Structure of the crystalline complex between ribonuclease A and D(pA)4.

Crystals of a complex formed between ribonuclease A and d(pA)4 were grown and their structure determined by a combination of multiple isomorphous replacement (MIR) and molecular replacement techniques. The known structure of ribonuclease A in the correct orientation in the unit cell yielded a conventional crystallographic R factor of 0.32 at 2.8 A resolution when refined as a rigid body. Difference Fourier syntheses permitted determination of the disposition of the DNA in the unit cell. Refinement of both protein and DNA by constrained-restrained least squares procedures resulted in an R factor of 0.22 at 2.5 A resolution. The structure of the crystalline complex is comprised of four ordered oligomers of d(pA)4 associated with each molecule of RNAse. If the sites of interaction between protein and d(pA)4 fragments are mapped on the surface of the protein, they describe an essentially continuous path into and through the active site, across the surface of the enzyme and finally into the basic amino acid cluster on the opposite side of the protein.     

Crystal structure of RNase A complexed with d(pA)4

Co-crystals of pancreatic RNase A complexed with oligomers of d(pA)4 were grown from polyethylene glycol 4000 at low ionic strength and the X-ray diffraction data were collected to 2.5 A resolution. From a series of heavy-atom derivatives a multiple isomorphous replacement-phased electron density map of the RNase-d(pA)4 complex was calculated to 3.5 A. By inspection, the disposition of the known structure of RNase in the unit cell was determined and this was confirmed by calculation of a standard crystallographic residual, R. Refinement of the protein alone in the unit cell as a strictly rigid body yielded an R factor of 0.32 at 2.8 A resolution. From difference Fourier syntheses DNA fragments were elucidated and incorporated into a model of the complex. The entire asymmetric unit was refined using a restrained-constrained least-squares procedure (CORELS) interspersed with difference Fourier syntheses. At the present time the crystal structure has been refined to an overall R value of 0.215 at 2.5 A resolution. The asymmetric unit of the complex crystals contains four oligomers of d(pA)4 associated with each molecule of RNase. In addition, there may also be partially ordered fragments of DNA at low occupancy present in the unit cell, but these have not, at this time, been incorporated into the model. One tetramer of d(pA)4 is entirely bound by a single protein molecule and occupies a portion of the active site cleft, filling the purine binding site and the phosphate site at the catalytic center with its 5' nucleotide. Two other tetramers are partly intermolecular. One passes from near the pyrimidine binding site over the surface of the protein toward arginine 39 and into a solvent region. A third tetramer is anchored at its 5' terminus by a salt link to lysine 98, passes near arginine and then through a solvent region to terminate with its 3' end near the surface of another protein molecule in the lattice. The fourth tetramer of d(pA)4 is bound at its 5' end on the opposite side of the protein from the active site in an electropositive anion trap that includes lysines 31 and 91 as well as arginine 33. There may be a DNA-DNA interaction involving the 5' phosphate of one tetramer and the 3' bases of two other tetramers and this may help to stabilize the crystalline complex.(ABSTRACT TRUNCATED AT 250 WORDS)     

RNA-ligase of bacteriophage T4. IV. Synthesis of pentadecaribonucleotide ApUpG(pU)6(pA)5pAp

Oligoribonucleotide ApUpG(pU)6(pA)5pAp (I) has been prepared by means of RNA ligase. ApUpG, synthesised by the phosphotriester approach, was elongated in the 3'-direction by adding (pU)6 and then (pA)6, which was 3'-blocked with the phosphate or with the periodate-oxidized AMP residue, the latter giving considerably lower level of by-products. Condensation of ApUpG(pU)6 with blocked (pA)6 was carried out under conditions optimal for poor acceptors (20 degrees C, 48 h, pH 8,7) to afford (I) with the yield of 20% (105 OE260); ApUpG(pU)6(pA)10pAp was identified as a byproduct.     

Relationship between pD2 and pA2 of neuroleptics

The differences in the pD2/pA2 ratio of nine tested neuroleptics were found to vary between 0.92 and 1.11. This result confirms the hypothesis that pD2 (as determined from the inhibition of spontaneous locomotor activity) and pA2 (as determined from the shift of apomorphine dose response curve induced by a fixed dose of the neuroleptic) should not differ markedly and is discussed as differences in receptor specifities on the basis of the concept of multiple binding sites fo neuroleptics in the brain.     

