Interaction of intracellular RNAase from Aspergillus clavatus with derivatives of its substrates]

Using spectrophotometric and kinetic methods and also the methods of protection of Aspergillus clavatus RNAse (EC 3.1.4.23) by adenine nucleotides and their components against inactivation by means of acylation or heating, it was found that RNAse-nucleotide complex was formed by association of one enzyme molecule with one nucleotide molecule. It was also shown that all components of nucleotides (base, ribose and phosphate) take part in the formation of such complex and the removal of one of them (base or phosphate) lead to loosening of bindings of remaining fragments (ribose-5'-monophosphate, adenine) with the active site of RNAse, and to disappearance of bends within the pH range of 3.0-4.0 on the plot of pKi (5'-MP) versus pH, within the pH range of 5.5-7.0 on the plot of oKi (Ado) versus pH. The possibility of participation of associative pair RNAse imidasole groups - nucleotide phosphate groups and RNAse carboxylic group - nucleotide base in the mechanism of formation of enzyme-nucleotide (enzyme-substrate) complexes is postulated.     

Assessing Dissimilarity of Genes by Comparing Their Rnase a Mismatch Cleavage Patterns

We propose a simple algorithm for estimating the number of nucleotide differences between a pair of RNA or DNA sequences through comparison of their RNAse A mismatch cleavage patterns. In the RNAse A mismatch cleavage technique two or more sample sequences are hybridized to the same RNA probe, the hybrids are partially digested with RNAse A, and the digestion products are compared on an electrophoretic gel. Here we provide an algorithm for converting the numbers of unique and matching electrophoretic bands into an estimate of the number of nucleotide differences between the sequences. Computer simulation indicates that the proposed method yields a robust estimate of the genetic distance despite stochastic errors and occasional violation of certain assumptions. Our study suggests that the method performs best when the distance between the sequences is <15 differences. When the sequences under analysis are likely to have larger distances, we advise to substitute one long riboprobe with a set of shorter nonoverlapping probes. The new algorithm is applied to infer the proximity of several strains of pseudorabies virus.     

Inhibitory effects of RraA and RraB on RNAse E-related enzymes imply conserved functions in the regulated enzymatic cleavage of RNA

RraA and RraB are recently discovered protein inhibitors of RNAse E, which forms a large protein complex termed the degradosome that catalyzes the initial step in the decay and processing of numerous RNAs in Escherichia coli . Here, we report that these E. coli protein inhibitors physically interact with RNAse ES, a Streptomyces coelicolor functional ortholog of RNAse E, and inhibit its action in vivo as well as in vitro ; however, unlike their ability to differentially modulate E. coli RNAse E action in a substrate-dependent manner by altering the composition of the degradosome, both proteins appear to have a general inhibitory effect on the ribonucleolytic activity of RNAse ES, which does not interact with E. coli polynucleotide phosphorylase, a major component of the degradosome. Our findings suggest that these regulators of RNAse activity have a conserved intrinsic property enabling them to directly act on RNAse E-related enzymes and inhibit their general ribonucleolytic activity.     

A conformational change in E. coli DNA polymerase I (Klenow fragment) is induced in the presence of a dNTP complementary to the template base in the active site

It is well established that the insertion of a nucleotide into a growing DNA chain requires a conformational change in the structure of a DNA polymerase. These enzymes have been shown to bind a primer-template in the open conformation and then upon binding of a complementary dNTP undergo a conformational rearrangement to the closed ternary complex. This movement results in the positioning of the incoming nucleotide in the proper geometry for the nucleophilic attack by the 3'-hydroxyl of the primer. In this work, tryptic digestion experiments were performed to detect this conformational change in the structure of the exonuclease-deficient DNA polymerase I (Klenow fragment). Three distinct digestion patterns were observed: one for the polymerase alone, one for the binary complex with the primer-template, and one for the ternary polymerase-DNA-dNTP complex. The latter conformational change leads to a stable ternary closed complex formation only when the correct nucleotide is present in the reaction mixture. Positioning of nucleotides with incorrect geometry in the protein active site inhibits or eliminates formation of the closed complex. Similarly, this conformational change is inhibited when the primer terminus of the DNA molecule is altered by the presence of the 2'-hydroxyl.     

