Cationic ruthenium allenylidene complexes as catalysts for ring closing olefin metathesis

A series of well accessible cationic ruthenium allenylidene complexes of the general type [(eta6-arene)(R3P)RuCl(=C=CR'2)]+ X- is described which constitute a new class of pre-catalysts for ring closing olefin metathesis reactions (RCM) and provide an unprecedented example for the involvement of metal allenylidenes in catalysis. They effect the cyclization of various functionalized dienes and enynes with good to excellent yields and show a great tolerance towards an array of functional groups. Systematic variations of their basic structural motif have provided insights into the essential parameters responsible for catalytic activity which can be enhanced further by addition of Lewis or Bronsted acids, by irradiation with UV light, or by the adequate choice of the "non-coordinating" counterion X-. The latter turned out to play a particularly important role in determining the rate and selectivity of the reaction. A similarly pronounced influence is exerted by remote substituents on the allenylidene residue which indicates that this ligand (or a ligand derived thereof) may remain attached to the metal throughout the catalytic process. X-ray crystal structures of the catalytically active allenylidene complexes 3b.PF6 and 15.OTf as well as of the chelate complex 10 required for the preparation of the latter catalyst are reported.

Modelling the three-dimensional elastic constants of parallel-fibred and lamellar bone

The complex hierarchical structure of lamellar bone makes understanding structure–mechanical function relations, very difficult. We approach the problem by first using the relatively simple structure of parallel-fibred bone to construct a mathematical model for calculating Young's moduli in three-dimensions. Parallel-fibred bone is composed essentially of arrays of mineralized collagen fibrils, which are also the basic structural motif of the individual lamellae of lamellar bone. Parallel-fibred bone structure has orthotropic symmetry. As the sizes and shapes of crystals in bone are not well known, the model is also used to compare the cases of platelet-, ribbon- and sheet-reinforced composites. The far more complicated rotated plywood structure of lamellar bone results in the loss of the orthotropic symmetry of individual lamellae. The mathematical model used circumvents this problem by sub-dividing the lamellar unit into a thin lamella, thick lamella, transition zone between them, and the recently observed “back-flip” lamella. Each of these is regarded as having orthotropic symmetry. After the calculation of their Young's moduli they are rotated in space in accordance with the rotated plywood model, and then the segments are combined to present the overall modulus values in three-dimensions. The calculated trends compare well with the trends in microhardness values measured for circumferential lamellar bone. Microhardness values are, as yet, the only measurements available for direct comparison. Although the model is not directly applicable to osteonal bone, which is composed of many hollow cylinders of lamellar bone, the range of calculated modulus values and the trends observed for off-axis calculations, compare well with measured values. © 1998 Chapman & Hall

Rotated plywood structure of primary lamellar bone in the rat: Orientations of the collagen fibril arrays

A basic structural motif of lamellar bone is the arrays of parallel collagen fibrils, with successive arrays having different orientations to form a plywood-like structure. Measurements of the angles between adjacent arrays from cryomicrotomed and vitrified thin sections of demineralized rat bone, cut approximately parallel to the lamellar boundary plane, show that most angles are around 30°, although a subset are around 70°. A structural model for collagen organization based on these measurements is proposed in which an individual lamellar unit (thick and thin lamellae together with transition zones) is composed of five arrays of parallel collagen fibrils, each offset by 30°.

The Reaction of a Triorganochloroindate with Dioxygen

AbstractThe reaction of CsCl with In(CH2Ph)3 yields the triorganochloroindate Cs[(PhCH2)3InCl] (1). Treatment of In(CH2Ph)3 with dry O2 gives the alkoxide [(PhCH2)2InOCH2Ph]2 (2), whereas the reaction of 1 with O2 leads to Cs2[O{PhCH2In(OCH2Ph)2}4] (3). According to X‐ray structural investigations, 1 contains Cs2Cl2 four‐membered rings as basic structural motif. The dimers are connected by Cs‐π‐electron interactions to form a layer structure. Compound 3 can be described as a metalla(crown ether) fragment coordinating two Cs+ ions. Additional shielding of the Cs centers by weak Cs‐π‐electron contacts was observed.

A Novel Phosphatidylserine-binding Peptide Motif Defined by an Anti-idiotypic Monoclonal Antibody: LOCALIZATION OF PHOSPHATIDYLSERINE-SPECIFIC BINDING SITES ON PROTEIN KINASE C AND PHOSPHATIDYLSERINE DECARBOXYLASE

A monoclonal anti-idiotypic antibody, Id8F7, previously shown to bind to a phosphatidylserine (PS)-specific binding site on protein kinase C (PKC) has been used to identify a 12-amino acid consensus sequence shared by PKC and phosphatidylserine decarboxylase (PSD). The 14-amino acid synthetic peptide derived from the corresponding region of PSD (amino acids 351-364 of the enzyme from Chinese hamster ovary cells) bound effectively and specifically to PS, and that derived from rat PKC gamma (amino acids 227-240) bound weakly but specifically to PS. Analysis of binding of Id8F7 to various synthetic peptides revealed that the consensus sequence motif, FXFXLKXXXKXR, is responsible for the interaction with both Id8F7 and PS. The results suggest that the conserved amino acid residues represent a basic structural motif for the specific interaction with PS, and the corresponding regions of PKC and PSD form the PS-specific binding sites of these enzymes.