The binding of pentaammineruthenium (III) to RNase B and RNase A+d(pA)4 in the crystalline state

The binding of pentaammineruthenium (III) to ribonuclease A and B both free and complexed with d(pA)₄ has been examined in the crystalline state through the application of X-ray diffraction and difference Fourier techniques. In crystals of native RNase B, the reagent was observed to have many binding sites, some entirely electrostatic in nature and others consistent with coordination to histidine residues. The primary histidine in the latter case was 105 with 119 also partially substituted. In crystals of RNase A+d(pA)₄ complex only a single, extremely strong site of substitution was observed, and this was 2.4 Å from the native position of the imidazole ring of histidine 105. Thus, the results of these X-ray diffraction studies appear to be quite consistent with the findings of earlier NMR studies and with the results obtained in crystals of the gene 5 DNA binding protein.     

The binding of pentaammineruthenium (III) to RNase B and RNase A+d(pA)4 in the crystalline state

The binding of pentaammineruthenium (III) to ribonuclease A and B both free and complexed with d(pA)₄ has been examined in the crystalline state through the application of X-ray diffraction and difference Fourier techniques. In crystals of native RNase B, the reagent was observed to have many binding sites, some entirely electrostatic in nature and others consistent with coordination to histidine residues. The primary histidine in the latter case was 105 with 119 also partially substituted. In crystals of RNase A+d(pA)₄ complex only a single, extremely strong site of substitution was observed, and this was 2.4 Å from the native position of the imidazole ring of histidine 105. Thus, the results of these X-ray diffraction studies appear to be quite consistent with the findings of earlier NMR studies and with the results obtained in crystals of the gene 5 DNA binding protein.     

The Absence of Cruciform Structures from pA03 Plasmid DNA In vivo

Abstract

We extracted pA03 plasmid DNA from E. coli cells, having “frozen” the transitions between cruciform and double-helical conformations in DNA. The characteristic feature of the DNA isolation procedure is that all steps were carried out at temperature between 0 and 4 C and no phenol deproteinization was used, since it has been discovered that phenol destabilizes cruciform structures in pA03 DNA. Two-dimensional gel electrophoresis has revealed no cruciform structures in the pA03 DNA preparations obtained this way, although the superhelical density of DNA was sufficient for them. Cruciform structures are absent from intracellular pA03 DNA at all growth stages of the bacterial culture: stationary and logarithmic, and under the induction of pA03 DNA replication in chloramphenicol-treated cells.     

Receptor regulation, competitive antagonism and pA2.

A growing body of evidence suggests that the number of drug receptors on cell surfaces is not fixed, but is dynamically regulated by circumstances that include exposure to the ligand itself. Because most traditional theories of drug action are based on the assumption of a fixed number of receptors, it is desirable to examine the importance of this regulatory process on the interpretation of dose-effect data. Of special interest is the impact of a variable receptor number on the equation of competitive antagonism and associated pA2 which, in the traditional theory, is a quantitative measure of antagonist-receptor affinity. Using a simple model of drug-induced endocytosis or exocytosis, it is shown that if the rate of either is appreciable, the pA2 is no longer a simple measure of affinity.     

The Ff gene 5 protein-d(pA)40-60 complex: 1H NMR supports a localized base-binding model

The interaction between Ff gene 5 protein (G5P) and d(pA)40-60 serves as an improved model system for a 1H NMR examination of the G5P-ssDNA interface under cooperative binding conditions. Selective deuteriation of aromatic residues enables individual Tyr (3,5)H and (2,6)H resonances to be monitored in spectra of high molecular weight nucleoprotein assemblies. Analysis of complexation-induced chemical shift changes and intermolecular NOEs indicates that Tyr 26 is the only tyrosine to interact directly with ssDNA. Tyr 41, which is immobilized upon binding, is implicated in a dimer-dimer contact role. These and other NMR data are consistent with a previously outlined model of the protein-DNA interface in which Phe 73', Leu 28, and Tyr 26 form components of a base-binding pocket or "dynamic clamp" fringed by a cluster of positively charged residues [King, G. C., & Coleman, J. E. (1987) Biochemistry 26, 2929-2937]. In the present version of this model, the Phe and Leu side chains are proposed to stack on either side of a single base, while there is the possibility that Tyr 26 may H-bond to the sugar-phosphate backbone in addition to or instead of stacking. Chemical-exchange effects underscore the dynamic nature of binding at the pocket. A comparison of d(pA)40-60 and oligo(dA)-induced chemical shift changes suggests that poly- and oligonucleotide complexes have indistinguishable base-binding loci but appear to differ in their dimer-dimer interactions.(ABSTRACT TRUNCATED AT 250 WORDS)     

Sequence and analysis of the 46.6-kb plasmid pA1 from Sphingomonas sp. A1 that corresponds to the typical IncP-1beta plasmid backbone without any accessory gene

