[Modification of the 5' End of mRNA Leader Sequence Alters the Set of Initiation Factors Essential for Initiation of Translation].

The abundance of noncanonical mechanisms of eukaryotic initiation of translation indicates their involvement in the regulation of protein synthesis during key events in a cell life. One of the well-known examples of a noncanonical cap-independent process is the initiation of translation of mRNA with the 5'-untranslated (leader) region of the messenger encoding for the photoprotein obelin (the obelin leader). In the present work, mRNA with the obelin leader was modified by adding 45 deoxycytidyl nucleotides and a fluorescent label to its 5'end. Formation of the 48S ribosomal initiation complexes at the start codon of the modified mRNA was studied using primer extension inhibition (toeprinting). In contrast to mRNA with the intact obelin leader, translation initiation of which strictly requires the eIF4F factor, initiation on the modified mRNA can take place in the absence of this factor, although with less efficiency. The finding thus indicates the unknown function of the eIF4F factor in the first step(s) of mRNA recognition by ribosomal subunits.

Trigger factor assists the refolding of heterodimeric but not monomeric luciferases.

The refolding of thermally inactivated protein by ATP-independent trigger factor (TF) and ATP-dependent DnaKJE chaperones was comparatively analyzed. Heterodimeric (αß) bacterial luciferases of Aliivibrio fischeri, Photobacterium leiognathi, and Vibrio harveyi as well as monomeric luciferases of Vibrio harveyi and Luciola mingrelica (firefly) were used as substrates. In the presence of TF, thermally inactivated heterodimeric bacterial luciferases refold, while monomeric luciferases do not refold. These observations were made both in vivo (Escherichia coli ΔdnaKJ containing plasmids with tig gene) and in vitro (purified TF). Unlike TF, the DnaKJE chaperone system refolds both monomeric and heterodimeric luciferases with equal efficiency.

Properties of intraribosomal part of nascent polypeptide.

This review analyzes the concept according to which the pathway of synthesized peptide from the ribosome peptidyl transferase center to the exit domain goes along the tunnel of the large subparticle. Experimental data on the accessibility of the nascent polypeptide chain to molecules of modifying agents and fluorescence quenchers are considered. Results of localization of the exit site for the nascent peptide on the ribosome surface, possible conformational states of the peptide, and its mobility and folding on the ribosome are analyzed. The analysis is based on the ribosomal tunnel parameters obtained using X-ray crystallography of whole ribosomes and large ribosomal subparticles. Special attention is given to data that do not fit in the concept of the "tunnel for peptide exit" and to results already obtained before the reliable tunnel visualization using X-ray crystallography was achieved.

[Folding of the firefly luciferase polypeptide chain with immobilized C-terminus].

Refolding of Photinus pyralis firefly luciferase from a denatured state is a slow process; its rate and productivity depend on molecular chaperones of the Hsp70 family. In contrast, cotranslational folding of the enzyme is fast and productive in the absence of chaperones [Svetlov et al., 2006. Protein Sci. 15, 242-247]. During cotranslational folding, the C-termini of polypeptides are bound to massive particles - ribosomes. The question arises whether the immobilization of the polypeptide C-terminus on a massive particle promotes the folding. To test this experimentally, the luciferase with oligohistidine tag at its C-terminus was prepared. This allowed us to immobilize the protein C-terminal segment on chelating Sepharose beads. Here we show that both immobilized and free chains of urea-denatured enzyme refold with the same rate. At the same time, the immobilization of luciferase results in higher refolding yield due to prevention of inter-molecular aggregation. Chaperones of the Hsp70 family promote refolding of both immobilized and free luciferase polypeptides. The results presented here suggest that the high rate of cotranslational folding is not caused by the immobilization of polypeptide C-termini by itself, but is rather due to a favorable start conformation of the growing polypeptide in the peptidyl-transferase center of the ribosome and/or the strongly vectorial character of the folding from N- to C-terminus during polypeptide synthesis.

Investigation of hormone-receptor interactions by means of fluorescence labeling.

