How many hydrogen-bonded α-turns are possible?

The formation of α-turns is a possibility to reverse the direction of peptide sequences via five amino acids. In this paper, a systematic conformational analysis was performed to find the possible isolated α-turns with a hydrogen bond between the first and fifth amino acid employing the methods of ab initio MO theory in vacuum (HF/6-31G*, B3LYP/6-311?+?G*) and in solution (CPCM/HF/6-31G*). Only few α-turn structures with glycine and alanine backbones fulfill the geometry criteria for the i←(i?+?4) hydrogen bond satisfactorily. The most stable representatives agree with structures found in the Protein Data Bank. There is a general tendency to form additional hydrogen bonds for smaller pseudocycles corresponding to β- and γ-turns with better hydrogen bond geometries. Sometimes, this competition weakens or even destroys the i←(i?+?4) hydrogen bond leading to very stable double β-turn structures. This is also the reason why an “ideal” α-turn with three central amino acids having the perfect backbone angle values of an α-helix could not be localized. There are numerous hints for stable α-turns with a distance between the \( {{\hbox{C}}_\alpha } \)-atoms of the first and fifth amino acid smaller than 6-7 Å, but without an i←(i?+?4) hydrogen bond.     

Amino acid esters of 9-(2′,3′-dihydroxypropyl-1′)-adenine are the specific inhibitors of protein synthesis on ribosomes

Peptide acceptor properties of phenylalanine and glycine esters of 9-(2,3-dihydroxypropyl-1)-adenine and 1-(2,3-dihydroxypropyl-1)-4-thiouracyl were investigated. All these esters appeared to be powerful inhibitors of polyphenylalanine synthesis in E. coli MRE-600 ribosomes charged with poly U. Like puromycin, esters of adenine derivatives accepted the AcPhe residue from Ac-[¹⁴C] Phe-tRNA in a ribosomal system charged with poly U. However, peptidyl esters of 9-(2,3-dihydroxypropyl-1)-adenine remained bound with ribosomes. The structure of the peptide esters synthesized was ascertained after dissociation of ribosomes into subparticles by direct comparison with the synthetic specimens.Abbreviations AcPhe acetyl-l-phenylalanine - HP-Ade 9-(2,3-dihydroxypropyl-1)-adenine - Phe-HP-Ade and Gly-HP-Ade l-phenylalanine and glycine esters of HP-Ade - Phe-HP-TUra l-phenylalanine ester 1-(2,3-dihydroxypropyl-1)-4-thiouracyl - AcPhePhe-HP-Ade and AcPheGly-HP-Ade acetyl-l-diphenylalanine and acetyl-l-phenylalanylglycine esters of HP-Ade respectively - AcPhe-puromycin acetyl-l-phenylalanyl-puromycin     

Silica,Alumina and Clay Catalyzed Peptide Bond Formation: Enhanced Efficiency of Alumina Catalyst

Catalytic efficiencies of clay (hectorite), silica and alumina were tested in peptide bond formation reactions of glycine (Gly), alanine (Ala), proline (Pro), valine (Val) and leucine (Leu). The reactions were performed as drying/wetting (hectorite) and temperature fluctuation (silica and alumina) experiments at 85 °C. The reactivity of amino acids decreased in order Gly > Ala > Pro Val Leu. The highest catalytic efficiency was observed for alumina, the only catalyst producing oligopeptides in all investigated reaction systems. The peptide bond formation on alumina is probably catalyzed by the same sites and via similar reaction mechanisms as some alumina-catalyzed dehydration reactions used in industrial chemistry.     

The use of bonding between tRNAs to implement early peptide synthesis

Summary Continuation of early evolutionary bonding between tRNAs would provide a solution to residence time problems between peptidyl-tRNA and mRNA. It could also improve the speed of peptide bond formation by holding the amino acid close to the growing peptide.The tRNA clover leaf structure would allow each tRNA to from a TC(GA)-loop bond to one side and a D-loop bond to the other, hence fixing itself within a group of tRNAs, all attached to the mRNA. This can be developed into a system for peptide elongation in which bonds are made and broken in an ordered sequence, with each step triggering the next. This leads to a model system that fits with some recent propsals for a three-site ribosome.     

