Bipartite gating in the outer membrane protein FecA.

The recent structure determination of FecA, with and without ligand, shows the existence of two gates. These are the extracellular loops closing over the binding site and the plug located inside the barrel. It indicates a process which is described as bipartite gating and allows for a rational distinction between the binding event and the transport process.

Aplidioxins A and B, two new dibenzo-p-dioxins from the ascidian aplidiopsis ocellata

Two new substituted dibenzo-p-dioxins, aplidioxins A (1) and B (2), were isolated from the ascidian Aplidiopsis ocellata. The structures of these compounds were elucidated by a combination of 1D and 2D NMR spectroscopy and an X-ray analysis of aplidioxin A.

Crystal structure of the outer membrane active transporter FepA from Escherichia coli.

Integral outer membrane receptors for iron chelates and vitamin B12 carry out specific ligand transport against a concentration gradient. Energy for active transport is obtained from the proton-motive force of the inner membrane through physical interaction with TonB-ExbB-ExbD, an inner membrane complex. Here we report the crystal structure of an active transport, outer membrane receptor at 2.4 A resolution. Two distinct functional domains are revealed: (i) a 22-stranded beta-barrel that spans the outer membrane and contains large extracellular loops which appear to function in ligand binding; and (ii) a globular N-terminal domain that folds into the barrel pore, inhibiting access to the periplasm and contributing two additional loops for potential ligand binding. These loops could provide a signaling pathway between the processes of ligand recognition and TonB-mediated transport. The blockage of the pore suggests that the N-terminal domain must undergo a conformational rearrangement to allow ligand transport into the periplasm.

Crystallization and preliminary X-ray analysis of ferric enterobactin receptor FepA, an integral membrane protein from Escherichia coli.

Diffraction-quality crystals have been obtained of the integral membrane protein ferric enterobactin receptor (FepA) from the outer membrane of Escherichia coli. Crystals were grown using the zwitterionic detergent lauryldimethylamine oxide (LDAO), the precipitants polyethylene glycol (PEG) 1000 and sodium chloride, and the additive heptane-1,2,3-triol; they have the symmetry of the orthorhomic space group C2221 with a = 112.2, b = 137.2 and c = 135. 4 A and diffract to 2.5 A resolution. The crystals were flash-cooled and a preliminary data set was collected at 103 K. The crystals are suitable for three-dimensional structure analysis.

Structure and absolute stereochemistry of salvimirzacolide, a new sesterterpene from Salvia mirzayanii.

A new sesterterpene, salvimirzacolide (1), was isolated from the aerial parts of Salvia mirzayanii and its structure established by X-ray diffraction analysis. Full assignments of 1H- and 13C-NMR spectral data of salvimirzacolide are presented.

6-L-alanineferrirubin, a ferrichrome-type siderophore from the fungus Aspergillus ochraceous.

The molecular structure of 6-L-alanineferrirubin tetradecahydrate, [Fe(C41H64N9O16)].14H2O, has been determined in order to confirm its chemical structure. The structural results show that the presence of an alanine in place of a serine or a glycine at position 6 in the cyclic hexapeptide has very little effect on the conformation of the 18-membered ring or on the geometry of the octahedral iron coordination.

Structures and characteristics of novel siderophores from plant deleterious Pseudomonas fluorescens A225 and Pseudomonas putida ATCC 39167.

