'Ribozoomin'--translation initiation from the perspective of the ribosome-bound eukaryotic initiation factors (eIFs)

Protein synthesis is a fundamental biological mechanism bringing the DNA-encoded genetic information into life by its translation into molecular effectors - proteins. The initiation phase of translation is one of the key points of gene regulation in eukaryotes, playing a role in processes from neuronal function to development. Indeed, the importance of the study of protein synthesis is increasing with the growing list of genetic diseases caused by mutations that affect mRNA translation. To grasp how this regulation is achieved or altered in the latter case, we must first understand the molecular details of all underlying processes of the translational cycle with the main focus put on its initiation. In this review I discuss recent advances in our comprehension of the molecular basis of particular initiation reactions set into the context of how and where individual eIFs bind to the small ribosomal subunit in the pre-initiation complex. I also summarize our current knowledge on how eukaryotic initiation factor eIF3 controls gene expression in the gene-specific manner via reinitiation.     

Structure and function of ferritin

Ferritin is the major iron storage protein of mammals and consists of up to 4500 atoms of ferric iron surrounded by a shell of protein subunits. The protein component, apoferritin, consists of 24 identical polypeptide chains each of molecular weight 18500. The function of ferritin is to store iron in a soluble form from which it can be readily mobilized. Recent results concerning the structure of the protein are reported, and progress in the elucidation of the mechanisms whereby iron is introduced into apoferritin and released from ferritin is reviewed.     

Structure and properties of conducting bacterial cellulose-polyaniline nanocomposites

Conducting composite membranes of bacterial cellulose (BC) and polyaniline doped with dodecylbenzene sulfonic acid (PAni.DBSA) were successfully prepared by the in situ chemical polymerization of aniline in the presence of hydrated BC sheets. The polymerization was performed with ammonium peroxydisulfate as the oxidant agent and different amounts of DBSA. The composites were characterized by X-ray diffraction, attenuation reflectance Fourier transform infrared spectroscopy, scanning electron microscopy (SEM), impedance spectroscopy and small angle X ray scattering (SAXS). The highest electrical conductivity value was achieved by using a DBSA/aniline molar ratio of 1.5 because this condition provided a better penetration of PAni.DBSA chains inside the hydrated BC sheet, as observed by SEM. The in situ polymerization gives rise to conducting membranes with the surface constituted by different degree roughness as indicated by Nyquist plots obtained from impedance spectroscopy and confirmed by SAXS measurements. This preliminary work provides a new way to prepare cellulose-polyaniline conducting membranes which find potential applications as electronic devices, sensors, intelligent clothes, etc.     

Structure and function of vanadium haloperoxidases

A quantum mechanics/molecular mechanics study of the resting state of the vanadium dependent chloroperoxidase from fungi Curvularia inaequalis and of the early intermediates of the halide oxidation is reported. The investigation of different protonation states indicates that the enzyme likely consists of an anionic H2VO4- vanadate moiety where one hydroxo group is in axial position. The calculations suggest that the hydrogen peroxide binding may not involve an initial protonation of the vanadate cofactor. A low free energy reactive path is found where the hydrogen peroxide directly attacks the axial hydroxo group, resulting in the formation of an hydrogen peroxide intermediate. This intermediate is promptly protonated to yield a peroxo species. The free energy barrier for the formation of the peroxo species does not depend significantly upon the protonation state of the cofactor. The most likely protonation states of the peroxo cofactor are neutral forms HVO2(O2) with a hydroxo group either H-bonded to Ser402 or coordinated to Arg360. The peroxo cofactor is also coordinated to an axial water molecule, which could be important for the stability of the peroxovanadate/His496 adduct. Our calculations strongly suggest that the halide oxidation may take place with the preliminary formation of a peroxovanadate/halogen adduct. Subsequently, the halogen reacts with the peroxo moiety yielding a hypohalogen vanadate. The most reactive protonation state of peroxovanadate is the neutral HVO2(O2) with the hydroxo group H-bonded to Ser402. The important role of Lys353 in determining the catalytic activity is also confirmed.     