The purification and properties of a ribonuclease of the roe of the fish Cyprinus carpio L.

• 1.1. An acid RNase was purified 620-fold from the roe of the fish Cyprinus carpio L. The recovery was 12.4% and the enzyme appeared to be homogenous as judged by the SDS-Polyacrylamide Gel Electrophoresis (SDS-PAGE).
• 2.2. The enzyme displays maximum activity at pH 5.50, I = 50 mM and the mol. wt is 22,000.
• 3.3. The purified enzyme shows two molecular forms (pI₁ = 4.04, pI₂ = 4.75) as revealed by the isoelectric focusing technique.
• 4.4. The enzyme hydrolyses both Poly(A) and Poly(U) showing a stronger preference for Poly(U), Neither Poly(G) nor Poly(C) was hydrolysed.

     

Extracellular silk fibres in Stannophyllum (Rhizopodea: Protozoa)

Summary The agglutinated shell or capsule of Stannophyllum zonarium, a deep sea rhizopod, contains a mass of extracellular proteinaceous fibres called linellae. They are 2–3 m diameter, weakly positively birefringent and on examination by X-ray diffraction give an amorphous type of diagram. An amino acid analysis is notable for its very high glycine content and indicates that the molecule may be related to those found in arthropod silk proteins.We wish to thank Mr. G. S. Bell and Mr. C. G. Ogden for their help with the amino acid analysis and electron microscopy respectively.     

A new hypothesis for the origin of life

This hypothesis suggests that calcium chelating sugars, and especially ribose, have determined the nature of the first molecular systems. The self-organization capacities of these molecules enabled them to form regular arrays with certain salts. These arrays then evolved to form polysaccharides. In this first step, ribose and particularly -D-ribofuranose predominated over other prebiotic components. In a second step, the purines invaded these polysaccharides (3–5-polyribophosphodiester). The purines best suited for this were adenine and deoxyguanine, arising from the polymerization of HCN. Just as the polysaccharides reacted with purines, so the purines reacted with other small molecules and in particular, certain alkylating agents and water. After several methylation and oxidation reactions, adenine and deoxyguanine evolved to adenine, methylguanine, cytosine, uracil and thymine. Slow evolution of the prebiotic components gradually brought about a transition from a ribose world to an RNA world. The environment of this prebiotic RNA was different from that of modern RNA. For example, interaction of prebiotic RNA with water, calcium salts and certain zwitterionic molecules like the amino acids glycine and alanine was unavoidable. The interaction of these two small amino acids with calcium evolved to form transient anhydride bonds that quickly reverted to the initial state, or transformed to a peptide bond or to a more stable activated state, the oxazolone ring. The formation of this ring in double-stranded prebiotic RNA is the critical event that allowed the synthesis of new -L-amino acids. The positioning of the lateral sides of the amino acids inside the RNA suggests a stereochemical relationship that could explain the origin of the genetic code.     

Structure and expression of a barley acidic β-glucanase gene

A barley acidic -1,3-glucanase gene was recovered from a barley genomic library by homology with a partial cDNA of barley basic -1,3-glucanase isoenzyme GII. The gene, Abg2, is homologous to the PR2 family of pathogenesis-related -1,3-glucanase genes. The ABG2 protein has 81% amino acid similarity to barley basic -1,3-glucanase GII. The ABG2 protein is encoded as a preprotein of 336 amino acids including a 28 amino acid signal peptide. A 299 bp intron occurs within codon 25. The mature ABG2 protein has a predicted mass of 32642 Da and a calculated isoelectric point of 4.9. The second exon of the Abg2 gene shows a strong preference for G+C in the third position of degenerate codons. The Abg2 gene was functionally expressed in Escherichia coli. Abg2 mRNA is constitutively expressed in barley root; leaf expression of Abg2 mRNA is induced by mercuric chloride and infection by Erysiphe graminis f. sp. hordei. Southern blot analysis indicates that Abg2 is a member of a small gene family.     