When Pseudomonas putida ATCC 39167 and plant-deleterious Pseudomonas fluorescens A225 were grown in an iron-deficient culture medium, they each produced two different novel yellow-green fluorescent pseudobactins: P39167-I, II and PA225-I, II. Pseudobactin P39167-I has a molecular formula of C46H65O23N13 and is monoanionic at neutral pH. P39167-II has the molecular formula of C46H63O22N13 and no charge at neutral pH. Pseudobactin PA225-I has a molecular formula of C46H65O24N13 and is monoanionic at neutral pH whereas pseudobactin PA225-II has the molecular formula of C46H63O23N13 and no charge at neutral pH. All four of the pseudobactins contain a dihydroxyquinoline-based chromophore. The amino acid sequence for the octapeptide in case of pseudobactins from P. putida ATCC 39167 is Chr-Ser(1)-Ala(1)-AcOHOrn-Gly-Ala(2)-OHAsp-Ser(2)-Thr. In case of pseudobactins from P. fluorescens A225, the octapeptide has the sequence Chr-Ser(1)-Ala-AcOHOrn-Gly-Ser(2)-OHAsp-Ser(3)-Thr. For all four pseudobactins (P39167-I, II and PA225-I, II), the serine(1) residue of the octapeptide is attached to the carboxylic acid group on the C-11 of the fluorescent quinoline via an amide bond. Additionally, for pseudobactin P39167-II and PA225-II, the hydroxyl group of the serine(1) residue is also attached to the carboxyl group of threonine residue at the carboxy terminus of the peptide via an ester bond, resulting in a cyclic depsipeptide in contrast to the linear peptide chain of P39167-I and PA225-I. For all four pseudobactins, a malamide group is attached to the C-3 of the quinoline derived chromophore. The three bidentate iron(III) chelating groups in all four pseudobactins consist of a 1,2-dihydroxy aromatic group of the fluorescent chromophore, a hydroxy acid group of beta-hydroxy aspartic acid, and a hydroxamate group from the acylated Ndelta-hydroxyornithine. The amino acid constituents of the pseudobactins P39167 I, II are the same as those in pseudobactin A214, whereas those in A225 I, II are the same as in 7SR1, but in both cases the sequences are different. The uptake results indicate a single outer membrane receptor protein for ferric-pseudobactins in both organisms. The receptor proteins in the two species are similar but not identical.

Makaluvic acids A and B: novel alkaloids from the marine sponge Zyzzya fuliginosus.

Two new substituted pyrrolecarboxylic acids, makaluvic acids A (5) and B (6), were isolated from the sponge Zyzzya fuliginosus, which was collected in Chuuk Atoll, Federated States of Micronesia. The known alkaloids 3,7-dimethylisoguanine (1) and makaluvamines A (2), E (3), and K (4) were also isolated.

Synthesis, physicochemical properties, and biological evaluation of hydroxypyranones and hydroxypyridinones: novel bidentate ligands for cell-labeling.

The synthesis of a range of hydroxypyranones and hydroxypyridinones with potential for the chelation of indium(III) is described. The crystal structures of two of the indium complexes are presented. The distribution coefficients of the ligands and the corresponding iron(III), gallium(III), and indium(III) complexes are reported. Good linear relationships between the distribution coefficients of the iron and gallium complexes and iron and indium complexes were obtained. In contrast a nonlinear relationship was obtained between the distribution coefficient of the free ligand and the distribution coefficient of the three groups of complexes. This latter relationship was used to identify compounds with optimal cell labeling properties. Two such compounds both 6-(alkoxymethyl)-3-hydroxy-4H-pyran-4-ones have been compared with tropolone for their ability to label human leucocytes with 111In. The leucocyte labeling efficiencies of the selected ligands were greater and the in-vitro plasma stabilities were similar to that of 111In-tropolonate. These results suggest that the new bidentate ligands may offer advantages over those currently used for cell-labeling.

Novel 3,7-diheterabicyclo[3.3.1]nonanes that possess predominant class III antiarrhythmic activity in 1-4 day post infarction dog models: X-ray diffraction analysis of 3-[4-(1H-imidazol-1-yl)benzoyl]-7-isopropyl-3,7-diazabicyclo[3.3.1]nona ne dihydroperchlorate.

Several 3,7-diheterabicyclo[3.3.1]nonanes (DHBCNs) were prepared and screened in the Harris dog model for their ability to abolish pace-induced and sustained ventricular tachycardia (SVT) or prevent induction of ventricular tachycardia. In addition, an electrophysiological examination was made in the infarcted hearts of each animal to determine if more than one class activity was present. The examples exhibited predominately class III antiarrhythmic activity via a prolongation of the ventricular effective refractory period (VERP) in the models, although there may well be an underlying class Ib action present as exemplified by the ability of several of the agents to slow conduction in the myocardial infarcted dog hearts. 3-[4-(1H-Imidazol-1-yl)benzoyl]-7-isopropyl-3,7-diazabicyclo[3.3.1]nonan e dihydroperchlorate displayed powerful class III activity in the model systems while several other DHBCNs exhibited various degrees of class III action. An X-ray diffraction analysis revealed that this compound has a 3,7-diazabicyclo[3.3.1]nonane bicyclic unit in a chair-chair conformation.

A pyrazoline derivative of eunicin acetate.