Structure and function of noncanonical nucleobases

DNA and RNA contain, next to the four canonical nucleobases, a number of modified nucleosides that extend their chemical information content. RNA is particularly rich in modifications, which is obviously an adaptation to their highly complex and variable functions. In fact, the modified nucleosides and their chemical structures establish a second layer of information which is of central importance to the function of the RNA molecules. Also the chemical diversity of DNA is greater than originally thought. Next to the four canonical bases, the DNA of higher organisms contains a total of four epigenetic bases: m(5) dC, hm(5) dC, f(5) dC und ca(5) dC. While all cells of an organism contain the same genetic material, their vastly different function and properties inside complex higher organisms require the controlled silencing and activation of cell-type specific genes. The regulation of the underlying silencing and activation process requires an additional layer of epigenetic information, which is clearly linked to increased chemical diversity. This diversity is provided by the modified non-canonical nucleosides in both DNA and RNA.     

Structure and function of annexin V-decorsin fusion

Decorsin is an antagonist of fibrinogen receptor on platelets and Annexin V is able to recognize stimulated platelets. Two recombinant proteins, Annexin V plus Decorsin (AnnV-D39) and Annexin V plus the C terminal 27 amino acids variant of Decorsin (AnnV-D27), were constructed, expressed, and purified. Platelet Aggregation assay results appear that AnnV-D39 shows good anti-platelet aggregation activity, but AnnV-D27 no such activities in any platelet aggregation assay test. And computational simulations reveal that AnnV-D39 showed good anti-platelet aggregation activity as a new antagonist of fibrinogen receptor, while Annv-D27 needs re-modification. Despite the AnnV_D39 fusion is more than decorsin, the former maintains the binding sites of decorsin interacton with its receptor, which contains Asp10, Arg28-Asp33, and Tyr37-Glu39. And the addition of Annexin V could not influence the interaction between its decorsin part with its receptor GPIIb–IIIa due to the linkage peptide (GGGGSGGGGS). Although the AnnV_D27 fusion is similar to the AnnV_D39 fusion, there are differences between them, where the former is in shortage of the linkage peptide and the N-terminal segment of decorsin whose one residue (Asp10) contribution to its interaction with GPIIb–IIIa. Meanwhile, these complex models suggest that decorsin plays a role in antiplatelet aggregation not only by its RGD motif interaction with its GPIIb–IIIa receptor, but also by other residues, especially Asp10 of its N-terminal segment and Tyr37-Glu39 of its C-terminal segment. On the other hand, the linkage peptide acts as avoidance of influence and blockage between domains of fusion. This is the cause that AnnV-D39 shows good anti-platelet aggregation activity.     

Structure and function of window glass and Pyrex

Window glass is a ternary mixture, while Pyrex (after window glass, the most common form of commercial glass) is a quaternary. Here, we investigate the chemical, physical, and mathematical factors that determine the compositions of these optimized glasses. Previously, we succeeded in deriving exactly the composition of window glass (sodium calcium silicate) without adjustable parameters. Borosilicates are a much more challenging problem, and Pyrex (sodium aluminum borosilicate) requires a different approach. Our analysis shows that mean-field (or global) models (networks without significant clustering) are sufficient for window glass and probably most other commercial silicate glasses. However, it appears that the most important property of pyrex, its ability to resist mechanical shocks, requires a cluster model (large medium range order). We propose such a model, and argue that it also follows from hierarchical principles. Our model is strongly supported by specific experiments, and we suggest further experiments to test the principles underlying commercial glasses.     

Structure of ascorbic acid and its biological function

Summary Only LAMMA spectra of negative ions of ascorbic acid and isoascorbic acid exhibit a deprotonated peak. In the case of the radicals Na-ascorbate and K-isoascorbate neither the positive nor the negative ion spectra show a similar peak. Only a peak at m_r/z=41 can be detected in the negative ion spectra of both of the radicals. Positive ion spectra exhibit peaks at m_r/z =63 (for Na-ASC) and at 95 (for K-Iso-ASC) in addition to the Na⁺ and K⁺ peaks in the corresponding radicals. The peaks at 41, 63, and 95 might represent Na and K complexes engulfed in the cyclic structure of the side chain. From the results obtained one can be certain, that both of the radicals are electroneutral.

