A model for histone H5-DNA interaction: simultaneous minor and major groove binding.

Using the tertiary structure of the globular domain of H5 (GH5) and based on an alternative sequence homology between GH5 and DNA-binding proteins containing the helix-turn-helix motif, a model for H5-DNA interaction is proposed. From molecular graphics it follows that helix II recognizes the major groove of the DNA, as does the second helix of the helix-turn-helix motif, while helix III makes minor groove contacts, in agreement with the hypothesis of Turnell et al. (FEBS letters 232, 263-268). In the resulting model GH5 makes contact with a full turn of DNA.     

Non-polyadenylated 22 s ribonucleoprotein particle is insensitive to translational inhibitor RNA of cryptobiotic gastrulae of Artemia salina.

A free cytoplasmic 22 S ribonucleoprotein particle exhibiting a major template activity in rabbit reticulocyte system has been identified in the cryptobiotic gastrulae of Artemia salina. This particle contains non-polyadenylated 9 S messenger RNA which codes primarily for a non-histone basic protein with an apparent molecular weight of 26 000 daltons. We have previously demonstrated the presence of a translational inhibitor RNA which is apparently responsible for transforming polyadenylated messenger (Slegers et al., FEBS Letters 80, 390-394, 1977). This inhibitor RNA was found to be completely ineffective on the template activity of non-polyadenylated 22 S messenger ribonucleoprotein, confirming the specificity of this regulatory RNA for polyadenylate sequences.     

Optical properties and structure of tetrapyrroles. A report of a symposium held at the University of Konstanz, FRG, August 12-17, 1984

Many basic life processes such as oxygen transport, electron transport, photosynthesis and plant development, are mediated by tetrapyrroles. It has long been recognized that optical and other physicochemical properties of tetrapyrroles are highly important not only for characterization of the various relevant systems but also to provide a key role in the understanding of their structural and functional aspects. The symposium described below was devoted mainly to recent advances in the optical and molecular properties of biologically important systems, involving both cyclic and open-chain tetrapyrroles. The topics presented and discussed ranged from physics and chemistry to plant biology and medicine. This interdisciplinary character of the meeting conforms with previous symposia also held in Konstanz: Protein-Ligand Interactions (1974) and Transport by Proteins (1978) [see FEBS Lett. (1975) 54, 1-4, and FEBS Lett. (1979) 103, 1-4]. In order to stimulate exchange of ideas, new experimental approaches and techniques, emphasis was placed on the discussions following each presentation, reports of which are also included in the book published. Preprints of the papers presented were distributed some time prior to the symposium. The symposium was mainly supported by the Stiftung Volkswagenwerk and the University of Konstanz. The meeting was based on 29 invited lectures which were divided into four sections.     

Identification and purification of a calcium-binding protein from Bacillus subtilis

A Ca(2+)-binding protein was identified in Bacillus subtilis in the log phase of growth. The molecular mass of this protein is about 38 kDa as estimated by polyacrylamide gel electrophoresis in the presence of SDS and by gel filtration. The protein was found to be resistant 10 min at 65 degrees C and was purified about 400 times, starting from heated crude extract, by conventional procedures. This novel protein is able to bind Ca2+ in the presence of an excess of MgCl2 and KCl both in solution and after SDS gel electrophoresis and electrotransfer. Since an impairment of the Ca2+ intake, in Bacillus subtilis, results in an impairment of chemotactic behavior (Matsushita, T. et al (1988) FEBS lett. 236, 437-440), 38 kDa protein may be involved in the regulation of chemotaxis.     

Purification and characterization of human bronchial proteinase inhibitor

We describe a purification procedure for the human bronchial proteinase inhibitor which involves trichloroacetic acid precipitation of sputum followed by ion-exchange and gel filtration chromatography. The inhibitor shows a major band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, but exhibits microheterogeneity on high-resolution chromatography. It has a molecular mass of 15.5-16 kDa as determined by electrophoresis and gel filtration and is 90% active against leukocyte elastase. The amino acid sequence of the N-terminal portion of the inhibitor was determined and was found to be identical (through 29 amino acids) to that recently reported for the human seminal plasma proteinase inhibitor I (Seemuller et al. (1986) FEBS Lett. 199, 43-48).     

