Affinity chromatography of Drosophila melanogaster ribosomal proteins to 5S rRNA

The binding of Drosophila melanogaster ribosomal proteins to D. melanogaster 5S rRNA was studied using affinity chromatography of total ribosomal proteins (TP80) on 5S rRNA linked via adipic acid dihydrazide to Sepharose 4B. Ribosomal proteins which bound 5S rRNA at 0.3 M potassium chloride and were eluted at 1 M potassium chloride were identified as proteins 1, L4, 2/3, L14/L16, and S1, S2, S3, S4, S5, by two-dimensional polyacrylamide gel electrophoresis. Using poly A-Sepharose 4B columns as a model of non-specific binding, we found that a subset of TP80 proteins is also bound. This subset, while containing some of the proteins bound by 5S rRNA columns, was distinctly different from the latter subset, indicating that the binding to 5S rRNA was specific for that RNA species.     

Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach

To explore the relationship between the assembly of the 30S ribosomal subunit and interactions among the constituent components, 16S RNA and proteins, relative binding free energies of the T. thermophilus 30S proteins to the 16S RNA were studied based on an implicit solvent model of electrostatic, nonpolar, and entropic contributions. The late binding proteins in our assembly map were found not to bind to the naked 16S RNA. The 5' domain early kinetic class proteins, on average, carry the highest positive charge, get buried the most upon binding to 16S RNA, and show the most favorable binding. Some proteins (S10/S14, S6/S18, S13/S19) have more stabilizing interactions while binding as dimers. Our computed assembly map resembles that of E. coli; however, the central domain path is more similar to that of A. aeolicus, a hyperthermophilic bacteria.     

The accessibility of antigenic determinants of ribosomal protein S4 in situ.

Antibodies to Escherichia coli ribosomal protein S4 react with S4 in subribosomal particles, eg, the complex of 16S RNA with S4, S7, S8, S15, S16, S17, and S19 and the RI reconstitution intermediate, but they do not react with intact 30S subunits. Antibodies were isolated by three different methods from antisera obtained during the immunization of eight rabbits. Some of these antibody preparations, which contained contaminant antibodies directed against other ribosomal proteins, reacted with subunits, but this reaction was not affected by removal of the anti-S4 antibody population. Other antibody preparations did not react with subunits. It is concluded that the antigenic determinants of S4 are accessible in some protein deficient subribosomal particles but not in intact 30S subunits.     

Calix[4]arenes containing ferrocene amide as carboxylate anion receptors and sensors

Calix[4]arene derivatives containing amide ferrocene units at the wide rim and ethyl ester groups at the narrow rim, L1-L3, were synthesized and their anion binding and sensing properties were investigated. It was found from (1)H NMR titrations that L1-L3 were able to bind selectively with carboxylate anions. Moreover, cyclic voltammetry and square wave voltammetry showed that L1-L3 were able to act as electrochemical sensors for carboxylate anions. [structure: see text]     

Synthesis of aminodisaccharide-nucleoside conjugates for RNA binding

Two types of aminodisaccharide-nucleoside conjugates were synthesized by the condensation of azidodisaccharide and nucleoside using aliphatic diamine as a linker. The corresponding azidodisaccharides could be yielded from neamine in good yield. The binding properties to 16S RNA of these conjugates were evaluated by SPR. It was found that the nucleobase played a significant role in the binding of these conjugates to 16S RNA and a shorter linker between the aminodisaccharide and nucleoside was favorable for 16S RNA binding.     