Molecular characterization of HLA-A28*, a novel HLA product,and its relationship to HLA-A28 and HLA-A2

The HLA-A28^* molecule expressed by the B-cell line IDF is serologically distinct and intermediate between HLA-A28 and HLA-A2. Comparative tryptic peptide mapping of biosynthetically labeled HLA-A28^*, A28, and A2 molecules showed that HLA-A28^* is also chemically distinct. Reverse-phase high pressure liquid chromatographic analysis of tryptic peptides labeled with ³H-arginine and ³H-lysine revealed that A28^*. A28, and A2 share 65% of their tryptic peptides. Multiple differences were observed between A28^* and both A28 and A2. No peptides unique to A28^* were detected and 25 peptides were shared with both A28 and A2. These results show that A28^* is a novel HLA product that is closely related to A28 and A2. Tryptic peptide map comparisons of these molecules labeled separately with 11 amino acids confirm these results. The data suggest that HLA-A28 ^* may have arisen from a genetic exchange event involving HLA-A28 and -A2. These data are consistent with the hypothesis that A28^* is identical with A28 in the first extracellular domain ( ₁) and identical with A2 in the second domain ( ₂).Abbreviations used in this paper EDTA ethylenediaminetetraacetic acid - HPLC high-pressure liquid chromatography - MHC major histocompatibility complex - NP40 Nonidet P40 - PMSF phenylmethylsulphonylfluoride - SDS-PAGE sodium dodecyl sulfate-polyacrylamide gel electrophoresis - TPCK L(tosylamido-2-phenyl) ethyl chloromethyl ketone - Tris tris (hydroxymethyl)-aminomethane - A alanine - C cysteine - D aspartic acid - E glutamic acid - G glycine - H histidine - K lysine - L leucine - M methionine - N asparagine - Q glutamine - R arginine - S serine - T threonine - V valine - W tryptophan - Y tyrosine     

Salinity dependence,uptake kinetics,and specificity of amino-acid absorption across the body surface of the oligochaete annelidEnchytraeus albidus

Enchytraeus albidus is able to absorb dissolved¹⁴C-labeled neutral amino acids (glycine, L-alanine, L-valine,-aminoisobutyric acid) and an amino-acid mixture from ambient water across the body surface against considerable concentration gradients. Saturation kinetics and susceptibility of glycine uptake to competitive inhibition by alanine suggest mediated transport. Absorption of neutral amino acids is an active process. Exchange diffusion of preloaded-aminoisobutyric acid against external glycine or-aminoisobutyric acid could not be detected. Results on inhibition of glycine uptake by a variety of low-molecular-weight substances indicate that glycine absorption is highly specific for neutral amino acids and somewhat less for basic amino acids; it is unspecific for non--amino acids, acidic amino acids, carbohydrates, and organic acids. Rates of transintegumentary net influx of glycine are nearly identical to¹⁴C-glycine influx, suggesting that only small amounts of amino acids are released, as compared with the capacity for uptake. Thus,¹⁴C-amino-acid influx data are used for characterization of the uptake system. Glycine uptake is positively correlated to external salinity. In fresh water, absorption is nearly zero; between 10 and 20 S, uptake increases markedly reaching maximum values at 30 S; these remain almost constant at 40 S. Transport constants and maximum uptake rates increase with rising salinities. Since absorption of glycine and L-valine is susceptible to sodium depletion, similar mechanisms presumably underly salinity-dependent uptake of amino acids and sodium-dependent solute transport. Oxygen consumption is not significantly modified by different external salinities. Estimates of nutritional profit gained from absorption of amino acids vary between 4 and 15 % of metabolic rate for glycine absorption and between 10 and 39 % for uptake of an amino-acid mixture, according to external concentrations (10 and 50 µM) and salinities (20 and 30 S).     