Nitrous oxide reductase and the 120,000 MW copper protein of N2-producing denitrifying bacteria are different entities

Zumft and Matsubara [1982) FEBS Lett. 148, 107-112) isolated a 120,000 MW copper protein from certain denitrifying bacteria which were capable of producing N2. The presence of this protein correlated with a nutritional requirement of copper for growth on and reduction of N2O by the bacteria. The copper protein was alleged by these workers to be nitrous oxide reductase. However, it is shown that the copper protein and nitrous oxide reductase have different molecular weights and exhibit different behavior upon anion exchange chromatography. The copper protein is therefore not nitrous oxide reductase.     

The sequence of an atriopeptigen: A precursor of the bioactive atrial peptides

The high molecular weight fraction (atriopeptigen-APG) obtained by gel filtration chromatography of rat atrial extracts was fractionated by isoelectric focusing and reverse phase HPLC to obtain a pure APG. Purification of cyanogen bromide digests of the crude high molecular weight fraction resulted in the isolation of a single biologically active cyanogen bromide cleavage peptide. Sequence analyses of these peptides coupled with recent reports of sequence analyses of intermediate molecular weight atrial peptides (Thibault, et al. (1984) FEBS Letters 167, 352–356, and Kangwa, et al., Biochem. Biophys. Res. Commun 119, 933–940) provide the complete primary structure of an 111 residue APG.     

Further comments on the logic of the application of uncoupler- inhibitor titrations for the elucidation of the mechanisms of energy coupling

Following the appearance of two papers in this journal commenting on the logic of the application of uncoupler-inhibitor titrations as a means of discriminating between 'delocalized' and 'localized' chemiosmotic mechanisms [(1984) FEBS Lett. 176,79-82; (1985) FEBS Lett. 186, 8-10], and in contrast with the arguments presented there and elsewhere, we show that in a linear model the increase in delta mu H which accompanies partial inhibition of the ATPases always leads to a relatively higher decrease of the rate of ATP synthesis by a given concentration of uncoupler in the presence of an ATPase inhibitor than in its absence. This is due to the fact that the same titre of uncoupler leads to a higher dissipative H+ flow in the presence of inhibitor, since the driving force delta mu H is higher.     

Human leukocyte granule elastase: rapid isolation and characterization.

Human granulocytic elastases have been purified by a two-step procedure involving affinity chromatography of crude extracts of leukocytic granules on Sepharose-Trasylol, followed by ion-exchange chromatography on CM-cellulose to resolve the isoelastases. All of these enzymes were found to be glycoproteins with the carbohydrate content of the major form being composed essentially of only neutral sugars. The molecular weight of this form was found to be near 30 000 daltons with the other forms being slightly higher. Preliminary structural analyses indicate that all of the elastase isozymes have identical NH2-terminal sequences suggesting that the differences in mobility of the four proteins are not due to different degrees of activation from a common zymogen but, more likely, from minor changes in carbohydrate content. Human granulocytic elastases are less active on ligament elastin than porcine pancreatic elastase, but both are inhibited by synthetic elastase active-site directed low molecular weight compounds (Tuhy, P. M., and Powers, J. C. (1975), FEBS Lett. 50, 359) as well as by plasma alpha-1-proteinase inhibitor (formerly called alpha-1-antitrypsin). In the latter case a stable complex with mol wt of 78 000 daltons is formed indicating the formation of a 1:1 complex.     

Molecular identification of the enzyme responsible for the mitochondrial NADH-supported ammonium-dependent hydrogen peroxide production

A homogeneous protein with a subunit apparent molecular mass of ∼50 kDa that catalyzes the previously described mitochondrial NADH-supported ammonium-stimulated hydrogen peroxide production (Grivennikova, V.G., Gecchini, G. and Vinogradov, A.D. (2008) FEBS Lett. 583, 1287–1291) was purified from the mitochondrial matrix of bovine heart. Chromatography of partially purified protein showed that the peaks of ammonium-stimulated NADH-dependent H₂O₂ production and that of NADH:lipoamide oxidoreductase activity coincided. The catalytic properties and mass spectrometry of the trypsin-digested protein revealed peptides that allowed identification of the protein as the Bos taurus dihydrolipoyl dehydrogenase.     