Engineering encodable lanthanide-binding tags into loop regions of proteins

Lanthanide-binding tags (LBTs) are valuable tools for investigation of protein structure, function, and dynamics by NMR spectroscopy, X-ray crystallography, and luminescence studies. We have inserted LBTs into three different loop positions (denoted L, R, and S) of the model protein interleukin-1β (IL1β) and varied the length of the spacer between the LBT and the protein (denoted 1?3). Luminescence studies demonstrate that all nine constructs bind Tb3+ tightly in the low nanomolar range. No significant change in the fusion protein occurs from insertion of the LBT, as shown by two X-ray crystallographic structures of the IL1β-S1 and IL1β-L3 constructs and for the remaining constructs by comparing the 1H?15N heteronuclear single-quantum coherence NMR spectra with that of the wild-type IL1β. Additionally, binding of LBT-loop IL1β proteins to their native binding partner in vitro remains unaltered. X-ray crystallographic phasing was successful using only the signal from the bound lanthanide. Large residual dipolar couplings (RDCs) could be determined by NMR spectroscopy for all LBT-loop constructs and revealed that the LBT-2 series were rigidly incorporated into the interleukin-1β structure. The paramagnetic NMR spectra of loop-LBT mutant IL1β-R2 were assigned and the Δχ tensor components were calculated on the basis of RDCs and pseudocontact shifts. A structural model of the IL1β-R2 construct was calculated using the paramagnetic restraints. The current data provide support that encodable LBTs serve as versatile biophysical tags when inserted into loop regions of proteins of known structure or predicted via homology modeling.     

The 3′-End of tRNA and Its Role in Protein Biosynthesis

In the course of protein biosynthesis, the 3′-ends of aminoacyl-tRNA (aa-tRNA) and peptidyl-tRNA specifically interact with macromolecules of the protein biosynthesis machinery. The 3′-end of tRNA consists of an invariant C-C-A single strand. Interaction of the aminoacyl-tRNA 3′-end with elongation factor Tu (EF-Tu) containing bound GTP is necessary for the formation of the aa-tRNA·EF-Tu·GTP complex and, after the complex binds to the ribosome, for the GTP hydrolysis. This process is followed by the specific binding of the aminoacyl-tRNA 3′-end to the aminoacyl (A) site of the ribosome. In this review, a model is proposed that involves Watson-Crick base pairing of the C? C sequence of the aminoacyl-tRNA 3′-end with a specific G? G sequence of the ribosomal 23S RNA. Similarly, peptidyl-tRNA binds with its 3′-end to the peptidyl (P) site of the ribosome. This binding may also involve Watson-Crick base pairing of the C-C-A sequence with a complementary sequence of 23S RNA. It is proposed that peptide bond formation is catalyzed by a functional site of the 23S RNA located near the 3′-ends of aminoacyl-tRNA and peptidyl-tRNA. A model is suggested in which two loops of the 23S RNA, brought into close proximity via folding, are involved both in binding the 3′-ends of the tRNAs and in catalyzing peptide bond formation. This model presumes a dynamic structure for ribosomal RNA, which is modulated by interaction with elongation factors and ribosomal proteins.     

Three-dimensional electron cryomicroscopy of ribosomes

Single particle electron cryomicroscopy is nowadays routinely used to generate three-dimensional structural information of ribosomal complexes without the need of crystallization. A large number of structures of functional important ribosomal complexes have thus been determined using this technique. In E. coli 70S ribosomes all three tRNA binding sites could be localized. The ternary complex of EF-TutRNAGTP that delivers the tRNA to the ribosome was directly visualized in a ribosomal complex blocked by the antibiotic kirromycin. Three different functional states of translocation have been studied and the respective EF-G binding sites have been mapped. The level of resolution achievable with electron cryomicroscopy allows conformational changes in the domain structures of elongation factors to be modelled in terms of rigid body movements. Structural information on eukaryotic ribosomes is also available for yeast and mammalian 80S ribosomes. The structural differences between rabbit 80S and E. coli 70S ribosomes could be interpreted in terms of ribosomal RNA expansion segments in the 18S and 23S RNA. The EF-G homologue EF2 was mapped analysing the structure of an 80SEF2sodarin complex and most recently the binding of a hepatitis C virus IRES element to a yeast 40S subunit has been studied. The first electron cryomicroscopical 3D reconstructions have further been used to overcome the initial phasing problems in X-ray crystallographic studies of the ribosome facilitating structure determination of the recent atomic resolution structures of the 30S and 50S ribosomal subunits. In turn, the knowledge of the atomic structure of the ribosome makes detailed interpretations of cryo-EM maps possible at approximately 20 A resolution.     