Prereplicative modulation of nuclear protein kinases in the regenerating rat liver

Treatment of carboxymethylated actin with o-iodosobenzoic acid (Mahoney, W.C., and Hermodson, M.A. (1979) Biochemistry, $\text{18}$, 3810–3814) did not produce the peptide pattern expected on the basis of specific peptide bond cleavage at tryptophanyl bonds. Isolation and amino acid sequence characterization of peptides from the digest indicated that in addition to cleavage at Trp residues, cleavages occurred at Tyr-53, Tyr-198, Tyr-218, Tyr-239 and probably at Tyr-91. These results indicate that the specificity of o-iodosobenzoic acid as a reagent for peptide bond cleavage is wider than previously reported. A simple explanation for the different susceptibilities of tyrosyl-containing peptide bonds to cleavage was not apparent from inspection of the sequences adjacent to these residues.     

Compact state of a protein molecule with pronounced small-scale mobility: bovine α-lactalbumin

We describe a novel physical state of a protein molecule which is nearly as compact as the native state and has pronounced secondary structure, but differs from the native state by the large increase of thermal fluctuations (in particular, by the large mobility of side groups). This state has been characterized in detail for the acid form of bovine -lactalbumin as a result of the study of physical properties of this state by a large variety of different methods (hydrodynamics, diffuse X-ray scattering, circular dichroism and infrared spectra, polarization of the luminescence, proton magnetic resonance, deuterium exchange and microcalorimetry). It has been shown that bovine -lactalbumin can be transformed into a similar state by thermal denaturation. This process is thermodynamically two state (i.e. all-or-none transition), which means that this state differs from the native one by a phase transition of the first order.Abbreviations B-LA bovine -lactalbumin - Gu·HCl guanidine hydrochloride - CD circular dichroism - UV ultraviolet - IR infra-red - NMR nuclear magnetic resonance. Differen forms of B-LA are abbreviated as follows - N native form - A acid form - T temperature-denatured form - U unfolded form (by 6 M Gu·HCl or 8 M urea). All forms have intact S-S bonds     

Effects of Anion Channel Blockers on Hyposmotically Induced Amino Acid Release From the In Vivo Rat Cerebral Cortex

A cortical cup model with continuous perfusion of artificial cerebrospinal fluid (containing 134 mM NaCl) was used to investigate the effects of anion channel blockers on the hyposmotically-induced release of amino acids from the in vivo rat cerebral cortex. The hyposmotic stimulus (25 mM NaCl) evoked a release of taurine, glutamate, aspartate, glycine, phosphoethanolamine and GABA. Topically applied anion channel blockers 4,4-diisothiocyanatostilbene-2,2-disulfonic acid (1 mM); 4-acetamido-4-isothiocyanatostilbene-2,2-disulfonic acid (2 mM); 5-nitro-2-(3-phenylpropylamino) benzoic acid (350 M); niflumic acid (500 M); tamoxifen (20 M) and arachidonic acid (0.5 M) all significantly reduced the hyposmotically-induced release of taurine. The releases of glutamate, aspartate, glycine, phosphoethanolamine and GABA were variably susceptible to inhibition by these compounds. These results demonstrate that osmoregulatory processes in cortical cells, in vivo, involve amino acids, with taurine playing a dominant role. The efflux of taurine and, to a lesser extent, the other amino acids may be mediated by anion channels.     

Effects of Salt Concentration and pH on the Absorption Spectra of Polynucleotides with Various S-Values

Poly (A) took stable double-stranded form in 0.02 m phosphate buffer pH 5.8 when its S-value was higher than 3.5. Poly (C) also took stable double-stranded form in 0.01 m acetate buffer pH 3.9 containing 0.1 m NaCl if its S-value was higher than 4.8.

Poly (I) with S-values higher than 6.5 stably formed triple-stranded form. Poly (A) with S-values over 3S and poly (I) with S-values over 7S were observed to aggregate in the presence of high concentration of salt, but poly (C) and poly (U) did not aggregate under the same condition. Effect of salt concentration differed with different polynucleotides and with different salts.     

