Conversion of cucumber linoleate 13-lipoxygenase to a 9-lipoxygenating species by site-directed mutagenesis

Multiple lipoxygenase sequence alignments and structural modeling of the enzyme/substrate interaction of the cucumber lipid body lipoxygenase suggested histidine 608 as the primary determinant of positional specificity. Replacement of this amino acid by a less-space-filling valine altered the positional specificity of this linoleate 13-lipoxygenase in favor of 9-lipoxygenation. These alterations may be explained by the fact that H608V mutation may demask the positively charged guanidino group of R758, which, in turn, may force an inverse head-to-tail orientation of the fatty acid substrate. The R758L+H608V double mutant exhibited a strongly reduced reaction rate and a random positional specificity. Trilinolein, which lacks free carboxylic groups, was oxygenated to the corresponding (13S)-hydro(pero)xy derivatives by both the wild-type enzyme and the linoleate 9-lipoxygenating H608V mutant. These data indicate the complete conversion of a linoleate 13-lipoxygenase to a 9-lipoxygenating species by a single point mutation. It is hypothesized that H608V exchange may alter the orientation of the substrate at the active site and/or its steric configuration in such a way that a stereospecific dioxygen insertion at C-9 may exclusively take place.

Microwave-assisted palladium-catalyzed highly regio- and stereoselective head to head dimerization of terminal aryl alkynes in water

A highly regio- and stereoselective oxime palladacycle/imidazolinium-catalyzed head to head dimerization of terminal aryl alkynes in water is presented. The reaction, which is carried out at 130 °C under microwave irradiation in the presence of 1,3-bis-(2,6-diisopropylphenyl)imidazolinium chloride as ligand, triethylamine as base, and TBAB as surfactant, allows the synthesis of (E)-1,4-enynes as single stereoisomers in good isolated yields.

Switching Axial Progenitors from Producing Trunk to Tail Tissues in Vertebrate Embryos

The vertebrate body is made by progressive addition of new tissue from progenitors at the posterior embryonic end. Axial extension involves different mechanisms that produce internal organs in the trunk but not in the tail. We show that Gdf11 signaling is a major coordinator of the trunk-to-tail transition. Without Gdf11 signaling, the switch from trunk to tail is significantly delayed, and its premature activation brings the hindlimbs and cloaca next to the forelimbs, leaving extremely short trunks. Gdf11 activity includes activation of Isl1 to promote formation of the hindlimbs and cloaca-associated mesoderm as the most posterior derivatives of lateral mesoderm progenitors. Gdf11 also coordinates reallocation of bipotent neuromesodermal progenitors from the anterior primitive streak to the tail bud, in part by reducing the retinoic acid available to the progenitors. Our findings provide a perspective to understand the evolution of the vertebrate body plan.

Capped acyclic permutants of the circular protein kalata B1

The cyclotides are a family of head-to-tail cyclized peptides that display exceptionally high stability and a range of biological activities. Acyclic permutants that contain a break in the circular backbone have been reported to be devoid of the haemolytic activity of the prototypic cyclotide kalata B1, but the potential role of the charges at the introduced termini in this loss of membraneolytic activity has not been fully determined. In this study, acyclic permutants of kalata B1 with capped N- and G termini were synthesized and found to adopt a native fold. These variants were observed to cause no measurable lysis of erythrocytes, strengthening the connection between backbone cyclization and haemolytic activity. (C) 2004 Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies.

A gradient descent algorithm for minimizing amino acid coupling reactions when synthesizing cyclic-peptide libraries

Combinatorial chemistry has become an invaluable tool in medicinal chemistry for the identification of new drug leads. For example, libraries of predetermined sequences and head-to-tail cyclized peptides are routinely synthesized in our laboratory using the IRORI approach. Such libraries are used as molecular toolkits that enable the development of pharmacophores that define activity and specificity at receptor targets. These libraries can be quite large and difficult to handle, due to physical and chemical constraints imposed by their size. Therefore, smaller sub-libraries are often targeted for synthesis. The number of coupling reactions required can be greatly reduced if the peptides having common amino acids are grouped into the same sub-library (batching). This paper describes a schedule optimizer to minimize the number of coupling reactions by rotating and aligning sequences while simultaneously batching. The gradient descent method thereby reduces the number of coupling reactions required for synthesizing cyclic peptide libraries. We show that the algorithm results in a 75% reduction in the number of coupling reactions for a typical cyclic peptide library.