Sphingomonas sp. A1 (strain A1) is capable of directly incorporating macromolecules (e.g., alginate) through the specialized import system--"super-channel." Here, we report the complete DNA sequence and genetic organization of plasmid pA1 from strain A1. Nucleotide sequence analysis revealed that pA1 comprises 46,557 bp encoding 49 open reading frames (ORFs) with 65% G+C content and abundant GCCG/CGGC motifs. Many predicted pA1 ORFs showed high similarity to pA81 ORFs; pA81 is supposedly a self-transmissible promiscuous incompatibility (Inc) group P-1beta plasmid. Unlike any reported IncP-1 plasmids, pA1 contains no inserted mobile genetic elements. The genetic organization and predicted pA1 ORFs showed greater similarity to the IncP-1beta plasmid backbone than to the IncP-1alpha plasmid backbone. pA1 contains restriction site-associated repeat sequences typical of the IncP-1beta but absent in the IncP-1alpha and delta subgroups. Thus, the overall pA1 structure corresponds to that of the typical IncP-1beta plasmids. Phylogenetic analysis of the replication-associated proteins suggested that pA1 may have diverged later along with the two IncP-1beta plasmids--pA81 and pB4. The 2.4-kb duplicates of stable inheritance genes klcAB and korC in pA1 possibly resulted from insertion and/or recombination events via the repeat sequences flanking these duplicates.     

Stability of plasmid pA387 derivatives in Amylcolatopsis mediterranei producing rifamycin

Genetic studies on the biosynthesis of rifamycins in producer strains such as Amylcolaptopsis mediterranei U-32 are severely hampered by the availability of efficient transformation procedures and stable plasmid vectors. Using an efficient electroporation procedure we have studied the replication and stability of a pA387 derivative, pDXM32. This plasmid confers enhanced plasmid stability and copy number compared to pA387 derivatives commonly used as cloning vectors in A. mediterranei. Deletion derivatives in the region previously identified as being a minimal replication origin were also examined with respect to their ability to transform A. mediterranei and at least one locus was essential for replication. A 5.4 kbp DNA fragment was sequenced and annotated encoding the replication and plasmid stability functions. A parA homologue was identified which is likely to confer plasmid stability.     

Presence of several plasmids in the fungus Ascobolus immersus, and homologies with the linear plasmid pA1

DNA analysis of several genetically unstable strains of the fungus Ascobolus immersus revealed the presence of at least seven different plasmids. These plasmids ranged from 2 to 20 kb in size, and showed homology to one of them, pA1. In 18 stocks directly isolated from nature, two-thirds harboured plasmids ranging from 3 to 17 kb. Plasmids with homology to pA1 had similar molecular masses (about 8.5 kb). A possible mechanism of plasmid formation from chromosomal DNA is discussed.     

Voltage- and calcium-activated currents in cultured olfactory receptor neurons of male Mamestra brassicae (Lepidoptera)

Insect olfactory receptor neurons (ORNs) grown in primary cultures were studied using the patch-clamp technique in both conventional and amphotericin B perforated whole-cell configurations under voltage-clamp conditions. After 10-24 days in vitro, ORNs had a mean resting potential of -62 mV and an average input resistance of 3.2 GOmega. Five different voltage-dependent ionic currents were isolated: one Na(+), one Ca(2+) and three K(+) currents. The Na(+) current (35-300 pA) activated between -50 and -30 mV and was sensitive to 1 microM tetrodotoxin (TTX). The sustained Ca(2+) current activated between -30 and -20 mV, reached a maximum amplitude at 0 mV (-4.5 +/- 6.0 pA) that increased when Ba(2+) was added to the bath and was blocked by 1 mM Co(2+). Total outward currents were composed of three K(+) currents: a Ca(2+)-activated K(+) current activated between -40 and -30 mV and reached a maximum amplitude at +40 mV (605 +/- 351 pA); a delayed-rectifier K(+) current activated between -30 and -10 mV, had a mean amplitude of 111 +/- 67 pA at +60 mV and was inhibited by 20 mM tetraethylammonium (TEA); and, finally, more than half of ORNs exhibited an A-like current strongly dependent on the holding potential and inhibited by 5 mM 4-aminopyridine (4-AP). Pheromone stimulation evoked inward current as measured by single channel recordings.     