Structural basis for contrasting activities of ribosome binding thiazole antibiotics

Thiostrepton and micrococcin inhibit protein synthesis by binding to the L11 binding domain (L11BD) of 23S ribosomal RNA. The two compounds are structurally related, yet they produce different effects on ribosomal RNA in footprinting experiments and on elongation factor-G (EF-G)-dependent GTP hydrolysis. Using NMR and an assay based on A1067 methylation by thiostrepton-resistance methyltransferase, we show that the related thiazoles, nosiheptide and siomycin, also bind to this region. The effect of all four antibiotics on EF-G-dependent GTP hydrolysis and EF-G-GDP-ribosome complex formation was studied. Our NMR and biochemical data demonstrate that thiostrepton, nosiheptide, and siomycin share a common profile, which differs from that of micrococcin. We have generated a three-dimensional (3D) model for the interaction of thiostrepton with L11BD RNA. The model rationalizes the differences between micrococcin and the thiostrepton-like antibiotics interacting with L11BD.     

Sequence of the amino-terminal region of rat liver ribosomal proteins S4, S6, S8, L6, L7a, L18, L27, L30, L37, L37a, and L39.

The sequence of the amino-terminal region of eleven rat liver ribosomal proteins--S4, S6, S8, L6, L7a, L18, L27, L30, L37a, and L39--was determined. The analysis confirmed the homogeneity of the proteins and suggests that they are unique, since no extensive common sequences were found. The N-terminal regions of the rat liver proteins were compared with amino acid sequences in Saccharomyces cerevisiae and in Escherichia coli ribosomal proteins. It seems likely that the proteins L37 from rat liver and Y55 from yeast ribosomes are homologous. It is possible that rat liver L7a or L37a or both are related to S cerevisiae Y44, although the similar sequences are at the amino-terminus of the rat liver proteins and in an internal region of Y44. A number of similarities in the sequences of rat liver and E coli ribosomal proteins have been found; however, it is not yet possible to say whether they connote a common ancestry.     

Synthesis and biological evaluation of novel neamine-nucleoside conjugates potentially targeting to RNAs

Eighteen novel neamine-nucleoside conjugates with ethylenediamine-lysine or ethylenediamine-arginine as the linker were synthesized and their potential binding to A site of 16S RNA and TAR RNA was evaluated using SPR (surface plasmon resonance). Compared with neamine, compounds 10i and 10q show 6.3 and 4.8 times potential in binding to A site of 16S RNA and eight and six times potential in binding to TAR RNA, respectively. According to the data of SPR, it indicates that amino acid residue and nucleobase moieties of the designed neamine-nucleosides conjugates exhibit the important contributions for the binding to A site of 16S RNA and TAR RNA. The molecular docking study on the interaction between the ligands and A site of 16S RNA is in agreement with the experimental data. The novel type of modification may provide a promising way for the development of neamine derivatives effectively targeting to RNAs.     

Homogenous time resolved fluorescence assay to identify modulators of cap-dependent translation initiation

Eukaryotic initiation factor (eIF) 4F plays a key role in recruiting 40S ribosomes and associated factors to mRNA templates during translation initiation. The function of this heterotrimeric complex is to deliver an RNA helicase to the 5' cap proximal region of mRNAs in preparation for ribosome binding. To study the interaction between subunits of this complex, as well as identify small molecules that could interfere with their association, we developed a time resolved fluorescence assay that allows monitoring of interactions between two subunits of eIF4F. We have performed a small molecule chemical screen of >73,000 compounds using this assay.     