Discovery and characterization of a linear cyclotide from Viola odorata: Implications for the processing of circular proteins

Cyclotides are mini-proteins of 28-37 amino acid residues that have the unusual feature of a head-to-tail cyclic backbone surrounding a cystine knot. This molecular architecture gives the cyclotides heightened resistance to thermal, chemical and enzymatic degradation and has prompted investigations into their use as scaffolds in peptide therapeutics. There are now more than 80 reported cyclotide sequences from plants in the families Rubiaceae, Violaceae and Cucurbitaceae, with a wide variety of biological activities observed. However, potentially limiting the development of cyclotide-based therapeutics is a lack of understanding of the mechanism by which these peptides are cyclized in vivo. Until now, no linear versions of cyclotides have been reported, limiting our understanding of the cyclization mechanism. This study reports the discovery of a naturally occurring linear cyclotide, violacin A, from the plant Viola odorata and discusses the implications for in vivo cyclization of peptides. The elucidation of the cDNA clone of violacin A revealed a point mutation that introduces a stop codon, which inhibits the translation of a key Asn residue that is thought to be required for cyclization. The three-dimensional solution structure of violacin A was determined and found to adopt the cystine knot fold of native cyclotides. Enzymatic stability assays on violacin A indicate that despite an increase in the flexibility of the structure relative to cyclic counterparts, the cystine knot preserves the overall stability of the molecule. (c) 2006 Elsevier Ltd. All rights reserved.

4-(2-hydroxyethyl)anilinium 3-carboxy-4-hydroxybenzenesulfonate monohydrate

In the structure of the title compound C8H12NO+ C7H5O6S- . H2O, from the reaction of 2-(4-aminophenyl)ethanol with 5-sulfosalicylic acid, the cations form head-to-tail hydrogen-bonded chains through C1/1(9) anilinium N+-H...O(hydroxyl} interactions while the anions also form similar but C1/1(8)-linked chains through carboxylic acid O-..O(sulfonate) interactions. The chains inter-associate through a number of N-H...O and O-H...O bridging interactions giving a two-dimensional array in the ab plane.

Three-dimensional hydrogen-bonded structures in the 1:1 proton-transfer compounds of L-tartaric acid with the associative-group monosubstituted pyridines 3-minopyridine, 3-carboxypyridine (nicotinic acid) and 2-carboxypyridine (picolinic acid).

The 1:1 proton-transfer compounds of L-tartaric acid with 3-aminopyridine [3-aminopyridinium hydrogen (2R,3R)-tartrate dihydrate, C5H7N2+·C4H5O6-·2H2O, (I)], pyridine-3-carboxylic acid (nicotinic acid) [anhydrous 3-carboxypyridinium hydrogen (2R,3R)-tartrate, C6H6NO2+·C4H5O6-, (II)] and pyridine-2-carboxylic acid [2-carboxypyridinium hydrogen (2R,3R)-tartrate monohydrate, C6H6NO2+·C4H5O6-·H2O, (III)] have been determined. In (I) and (II), there is a direct pyridinium-carboxyl N+-HO hydrogen-bonding interaction, four-centred in (II), giving conjoint cyclic R12(5) associations. In contrast, the N-HO association in (III) is with a water O-atom acceptor, which provides links to separate tartrate anions through Ohydroxy acceptors. All three compounds have the head-to-tail C(7) hydrogen-bonded chain substructures commonly associated with 1:1 proton-transfer hydrogen tartrate salts. These chains are extended into two-dimensional sheets which, in hydrates (I) and (III) additionally involve the solvent water molecules. Three-dimensional hydrogen-bonded structures are generated via crosslinking through the associative functional groups of the substituted pyridinium cations. In the sheet struture of (I), both water molecules act as donors and acceptors in interactions with separate carboxyl and hydroxy O-atom acceptors of the primary tartrate chains, closing conjoint cyclic R44(8), R34(11) and R33(12) associations. Also, in (II) and (III) there are strong cation carboxyl-carboxyl O-HO hydrogen bonds [OO = 2.5387 (17) Å in (II) and 2.441 (3) Å in (III)], which in (II) form part of a cyclic R22(6) inter-sheet association. This series of heteroaromatic Lewis base-hydrogen L-tartrate salts provides further examples of molecular assembly facilitated by the presence of the classical two-dimensional hydrogen-bonded hydrogen tartrate or hydrogen tartrate-water sheet substructures which are expanded into three-dimensional frameworks via peripheral cation bifunctional substituent-group crosslinking interactions.