Conservation in rat liver of light and heavy subunit sequences of mammalian ferritin. Presence of unique octopeptide in the light subunit

Ferritin, an iron-storage protein found in all life forms examined, is composed of varying proportions of two subunits of different molecular weight, heavy (H) and light (L). Using cDNA clones, we have determined the nucleotide sequence corresponding to the mRNA of the L-subunit of rat liver ferritin. The coding region of 546 nucleotides (182 amino acids) is flanked by 5'- and 3' -untranslated regions of approximately 130 and 150 nucleotides, respectively. The rat liver L-subunit amino acid sequence derived from the reading frame of the cDNA showed 88% and 82% homology, respectively, with the amino acid sequences of horse spleen ferritin (Heusterspreute, M., and Crichton, R. R. (1981) FEBS Lett. 129, 322-327), and human spleen ferritin (Wustefeld, C., and Crichton, R. R. (1982) FEBS Lett. 150, 43-48), thus demonstrating evolutionary conservation of the L-subunit sequence. However, a major difference between the rat and the horse and human sequences is the insertion of an octopeptide near the COOH-terminus of the rat protein resulting in a slightly longer peptide chain in this species. The reading frame and parts of the derived amino acid sequence including the octopeptide sequence were confirmed by direct amino acid sequencing of cyanogen bromide peptides from rat liver ferritin. Minor fragments of rat liver ferritin, presumably derived from the H-subunit, were also isolated after cyanogen bromide treatment. On sequencing, these H-peptides showed limited homology with regions of the L-sequence but extensive homology with published H-sequences from human liver and spleen. The H-subunit sequence did not contain the octopeptide found as part of the L-subunit sequence.     

Gamma-subunit of mouse retinal cyclic-GMP phosphodiesterase: cDNA and corresponding amino acid sequence

The cDNA nucleotide and corresponding amino acid sequences of the gamma-subunit of cyclic-GMP phosphodiesterase (cGMP-PDE gamma) from mouse retina have been determined. The cDNA translated region was found to be 91.5% homologous to the cDNA coding region for the enzyme from bovine retina [(1986) FEBS Lett. 204, 288-292]. On Northern blots of normal mouse retinal RNAs this cDNA hybridized the cGMP-PDE gamma mRNA which is 900 bp long. The mouse gamma-subunit contains 87 amino acid residues which share 97.7% homology with the bovine polypeptide [(1986) FEBS Lett. 204, 288-292]. Only two amino acids have been changed, Ala 8 to Gly and Met 17 to Ile.     

Quaternary structure of bovine cytochrome oxidase

A hydrodynamically homogeneous preparation of bovine mitochondrial cytochrome c oxidase can be obtained by anion-exchange chromatography of alkaline-treated enzyme, followed by a gel permeation chromatography step, which further removes some (aggregated) apoprotein. The molecular weight, Mr, of the monodisperse enzyme in Triton X-100 was found to be 210000. This complex is composed of six different polypeptides, with Mr summing up to about 110000 in toto, in a relative one-to-one stoichiometry. Two sets of these subunits constitute the 210000-Mr enzyme complex. In contrast to our earlier report [Saraste, Penttil?, Coggins, and Wikstr?m, FEBS Lett. 114 (1980) 35-38] the 210000-Mr enzyme contains four (and not two) haems A, and therefore represents the dimer of cytochrome aa3. One of the proposed seven subunits, number III, is lacking in this enzyme preparation.     

Amyloid fibrillogenesis of silkmoth chorion protein peptide-analogues via a liquid-crystalline intermediate phase

Chorion, the major component of silkmoth eggshell, consists of the A and B classes of low-molecular weight structural proteins. Chorion protects the oocyte and the developing embryo from environmental hazards and this is due to the extraordinary physical and chemical properties of its constituent proteins. We have shown previously [FEBS Lett. 479 (2000) 141; 499 (2001) 268] that peptide-analogues of the A and B classes of chorion proteins form amyloid fibrils under a variety of conditions, which led us to propose that silkmoth chorion is a natural, protective amyloid. In this work, we present data showing conclusively that, the first main step of amyloid-like fibrillogenesis of chorion peptides is the formation of nuclei of liquid crystalline nature, which is reminiscent of spider-silk formation. We show that these liquid-crystalline nuclei (spherulites) 'collapse'/deteriorate to form amyloid fibrils in a spectacular manner, important, it seems, for chorion morphogenesis and amyloid fibrillogenesis in general. The molecular 'switch' causing this spectacular transformation is, most probably, a conformational transition to the structure of chorion peptides, from a left-handed parallel beta-helix to an antiparallel beta-pleated sheet. Apparently, these peptides were suitably designed to play this role, after millions of years of molecular evolution.     