Conformation properties and enzymatic activity of pancreatic ribonuclease in soluble complexes with sodium dextran sulfate

Effect of complex formation with dextran sulfate (DS) (substitution degree 1.3, molecular mass 500 thousand) on RNAse enzymic activity. its spatial structure and conformation stability was studied. Hydrolytic activity of the enzyme in complex in inhibited already at small additions of DS, while the transferase one is changed only at a great excess of the polyelectrolyte. It has been shown by CD spectra that no notable conformation changes proceed in the enzyme during complex formation, although the enzyme turns destabilized to the denaturing effect of heat at the expense of strengthened interactions between DS and RNAse during its denaturation. Thus the inhibition of hydrolytic activity in the complex is primarily related to limitations for the formation of the enzyme-substrate complex on polyelectrolyte charged likely with the substrate, and not to the protein conformation changes.     

An intracellular inhibitory activity of RNase secreted by Bacillus intermedius

Bacillus intermedius cells producing extracellular RNAse were found to contain its inhibitor and an RNAse-inhibitor complex. Bacillus subtilis and Escherichia coli cell lysates did not inhibit the activity of homogeneous extracellular RNAse produced by B. intermedius. The inhibitor was shown to be specific for this RNAse and did not interact with other RNAses. As was demonstrated by biochemical tests and electrophoretic analysis, the inhibitor is released when the protoplasts are disintegrated, i.e. it is located in the cytoplasm. A correlation has been established between the biosynthesis of extracellular RNAse and its intracellular inhibitor.     

Activation of ras p21 transforming properties associated with an increase in the release rate of bound guanine nucleotide.

An Ala-to-Thr substitution at position 59 activates the transforming properties of the p21ras protein without impairment of GTPase activity, a biochemical alteration associated with other activating mutations. To investigate the basis for the transforming properties of the Thr-59 mutant, we characterized guanine nucleotide release. This reaction exhibited a slow rate and stringent temperature requirements. To further dissect the release reaction, we used monoclonal antibodies directed against different epitopes of the p21 molecule. One monoclonal specifically interfered with nucleotide release, while others which recognized different regions of the molecule blocked nucleotide binding. Mutants with the Thr-59 substitution exhibited a three- to ninefold-higher rate of GDP and GTP release than normal p21 or mutants with other activating lesions. This alteration in the Thr-59 mutant would have the effect of increasing its rate of nucleotide exchange. In an intracellular environment with a high GTP/GDP ratio, this would favor the association of GTP with the Thr-59 mutant. Consistent with knowledge of known G-regulatory proteins, these findings support a model in which the p21-GTP complex is the biologically active form of the p21 protein.     

Photo-oxidation and carboxymethylation of guanylribonuclease Pch1]

The effect of photo-oxidation and carboxymethylation on the activity of RNAse Pch1 has been studied. Photoinactivation in the presence of rose bengal results in a selective oxidation of two histidine residues. The process is inhibited by the nucleotide substrate analogs. This suggests that one or two imidazole groups may be localized in the active site of RNAse Pch1. The pH dependence of the enzyme inactivation by bromoacetic acid is indicative of the contribution of a functional group with pKa 4,0, presumably of a beta- or gamma-carboxyl group of dicarbonic amino acid. The reaction is inhibited by the substrate analogs 2'(3')-GMP and 2'(3')-AMP. The data on the similarity of active sites in several guanyloribonucleases are discussed.     

Nucleotide binding by TAP mediates association with peptide and release of assembled MHC class I molecules

Background: Newly synthesised peptide-receptive major histocompatibility complex (MHC) class I molecules form a transient loading complex in the endoplasmic reticulum with the transporter associated with antigen processing (TAP) and a set of accessory proteins. Binding of peptide to the MHC class I molecule is necessary for dissociation of the MHC class I molecule from the complex with TAP, but other components of the complex might also be involved. To investigate the role of TAP in this process, mutations that block nucleotide binding were introduced into the ATP-binding site of TAP.Results: Mutant TAP formed apparently normal loading complexes with MHC class I molecules and accessory components, but had no nucleotide-binding or peptide-transport activity. Nevertheless, whereas wild-type loading complexes in detergent lysates could be dissociated by addition of peptides that bind MHC class I molecules, mutant complexes could not be dissociated in this way. Depletion of nucleotide diphosphates or triphosphates from wild-type lysates blocked peptide-mediated dissociation of MHC class I molecules, which could be reversed by readdition of nucleotide diphosphates or triphosphates. Complexes between mutant TAP and MHC class I molecules remained associated in vivo until they were degraded. Disruption of nucleotide binding also eliminated TAP's peptide-binding activity.Conclusions: Peptide-mediated dissociation of the MHC class I molecule from the loading complex depends on conformational signals arising from TAP. Integrity of the nucleotide-binding site is required not only for transmission of this conformational signal to the loading complex, but also for binding of peptide to TAP. Thus, the dynamic activity of the loading complex is synchronised with the nucleotide-mediated peptide-binding and transport cycle of TAP.     

