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PubMed1980

Site-specific recombination functions of bacteriophage lambda: DNA sequence of regulatory regions and overlapping structural genes for Int and Xis.

Site-specific recombination in bacteriophage lambda is mediated by two phage-encoded proteins, Int and Xis. The structural genes encoding these proteins are located immediately to the right of their site of action, the phage att site. The DNA sequence for both the structural and regulatory regions of these genes has been determined. The location and reading frame of the xis gene were ascertained by sequence comparisons with the b538 deletion (that ends within xis) and with the xis6 amber mutation. From the DNA sequence Xis has a molecular weight of 8630; it is rich in basic amino acids with lysine and arginine comprising 25% of the 72 amino acids. Identification of the int reading frame was also unambiguous. From the DNA sequence, Int has a molecular weight of 40,330; of the 356 amino acids, 69 are basic and 46 are acidic. In the NH(2)-terminal portion of Int, 35% of the first 20 amino acids are basic. The site-specific recombination functions form a very tight cluster (att-int-xis) on the lambda chromosome. The combined protein-encoding sequences of xis and int start 1347 base pairs, and terminate 84 base pairs, from the center of the phage att site. The two genes overlap one another by 20 base pairs (xis is upstream of int) and a possible means of controlling the relative synthesis rates of Int and Xis at the level of translation is proposed. Control at the level of transcription is also considered. The mutation intc226 leads to constitutive production of Int, independent of cII/cIII activator proteins normally required for transcription from the p(I) promoter. It is shown that this mutation is the result of a single base change (in the fMet codon of the xis gene) that generates an improved promoter heptamer sequence. This result, in conjunction with comparisons with other promoter sequences and other sequences responding to cII/cIII action, leads to a tentative identification of the p(I) promoter and site of cII/cIII action.

Bacteriophage lambda↗
PubMed1976

Structure-activity studies on mammalian tissue lytic enzymes: chemical characterization and substrate specificity of rat kidney nuclear lysozyme.

Studies on the structure and substrate specificity of purified rat kidney nuclear (RKN) lysozyme are reported. The carboxyl and amino terminal residues of RKN-lysozyme were found to be leucine and alanine respectively. The amino acid composition indicated similarities and differences as compared with that of hen egg white (HEW) lysozyme. There were alterations in the nine amino acid residues, Lys, His, Arg, Asp, Glu, Pro, 1/2 Cys, Tyr and Trp. The other nine residues were present in identical proportions to those of HEW-lysozyme. The decrease in the arginine and aspartic acid residues was found to be compensated by the increase in the number of lysine, histidine and glutamic acid residues. The overall ratio of the acidic to basic amino acids has thus been conserved in the mammalian enzyme. In addition, RKN-lysozyme contained decreased numbers of Trp, Tyr and 1/2 Cys, and increased numbers of proline residues as found in HEW-lysozyme. RKN-lysozyme did not cross react with heterologous antibodies produced against HEW-lysozyme, and vice versa. RKN-lysozyme showed distinct specificity towards the lysis of M. luteus. Against this substrate, it was three times more efficient than HEW-lysozyme. It also cleaved E. coli B, but its efficiency was half as much as with M. luteus. However, it cleaved P. septica and B. subtilis at a rate similar to HEW-lysozyme under identical conditions.

Amino Acid Sequence↗
PubMed1985

Distinction and similarity in the structure of histones H1 and H5 as indicated by 13C nuclear-magnetic-resonance spectroscopy.

The 13C nuclear magnetic resonance studies have been carried out on histones H1 and H5, by focusing our interest on possible formation of specific salt bridges between acidic and basic amino acid residues in the proteins and also on the structural difference between the two proteins. The 13C chemical shift and pKa values of the carboxyl group of glutamic acid residues in the histones coincided with those of free glutamic acid. Based on this result and another experiment using completely modified lysine residues in the histones, no evidence for a specific interaction between acidic and basic residues has been found. It has also been shown that the pH-effects of aliphatic and aromatic resonances are quite different between H1 and H5, suggesting that the globular domain of H5 is more stable than that of H1. The correlation time (1.5 ns) for the alpha-carbons of H5 estimated from 13C nuclear Overhauser enhancement was twice as long as that of H1 (0.9 ns), indicating that the backbone in the N-terminal and C-terminal domains of H5 is less mobile than that of H1.

Arginine↗
PubMed1986

Roles of urea production, ammonium excretion, and amino acid oxidation in acid-base balance.