Molecular Sizes of the Catalytic Units of Oxygen Evolution and the Reaction Center in Photosystem II of Spinach Thylakoids

Target analysis of the PS II reaction in spinach thylakoidsshowed that the respective molecular masses of the catalyticunits for oxygen evolution and the reaction center are about120 kDa and 250 kDa based on a kinetic separation of the tworeaction rates. The size of the oxygen-evolving enzyme agreedwith that determined for the PS II preparation from a thermophiliccyanobacterium by the same means [Nugent and Atkinson (1984)FEBS Lett. 170: 89]. Single hit-inactivation of oxygen evolutionand the PS II reaction center units indicates that each functionis driven by a structurally assembled unit. (Received August 6, 1984; Accepted December 17, 1984)     

Redox loops and proton pumps

In a Review-Hypothesis, Mitchell [(1987) FEBS Lett. 222,235-245] has recently suggested possible molecular mechanisms for proton translocation by cytochrome oxidase. In describing these mechanisms, he extended his own concept of a redox loop in a manner expected to lead to confusion. He also stated that the term redox-linked proton pump implies an indirect coupling between electron transfer and proton translocation, and that this type of coupling is very difficult to test experimentally. Here it is argued that the original meaning of a redox loop should be maintained, and proper definitions of the terms redox-linked proton pump and direct or indirect coupling are formulated. In addition, it is reasoned that both types of coupling are amenable to experimental tests.     

BOOK REVIEW

Book Reviewed in this Article:
Biochemistry of Cell Differentiation. FEBS Symposium Volume 24. Edited by A. Monroy and R. Tsanev.     

Design of ET(B) receptor agonists: NMR spectroscopic and conformational studies of ET7-21[Leu7, Aib11, Cys(Acm)15

In a previous report we have shown that the endothelin-B receptor-selective linear endothelin peptide, ET-1[Cys (Acm)1,15, Ala3, Leu7, Aib11], folds into an alpha-helical conformation in a methanol-d3/water co-solvent [Hewage et al. (1998) FEBS Lett., 425, 234-238]. To study the requirements for the structure-activity relationships, truncated analogues of this peptide were subjected to further studies. Here we report the solution conformation of ET7-21[Leu7, Aib11, Cys(Acm)15], in a methanol-d3/water co-solvent at pH 3.6, by NMR spectroscopic and molecular modelling studies. Further truncation of this short peptide results in it displaying poor agonist activity. The modelled structure shows that the peptide folds into an alpha-helical conformation between residues Lys9-His16, whereas the C-terminus prefers no fixed conformation. This truncated linear endothelin analogue is pivotal for designing endothelin-B receptor agonists.     

Amyloid-like fibrils from an 18-residue peptide analogue of a part of the central domain of the B-family of silkmoth chorion proteins.

Chorion is the major component of silkmoth eggshell. More than 95% of its dry mass consists of the A and B families of low molecular weight structural proteins, which have remarkable mechanical and chemical properties, and protect the oocyte and the developing embryo from the environment. We present data from negative staining, Congo red binding, X-ray diffraction, Fourier transform-Raman, attenuated total reflectance infrared spectroscopy and modelling studies of a synthetic peptide analogue of a part of the central domain of the B family of silkmoth chorion proteins, indicating that this peptide folds and self-assembles, forming amyloid-like fibrils. These results support further our proposal, based on experimental data from a synthetic peptide analogue of the central domain of the A family of chorion proteins, that silkmoth chorion is a natural, protective amyloid [Iconomidou et al., FEBS Lett. 479 (2000) 141-145].     

Potassium permeation through the KcsA channel: a density functional study

We present a theoretical study on structural and electronic aspects of K+ permeation through the binding sites of the KcsA channel's selectivity filter. Density functional calculations are carried out on models taken from selected snapshots of a molecular dynamics simulation recently reported [FEBS Lett. 477 (2000) 37]. During the translocation process from one binding site to the other, the coordination number of the permeating K+ ion turns out to decrease and K+ ion polarizes significantly its ligands, backbone carbonyl groups and a water molecule. K+-induced polarization increases significantly at the transition state (TS) between the two binding sites. These findings suggest that polarization effects play a significant role in the microscopic mechanisms regulating potassium permeation.