Fluorescent-labeled hormones can be used to study hormone-receptor interactions by means of fluorescence polarization, visualization by fluorescence microscopy, or separation methods, e.g., dextran-coated charcoal. Subcellular fragments, single cells, and tissue preparations are amenable to study; in this work rat uterine cytosol was used unless otherwise noted. Estrone labeled with fluorescein at position 17 gives 50% inhibition in the radiometric dextran-coated charcoal assay at 8.3 X 10(-7) M as compared to 3.4 and 3.5 X 10(-8) M for diethylstilbestrol and estradiol, respectively. Scatchard plots from fluorescence polarization are hyperbolic and consistent with two classes of binding sites having association constants 5.6 X 10(10) and 6.4 X 10(7) M-1. Binding by high-affinity sites, which were present at about 3 times the concentraion of "specific" sites (radiometric dextran-coated charcoal assay), was abrogated by estradiol or diethylstilbestrol. Kinetic measurements showed that binding sites that can be blocked by excess estradiol or diethylstilbestrol are those that are both slowly associating and slowly dissociating. Staining of tissues by estrone labeled with fluorescein at position 17 as seen in the fluorescence microscope showed specificity. In normal rat uterus only epithelial cells were stained. In one human infiltrating ductal carcinoma only the malignant ductoid elements stained, while in another there was essentially no staining.

Enzymatic activity of the ribosome-bound nascent polypeptide.

Firefly luciferase was shown to be completely folded and thus enzymatically active immediately upon release from the ribosome [Kolb et al. (1994) EMBO J. 13, 3631-3637]. However, no luciferase activity was observed while full-length luciferase was attached to the ribosome as a peptidyl-tRNA, probably because the C-terminal portion of the enzyme is masked by the ribosome and/or ribosome-associated proteins. Here we have demonstrated that the ribosome-bound enzyme acquires the enzymatic activity when its C-terminus is extended by at least 26 additional amino acid residues. The results demonstrate that the acquisition of the final native conformation by a nascent protein does not need the release of the protein from the ribosome.

Cell-free immunology: construction and in vitro expression of a PCR-based library encoding a single-chain antibody repertoire.

A novel cloning-independent strategy has been developed to generate a combinatorial library of PCR fragments encoding a murine single-chain antibody repertoire and express it directly in a cell-free system. The new approach provides an effective alternative to the techniques involving in vivo procedures of preparation and handling large libraries of antibodies. The possible use of the described strategy in the ribosome display is discussed.

Biomimicry as a basis for drug discovery.

Selected works are discussed which clearly demonstrate that mimicking various aspects of the process by which natural products evolved is becoming a powerful tool in contemporary drug discovery. Natural products are an established and rich source of drugs. The term "natural product" is often used synonymously with "secondary metabolite." Knowledge of genetics and molecular evolution helps us understand how biosynthesis of many classes of secondary metabolites evolved. One proposed hypothesis is termed "inventive evolution." It invokes duplication of genes, and mutation of the gene copies, among other genetic events. The modified duplicate genes, per se or in conjunction with other genetic events, may give rise to new enzymes, which, in turn, may generate new products, some of which may be selected for. Steps of the inventive evolution can be mimicked in several ways for purpose of drug discovery. For example, libraries of chemical compounds of any imaginable structure may be produced by combinatorial synthesis. Out of these libraries new active compounds can be selected. In another example, genetic system can be manipulated to produce modified natural products ("unnatural natural products"), from which new drugs can be selected. In some instances, similar natural products turn up in species that are not direct descendants of each other. This is presumably due to a horizontal gene transfer. The mechanism of this inter-species gene transfer can be mimicked in therapeutic gene delivery. Mimicking specifics or principles of chemical evolution including experimental and test-tube evolution also provides leads for new drug discovery.

Study of the syn and anti isomerism of the long-lasting opiate antagonist naloxazone and related compounds.

A 13C-NMR study of the long-acting opiate antagonists naloxazone (I) and naltrexazone (II) and the long-acting opiate agonist oxymorphazone (III) revealed that these compounds are formed as mixtures of their anti and syn isomers. The less crowded anti isomer was found to be the major product in all cases (ca. 80%). N,N-Dimethyl derivatives of naloxazone (IV), naltrexazone (V), and oxymorphazone (VI), which are sterically more crowded than the corresponding unsubstituted hydrazones I-III, were formed as almost exclusively anti isomers. Pure anti isomer of II was obtained as a 1:1 complex with ethanol. No syn-anti equilibration was observed during the 13C-NMR experiment in any of the cases studied. The relevance of our finding about the syn-anti isomerism of the opiate hydrazones to the understanding of their interactions with the opiate receptor is discussed.

Fluorescent probes for opioid receptors.