Atkinson and colleagues recently proposed several concepts that contrast with traditional views: first, that acid-base balance is regulated chiefly by the reactions leading to urea production in the liver; second, that ammonium excretion by the kidney plays no role in acid-base homeostasis; and third, that ammonium does not stimulate ureagenesis (except indirectly). To examine these concepts, plasma ions other than bicarbonate are categorized as 1) fixed cations (Na+, K+, Ca2+, and Mg2+, symbolized M+) and anions (Cl-), 2) buffer anions (A-), 3) other anions (X-), and 4) ammonium plus charged amino groups (N+). Since electroneutrality dictates that M+ + N+ = Cl- + HCO3- + A- + X-, it follows that delta HCO3- = delta(M+ - Cl-) - delta A- - delta X- + delta N+. Therefore acid-base disturbances (changes in HCO3-) can be categorized as to how they affect bodily content and hence plasma concentration of each of these four types of ions. The stoichiometry of ureagenesis, glutamine hydrolysis, ammonium and titratable acid excretion, oxidation of neutral, acidic, and basic amino acids, and oxidation of methionine, phosphoserine, and protein are examined to see how they alter these quantities. It is concluded that 1) although ureagenesis is pH dependent and also counteracts a tendency of amino acid oxidation to cause alkalosis, this tendency is inherently limited by the hyperammonemia (delta N+) that necessarily accompanies it, 2) ammonium excretion is equivalent to hydrogen excretion in its effects on acid-base balance if, and only if, it occurs in exchange for sodium or is accompanied by chloride excretion and only when the glutamate generated by glutamine hydrolysis is oxidized.(ABSTRACT TRUNCATED AT 250 WORDS)

Acid-Base Equilibrium↗
PubMed1985

Studies on the primary structure and antigenic determinants of pilin isolated from Pseudomonas aeruginosa K.

The complete amino acid sequence of Pseudomonas aeruginosa K (PAK) pilin was determined using a combination of automated and manual Edman degradation techniques. Suitable peptides were derived from cyanogen bromide, tryptic, chymotryptic, peptic, thermolytic, and citraconylated tryptic cleavages of unmodified or carboxymethylated pilin. The protein, a single polypeptide chain, has N-methylphenylalanine at the NH2-terminus, a total of 144 residues, a molecular weight of 15013, and an equal number of acid and basic amino acids. The NH2-terminal region (residues 1-43) is very hydrophobic with only three charged residues, suggesting a possible role in subunit-subunit interaction. The two half-cystines, residues 129 and 142, are shown to be linked through a disulfide bridge in the native protein. To delineate the antigenic regions of pilin, the protein was cleaved at Arg-30, Arg-53, and Arg-120 to produce peptide fragments cTI (residues 1-30), cTII (residues 31-53), cTIII (residues 54-120), and cTIV (residues 121-144). cTIII and cTIV were further degraded into several subfragments. The purified peptides were subjected to immunological analysis using direct and competitive enzyme-linked immunosorbent assay procedures. A major antigenic determinant was delineated in a region of the protein encompassing residues 82-101. Three other epitopes were also identified, but reacted with only minor amounts of antibody in the rabbit polyclonal antiserum.

Amino Acid Sequence↗
PubMed2002

Ionic interaction of the HIV-1 V3 domain with CCR5 and deregulation of T lymphocyte function.

We have reported that the principal neutralizing domain of V3 of the HIV-1 gp120 induces an antigen-specific activation apoptosis of responding effector CD4+ T lymphocytes, a phenomenon inhibited by RANTES, an agonist of CCR5. Here, addressing the question of how a hypervariable region could induce such a selective reaction, we demonstrated that the magnitude of the activation phase was dependent on the number of basic amino acids present in the V3 peptide, an observation confirmed by using V3 peptides with appropriate basic amino acid substitutions. The relative position of the amino acids in the V3 peptide did not affect the biological phenomenon. Using surface plasmon resonance biosensor analysis, we also provided direct evidence of the influence of basic amino acids in the interaction between V3 and the amino terminal domain of CCR5. Sulphation of tyrosines in the CCR5 peptide was essential. Our results confirm gp120 modelling predictions and demonstrate simple molecular ionic interactions as capable of affecting key cell events, the wider biological implications of which need to be further explored.

Amino Acid Sequence↗
PubMed2004

Cloning, expression and partial characterization of a gene encoding the S15a ribosomal protein of Taenia solium.