Crystallographic characterization of the first reported crystalline form of the potent hallucinogen (R)-2-amino-1-(8-bromobenzo[1,2-b;5,4-b']difuran-4-yl)propane or `bromodragonfly': the 1:1 anhydrous proton-transfer compound with 3,5-dinitrosalicylic acid

The 1:1 proton-transfer compound of the potent substituted amphetamine hallucinogen (R)-1-(8-bromobenzo[1,2-b; 4,5-b']difuran-4-yl)-2-aminopropane (common trivial name 'bromodragonfly') with 3,5-dinitrosalicylic acid, 1-(8-bromobenzo[1,2-b;4,5-b']difuran-4-yl)-2-mmoniopropane 2-carboxy-4,6-dinitrophenolate, C13H13BrNO2+ C7H3N2O7- forms hydrogen-bonded cation-anion chain substructures comprising undulating head-to-tail anion chains formed through C(8) carboxyl O-H...O(nitro) associations and incorporating the aminium groups of the cations. The intra-chain cation-anion hydrogen-bonding associations feature proximal cyclic R33(8) interactions involving both a N+-H...O(phenolate) and the carboxyl O--H...O(nitro)associations. Also present are aromatic pi-pi ring interactions [minimum ring centroid separation, 3.566(2)A; inter-plane dihedral angle, 5.13(1)deg]. A lateral hydrogen-bonding interaction between the third aminium proton and a carboxyl O acceptor link the chain substructures giving a two-dimensional sheet structure. This determination represents the first of any form of this compound and confirms that it has the (R) absolute configuration. The atypical crystal stability is attributed both to the hydrogen-bonded chain substructures provided by the anions, which accommodate the aminium proton-donor groups of the cations and give cross-linking, and to the presence of cation--anion aromatic ring pi-pi interactions.

Hydrate stabilization in the three-dimensional hydrogen-bonded structure of the brucinium compound, bis(2,3-dimethoxy-10-oxostrychnidinium) biphenyl-4,4'-disulfonate hexahydrate

The crystal structure of the 2:1 proton-transfer compound of brucine with biphenyl-4,4’-disulfonate, bis(2,3-dimethoxy-10-oxostrychnidinium) biphenyl-4,4'-disulfonate hexahydrate (1) has been determined at 173 K. Crystals are monoclinic, space group P21 with Z = 2 in a cell with a = 8.0314(2), b = 29.3062(9), c = 12.2625(3) Å, β = 101.331(2)o. The crystallographic asymmetric unit comprises two brucinium cations, a biphenyl-4,4'-disulfonate dianion and six water molecules of solvation. The brucinium cations form a variant of the common undulating and overlapping head-to-tail sheet sub-structure. The sulfonate dianions are also linked head-to-tail by hydrogen bonds into parallel zig-zag chains through clusters of six water molecules of which five are inter-associated, featuring conjoint cyclic eight-membered hydrogen-bonded rings [graph sets R33(8) and R34(8)], comprising four of the water molecules and closed by sulfonate O-acceptors. These chain structures occupy the cavities between the brucinium cation sheets and are linked to them peripherally through both brucine N+-H...Osulfonate and Ocarbonyl…H-Owater to sulfonate O bridging hydrogen bonds, forming an overall three-dimensional framework structure. This structure determination confirms the importance of water in the stabilization of certain brucine compounds which have inherent crystal instability.