The present crystal structure determination established spiro [¿3a,4,5,6,7,8,11,12,13,14,15,15a-dodecahydro-6,10,14-trimet hyl-2-oxo-5, 15-epoxy-3H-cyclotetradeca-[b]furan¿-3,3'-1'-pyrazoline]-6-yl acetate, C23H34N2O5, as a pyrazoline derivative of eunicin acetate. The spiro substitution of the pyrazoline ring causes elongation of the bonds within the lactone ring and also shortening of the carbonyl bond. The cembranolide skeleton is slightly more bent than that observed in the parent eunicin molecule.

7-Benzyl-3-thia-7-azabicyclo[3.3.1]nonane 3-oxide.

The molecular geometry of a major metabolite, C14H19NOS, of a potent anti-arrhythmic drug, 7-benzyl-3-thia-7-azabicyclo[3.3.1]nonane (BRB-I-28), has been determined by X-ray diffraction. The 3,7-dihetero bicyclic system of the sulfoxide molecule adopts a chair--chair conformation like that of the HCLO4 salt of the BRB-I-28 molecule. The S...N contact distance of 2.863(2)A in the present molecule is significantly shorter than that found in the crystal structure of its precursor [3.038(4)A]. The overall molecule possesses pseudo-mirror symmetry.

Crystal and molecular structure of didemnin A, an antiviral depsipeptide.

The molecular structure of didemnin A, the parent compound of a series of antiviral cytotoxic depsipeptides extracted from a marine tunicate Trididemnum solidum of the family of Didemnidae, has been determined by single-crystal X-ray diffraction. In the crystal, didemnin A molecules form pseudo-symmetric dimeric pair. The two molecules in the dimer are held together by strong N--H center dot center dot center dot O and N--H center dot center dot center dot N hydrogen bonds. A chloride ion, placed almost symmetrically between the dimeric pair, forms N--H center dot center dot center dot Cl hydrogen bonds (3.19 and 3.23 Angstrom) with both the molecules. The two independent molecules in the structure have closely similar geometry. For each molecule, the 23-membered depsipeptide ring assumes a folded conformation in the shape of a 'bent figure-of-eight' similar to that observed in the didemnin B crystal structure. The major conformational differences in the macrocycle of didemnin A and didemnin B are around the Hip residue. The root mean-square (RMS) difference of 20 of the 23 endocyclic torsion angles for the two structures is less than 10 degrees, while the three bond torsions in the Hip residue vary by about 50 degrees. The macrocycle conformation is stabilized by a transannular N--H center dot center dot center dot O hydrogen bond linking the isostatine amide group with the leucine carbonyl group. The truncated linear chain is folded back toward the macrocyclic ring and is held by a N--H center dot center dot center dot O hydrogen bond between the leucine amide group and Me-Leu carbonyl group. The transannular hydrogen bond in the didemnin A structure (N4--H center dot center dot center dot O3 = 2.83 Angstrom in both molecule a and molecule b) is noticeably stronger than that observed in the didemnin B structure (3.02 Angstrom). The X-ray structure of didemnin A is generally consistent with that obtained by NMR studies. Within the crystal, the molecules are packed in zig-zag chains formed by intermolecular O--H center dot center dot center dot O hydrogen bonds. The crystal structure and packing of didemnin A are quite different from that of the didemnin B structure.

Binding characterization of the iron transport receptor from the outer membrane of Escherichia coli (FepA): differentiation between FepA and FecA.

The dissociation constants for the binding of ferric enterobactin with FepA and FecA are quantitated with displacement experiments. It is found that Kd for FepA is 12 times lower than the one for FecA. This indicates that FepA is an high-affinity receptor while FecA binds ferric enterobactin with a lower affinity. Monoclonal antibodies specific for binding epitopes of FepA inhibit the binding of ferric enterobactin with purified FepA. These same antibodies do not inhibit the binding of ferric enterobactin with purified FecA. This indicates that the binding epitopes in FecA and FepA are different.

Molecular structures of CPF-dipeptides, inhibitors for the binding of CD4 with gp120.

