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PubMed1977

[Set of biochemical tests for studying the metabolic pathways of arginine and other basic amino acids in bacteria].

The author suggests a set of biochemical methods permitting to identify the enzymes participating in the utilization of arginine and some other amino acids. Use of the whole complex of the suggested tests permits to determine reliably the presence of one or another enzymatic activity. The described methods permitted quantitative recording and could be used both to ascertain the peculiarities of the amino acid metabolism in various bacterial species and possibly for the purpose of differential diagnosis and identification of bacteria.

Amino Acids↗
PubMedDate not supplied

Synthesis and cytotoxic activity of peptides containing basic amino acids residues.

We synthesized eight peptides containing from three to twenty residues of arginine, lysine and histidine, using an automated synthetiser and Fmoc strategy. All peptides were purified by preparative reverse-phase HPLC and characterized by electrospay mass spectometry. Cytotoxic activity was assessed on HeLa cells. One peptide inhibited the colony-forming ability of tumor cells.

Amino Acid Sequence↗
PubMed1980

Electrical evidence for different mechanisms of uptake for basic, neutral, and acidic amino acids in oat coleoptiles.

The application of neutral or acidic amino acids to oat coleptiles induced transient depolarizations of the membrane potentials. The depolarizations are considered to reflect H(+) -amino acid co-transport, and the spontaneous repolarizations are believed to be caused by subsequent electrogenic H(+) extrusion. The basic amino acids depolarized the cell membrane strongly, but the repolarizations were weak or absent. The depolarizations induced by the basic amino acids were weakly sensitive to manipulations of the extracellular and intracellular pH. The depolarizations induced by the other amino acids, in contrast, were more strongly affected by the pH changes. Several amino acids induced distinct but diminished depolarizations in the presence of 2,4-dinitrophenol or cyanide, but the repolarizations were generally eliminated. These experiments support the co-transport theory but suggest somewhat different mechanisms for the transport of the neutral, acidic, and basic amino acids. We suggest that the neutral amino acids are co-transported with a single H(+) and that accumulation depends upon both the DeltapH and the membrane potential components of the proton motive force. The acidic amino acids appear to be accumulated by a similar mechanism except that the transport of each molecule may be associated with a cation in addition to a single proton. The permanently protonated basic amino acids appear not to be co-transported with an additional proton. Accumulation would depend only on the membrane potential component of the proton motive force.

Journal Article↗
PubMed1999

Amino acid-mediated induction of the basic amino acid-specific outer membrane porin OprD from Pseudomonas aeruginosa.

Pseudomonas aeruginosa can utilize arginine and other amino acids as both carbon and nitrogen sources. Earlier studies have shown that the specific porin OprD facilitates the diffusion of basic amino acids as well as the structurally analogous beta-lactam antibiotic imipenem. The studies reported here showed that the expression of OprD was strongly induced when arginine, histidine, glutamate, or alanine served as the sole source of carbon. The addition of succinate exerted a negative effect on induction of oprD, likely due to catabolite repression. The arginine-mediated induction was dependent on the regulatory protein ArgR, and binding of purified ArgR to its operator upstream of the oprD gene was demonstrated by gel mobility shift and DNase assays. The expression of OprD induced by glutamate as the carbon source, however, was independent of ArgR, indicating the presence of more than a single activation mechanism. In addition, it was observed that the levels of OprD responded strongly to glutamate and alanine as the sole sources of nitrogen. Thus, that the expression of oprD is linked to both carbon and nitrogen metabolism of Pseudomonas aeruginosa.

Amino Acids↗
PubMed1967

Growth of Bacillus coagulans in chemically defined media.

A nutritional study was made of five strains of Bacillus coagulans obtained from various culture collections. These five strains were descendants of two original isolates; three had been derived from one parent culture in years past and the other two were transfers from another parent culture. Therefore, the five cultures should have represented two distinct groups of genetically identical cultures. Three of the strains obtained from one culture collection had become methyl red-negative and sorbitol-negative and had gained abilities to hydrolyze gelatin and ferment arabinose. Nutritional requirements of the five cultures, determined at 37, 45, and 55 C, differed considerably among strains; however, thiamine and biotin were required by all cultures at all temperatures. Aspartic acid was stimulatory at 37 C and was required at 45 C; folic acid, basic amino acids, and certain other nutrilites were required at 55 C. Adenine supplementation was necessary for two strains at 55 C to prevent autolysis; this phenomenon is discussed. The response of these organisms to both serine and the basic amino acids at the three growth temperatures seems especially significant. The media devised for the growth of the five strains of B. coagulans used in this study permit excellent growth at three incubation temperatures.