Naloxone, naltrexone and oxymorphone were labeled in position 6 with fluorescein by coupling their hydrazone analogs with fluorescein isothiocyanate. Naloxone was also coupled in a similar way with rhodamine-B. The compounds thus obtained were: "6-FN", [1-(N)-fluoresceinyl naloxone thiosemicarbazone]; "6-FNX", [1-(N)-fluoresceinyl naltrexone thiosemicarbazone]; "6-FO", [1-(N)-fluoresceinyl oxymorphone thiosemicarbazone]; "6-RN", [1-(N)-tetramethylrhodaminyl-B naloxone thiosemicarbazone]. These compounds were tested for opioid receptor binding in rat brain synaptosomal plasma membranes and for biological activity on the guinea pig ileum. All compounds retained activity, showing some changes in affinity and binding profile compared to their parent compounds. "6-FN", for example, showed decreased (approximately 10x) affinity compared to naloxone in opiate displacement analysis but retained potency in displacement of opioid peptides. Antagonist activity of "6-FN" in the guinea pig ileum bioassay was about ten-fold less than that of naloxone.

Effects of the opioid antagonist naltrexone-estrone azine on the luteinizing hormone-releasing hormone induced release of luteinizing hormone from the pituitary glands of ovariectomized rats.

The effects were studied of in vivo administration of the new opioid antagonist-estrogen hybrid, naltrexone-estrone azine (EH-NX), on subsequent luteinizing hormone-releasing hormone (LHRH)-stimulated luteinizing hormone (LH) release by the pituitary gland in vitro. It is well known that administration of estrogen exerts negative and positive effects on the pituitary LH response to LHRH, respectively after short-term and long-term treatment. Rats were injected subcutaneously with either 17 beta-estradiol-3-benzoate (EB), EH-NX or oil on days 18 and 19 (long-term treatment), and on day 21 (short-term treatment) following ovariectomy. Twenty minutes later the animals were killed and the pituitary glands were incubated in the presence of LHRH (1000 ng/ml) for 4 h. Whereas short-term treatment with EB on day 21 did not affect LH release in vitro, EH-NX significantly decreased the pituitary LH response to LHRH in oil pretreated rats. This inhibitory effect was partially blocked by the opioid antagonist naltrexone. After long-term EB or EH-NX, followed by short-term oil treatment, the pituitary LH response to LHRH was increased considerably, compared to the long-term oil controls. These observations demonstrate that the opioid antagonist estrogen hybrid EH-NX has estrogenic activity at the level of the pituitary gland. This hybridized drug is more effective in time than EB and an equimolar amount of EH (estrone hydrazone) to induce the negative estrogenic effect.

Estrogenic effects of the new opioid antagonist naltrexone-estrone azine on pituitary luteinizing hormone secretion in ovariectomized rats.

The effect of the new opioid antagonist naltrexone-estrone azine (EH-NX) on pituitary luteinizing hormone (LH) secretion in the ovariectomized rat was studied. EH-NX is a hybrid between the steroid component estrone and the opioid antagonist naltrexone (NX). It is a potent and long-acting opioid antagonist in vitro and in vivo, but its effect upon in vivo LH secretion has not been tested before. The aims of the study were to investigate whether, unlike naltrexone, EH-NX can stimulate LH secretion without the need of additional estrogen pretreatment and whether EH-NX has peripheral estrogenic effects upon the uterine weight, when administered chronically to long-term ovariectomized rats. Female rats were injected subcutaneously with EH-NX 21 days after ovariectomy. The effects of EH-NX injections on LH secretion were compared to the effects of NX and estrone hydrazone (EH) alone, or in combination, with or without estradiol-benzoate (EB) pretreatment. Inhibition of LH secretion and uterine proliferation were observed in rats treated chronically with EH-NX in dosages of 0.250 mg/kg bw and higher. These effects were similar to those caused by EH and EB. In short-term OVX rats EH-NX appeared to act faster than EH. In contrast to NX, no stimulatory effect on LH secretion was seen with EH-NX in EB primed OVX rats. These results surprisingly demonstrate that EH-NX behaves like an estrogen and not like an opioid antagonist. The unexpected pharmacological profile of this new drug may open up doors for several medical applications.

New opiate-receptor model.

A new opiate-receptor model is proposed in which only one conformation of the receptor is needed for binding of both agonists and antagonists. There are two different spacially fixed amine-binding sites in this model: one agonist and one antagonist. The opiates undergo binding to their amine-binding sites via the lone electron pair on nitrogen. The role of the N-allyl or other such group in imparting antagonist properties is explained in terms of the steric requirements of this group. For this group to be accommodated without imposing severe steric interactions in the rest of the opiate molecule, the piperidine ring must assume a flexible (skew boat) conformation; in this conformation, the N-lone-pair electron lobe assumes the characteristic directionality of an antagonist toward its amine-binding site. If the N-lone-pair lobe is not rigorously maintained in this direction, the opiate molecule assumes both antagonist and agonist conformations and mixed antagonist-agonist activity is observed. The observed differences in the effect of sodium on the degree of binding of an agonist versus an antagonist can be explained in this model by the different effects of sodium on the two amine-binding sites. The antagonist activity of an N-methyl antagonist can be rationalized on the basis of the proposed model.