Phenyl-ring disorder in the two-dimensional hydrogen-bonded structure of the 1:1 proton-transfer salt of the diazo-dye precursor 4-(phenyldiazenyl)aniline (aniline yellow) with L-tartaric acid

The structure of the 1:1 proton-transfer compound from the reaction of L-tartaric acid with the azo-dye precursor aniline yellow [4-(phenylazo)aniline], 4-(phenyldiazenyl)anilinium hydrogen 2R,3R-tartrate C12H12N3+ . C4H6O6- has been determined at 200 K. The asymmetric unit of the compound contains two independent phenylazoanilinium cations and two hydrogen L-tartrate anions. The structure is unusual in that all four phenyl rings of both cations have identical 50% rotational disorder. The two hydrogen L-tartrate anions form independent but similar chains through head-to-tail carboxylic O--H...O~carboxyl~ hydrogen bonds [graph set C7] which are then extended into a two-dimensional hydrogen-bonded sheet structure through hydroxyl O--H...O hydrogen-bonding links. The anilinium groups of the phenyldiazenyl cations are incorporated into the sheets and also provide internal hydrogen-bonding extensions while their aromatic tails layer in the structure without significant interaction except for weak \p--\p interactions [minimum ring centroid separation, 3.844(3) \%A]. The hydrogen L-tartrate residues of both anions have the common short intramolecular hydroxyl O--H...O~carboxyl~ hydogen bonds. This work has provided a solution to the unusual disorder problem inherent in the structure of this salt as well as giving another example of the utility of the hydrogen tartrate in the generation of sheet substructures in molecular assembly processes.

Anhydrous 1:1 proton-transfer compounds of isonipecotamide with picric acid and 3,5-dinitrosalicylic acid: 4-carbamoylpiperidinium 2,4,6-trinitrophenolate and two polymorphs of 4-carbamoylpiperidinium 2-carboxy-4,6-dinitrophenolate

The structures of the anhydrous 1:1 proton-transfer compounds of isonipecotamide (4-carbamoylpiperidine) with picric acid and 3,5-dinitrosalicylic acid, namely 4-carbamoylpiperidinium 2,4,6-trinitrophenolate, C6H13N2O8+ C6H2N3O7- (I) and 4-carbamoylpiperidinium 2-carboxy-4,6-dinitrophenolate, C6H13N2O8+ C7H3N2O7-: two forms, the monoclinic alpha-polymorph (II) and the triclinic beta-polymorph (III) have been determined at 200 K. All compounds form hydrogen-bonded structures, one-dimensional in (II), two-dimensional in (I) and three-dimensional in (III). In (I), the cations form centrosymmetric cyclic head-to-tail hydrogen-bonded homodimers [graph set R2/2(14)] through lateral duplex piperidinium N---H...O(amide) interactions. These dimers are extended into a two-dimensional network structure through further interactions with anion phenolate-O and nitro-O acceptors, including a direct symmetric piperidinium N-H...O(phenol),O(nitro) cation--anion association [graph set R2/1(6)]. The monoclinic polymorph (II) has a similar R2/1(6) cation-anion hydrogen-bonding interaction to (I) but with an additional conjoint symmetrical R1/2(4) interaction as well as head-to-tail piperidinium N-H...O(amide) O hydrogen bonds and amide N-H...O(carboxyl) hydrogen bonds, give a network structure which include large R3/4(20) rings. The hydrogen bonding in the triclinic polymorph (III) is markedly different from that of monoclinic (II). The asymmetric unit contains two independent cation-anion pairs which associate through cyclic piperidinium N-H...O,O'(carboxyl) interactions [graph set R2/1(4)]. The cations also show the zig-zag head-to-tail piperidinium N-H...O(amide) hydrogen-bonded chain substructures found in (II) but in addition feature amide N-H...O(nitro) and O(phenolate) and amide N-H...O(nitro) associations. As well there is a centrosymmetric double-amide N-H...O(carboxyl) bridged bis(cation-anion) ring system [graph set R2/4(8)] in the three-dimensional framework. The structures reported here demonstrate the utility of the isonipecotamide cation as a synthon with previously unrecognized potential for structure assembly applications. Furthermore, the structures of the two polymorphic 3,5-dinitrosalicylic acid salts show an unusual dissimilarity in hydrogen-bonding characteristics, considering that both were obtained from identical solvent systems.