Adenine↗
PubMed1997

Determinants for substrate phosphorylation by p21-activated protein kinase (gamma-PAK).

gamma-PAK, originally designated PAK I and subsequently identified as a member of the p21-activated protein kinase family, has been shown to have cytostatic properties and to be involved in maintaining cells in a nondividing state [Rooney, R. D., et al., (1996) J. Biol. Chem. 271, 21498-21504]. The determinants for phosphorylation of substrates by gamma-PAK have been identified by examining the kinetics of phosphorylation of a series of synthetic peptides patterned after the sequence KKRKSGL, which is the site phosphorylated by gamma-PAK in the Rous sarcoma virus nucleocapsid protein NC in vivo and in vitro. With these peptides, the recognition sequence for gamma-PAK has been shown to contain two basic amino acids in the -2 and -3 positions, as represented by (K/R)RXS, in which the -2 position is an arginine, the -3 position is an arginine or a lysine, and X can be an acidic, basic, or neutral amino acid. A basic amino acid in the -1 or -4 position improves the rate of phosphorylation by increasing the Vmax and decreasing the Km. An acidic amino acid in the -1 position increases the rate (2.5-fold), as does an acidic residue in the -4 position, although to a lower extent (1.6-fold). Proline in the -1 or +1 position has a deleterious effect and inhibits phosphorylation by gamma-PAK. The substrate requirements of protein kinases that recognize basic amino acids on the N-terminal side of the phosphorylatable residue such as cAMP-dependent protein kinase (PKA) and Ca2+/phospholipid-dependent protein kinase (PKC) have been compared with gamma-PAK using the same peptides. An acidic residue in the -1 position negatively affects PKA and PKC; thus, peptides containing the sequence KRES can be used to identify gamma-PAK.

Amino Acid Sequence↗
PubMed1975

Physicochemical properties of chromatin digested with trypsin.

Chromatin was prepared from calf thymus and digested with trypsin. Some physicochemical properties of chromatin were examined in connection with the time-course of the tryptic digestion. As the tryptic digestion proceeded, chromatin showed increases in viscosity and susceptibility to DNAase II and exhibited considerable alteration in thermal denaturation. A monophasic melting profile was found in the trypsic (digested) chromatin, but a biphasic one in the native (undigested) chromatin. The melting temperature descended from 78.2 degrees C for the native chromatin to 70.2 degrees C for the chromatin after only 10 min and further to 65.3 degrees C after 180 min tryptic digestions. The molar percent of total basic amino acid or lysine plus arginine in the chromatin increased with the time-course of the tryptic digestion whereas that of the total hydrophobic amino acid decreased. The molar ratio of hydrophobic amino acids to basic amino acids thus descended from 1.46 for the native chromatin to 1.05 for the chromatin after a 180-min tryptic digestion. These findings suggest that the neutral or hydrophobic portions in chromatin protein might play a role in the maintenance of the tertiary structure of chromatin.

Amino Acids↗
PubMed1990

Promotion of acid-induced membrane fusion by basic peptides. Amino acid and phospholipid specificities.

The ability of oligo- and polymers of the basic amino acids L-lysine, L-arginine, L-histidine and L-ornithine to induce lipid intermixing and membrane fusion among vesicles containing various anionic phospholipids has been investigated. Among vesicle consisting of either phosphatidylinositol or mixtures of phosphatidic acid and phosphatidylethanolamine rapid and extensive lipid intermixing, but not complete fusion, was induced at neutral pH by poly-L-ornithine or L-lysine peptides of five or more residues. When phosphatidylcholine was included in the vesicles, the lipid intermixing was severely inhibited. Such lipid intermixing was also much less pronounced among phosphatidylserine vesicles. Poly-L-arginine provoked considerable leakage from the various anionic vesicles and caused significantly less lipid intermixing than L-lysine peptides at neutral pH. When the addition of basic amino acid polymer was followed by acidification to pH 5-6, vesicle fusion was induced. Fusion was more pronounced among vesicles containing phosphatidylserine or phosphatidic acid than among those containing phosphatidylinositol, and occurred also with vesicles whose composition resembles that of cellular membranes (i.e., phosphatidylcholine/phosphatidylethanolamine/phosphatidylserine, 50:30:20, by mol). Liposomes with this composition are resistant to fusion by Ca2+ or by acidification after lectin-mediated contact. The tight interaction among vesicles at neutral pH, resulting in lipid intermixing, does not seem to be necessary for the fusion occurring after acidification, but the basic peptides nevertheless appear to play a more active role in the fusion process than simply bringing the vesicles in contact. However, protonation of the polymer side chains and transformation of the polymer into a polycation does not explain the need for acidification, since the pH-dependence was quite similar for poly(L-histidine)- and poly(L-lysine)-mediated fusion.