Long-range substituent effects in morphine-type agonists and antagonists: a possible explanation for some opiate anomalies.

Anomalous variations in the pKa values of variously substituted morphine-type agonists and antagonists are interpreted as a reflection of long-range substituent effects operating in these molecules. Based on the operation of long-range effects, a mechanism is proposed by which substitution into the N-normorphine portion of morphine-type agonists and antagonists changes the activity of the parent molecule. Thus, a remote substituent would distort the whole molecule via a conformational transmission effect and thereby (a) change the fit between the opiate and its receptor; (b) change the electron density distribution throughout the molecule and, therefore, at the nitrogen; (c) modify the directionality of the lone electron pair on the nitrogen; and (d) affect the pKa of the drug. The operation of long-range effects as proposed here could account for some of the anomalous changes in opiate activity effected by substitution into the parent molecule.

New insights in the clastic binding hypothesis for opiate-receptor interactions I: Electron-transfer mechanism.

A clastic binding hypothesis for opiate-receptor interactions, in which the key step in eliciting the opiate response is an electron transfer from the opiate nitrogen to the receptor, is analyzed from a chemical point of view and is found to be chemically feasible. An extended form of this hypothesis is proposed in order to accommodate recent observations about the N-demethylation of morphines in the brain. An in vitro model system for studying the electron-transfer reactions of morphines is proposed, and the initial experiments in this system are reported.

Angular dependence of the interaction energy between the N lone pair of amines and a proton: relevance to drug-receptor systems.

Ab initio molecular orbital calculations with a 4-31G basis set have been performed to study the angular dependence of the interaction energy between a lone electron pair of nitrogen and a proton. In this study ammonia and trimethylamine were used as models of biologically active amines. A proton was used as a model of an electrophilic site at the receptor. Results obtained confirm previous indications that the energy required to bend the proton from the lone pair direction decreases markedly as the two species are further separated from one another. Implications regarding the interactions of drugs and hormones at specific receptors are discussed.

New insights in the clastic binding hypothesis for opiate-receptor interactions II: Proton-transfer mechanism.

Ab initio (4-31G) molecular orbital calculations were performed on model systems to investigate the proton-transfer version of the clastic binding hypothesis for opiate-receptor interactions. Ammonia was chosen as the model for the nitrogen-containing portion of the opiate molecule, while ammonia and water were chosen as models for the proton acceptor at the receptor. The equilibrium position of a proton situated between the two molecules is found to be determined primarily by the orientation of the proton-donor molecule with some influence also from the other molecule. Misalignments of the lone pairs can significantly alter equilibrium populations when the proton affinities of the two molecules are similar.

Operation of long-range substituent effects in rigid opiates: protonated and unprotonated oxymorphone.

The structure of protonated oxymorphone (amine salt) was determined by an X-ray crystallographic study. Significant differences were found with the previously determined structure of unprotonated oxymorphone (free base). Upon protonation on nitrogen, an elongation of the N-C bound occurred, accompanied by subtle changes in bond lengths and angles distant from the site of protonation. These changes in geometry are interpreted as a reflection of long-range substituent effects.

Synthesis of octyl O- and S-glycosides related to the GPI anchor of Trypanosoma brucei and their in vitro galactosylation by trypanosomal alpha-galactosyltransferases.

Octyl O- and S-glycosides of mono- to tri-saccharides related to the core structure alpha-D-Manp-(1-->2)-alpha-D-Manp-(1-->6)-alpha-D-Manp of the GPI anchor of Trypanosoma brucei have been prepared via regioselective protodesilylation and glycodesilylation of octyl O- and S-glycosides of 2-O-benzoyl-4,6-O-(1,1,3,3-tetraisopropyl-1,3-disiloxane-1, 3-diyl)-alpha-D-mannopyranoside. The synthetic saccharides have been used as substrates for enzymatic alpha-galactosylation with membrane fractions of bloodstream forms of T. brucei strain 427 variants MITat 1.4, MITat 1.2, and MITat 1.5, respectively.

[Cotranslational protein folding]. / Kotransliatsionnoe svorachivanie belkov.

The review analyzes the research concerning the folding of proteins in the course of their synthesis on ribosomes. The experimental data obtained for various proteins using various methods give grounds for concluding that a nascent protein largely acquires its spatial structure while still attached to the ribosome, and final folding into the biologically active conformation takes place as soon as the completed protein is released therefrom. Cotranslational folding is characteristic of both bacterial and eukaryotic cells, and appears to be the universal and the most evolutionarily ancient mechanism.