Selective Formation of Ser-His Dipeptide via Phosphorus Activation

The Ser-His dipeptide is the shortest active peptide. This dipeptide not only hydrolyzes proteins and DNA but also catalyzes the formation of peptides and phosphodiester bonds. As a potential candidate for the prototype of modern hydrolase, Ser-His has attracted increasing attention. To explore if Ser-His could be obtained efficiently in the prebiotic condition, we investigated the reactions of N-DIPP-Ser with His or other amino acids in an aqueous system. We observed that N-DIPP-Ser incubated with His can form Ser-His more efficiently than with other amino acids. A synergistic effect involving the two side chains of Ser and His is presumed to be the critical factor for the selectivity of this specific peptide formation.     

Dynamics of β-CH and β-CH2 Groups of Amino Acid Side Chains in Proteins

The dynamics of amino acid side chains of uniformly 13C/15N-enriched ribonuclease T1 (RNase T1) have been investigated. Heteronuclear longitudinal relaxation rates, 1H/13C NOEs, and transverse cross-correlated cross-relaxation rates between the Sx and the SxIz1Iz2 operators (SIIS cross relaxation) [Ernst and Ernst (1994) J. Magn. Reson., A110, 202-213] have been determined in this study. New pulse sequences for measuring the longitudinal relaxation time and the heteronuclear NOE of aliphatic side chain carbon nuclei were developed using the CCONH type of magnetization transfer and 1HN detection. In addition, an improved pulse sequence for the determination of the SIIS cross relaxation is presented. For the analysis of the relaxation rates, the model of restricted rotational diffusion around the 1 dihedral angle has been applied [London and Avitabile (1978) J. Am. Chem. Soc., 100, 7159-7165]. These techniques were used in order to describe the side chain dynamics of the small globular protein RNase T1 (104 amino acids, MW about 11 kDa). Qualitative values of microdynamical parameters were obtained for 73 out of 85 amino acid side chains (glycine and alanine residues excepted) whereas more quantitative values were derived for 67 -CH and -CH2 groups.     

Adsorption of small biological molecules on silica from diluted aqueous solutions: Quantitative characterization and implications to the Bernal's hypothesis

To describe quantitatively the adsorption of prebiotically important compounds of low molecular weight (amino acids, short linear peptides, cyclic dipeptides, the Krebs's cycle and other carboxylic acids, nucleosides and related phosphates) on silica surface from diluted neutral aqueous solutions, equilibrium constants (K) and free energies (–G) of adsorption were determined from the retention values measured by means of high-performance liquid chromatography on a silica gel column and from the isotherms measured under static conditions. For most carboxylic acids (including amino acids and linear peptides) –G values were negative and K<1, thus showing very weak adsorption. Cyclic dipeptides (2,5-piperazinediones) exhibited higher adsorbability; –G>0 and K>1 were found for most of them. Influence of the structure of -substituent on the adsorbability is analyzed. A linear dependence of –G on the number of aliphatic carbon atoms in a sorbate molecule was found for the series of aliphatic bifunctional amino acids, related dipeptides and 2,5-piperazinediones, as well as for the row from glycine to triglycyl glycine. The adsorption of nucleosides and their phosphates is characterized by much higherK and –G values (of the order of 10² and 10⁴, respectively). The adsorption data available from our work and literature are summarized and discussed with implications to the Bernal's hypothesis on the roles of solid surfaces in the prebiotic formation of biopolymers from monomeric building blocks.corresponding author: on leave of absence from Institute of Surface Chemistry, Academy of Sciences of the Ukraine, Kiev, Ukraine.     