Arginine↗
PubMed2002

Low and high affinity amino acid H+-cotransporters for cellular import of neutral and charged amino acids.

Amides and acidic amino acids represent the major long distance transport forms of organic nitrogen. Six amino acid permeases (AAPs) from Arabidopsis mediating transport of a wide spectrum of amino acids were isolated. AAPs are distantly related to plasma membrane amino acid transport systems N and A and to vesicular transporters such as VGAT from mammals. A detailed comparison of the properties by electrophysiology after heterologous expression in Xenopus oocytes shows that, although capable of recognizing and transporting a wide spectrum of amino acids, individual AAPs differ with respect to specificity. Apparent substrate affinities are influenced by structure and net charge and vary by three orders of magnitude. AAPs mediate cotransport of neutral amino acids with one proton. Uncharged forms of acidic and basic amino acids are cotransported with one proton. Since all AAPs are differentially expressed, different tissues may be supplied with a different spectrum of amino acids. AAP3 and AAP5 are the only transporters mediating efficient transport of the basic amino acids. In vivo competition shows that the capability to transport basic amino acids in planta might be overruled by excess amides and acidic amino acids in the apoplasm. With the exception of AAP6, AAPs do not recognize aspartate; only AAP6 has an affinity for aspartate in the physiologically relevant range. This property is due to an overall higher affinity of AAP6 for neutral and acidic amino acids. Thus AAP6 may serve a different role either in cooperating with the lower affinity systems to acquire amino acids in the low concentration range, as a system responsible for aspartate transport or as an uptake system from the xylem. In agreement, a yeast mutant deficient in acidic amino acid uptake at low aspartate concentrations was complemented only by AAP6. Taken together, the AAPs transport neutral, acidic and cationic amino acids, including the major transport forms, i.e. glutamine, asparagine and glutamate. Increasing proton concentrations strongly activate transport of amino acids. Thus the actual apoplasmic concentration of amino acids and the pH will determine what is transported in vivo, i.e. major amino acids such as glutamine, asparagine, and glutamate will be mobilized preferentially.

Algorithms↗
PubMed2005

Alanine-scanning mutagenesis of HM-1 killer toxin and the essential residues for killing activity.

Each of the aromatic, acidic and basic amino acid residues in HM-1 were separately substituted with alanine by site-directed mutagenesis. The mutant genes were successfully expressed in HM-1 resistant Saccharomyces cerevisiae. HM-1 gene analogues corresponding to the aromatic substitutions resulted in lower production of HM-1 analogues. In the case of the acidic amino acid residue and basic amino acid residue substitutions, some analogues were produced in the same amount as and exhibited similar killing activity to that of the wild type HM-1. But the H35A HM-1 analogue had completely lost the killing activity, and D44A, K21A, K46A, R82A, R85A and R86A HM-1 showed highly decreased killing activities. These results strongly indicate the importance of histidine-35, aspartic acid-44, lysine-21, lysine-46, and C-terminal arginine residues in HM-1 for the killing activity.

Alanine↗
PubMed1989

Characteristics of acidic, basic and neutral amino acid transport in the perfused rat hindlimb.