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Struktur von Ascorbinsäure und ihre biologische Funktion: IV. Untersuchung der Struktur durch laser-induzierte Massenspektrometrie

Zusammenfassung Nur die LAMMA-Spektren der negativen Ionen von Ascorbinsäure und Isoascorbinsäure haben einen deprotonierten Peak. Bei den Radikalen Na-Ascorbat und K-Isoascorbat ist dieser weder bei den positiven noch bei den negativen Ionen-Spektren vorhanden. Bei beiden Radikalen kann nur bei m_r/z=41 ein Peak im negativen Ionen-Spektrum nachgewiesen werden. Die positiven Ionen-Spektren haben neben den Na⁺- und K⁺-Peaks solche bei m_r/z=63 (für Na-ASC) und 95 (für K-Iso-ASC). Die Peaks bei 41,63 und 95 stellen wahrscheinlich Na- und K-Komplexe dar, die in der cyclischen Struktur der Seitenkette eingebettet sind. Auf jeden Fall kann aus den erhaltenen Ergebnissen geschlossen werden, daß beide Radikale elektroneutral sind.

     

Structure and function of Buthus eupeus scorpion neurotoxins

At present the investigation of the complex mechanism of the signal conductance between nerve cells and their target organ is closely connected with application of neurotoxins as a valuable tool for study of important sites involved in nerve transmission. Particular interest is attributed to neurotoxins from scorpion venoms which slow down the inactivation rate of fast sodium channels of the excitable membrane. Fifteen different toxins have been isolated from Buthus eupeus scorpion venom by means of the combination of gel and ion exchange chromatography. The homologous insectotoxins I₁, I₃, I₄, and I₅ belong to the new structural type of scorpion toxins. The essential features of these toxins are low molecular weight (ca. 4000) and the presence of two or three methionine residues in their amino acid compositions. The complete amino acid sequences of two insectotoxins and one mammalian toxin have been estimated. All mammalian neurotoxins in concentration from 10^?9M to 10^?7M slow down the inactivation rate of fast sodium channels. The direct covalent binding of photosensitive radioactive neurotoxin derivatives presents one of the most effective approaches to the localization of the functionally important components of the fast sodium channels. Thus far 2,4-dinitro-5-fluorophenylazide has been used for chemical modification of the mammalian neurotoxin M₁₀. The prepared monosubstituted photosensitive neurotoxin derivative possessed a high biological activity according to the voltage clamp data. The neurotoxin derivative has been iodinated by ¹²⁵I, the resulted product being both radioactively and photoaffinity labeled. Both native neurotoxin M₁₀ and sea anemone toxin competitively inhibit the reception of the scorpion toxin derivative by rat brain synaptosomes. It was shown that covalent toxin-receptor complexes are composed of two protein components with molecular weights 76,000 and 51,000, being near equal for synaptosomes, neuroblastoma cells, and crab nerve plasma membranes.     

Structure and function of cis-prenyl chain elongating enzymes

All carbon skeletons of isoprenoids, whose chain lengths vary widely from geranyl diphosphate (C10) to natural rubber (C>10,000), are synthesized by sequential condensation of isopentenyl diphosphate with an allylic diphosphate through catalytic functions of a group of enzymes commonly called "prenyltransferases." Prenyltransferases are classified into two major groups, trans- or (E)-prenyltransferases and cis- or (Z)-prenyltransferases, according to the geometry of the prenyl chain units in the products. From the year 1987, many genes encoding trans-prenyltransferases were cloned and clearly characterized. In contrast, the structure and detailed mechanism of cis-prenyltransferase was completely unknown until the identification of a gene encoding the undecaprenyl diphosphate (UPP) synthase from Micrococcus luteus B-P 26 in 1998. Not only the primary but also the tertiary structure of the UPP synthase is quite different from that of the trans-prenyltransferases. Multiple alignment of the primary structures of cis-prenyltransferases identified from various organisms reveals five highly conserved regions. Site-directed mutagenesis of the conserved amino acid residues in UPP synthases based on the crystal structure has elucidated the basic catalytic mechanisms. Moreover, comparison of the structures of short-, medium-, and long-chain cis-prenyltransferases reveals important amino acid residues for product chain length determination, which enabled us to understand the regulation mechanism of the ultimate chain length among cis-prenyltransferases.     