Site of fasciculin interaction with acetylcholinesterase

Fasciculin, a 6750-Da peptide from the venom of Dendroaspis, is known to inhibit reversibly mammalian and fish acetylcholinesterases at picomolar concentrations, but is a relatively weak inhibitor of avian, reptile, and insect acetylcholinesterases and mammalian butyryl-cholinesterases. An examination of fasciculin association with several mutant forms of recombinant DNA-derived acetylcholinesterase from mouse shows that it interacts with a cluster of residues near the rim of the gorge on the enzyme. The aromatic residues, Trp286, Tyr72, and Tyr124, have the most marked influence on fasciculin binding, whereas Asp74, a charged residue in the vicinity of the binding site that affects the binding of low molecular weight inhibitors, has little influence on fasciculin binding. The 3 aromatic residues are unique to the susceptible acetylcholinesterases and, along with Asp74, constitute part of the peripheral anionic site. Fasciculin falls in the family of three-loop toxins that include the receptor blocking alpha-toxins and cardiotoxins. From this basic structural motif, a binding site has evolved on fasciculin to be highly specific for the peripheral site on acetylcholinesterase. Acetylthiocholine affects rates of fasciculin binding at concentrations causing substrate inhibition. In the case of the mutant cholinesterases where rates of fasciculin dissociation are more rapid, steady state kinetic parameters also show acetylthiocholine-fasciculin competition to be consistent with occupation at a peripheral or substrate inhibition site rather than the active center.

Centromeres of the fission yeast Schizosaccharomyces pombe are highly variable genetic loci.

Gross variations in the structure of the centromere of Schizosaccharomyces pombe chromosome III (cen3) were apparent following characterization of this centromeric DNA in strain Sp223 and comparison of the structure with that of cen3 in three other commonly used laboratory strains. Further differences in centromere structure were revealed when the structure of the centromere of S. pombe chromosome II (cen2) was compared among common laboratory strains and when the structures of cen2 and cen3 from our laboratory strains were compared with those reported from other laboratories. Differences observed in cen3 structure include variations in the arrangement of the centromeric K repeats and an inverted orientation of the conserved centromeric central core. In addition, we have identified two laboratory strains that contain a minimal cen2 repeat structure that lacks the tandem copies of the cen2-specific block of K-L-B-J repeats characteristic of Sp223 cen2. We have also determined that certain centromeric DNA structural motifs are relatively conserved among the four laboratory strains and eight additional wild-type S. pombe strains isolated from various food and beverage sources. We conclude that in S. pombe, as in higher eukaryotes, the centromere of a particular chromosome is not a defined genetic locus but can contain significant variability. However, the basic DNA structural motif of a central core immediately flanked by inverted repeats is a common parameter of the S. pombe centromere.

Centromeres of the Fission Yeast Schizosaccharomyces pombe Are Highly Variable Genetic Loci

Gross variations in the structure of the centromere of Schizosaccharomyces pombe chromosome III (cen3) were apparent following characterization of this centromeric DNA in strain Sp223 and comparison of the structure with that of cen3 in three other commonly used laboratory strains. Further differences in centromere structure were revealed when the structure of the centromere of S. pombe chromosome II (cen2) was compared among common laboratory strains and when the structures of cen2 and cen3 from our laboratory strains were compared with those reported from other laboratories. Differences observed in cen3 structure include variations in the arrangement of the centromeric K repeats and an inverted orientation of the conserved centromeric central core. In addition, we have identified two laboratory strains that contain a minimal cen2 repeat structure that lacks the tandem copies of the cen2-specific block of K-L-B-J repeats characteristic of Sp223 cen2. We have also determined that certain centromeric DNA structural motifs are relatively conserved among the four laboratory strains and eight additional wild-type S. pombe strains isolated from various food and beverage sources. We conclude that in S. pombe, as in higher eukaryotes, the centromere of a particular chromosome is not a defined genetic locus but can contain significant variability. However, the basic DNA structural motif of a central core immediately flanked by inverted repeats is a common parameter of the S. pombe centromere.

Nuclear magnetic resonance and circular dichroism studies of a triple-helical peptide with a glycine substitution

The triple-helical conformation has the stringent amino acid sequence constraint that every third residue must be a glycine, (X-Y-Gly) n . We use nuclear magnetic resonance and circular dichroism to quantify the consequences of a substitution in the glycine position of a triple-helical peptide, and to enhance our understanding of interactions in this basic structural motif. A 30-residue peptide with a Gly → Ala change forms a stable trimer at a folding rate somewhat less than that of the unsubstituted peptide, and the substitution results in a marked decrease in thermal stability and a conformational perturbation of about 30% of the triple-helical structure. Two models were generated for this peptide, one with the alanine residues packed inside the triple helix and one with a looping out of the chain at the substitution site. Studies on the Gly → Ala peptide are useful in understanding connective tissue diseases which result from the substitution of one glycine residue in the triple-helix of fibrillar collagens.

A common channel-forming motif in evolutionarily distant porins

Four new crystal packings of Escherichia coli porins are presented (phosphoporin, maltoporin, and two crystal forms of matrix porin). These were determined by molecular replacement methods using a polyalanine trial model acquired from the refined coordinates of porin from Rhodobacter capsulatus. The successful molecular replacement shows that the dominant motif found in R. capsulatus porin (a 16-stranded antiparallel (β-barrel) also applies to the E. coli porins, despite the lack of significant amino acid sequence homology. A 30°–40° tilt of the β-strands with respect to the membrane normal was derived from the intensity distributions in the X-ray diffraction patterns for each porin studied, stressing their similarity. In view of the evolutionary distance between enteric and photosynthetic bacteria, the antiparallel β-barrel may have significance as a basic structural motif for the formation of bacterial membrane channel structures.