1. We have employed a paired-tracer isotope dilution technique in a perfused rat hindlimb preparation to obtain information on the kinetics of transport across the sarcolemmal membranes of acidic, neutral and basic amino acids. 2. We have defined the characteristics of the saturable transport of amino acids normally regarded as paradigm substrates for the A, ASC, L, y+(basic) and the dicarboxylic amino acid transport systems. Their maximal transport capacities (Vmax, nmol min-1 (g muscle)-1 and substrate concentrations for half-maximal transport (Km, mM) of representative amino acid substrates are as follows: 2-aminoisobutyrate (AIB), Vmax = 15 +/- 7, Km = 1.26 +/- 0.6; alanine, Vmax = 332 +/- 53, Km = 3.9 +/- 0.9; serine, Vmax = 410 +/- 61, Km 3.4 +/- 0.5; leucine, Vmax = 2800 +/- 420, Km = 20 +/- 2; lysine, Vmax = 136 +/- 46, Km = 2.1 +/- 1.3; glutamate, Vmax = 86 +/- 6, Km = 1.05 +/- 0.05; proline, Vmax = 196 +/- 48, Km = 4.1 +/- 0.6. 3. Glycine uptake was faster than expected on the basis of diffusion but was not saturable and showed uptake that could be best described by a first-order rate constant of 0.07 +/- 0.003 min-1. 4. We have attempted to discriminate kinetically between possible routes of entry for an amino acid on the basis of competitive and non-competitive interaction between substrates potentially sharing common routes. On this basis, the major routes of alanine entry appear to be via the ASC and L systems with the A system playing a quantitatively minor role. Glutamate and aspartate appear to be transported exclusively by a dicarboxylate amino acid carrier. The branched-chain amino acids (BCAA) and the aromatic amino acid, phenylalanine, are almost equivalent substrates for an L-like system. 5. Insulin had no detectable effect on the uptake of paradigm substrates for ASC, L, y+, the dicarboxylic amino acid or glycine transport systems. 6. Transport of serine and lysine was Na+ dependent. Lysine transport apparently occurred with a stoichiometry of 2 Na+: 1 lysine. With the exception of alanine, whose transport was partially Na+ dependent, all other amino acids examined in the present study were transported in a Na+-independent manner.

Alanine↗
PubMed2000

Adsorption Behavior of Amino Acids on a Stainless Steel Surface.

The adsorption behavior of various amino acids on a stainless steel surface was investigated at 30 degrees C and over a pH range of 3-10. Acidic and basic amino acids except histidine adsorbed remarkably at pH 3-4 and 7-10, respectively, and showed Langmuir-type adsorption isotherms. The effects of pH and ionic strength on the adsorption isotherms were investigated to analyze the interactions between amino acids and adsorption sites on the stainless steel. Hydrophobic amino acids and glycine showed only small adsorbed amounts at all pHs tested. For the acidic and basic amino acids, reversibility of the absorption and the influence of the ionic strength on the adsorption behavior were examined. The adsorption isotherms of the derivatives of aspartic acid were also measured in order to examine the contribution of the carboxylic groups of acidic amino acids to the adsorption. Furthermore, a Fourier-transform infrared spectroscopic analysis and semiempirical molecular orbital calculation were carried out to analyze the ionization states and the configuration of the amino acids adsorbed on a stainless steel surface. These investigations suggest that the acidic and basic amino acids adsorb through two electrostatic interactions of two ionized groups in the amino acid with a stainless steel surface. Copyright 2000 Academic Press.

Journal Article↗
PubMed1977

Isolation and characterization of nonhistone chromosomal protein C-14 which stimulates RNA synthesis.

The nonhistone chromatin protein, C-14, was extracted from chromatin of Novikoff hepatoma ascites cells and isolated in high purity as shown by its migration as a single dense spot on two-dimensional polyacrylamide gels. Its mobility on sodium dodecyl sulfate gels is consistent with a molecular weight of approximately 70 000. The amino acid composition shows that protein C-14 has an acidic:basic amino acid ratio of 1.8. Its amino terminal amino acid is lysine. Protein C-14 stimulated the incorporation of [3H]UMP into RNA by approximately 30% when added to naked DNA and homologous RNA polymerase I. A 30% stimulation of [3H]UMP incorporation into RNA was also found when protein C-14 was added to an E. coli RNA polymerase system containing either E. coli or Novikoff hepatoma DNA.

Amino Acid Sequence↗
PubMed1981

Isolation of the 12 S globulin from rapeseed (Brassica napus L.) and characterization as a "neutral" protein. On seed proteins. Part 13.

An isolation procedure for the 12 S rapeseed globulin is described which includes precipitation by dialysis, purification using gel chromatography on Sephadex G-200, and ion-exchange chromatography on DEAE-Sephadex A-50. The isolated globulin represents a neutral protein with an isoelectric point at pH 7.25--determined by isoelectric focusing--and a relation of the acidic to basic amino acid residues (epsilon Glu, Asp--Amide ammonia: epsilon Arg, Lys, His) of 1.0. As in other storage globulins high contents of glutamic (19%) and aspartic (10%) acid and a low content of sulphur containing amino acids are characteristic for the amino acid composition. Amongst the basic amino acids arginine has the highest percentage (7%). Opposite to results of other authors the sugar content of the globulin is low (0.5%). From the amino acid composition an average hydrophobicity according to Bigelow was calculated which amounts to be 1041 cal/res. (4.36 kJ/res.).