The presence of two UvrB subunits in the UvrAB complex ensures damage detection in both DNA strands

It is generally accepted that the damage recognition complex of nucleotide excision repair in Escherichia coli consists of two UvrA and one UvrB molecule, and that in the preincision complex UvrB binds to the damage as a monomer. Using scanning force microscopy, we show here that the damage recognition complex consists of two UvrA and two UvrB subunits, with the DNA wrapped around one of the UvrB monomers. Upon binding the damage and release of the UvrA subunits, UvrB remains a dimer in the preincision complex. After association with the UvrC protein, one of the UvrB monomers is released. We propose a model in which the presence of two UvrB subunits ensures damage recognition in both DNA strands. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one of the UvrB monomers, which will subsequently probe one of the DNA strands for the presence of a lesion. When no damage is found, the DNA will wrap around the second UvrB subunit, which will check the other strand for aberrations.     

Small-angle neutron scattering study of the association between porcine pancreatic colipase and taurodeoxycholate micelles

Small-angle neutron scattering studies have shown the association of porcine colipase with bile salts micelles to be a lateral one. The molecular structure parameters of the individual components were determined first. A radius of gyration of 13.9 Å is found for colipase, which implies a non-spherical shape for this molecule. The size of taurodeoxycholate micelles is controlled by the ionic strength of the solution. In 0.15 m-NaCl their volume is comparable to that of colipase; they are elongated with an axial ratio of about 2. At higher ionic strengths the elongation of the micelles increases.In 0.15 m-NaCl the complex is found to be an association of one colipase molecule with a volume of detergent corresponding to that of one free micelle. The contrast variation study of the radius of gyration shows that in the complex the centre of masses of the protein and of the detergent are well-separated: a distance between 29 and 45 Å has been estimated. The value of the radius of gyration of the complex at high contrast, and the agreement between the contrast variation analysis and a straightforward application of the parallel axes theorem indicate that the complex is formed by the juxtaposition of the protein and a preformed micelle, which has approximately the same size and shape as a free micelle. There is only one localized surface contact between the protein and the micelle, which implies that colipase possesses a relatively well-defined binding site.     

Kinetics of interaction of 2-amino-6-mercapto-9-beta-ribofuranosylpurine 5'-triphosphate with bovine brain tubulin

The binding of the guanine nucleotide analogue 2-amino-6-mercapto-9-beta-ribofuranosylpurine 5'-triphosphate (S6-GTP) to tubulin from which the associated proteins and exchangeably bound nucleotide have been removed produces about a 15% decrease in intrinsic tubulin fluorescence. Using a fluorescence stopped-flow technique, we have examined the kinetics and mechanism of this process. Analysis of the data reveals that the binding is complex, involving at least one conformational change subsequent to nucleotide binding. The bimolecular association rate constant for binding of S6-GTP to tubulin is approximately 6 X 10(5) M-1 s-1, suggesting that the orientation requirements are stringent. The kinetic parameters for dissociation of GDP, S6-GTP, and S6-GDP from the exchangeable nucleotide binding site have also been determined. S6-GDP and GDP were found to have comparable rates of dissociation; S6-GTP dissociated approximately twice as slowly as either GDP or S6-GDP. Glycerol produces a significant decrease in the rates of nucleotide dissociation. The mechanism whereby glycerol produces such an effect is not known; however, it may involve slight changes in the conformation of the tubulin protomer.     