Structure and function of the energy-converting system of mitochondria

The main energy source for all endergonic processes occurring in living organisms is the phosphate bond energy of nucleoside triphosphates, especially adenosine triphosphate (ATP). In aerobic organisms, as for instance in mammals, more than 90% of ATP is formed during the process called oxidative phosphorylation. In this process, similar to that of muscle contraction and nerve excitation, nature works with vectorial processes taking place at a membrane separating distinct spaces from each other. The present article deals with the operation of a set of water-insoluble membrane proteins and enzymes vectorially transporting electrons, protons and other ions, which finally leads to the formation of ATP. This machinery transforming substrate oxidation energy into chemical energy in the form of the phosphoric anhydride bond of ATP operates with a very high efficiency. The structure and function of the machinery of mitochondrial oxidative phosphorylation are described. It consists of the electron transfer chain, the ATP-synthetase, the adenine nucleotide translocase and the phosphate carrier. The electron transfer chain can be resolved into multiprotein complexes—at three of them energy conversion takes place—and into the electron carriers ubiquinone and cytochrome c. The substrate oxidation energy is converted into the chemical energy of ATP with an electrochemical proton gradient as intermediary form. The energetic aspects of the processes are analyzed by linear irreversible thermodynamics. Great success has been gained during the past few years on the structural characterization of the participating proteins. The function of the various systems is partially elucidated on the molecular level; this concerns especially the mechanism of proton and adenine nucleotide translocation, as well as ATP formation.     

Structure and function of the acidic ribosomal stalk proteins

The acidic L7/L12 (prokaryotes) and P1/P2 (eukaryotes) proteins are the only ribosomal components that occur in more than one, specifically four, copies in the translational machinery. These ribosomal proteins are the only ones that do not directly interact with ribosomal RNA but bind to the particles via a protein, L10 and P0, respectively. They constitute a morphologically distinct feature on the large subunit, the stalk protuberance. Since a long time proteins L7/L12 have been implicated in translation factor binding and in the stimulation of the factor-dependent GTP-hydrolysis. Recent studies reproduced such activities with the isolated components and L7/L12 can therefore in retrospect be regarded as the first GTPase activating proteins identified. GTP-hydrolysis induces a drastic conformational change in elongation factor (EF) Tu, which enables it to dissociate from the ribosome after having successfully delivered aminoacylated tRNA into the A-site. It is also used as a driving force for translocation, mediated by EF-G. The in vitro stimulation of translation-uncoupled EF-G-dependent GTP-hydrolysis seems to be an intrinsic property of the ribosome that is dependent on L7/L12, reaches a maximum with four copies of the proteins per particle, and reflects the in vivo hydrolysis rate during translation. It is much larger than the analogous activity observed for EF-Tu, which is correlated with the in vitro polypeptide synthesis rate. Therefore, at least certain stimulatory activities of L7/L12 are controlled by the ribosomal environment, which in the case of EF-Tu senses the successful codon-anticodon pairing. Present knowledge is consistent with a picture in which proteins L7/L12 constitute a "landing platform" for the factors and after rearrangements induce GTP-hydrolysis. The molecular mechanism of the GTPase activation is unknown. While sequence comparisons show a large diversity in the stalk proteins across the kingdoms, a conserved functional domain organization and conserved designs of their genetic units are discernible. Consistently, stalk transplantation experiments suggest that coevolution took place to maintain functional L7/L12 EF-G and P-protein EF-2 couples. The acidic proteins are organized into three distinct functional parts: An N-terminal domain is responsible for oligomerization and ribosome association, a C-terminal domain is implicated in translation factor interactions, and a hinge region allows a flexible relative orientation of the latter two portions. The bacterial L7/L12 proteins have long been portrayed as highly elongated dimers displaying globular C-terminal domains, helical N-termini, and unstructured hinges. Conversely, recent crystal structures depict a compact hetero-tetrameric assembly with the hinge region adopting either an alpha-helical or an open conformation. Two different dimerization modes can be discerned in these structures. Models suggest that dimerization via one association mode can lead to elongated dimeric complexes with one helical and one unstructured hinge. The physiological role of the other dimerization mode is unclear and is in apparent contradiction to distances measured by fluorescence resonance energy transfer. The discrepancies between the crystal structures and results from other physico-chemical methods may partly be a consequence of the dynamic functions of the proteins, necessitating a high flexibility.     