Ribosomes, ribosomal proteins (r-proteins), and messenger and transfer RNAs catalyze the synthesis of proteins in organisms. To understand and define the components involved in this event in Taenia solium, we isolated and characterized a T. solium cDNA encoding the basic ribosomal protein S15a (TsS15a). The TsS15a cDNA produces a protein with M(r) (relative molecular mass) 14,988, which contains 22.3% of basic amino acids. Analysis comparing TsS15a protein with other S15a r-proteins indicates that this protein is highly conserved. A recombinant TsS15a protein with similar M(r) was produced in bacteria. Antibodies against recombinant TsS15a react with a 15-kDa protein in extracts from all life stages of T. solium and from all helminths tested. Hybridization studies showed the presence of two genes encoding a mRNA of 0.5 kb. Moreover, the gene presents an intron of 30 bp. Our phylogenetic analysis using S15a r-proteins reproduced the topologies reported for 16/18S rRNA.

Amino Acid Sequence↗
PubMed1989

Interplay between carbohydrate in the stalk and the length of the connecting peptide determines the cleavability of influenza virus hemagglutinin.

The ability of many viruses to replicate in host cells depends on cleavage of certain viral glycoproteins, including hemagglutinin (HA). By generating site-specific mutant HAs of two highly virulent influenza viruses, we established that the relationship between carbohydrate in the stalk and the length of the connecting peptide is a critical determinant of cleavability. HAs that lacked an oligosaccharide side chain in the stalk were cleaved regardless of the number of basic amino acids at the cleavage site, whereas those with the oligosaccharide side chain resisted cleavage unless additional basic amino acids were inserted. This finding suggests that the oligosaccharide side chain interferes with HA cleavage if the number of basic amino acids at the cleavage site is not adequate to nullify this effect. Similar interplay could influence cleavage of other viral glycoproteins, such as those of human and simian immunodeficiency viruses and paramyxoviruses.

Amino Acid Sequence↗
PubMed2006

Arginine mimetic structures in biologically active antagonists and inhibitors.

Peptidomimetics have found wide application as bioavailable, biostable, and potent mimetics of naturally occurring biologically active peptides. L-Arginine is a guanidino group-containing basic amino acid, which is positively charged at neutral pH and is involved in many important physiological and pathophysiological processes. Many enzymes display a preference for the arginine residue that is found in many natural substrates and in synthetic inhibitors of many trypsin-like serine proteases, e.g. thrombin, factor Xa, factor VIIa, trypsin, and in integrin receptor antagonists, used to treat many blood-coagulation disorders. Nitric oxide (NO), which is produced by oxidation of L-arginine in an NADPH- and O(2)-dependent process catalyzed by isoforms of nitric oxide synthase (NOS), exhibits diverse roles in both normal and pathological physiologies and has been postulated to be a contributor to the etiology of various diseases. Development of NOS inhibitors as well as analogs and mimetics of the natural substrate L-arginine, is desirable for potential therapeutic use and for a better understanding of their conformation when bound in the arginine binding site. The guanidino residue of arginine in many substrates, inhibitors, and antagonists forms strong ionic interactions with the carboxylate of an aspartic acid moiety, which provides specificity for the basic amino acid residue in the active side. However, a highly basic guanidino moiety incorporated in enzyme inhibitors or receptor antagonists is often associated with low selectivity and poor bioavailability after peroral application. Thus, significant effort is focused on the design and preparation of arginine mimetics that can confer selective inhibition for specific trypsin-like serine proteases and NOS inhibitors as well as integrin receptor antagonists and possess reduced basicity for enhanced oral bioavailability. This review will describe the survey of arginine mimetics designed to mimic the function of the arginine moiety in numerous peptidomimetic compounds (thrombin inhibitors, factor Xa inhibitors, factor VIIa inhibitors, integrin receptor antagonists, nitric oxide synthase inhibitors), with the aim of obtaining better activity, selectivity and oral bioavailability.

Arginine↗
PubMed2005

Essential role of cytoplasmic sequences for cell-surface sorting of the lectin-like oxidized LDL receptor-1 (LOX-1).

Lectin-like oxidized LDL receptor-1 (LOX-1) is an oxidized low-density lipoprotein (OxLDL) receptor found in endothelial cells and a member of the natural killer (NK) receptor gene complex. Here, we demonstrate that the ability of LOX-1 binding to OxLDL distinguishes it from other NK receptors. Domain swapping of the lectin-like domain between LOX-1 and the NK cell receptors CD94, NKG2D, and LY-49A demonstrated the crucial role of this domain for recognition of OxLDL by LOX-1, but not for the correct cell-surface sorting of LOX-1. Using LOX-1 GFP fusion constructs, we find that the combination of cytoplasmic and transmembrane domains of LOX-1 is sufficient to target the chimeric protein to the cell-surface. Using N-terminal deletions we determined that the correct cell-surface localization is dependent on a positively charged motif present in the cytosolic juxtamembrane region of LOX-1. Furthermore, the extracellular localization of the LOX-1 C-terminus is disrupted when we mutated the cytoplasmic basic amino acids, Lys-22, Lys-23 and Lys-25 to Glu. Collectively, these results indicate that the N-terminal cytoplasmic domain of LOX-1 determines the correct expression of the lectin domain on the cell-surface.