The dipeptides N-carbomethoxycarbonyl-prolyl-phenylalanyl-benzyl esters (CPFs) play a significant role in the prevention of HIV-1 virus infection by interacting with the glycoprotein gp120, one of the envelope proteins of the HIV-1 virus. Of the four possible isomers of CPF, (L-pro-L-phe), (L-pro-D-phe), (D-pro-L-phe) and (D-pro-D-phe), herein denoted LL etc., the crystal structures of LL, stereoisomeric LD and the racemic mixture of LD/DL have been determined. All three peptides crystallize in the orthorhombic system and they all have similar cell dimensions: (i) LL, P2(1)2(1)2(1), a = 13.699(2), b = 25.893(5), c = 6.155(1) A, Z = 4, Dcale = 1.333 g cm-3, R = 0.070 for 1247 observed reflections; (ii) LD, P2(1)2(1)2(1), a = 11.663(2), b = 26.557(2), c = 7.281(1) A, Z = 4, Dcalc = 1.290 g cm-3, R = 0.054 for 1918 observed reflections; (iii) LD/DL, Pbc2(1), a = 11.953(2), b = 24.208(8), c = 7.782(2) A, Z = 4, Dcalc = 1.292 g cm-3, R = 0.080 for 894 observed reflections. Both the enantiomeric LD and the LD in racemic LD/DL have a similar conformation, an extended peptide chain with phi 1 = -76, -73 degrees; psi 1 = 160, 158 degrees, psi 2 = 123, 131 degrees and psi 2 = -172, -167 degrees, while peptide LL adopts a bent conformation at the Phe residue, phi 1 = -69 degrees, psi 1 = 158 degrees, phi 2 = -60 degrees and psi 2 = -34 degrees.(ABSTRACT TRUNCATED AT 250 WORDS)

Molecular structures and conformational studies of triarylcyclopropyl and related nonsteroidal antiestrogens.

Molecular structures and conformational characteristics of a series of 1,1-dichloro-2,2,3-triarylcyclopropanes (DTACs), which were reported previously to be distinctly antiestrogenic and inhibitors of the estrogen-receptor-positive MCF-7 human breast cancer cells in culture, are reported. In addition, structural and conformational features of the DTACs were compared to the first-known nonsteroidal antiestrogen, MER25, and the clinically useful antiestrogen Tamoxifen. The molecular structures of four DTAC compounds were determined by X-ray diffraction. Crystallographic structures show that the DTAC molecules have nearly the same relative conformation for the three aryl rings which is designated as a "nonpropeller" conformation in contrast to the observed "propeller" conformation for the three rings in all known triarylethylenes. Systematic conformational searches were performed to find the conformational preferences of DTACs, MER25, and Tamoxifen using idealized model compounds built from their respective crystal structure. Energy-minimization and conformational-search studies demonstrated that all DTAC molecules have a common, single global minimum energy conformer for their central core containing the dichlorotriarylcyclopropyl system, which is similar to that found in their crystal structures. Conformational search of MER25 showed that the molecule can assume a number of low-energy conformers of which two, one anti (A1) and one gauche (G1A), have about the same energy. The anti conformation is similar to the one observed in its crystal structure and resembles the estrogenic E-isomer of Tamoxifen, while the lowest energy gauche conformer of MER25 resembles more closely the antiestrogenic Z-isomer of Tamoxifen. NMR spectroscopic analysis of MER25 showed that the molecule exists predominantly in the anti conformation in solution. A comparative review of the structural features and bioactivities of Tamoxifen, DTACs, and MER25 provides a possible explanation for their low estrogen receptor binding affinity which is common to these compounds together with their antiestrogenic activity.

Patagonicol: a diterpenoid from the Chinese soft coral Alcyonium patagonicum.

Patagonicol [1], a diterpenoid with a eunicellin skeleton, was isolated from the soft coral Alcyonium patagonicum. The structure of 1 was determined by X-ray diffraction, and detailed 1H and 13C assignments were made via 1D and 2D nmr experiments.

Structures of 3-hydroxy-1-(2-methoxyethyl)-2-methyl-4-pyridinone, its hydrochloride and 1-ethyl-3-hydroxy-2-methyl-4-pyridinone hydrochloride hydrate.

3-Hydroxy-1-(2-methoxyethyl)-2-methyl-4(1H)-pyridinone (1) exists mainly in the quinoid form with a small contribution from the aromatic zwitterion form, while 3-hydroxy-1-(2-methoxyethyl)-2-methyl-4(1H)-pyridinone hydrochloride (2) and 1-ethyl-3-hydroxy-2-methyl-4(1H)-pyridinone hydrochloride hydrate (3) are observed to occur in the aromatic form with a minor contribution from the quinoid resonance form. Different substituents at the ring N position do not have significant geometric effects in either the neutral molecules, as a group, or in the hydrochloride salts.