Molecular organization of the uvomorulin-catenin complex

The Ca(2+)-dependent cell adhesion molecule uvomorulin is a member of the cadherin gene family. Its cytoplasmic region complexes with structurally defined proteins termed alpha-, beta-, and gamma-catenins. Here we show that A-CAM (N-cadherin), another member of this gene family, also associates with catenins suggesting that this complex formation may be a general property of the cadherins. For uvomorulin it has been found that this association with catenins is of crucial importance for the adhesive function, but little is known about the molecular organization of the uvomorulin-catenin complex. Using a combination of biochemical analyses we show that a single complex is composed of one molecule of uvomorulin, one or two molecules of beta-catenin, and one molecule of alpha-catenin. Furthermore, beta-catenin seems to interact more directly with uvomorulin. In pulse-chase experiments beta-catenin is already associated with the 135-kD uvomorulin precursor molecule but the assembly of the newly synthesized alpha-catenin into the complex is only detected around the time of endoproteolytic processing.     

Reactions of the amino groups of RNAse A: III. The existence of pH-dependent values of pK

The rates of the trinitrophenylation of the amino groups of ribonuclease A (RNAse) with the specific reagent trinitrobenzene sulfonic acid have been studied at 27°C, between pH 7.0 and 9.9. From the variation of the velocity constants with pH it has been shown that the reaction is biphasic in the sense that for each amino group two pKs have been found: one (pK = 7.3–7.52) in the range of pH between 7.0 and 8.3 and the other (pK = 9.28–9.69) in the pH range 8.5–9.9. It is pointed out that when the experimental conditions approached one another, there was agreement between the pK values obtained from titrimetric and kinetic studies. Evidence is presented from the literature concerning the validity of the pK value near 7.5 for the ε-amino groups in RNAse. The studies were repeated with performic acid oxidized RNAse and the 10 ε-amino groups were found to be monophasic with pK values between 8.01 and 8.10. The α-amino group of the N-terminal lysine was biphasic with a pK of 7.26 (pH range 7–8) and 8.13 (pH range 8.2–9.5).     

Ribonuclease of Bacillus intermedius 7 P. Purification by chromatography on phosphocellulose and several characteristics of the homogeneous enzyme]

A new procedure for isolation of homogenous ribonuclease of Bac. intermedius from a commercial source is described. The yields of 140 mg of RNAse from 200 g of the enzymic powder were attained. The amino acid composition of the enzyme was determined. The RNAse contains neither the sulfhydryl groups nor the disulfide bonds and has only one histidine residue. At the same time the amount of aromatic amino acid residues is relatively high. The enzyme is highly resistant to heat and acid treatment but is less stable in an alkaline solution. The pH optimum of the RNAse for the RNA digestion is 8,5; the temperature optimum for this reaction is 37 degrees. A spectrophotometric method for the RNAse activity assay using polyA as a specific substrate was developed. The purified product provides a suitable starting material for structural studies.     

The human T-cell lymphotropic virus type-I dimerization initiation site forms a hairpin loop, unlike previously characterized retroviral dimerization motifs

The formation of genomic RNA dimers during the retroviral life cycle is essential for optimal viral replication and infectivity. The sequences and RNA structures responsible for this interaction are located in the untranslated 5' leader RNA, along with other cis-acting signals. Dimer formation occurs by specific interaction between identical structural motifs. It is believed that an initial kissing hairpin forms following self-recognition by autocomplementary RNA loops, leading to formation of an extended stable duplex. The dimerization initiation site (DIS) of the deltaretrovirus human T-cell lymphotropic virus type-I (HTLV-I) has been previously localized to a 14-nucleotide sequence predicted to contain an RNA stem loop. Biochemical probing of the monomeric RNA structure using RNAse T1, RNAse V1, RNAse U2, lead acetate, and dimethyl sulfate has led to the generation of the first structural map of the HTLV-I DIS. A comprehensive data set of individual nucleotide modifications reveals that the structural motif responsible for HTLV-I RNA dimerization forms a trinucleotide RNA loop, unlike any previously characterized retroviral dimerization motif. Molecular modeling demonstrates that this can be formed by an unusual C:synG base pair closing the loop. Comparative phylogeny indicates that such a motif may also exist in other deltaretroviruses.     