Selection of peptides targeting helix 31 of bacterial 16S ribosomal RNA by screening M13 phage-display libraries

Ribosomal RNA is the catalytic portion of ribosomes, and undergoes a variety of conformational changes during translation. Structural changes in ribosomal RNA can be facilitated by the presence of modified nucleotides. Helix 31 of bacterial 16S ribosomal RNA harbors two modified nucleotides, m2G966 and m?C967, that are highly conserved among bacteria, though the degree and nature of the modifications in this region are different in eukaryotes. Contacts between helix 31 and the P-site tRNA, initiation factors, and ribosomal proteins highlight the importance of this region in translation. In this work, a heptapeptide M13 phage-display library was screened for ligands that target the wild-type, naturally modified bacterial helix 31. Several peptides, including TYLPWPA, CVRPFAL, TLWDLIP, FVRPFPL, ATPLWLK, and DIRTQRE, were found to be prevalent after several rounds of screening. Several of the peptides exhibited moderate affinity (in the high nM to low μM range) to modified helix 31 in biophysical assays, including surface plasmon resonance (SPR), and were also shown to bind 30S ribosomal subunits. These peptides also inhibited protein synthesis in cell-free translation assays.     

Specificity of aminoglycoside antibiotics for the A-site of the decoding region of ribosomal RNA

Background: Aminoglycoside antibiotics bind to the A-site of the decoding region of 16S RNA in the bacterial ribosome, an interaction that is probably responsible for their activity. A detailed study of the specificity of aminoglycoside binding to A-site RNA would improve our understanding of their mechanism of antibiotic activity.Results: We have studied the binding specificity of several aminoglycosides with model RNA sequences derived from the 16S ribosomal A-site using surface plasmon resonance. The 4,5-linked (neomycin) class of aminoglycosides showed specificity for wild-type A-site sequences, but the 4,6-linked class (kanamycins and gentamicins), generally showed poor specificity for the same sequences. Methylation of a cytidine in the target RNA, as found in the Escherichia coli ribosome, had negligible effects on aminoglycoside binding.Conclusions: Although both 4,5- and 4,6-linked aminoglycosides target the same ribosomal site, they appear to bind and effect antibiotic activity in different manners. The aminoglycosides might recognize different RNA conformations or the interaction might involve different RNA tertiary structures that are not equally sampled in our ribosome-free model. These results imply that models of ribosomal RNA must be carefully designed if the data are expected to accurately reflect biological activity.     

Ruthenium complexes with chiral tetradentate imino-sulfoxide ligands

Treatment of 2-(methylsulfinyl)benzaldehyde (1) with ethylenediamine or (1R,2R)-(-)-1,2-diaminocyclohexane afforded N,N'-bis[2-(methylsulfinyl)benzylidene]ethylenediamine (L(1)) or (1R,2R)-N,N'-bis[2-(methylsulfinyl)benzylidene]-1,2-cyclohexanedia mine (L(2)), respectively. Lithiation of 2-bromobenzaldehyde diethylacetal with n-BuLi/TMEDA followed by reaction with (1R,2S,5R)-(-)-menthyl-(S)-p-toluenesulfinate afforded 2-(S)-(p-tolylsulfinyl)benzaldehyde diethyl acetal (2). Deprotection of 2 with pyridinium tosylate followed by condensation with ethylenediamine, (1R,2R)-(-)-diaminocyclohexane, or (S,S)-(+)-diaminocyclohexane afforded N,N'-bis[2-(S)-(p-tolylsulfinyl)benzylidene]ethylenediamine (L(3)), (1R,2R)-N,N'-bis[2-(S)-(p-tolylsulfinyl)benzylidene]-1,2-cyclohexanediamine ((R,R)-L(4)), or (S,S)-N,N'-bis[2-(S)-(p-tolylsulfinyl)benzylidene]-1,2-cyclohexanediamine ((S,S)-L(4)), respectively. Treatment of [Ru(PPh(3))(3)Cl(2)] with L afforded trans-[Ru(L)Cl(2)] [L = L(1) (3), L(2) (4), L(3) (5), (R,R)-L(4) ((R,R)-6), (S,S)-L(4) ((S,S)-6)]. The X-ray structures of (S(S),R(S))-4, (R,R)-6, and (S,S)-6 have been determined. The average Ru-N, Ru-S, and Ru-Cl distances in (S(S),R(S))-4 are 2.063, 2.2301, and 2.4039 A, respectively. The corresponding distances in (R,R)-6 are 2.071, 2.256, and 2.411 A, and those in (S,S)-6, 2.058, 2.2275, and 2.3831 A. Compound 3 exhibited a reversible Ru(III/II) couple at 0.56 V vs Cp(2)Fe(+/0) in CH(2)Cl(2). Treatment of 3 with AgNO(3) in water afforded the aqua compound trans-[Ru(L(1))Cl(H(2)O)][PF(6)] (7), which has been characterized by X-ray crystallography. The Ru-Cl, Ru-O, average Ru-N, and average Ru-S distances in 7 are 2.3733(6), 2.1469(16), 2.071, and 2.2442 A, respectively. Treatment of 3 with AgNO(3) followed by reaction with PPh(3) afforded [Ru(L(1))(PPh(3))(2)][PF(6)](2) (8). Treatment of [Os(PPh(3))(3)Cl(2)] with L(1) resulted in deoxygenation of one sulfoxide group of L(1) and formation of [Os(L(5))Cl(2)(PPh(3))] (9) (L(5) = N-[2-(methylsulfinyl)benzylidene]-N'-[2-(methylthio)benzylididene]ethylenediamine), which has been characterized by X-ray crystallography. The average Os-S(O), Os-N(trans to P), Os-N(trans to S), Os-P, and Os-Cl distances are 2.1931, 2.085, 2.175, 2.3641, and 2.4266 A, respectively.     