Rrp6p controls mRNA poly(A) tail length and its decoration with poly(A) binding proteins

Poly(A) (pA) tail binding proteins (PABPs) control mRNA polyadenylation, stability, and translation. In a purified system, S. cerevisiae PABPs, Pab1p and Nab2p, are individually sufficient to provide normal pA tail length. However, it is unknown how this occurs in more complex environments. Here we find that the nuclear exosome subunit Rrp6p counteracts the in vitro and in vivo extension of mature pA tails by the noncanonical pA polymerase Trf4p. Moreover, PABP loading onto nascent pA tails is controlled by Rrp6p; while Pab1p is the major PABP, Nab2p only associates in the absence of Rrp6p. This is because Rrp6p can interact with Nab2p and displace it from pA tails, potentially leading to RNA turnover, as evidenced for certain pre-mRNAs. We suggest that a nuclear mRNP surveillance step involves targeting of Rrp6p by Nab2p-bound pA-tailed RNPs and that pre-mRNA abundance is regulated at this level.     

Nuclear magnetic resonance investigation of lysine–oligopeptides and a complex with d(pA)3pGpC(pT)3

We report proton magnetic resonance studies of a series of lysine oligopeptides in H₂O solution. At pH 5 the protonated ε-amino groups are seen as broad resonances; the peptide NH proton resonances are split by spin–spin coupling with the C^α-H proton, and appear at positions which depend on position in the chain and on chain length. Assignments were made by the europium shift method, and we observed the expected effect of catalysis by the terminal —NH₃⁺ of exchange of the adjacent peptide NH. Coupling constants and the temperature coefficient of chemical shift values were consistent with a non-hydrogen-bonded structure for the oligolysines. The rate and mechanism of NH hydrogen exchange were investigated by line-broadening measurements of the peptide protons as a function of pH. Exchange was found to be OH^? catalyzed, with large differences in the rate depending on position in the chain. Preliminary studies of the complex between double-helical d(pA)₃pGpC(pT)₃ and tetra(L -lysine) were performed using ¹H- and ³¹P-nmr techniques. Pmr spectra of the complex at pH values ranging from 3.98 to 8.15 showed very complicated patterns. Downfield shifts and reduction in exchange rates were observed for several tetra(L -lysine) protons. ³¹P-nmr spectra of the complex reveal an upfield shift of 1 ppm for 3′-5′ phosphate diester resonances on complexation. ³¹P T₁ relaxation times change little on complex formation at low temperature but are altered at higher temperature.     

Studies of oligoadenylate formation on a poly(U) template

We have studied a variety of condensation reactions involving poly (U) as template and isomeric adenosine dinucleotides as substrates. We find that [3'-5']-linked dinucleotides such as A3pA and pA3pA are better acceptors than the corresponding [2'-5']-linked compounds, while ImpA2pA is a better donor than ImpA3pA. The reaction between A2pA and ImpA3pA, for example, yields only 4% of product while the reaction of A3pA with ImpA2pA yields 86% of product. The more efficient condensation reactions of dimers are about as efficient as the self-condensation of ImpA. They yield a few percent of material in which five or more substrate molecules are linked together. The percentage of the natural [3'-5']-linkage in the product varies greatly, from as little as 1% to as much as 45%.     

Structure of deoxy hemoglobin C (beta six Glu replaced by Lys) in two crystal forms

Five crystal forms of the abnormal human hemoglobin Hb³ C (beta six Glu → Lys) have been grown. Two of them are grown with liganded Hb C, three with deoxy Hb C. The structures of two of the deoxy crystal forms were determined by the method of molecular replacement, using deoxy Hb A as the model structure. Fourier maps were calculated for each Hb C structure, using data to a resolution of 5 Å in one case and 4 Å in the second case. The structural differences between each deoxy Hb C structure and the deoxy Hb A model are found mostly at the molecular surface. Energetically favorable interactions involving the variant residue, beta six lysine, occur in both Hb C crystal forms, and could explain the lowered solubility and enhanced tendency of deoxy Hb C to crystallize in vivo.     

Oxantel is an N-type (methyridine and nicotine) agonist not an L-type (levamisole and pyrantel) agonist: classification of cholinergic anthelmintics in Ascaris