Amino Acids↗
PubMed1999

Npw38, a novel nuclear protein possessing a WW domain capable of activating basal transcription.

We have found a novel cDNA encoding a 265 amino acid protein possessing a WW domain in our full-length cDNA bank. The WW domain was sandwiched between an acidic region and an acidic-basic amino acid repetitive region. In vitro transcription/translation of the cDNA produced a 38 kDa product that was also found in the cell lysate by western blot analysis. Thus this protein is named the nuclear protein containing a WW domain with a molecular mass of 38 kDa, Npw38. Immunofluorescence studies and expression of a fusion protein to a green fluorescent protein revealed that this protein is localized in the nucleus. Npw38 was shown to be capable of binding to a poly(rG) resin. Interestingly, the WW domain of Npw38 was found to function as a transcriptional activator in CHO cells using the GAL4 DNA-binding fusion system. Furthermore, the WW domains of human YAP and Pin1 were demonstrated to have a similar transcription-promoting activity. Combined mutation of the conserved first and second Trp residues and a hydrophobic triplet of TyrTyrTrp in the WW domain of Npw38 abolished the transcription-promoting activity, but single mutations of these sites did not. These results suggest that some WW domains potentially possess transcription-promoting activity in mammalian cells.

Amino Acid Sequence↗
PubMed1965

PURIFICATION AND PROPERTIES OF DIAMINOPIMELATE DECARBOXYLASE FROM ESCHERICHIA COLI.

1. Diaminopimelate decarboxylase from a soluble extract of Escherichia coli A.T.C.C. 9637 was purified 200-fold by precipitation of nucleic acids, fractionation with acetone and then with ammonium sulphate, adsorption on calcium phosphate gel and chromatography on DEAE-cellulose or DEAE-Sephadex. 2. The purified enzyme showed only one component in the ultracentrifuge, with a sedimentation coefficient of 5.4s. One major peak and three much smaller peaks were observed on electrophoresis of the enzyme at pH8.9. 3. The mol.wt. of the enzyme was approx. 200000. The catalytic constant was 2000mol. of meso-diaminopimelic acid decomposed/min./mol. of enzyme, at 37 degrees . The relative rates of decarboxylation at 25 degrees , 37 degrees and 45 degrees were 0.17:1.0:1.6. At 37 degrees the Michaelis constant was 1.7mm and the optimum pH was 6.7-6.8. 4. There was an excess of acidic amino acids over basic amino acids in the enzyme, which was bound only on basic cellulose derivatives at pH6.8. 5. The enzyme had an absolute requirement for pyridoxal phosphate as a cofactor; no other derivative of pyridoxine had activity. A thiol compound (of which 2,3-dimercaptopropan-1-ol was the most effective) was also needed as an activator. 6. In the presence of 2,3-dimercaptopropan-1-ol (1mm), heavy-metal ions (Cu(2+), Hg(2+)) did not inhibit the enzyme, but there was inhibition by several amino acids with analogous structures to diaminopimelate, generally at high concentrations relative to the substrate. Penicillamine was inhibitory at relatively low concentrations; its action was prevented by pyridoxal phosphate.

Amino Acids↗
PubMed1995

The structure of satellite panicum mosaic virus at 1.9 A resolution.

The crystal structure of satellite panicum mosaic virus (SPMV) has been solved by multiple isomorphous replacement and molecular replacement and refined at 1.9 A resolution. SPMV, a T = 1 icosahedral virus, is the smallest virus structure determined. The coat protein is an eight-stranded 'jelly roll' beta-barrel with an amino-terminal strand that extends into the interior of the virus, presumably interacting with the RNA. Regions of electron density on the interior of the protein capsid may be RNA, although it is not possible to construct any detailed model of the nucleic acid. Basic amino acid residues in contact with the nucleic acid show a considerable degree of disorder. The carboxy-terminal strand of the virus coat protein interacts with adjacent subunits, forming an additional beta-strand.

Amino Acid Sequence↗