Structure, function and biological relevance of prolyl oligopeptidase

A group of serine peptidases, the prolyl oligopeptidase family, cannot hydrolyze proteins and peptides containing more than 30 residues. The crystal structure of prolyl oligopeptidase (POP) has shown that the enzyme is composed of a peptidase domain with an alpha/beta hydrolase fold and a seven-bladed beta-propeller domain. This domain covers the catalytic triad and excludes large, structured peptides from the active site. The mechanism of substrate selection has been reviewed, along with the binding mode of the substrate and the catalytic mechanism, which differ from that of the classical serine peptidases in several features. POP is essentially a cytosolic enzyme and has been shown to be involved in a number of biological processes, but its precise function is still unknown. Many reports addressed experimentally the possible role of POP in cognitive and psychiatric processes, its involvement in the inositol phosphate signaling pathway, and its ability to metabolize bioactive peptides. Inhibitors were designed to reveal the cellular functions of POP and to treat neurological disorders. Other studies concerned the cellular localization of POP, its presumed interaction with the cytoskeletal elements, and its involvement in peptide/protein transport/secretion processes. The possible role of POP in Alzheimer disease is an intriguing issue, which is still debated. Recently, recombinant bacterial POPs have been investigated as potential therapeutics for celiac sprue, an autoimmune disease of small intestine caused by the intake of gluten proteins.     

Identifying bacterial species using CE-MS and SEQUEST with an empirical scoring function

CE-MS/MS analysis of proteolytic digests of bacterial cell extracts was combined with SEQUEST searching and a new scoring system to identify bacteria species in bacterial mixtures. Searches of MS/MS spectra against protein databases enabled the identification of bacterial species by the matching of the proteins associated with the corresponding species. An empirical scoring function was obtained by evaluating the SEQUEST search results of 38 samples that contained single bacterial species. The scoring by the empirical function helped move up the positive identification results from their original positions in the ranking based on Xcorr values alone. Therefore, the identification of bacteria in the samples that contained bacterial mixtures was improved. Bacterial species in 20 bacterial mixtures, including one real sample, were correctly identified by database searches and the new scoring function.     

Structure, function, and antigenicity of cholera toxin.

Chemical modification of intact cholera toxin or its B subunit by either partial nitration or reduction and alkylation did not result in significant loss of biological activity as determined by measurement of cyclic AMP in Chinese hamster ovary cells. Complete nitration or succinylation in the presence of guanidine hydrochloride resulted in complete loss of biological activity and significantly affected the immunoreactivity of the toxin and B subunit. Compositional analyses of both the isolated alpha and gamma chains of the toxin were typical of globular proteins and did not reveal significant hydrophobicity. Analysis of antigenic relationships by radioimmunoassay indicated a partial crossreactivity between the alpha chain and the B subunit of cholera toxin. Since previous structural studies of the beta chain of cholera toxin indicated chemical similarity with the glycoprotein hormones [Kurosky et al. Science 195:299 (1977)], radioimmunoassay procedures were employed to investigate for possible crossreactivity. No evidence of crossreactivity between cholera toxin subunits and subunits of ovine luteinizing hormone was found.