Amino acid replacements in proteins S5 and S12 of two Escherichia coli revertants from streptomycin dependence to independence

Summary Ribosomes were isolated from two E. coli revertants from streptomycin dependence to independence, N660 and d1023. After separation of subunits, proteins were extracted from ribosomal 30S subunits and separated by CM-cellulose column chromatography and gel filtration. Pure S5 and S12 proteins of the two mutants were digested with trypsin and all resulting peptides were isolated by column and paper chromatography. The amino acid compositions of the peptides from the four mutant proteins were compared with the corresponding peptides of the wild type strain A19. The amino acid sequences of non-identical peptides were determined.The following amino acid replacements were found: Glycine by arginine in peptide T2 of protein S5 from mutant N660 and glycine by aspartic acid in peptide T15 of protein S12 from the same mutant. In the other mutant, d1023, arginine in peptide T2 of protein S5 was replaced by leucine and furthermore arginine by serine in peptide T10 of protein S12. Besides the single amino acid replacements mentioned above which are compatible with alterations of single nucleotides, a rather drastic difference between peptides T15 of proteins S12 isolated from strain A19 and mutant d1023 has been detected.The results presented in this paper are compared with amino acid replacements in proteins S5 and S12 from other ribosomal mutants of E. coli.Paper No. 62 on Ribosomal Proteins. Preceding paper is by Wittmann et al., Molec. gen. Genet., in press.     

Formation of peptides from amino acids by single or multiple additions of ATP to suspensions of nucleoproteinoid microparticles

When lysine-rich proteinoid, which catalyzes the formation of peptides from amino acids and ATP, is complexed with acidic proteinoid to form microspheres of mixed constitution, the normal synthesis by basic proteinoid alone is multiplied several-fold. The product consists not only of small peptides but also of a high-molecular-weight fraction of substituted proteinoid.Suspensions of particles of lysine-rich proteinoid complexed with polyadenylic acid catalyze the synthesis of peptides from each of the amino acids tested with ATP. When equimolar solutions of mixtures of glycine and phenylalanine with ATP are tested in suspensions of complexes of lysine-rich proteinoid and each of various polyribonucleotides, both homopeptides and heteropeptides are produced. Glycylphenylalanine or phenylalanylglycine is the principal product; the preference is related to which polyribonucleotide is in the complex.The rate of conversion of amino acid to peptide is a function of whether ATP is added in a single batch or in repeated amounts adding to the same amount as in the single batch. Related experiments indicate a relatively rapid initial rate of decay of ATP in this system. These results are discussed relative to the mechanisms for continuous generation in modern organisms, as are the results in peptide formation.     

Structure of a rice β-glucanase gene regulated by ethylene,cytokinin, wounding,salicylic acid and fungal elicitors

A rice -glucanase gene was sequenced and its expression analyzed at the level of mRNA accumulation. This gene (Gns1) is expressed at relatively low levels in germinating seeds, shoots, leaves, panicles and callus, but it is expressed at higher levels in roots. Expression in the roots appears to be constitutive. Shoots expressGns1 at much higher levels when treated with ethylene, cytokinin, salicylic acid, and fungal elicitors derived from the pathogenSclerotium oryzae or from the non-pathogenSaccharomyces cereviseae. Shoots also expressGns1 at higher levels in response to wounding. Expression in the shoots is not significantly affected by auxin, gibberellic acid or abscisic acid. The -glucanase shows 82% amino acid similarity to the barley 1,3;1,4--D-glucanases, and from hybridization studies it is the -glucanase gene in the rice genome closest to the barley 1,3;1,4--glucanase EI gene. The mature peptide has a calculated molecular mass of 32 kDa. The gene has a large 3145 bp intron in the codon for the 25th amino acid of the signal peptide. The gene exhibits a very strong codon bias of 99% G+C in the third position of the codon in the mature peptide coding region, but only 61% G+C in the signal peptide region.Abbreviations ABA abscisic acid - 2,4-D 2,4-dichlorophenoxyacetic acid - EtBr ethidium bromide - GA gibberellic acid - n.p. nucleotide position in gene sequence - PCR polymerase chain reaction - 1×SSPE 150 mM NaCl, 10 mM NaH₂PO₄, 1 mM EDTA pH 7.4