The transitory complex between photoexcited rhodopsin and transducin. Reciprocal interaction between the retinal site in rhodopsin and the nucleotide site in transducin

In the first step of the visual transduction cascade a photoexcited rhodopsin molecule, R*ret, binds to a GDP-carrying transducin molecule, TGDP. The R*-T interaction causes the opening of the nucleotide site in T and catalyzes the GDP/GTP exchange by allowing the release of the GDP. We have studied the influences on this R*-T transitory complex of the occupancies of the nucleotide site in T and the retinal site in rhodopsin. After elimination of the GDP released from the bound transducin, the complex, named R*ret-te (ret for retinal present, e for nucleotide site empty) remains stabilized almost indefinitely in a medium whose ionic composition is close to physiological. In this complex the bound Te retains a lasting ability to interact with GDP or GTP, and R*ret remains spectroscopically in the meta-II state, by contrast with free R*ret which decays to opsin and free retinal. Hence the R*-T interaction which opens the nucleotide site in T conversely blocks the retinal site in R*ret. Upon prolonged incubation in a low-ionic-strength medium the R*ret-Tc complex dissociates partially, but the liberated Te is then unable to rebind GDP or GTP, even in the presence of R*ret, it is probably denaturated. Upon treatment of the R*ret-Te complex by a high concentration of hydroxylamine, the retinal can be removed from the rhodopsin. The Re-Te complex remains stable and the complexed transducin keeps its capacity to bind GTP. TGTP then dissociates from Re. The liberated Re loses its capacity to interact with a new transducin. These data are integrated into a discussion of the development of the cascade. We stress that affinities, i.e. dissociation equilibrium constants, are insufficient to describe the flow of reactions triggered by one R*ret molecule. It depends on a few critical rapid binding and dissociation processes, and is practically insensitive to other slow ones, hence to the values of affinities that express only the ratio of kinetics constants. The effect of the R*-T interaction on the retinal site in rhodopsin is analogous to the effect of the binding of a G-protein on the apparent affinity of a receptor for its agonist.     

RNA interference: past, present and future

RNA interference (RNAi) is the sequence-specific gene silencing induced by double-stranded RNA. RNAi is mediated by 21-23 nucleotide small interfering RNAs (siRNAs) which are produced from long double-stranded RNAs by RNAse II-like enzyme Dicer. The resulting siRNAs are incorporated into a RNA-induced silencing complex (RISC) that targets and cleaves mRNA complementary to the siRNAs. Since its inception in 1998, RNAi has been demonstrated in organisms ranging from trypanosomes to nematodes to vertebrates. Potential uses already in progress include the examination of specific gene function in living systems, the development of anti-viral and anti-cancer therapies, and genome-wide screens. In this review, we discuss the landmark discoveries that established the contextual framework leading up to our current understanding of RNAi. We also provide an overview of current developments and future applications.     

Crystal structures and spectroscopic studies of ternary compounds of Ni(II) with ethylenediamine and 5'GMP and 5'IMP

Two metal complexes [Ni(en)5'GMPH)2(H2O)2] (en).6.5H2O and [Ni(en)(5'IMPH)2(H2O)2].13H2O have been synthesized in the form of suitable crystals for x-ray crystallography (en = ethylenediamine, 5'GMP = guanosine 5'-monophosphate, 5'IMP = inosine 5'-monophosphate). The 5'GMP complex crystallizes in a monoclinic space group P21 (Z = 4) with a = 12.317(2), b = 28.417(4), c = 12.290(2)A, beta (deg) = 89.59(2). The 5'IMP complex is tetragonal, space group P4122 (Z = 4), with a = 12.119(3), b = 12.119(3), c = 28.560(4)A, beta (deg) = 90.0. The crystal structures of both complexes were refined from diffractometer data to conventional R values of 0.073 for the 5'GMP compound (5,284 observed reflections, 1,322 variables) and 0.030 for the 5'-IMP compound (1,529 observed reflections, 296 variables). In both structures, the Ni(II) is surrounded by two water molecules, one chelate ethylenediamine, and two nucleotide molecules. The synthesis was carried out from Ni(en)2Cl2.0.5H2O and the nucleotide in water medium. The dimer structure of the initial complex is broken, and one ethylenediamine is substituted by two molecules of the nucleotide with the N(7) of the purine ring in cis-position. Differences between both structures are largely due to retention in the structure or loss of the en molecule substituted and to the intermolecular hydrogen bonds of the en molecule coordinated. A third complex of composition [Ni(en)(5'IMPH)2(H2O)2] (en).6H2O similar to the 5'GMP complex has been obtained in the form of blue crystals, but unfortunately its crystal structure failed to be refined. This complex is isostructural with the monoclinic one.