Macrocyclic nickel(II) complexes coligated by hydrosulfide and hexasulfide ions: syntheses, structures, and magnetic properties of [NiII2L(mu-SH)]+ and [(LNiII2)2(mu-S6)]2+

The borohydride complex [Ni(II)2L(mu-BH4)]+ (3) where L(2-) represents a sterically demanding hexaaza-dithiophenolate ligand reacts rapidly with elemental sulfur in acetonitrile at ambient temperature to produce the cationic complexes [Ni(II)2L(mu-SH)]+ (4) and [(Ni(II)2L) 2(mu-S6)]2+ (6). Both complexes were isolated as ClO4(-) or BPh4(-) salts and characterized by IR and UV/vis spectroscopy and X-ray crystallography. Complex 4 (also accessible from [Ni(II)2L(ClO4)]+ (5) and Na2S.9H2O) features an unprecedented N3Ni(II)(mu-SR)2(mu-SH)Ni(II)N3 core structure, the hydrosulfide ligand being deeply buried in the binding-cavity of the bowl-shaped [Ni(II)2L]2+ complex. In 6, a helical S6(2-) chain, with a structure reminiscent to that of plastic sulfur, is almost completely encapsulated by two [Ni(II)2L]2+ subunits. In contrast to other triply sulfur-bridged N3Ni(II)(SR)3Ni(II)N3 structures whose ground states are typically of S = 0, 4 reveals an S = 2 ground-state which is attained by a ferromagnetic exchange interaction between the two Ni(II) (S = 1) ions ( J = 18 cm (-1), H = -2JS1S2). Intradimer ferromagnetic exchange interactions are also present in 6 ( J = 23 cm (-1)). A qualitative explanation for this difference is offered.     

MCSS-based predictions of RNA binding sites

The diversity of RNA tertiary structures provides the basis for specific recognition by proteins or small molecules. To investigate the structural basis and the energetics which control RNA-ligand interactions, favorable RNA binding sites are identified using the MCSS method, which has been employed previously only for protein receptors. Two different RNAs for which the structures have been determined by NMR spectroscopy were examined: two structures of the TAR RNA which contains an arginine binding site, and the structure of the 16S rRNA which contains an aminoglycoside binding site (paromomycin). In accord with the MCSS methodology, the functional groups representing the entire ligand or only part of it (one residue in the case of the aminoglycosides) are first replicated and distributed with random positions and orientations around the target and then energy minimized in the force field of the target RNA. The Coulombic term and the dielectric constant of the force field are adjusted to approximate the effects of solvent-screening and counterions. Optimal force field parameters are determined to reproduce the binding mode of arginine to the TAR RNA. The more favorable binding sites for each residue of the aminoglycoside ligands are then calculated and compared with the binding sites observed experimentally. The predictability of the method is evaluated and refinements are proposed to improve its accuracy. Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 7 December 1998