Three pharmacological subtypes of cholinergic receptors have been distinguished in Ascaris suum using a muscle contraction assay and classical pharmacological techniques. The receptor subtypes are: a B-subtype (sensitive to bephenium); an L-subtype (sensitive to levamisole and pyrantel); and an N-subtype (sensitive to nicotine and methyridine). Oxantel is a cholinergic anthelmintic that was first introduced for the treatment of whipworm, Trichuris, infections in children. Here, we compare the subtype selectivity of oxantel with thenium and other cholinergic anthelmintics. We used the A. suum assay to derive pA(2) values for the agonists: oxantel, thenium, bephenium, levamisole, pyrantel, nicotine and methyridine with the antagonists: paraherquamide, 2-desoxyparaherquamide and methyllycaconitine. pA(2) values, rather than pK(B) values, were determined for all agonists when it was found that Schild slopes for some agonists were significantly less than 1.0. The pA(2) of oxantel was 6.58+/-0.25 for paraherquamide; 5.39+/-0.28 for 2-desoxyparaherquamide; 7.01+/-0.19 for methyllycaconitine. Comparison of pA(2) values using cluster analysis showed that oxantel was grouped with nicotine and methyridine, the N-subtype agonists. Thenium had pA(2)s of 7.84+/-0.41 for paraherquamide; 5.52+/-0.50 for 2-desoxyparaherquamide; 6.33+/-0.19 for methyllycaconitine. Cluster analysis placed thenium between the L-subtype agonists and the B-subtype agonist. The therapeutic significance of classification of cholinergic anthelmintics is discussed. Combination of oxantel and pyrantel would have therapeutic advantages, covering N- and L-subtypes, and so increasing spectrum of action and reducing the potential for development of resistance. Our results predict that oxantel may remain effective in some nematode isolates that have become levamisole- and pyrantel-resistant.     

L-641,953 (R-8-fluoro-dibenzo[b, f]thiepin-3-carboxylic acid-5-oxide): a novel thromboxane-prostaglandin endoperoxide antagonist

The effects of L-641,953 (R-8-fluoro-dibenzo[b, f]thiepin-3-carboxylic acid-5-oxide) have been studied on pulmonary and other smooth muscle preparations in vitro and in vivo. When studied in vitro on guinea-pig tracheal chains, L-641,933 produced significant shifts in the dose-response curves to the prostaglandin endoperoxide analogues, U-44069 (pA2 7.06) and U-46619 (pA2 7.14), and prostaglandin (PG) F2 alpha (pA2 6.33) had minimal activity against contractions induced by histamine (pA2 4.38), 5-hydroxytryptamine (pA2 4.63), and acetylcholine (pA2 4.56) and slightly enhanced relaxation induced by PGE2. When tested on the guinea-pig gall bladder strip in vitro, L-641,953 antagonized contractions induced by U-44069 (pA2 7.03) but was less active against those induced by PGF2 alpha (pA2 6.03), PGE1 (pA2 5.62), and histamine (pA2 4.84). When tested in vitro on the guinea-pig pulmonary artery, L-651-953 significantly antagonized contractions induced by U-44069 (pA2 7.04), U-46619 (pA2 7.14), and PGF2 alpha (pA2 7.16) but was less effective against contractions induced by histamine (pA2 4.19). Schild analysis indicated that L-641,953 was fully competitive against contractions of either the guinea-pig tracheal chain induced by U-46619 or the guinea-pig pulmonary artery induced by U-44069 and U-46619. When tested on human platelets in vitro L-641,953 inhibited aggregation induced by U-44069 (IC50 1.3 X 10(-6) M) but not ADP.(ABSTRACT TRUNCATED AT 250 WORDS)     

Human serum amyloid A (SAA): biosynthesis and postsynthetic processing of preSAA and structural variants defined by complementary DNA

To study structural variants of human serum amyloid A (SAA), an apoprotein of high-density lipoprotein, complementary DNA clones were isolated from a human liver library with the use of two synthetic oligonucleotide mixtures containing sequences that could code for residues 33-38 and 90-95 of the protein sequence. The SAA-specific cDNA clone (pA1) contains the nucleotide sequence coding for the mature SAA and 10 amino acids of the 18-residue signal peptide. It also includes a 70 nucleotide long 3'-untranslated region and approximately 120 bases of the poly(A) tail. The derived amino acid sequence of pA1 is identical with the alpha form of apoSAA1. A fragment of pA1 containing the conserved (residues 33-38) region of SAA also hybridized with RNA from human acute phase liver and acute phase stimulated, but not unstimulated, mouse and rabbit liver. In contrast, a fragment corresponding to the variable region hybridized to a much greater extent with human than with rabbit or murine RNA. Human acute phase liver SAA mRNA (approximately 600 nucleotides in length) directs synthesis of preSAA (Mr 14 000) in a cell-free translating system. In a Xenopus oocyte translation system preSAA is synthesized and processed to the mature Mr 12 000 product. The complete 18 amino acid signal peptide sequence of preSAA was derived from sequencing cDNA synthesized by "primer extension" from the region of SAA mRNA corresponding to the amino terminus of the mature product. Two other SAA-specific cDNA clones (pA6 and pA10) differed from pA1 in that they lack the internal PstI restriction enzyme site spanning residues 54-56 of pA1.(ABSTRACT TRUNCATED AT 250 WORDS)