Amino Acid Motifs↗
PubMed1985

Interspersed blocks of repetitive and charged amino acids in a dominant immunogen of Plasmodium falciparum.

We describe an antigen of Plasmodium falciparum that is a dominant immunogen in man. The corresponding cDNA clone, Ag231, expressing this antigen in Escherichia coli reacted in an in situ colony assay with sera from up to approximately equal to 93% of 65 people living in an area in which P. falciparum is endemic. Human antibodies affinity purified on immobilized Ag231 lysates identified the corresponding parasite antigen as a polypeptide of Mr approximately equal to 300,000. It was present in schizonts and also in ring-stage trophozoites, where a speckled immunofluorescence pattern suggested an association with the erythrocyte. Its mRNA was enriched in merozoites relative to other blood stages, a distinctive property shared by a recently described antigen located on the surface of ring-infected erythrocytes, and it is encoded by a single gene having a number of allelic variants. The complete nucleotide sequence of Ag231 revealed a structural unit composed of 13 hexapeptide repeats flanked by a highly charged region containing both acidic and basic amino acids. This structural unit is itself repeated, so that blocks of repeats and charged units are interspersed along the molecule. The sequences within the repeats vary much more extensively than those in the charged units.

Amino Acid Sequence↗
PubMed1993

A leucine to arginine amino acid substitution at codon 46 of rhodopsin is responsible for a severe form of autosomal dominant retinitis pigmentosa.

To evaluate the extent to which rhodopsin mutations are involved in autosomal dominant forms of retinitis pigmentosa (adRP) we collected DNAs from patients with adRP and screened the rhodopsin coding sequence with single-strand conformational polymorphism (SSCP) analysis and DNA sequencing. This screening revealed a thymidine to guanine transversion at nucleotide 431 (nucleotide sequence numbers as per Genebank) in affected members of one family (RFS04). The nucleotide substitution leads to a missense mutation at the 46th amino acid of rhodopsin. The mutation occurs at an amino acid conserved in mammals and changes the hydrophobic nature of the protein at a transmembrane-spanning region. The mutation causes the substitution of a non-polar hydrophobic amino acid, leucine, for the basic amino acid arginine (Leu46Arg). This nucleotide substitution is unique to the family studied and occurs in the affected individuals in the family. Full-field electroretinograms (ERGs) in four affected members of the family showed nondetectable rod responses at an early age, with markedly reduced cone responses, and a faster than average rate of progression of the phenotype as measured by yearly ERGs.

Adolescent↗
PubMed1978

Characterization of the glucose transporter from human erythrocytes.

The D-glucose transporter from human erythrocytes has been purified and reconstituted by Kasahara and Hinkle (J Biol Chem 252:7394--7390). Using a similar purification scheme, we have isolated the protein with 65% of the extracted phospholipid at a lipid-protein ratio of 14:1 by weight. The KD (0.14 micrometer) and extent (11 nmoles/mg protein) for binding of 3H-cytochalasin B was determined by equilibrium dialysis. Glucose was a linear competitive inhibitor of binding of cytochalasin B, with an inhibition constant of 30 mM. To further characterize the protein, samples were filtered in the presence of sodium dodecyl sulfate (SDS) through Sepharose 6B to remove 95% of the lipid followed by filtration of Sephadex G150 to remove the remaining lipid and a contaminating amount of a minor, lower-molecular-weight protein. This preparation contains only 24% acidic and basic amino acids. The protein also contains 5% neutral sugars (of which 3% is galactose), 7% glucosamine, and 5% sialic acid.

Biological Transport↗
PubMed1979

Structural states of dictyostelium myosin.

Myosin purified from Dictyostelium amoebae has approximately 10% by weight of RNA associated with it, unless specific steps (DEAE cellulose chromatography or RNase digestion) are taken to remove it. This RNA has significant effects on the structural states formed by the myosin at low ionic strength in the presence of Mg2+. Rapid precipitation of RNA-free myosin by dilution generates bipolar thick filaments (540 nm long, 33 nm thick), often with a bare zone and a 15-nm transverse repeat. Rapid precipitation of myosin with copurified RNA yields linear aggregates of bipolar filaments, showing some lateral association. Slow precipitation of RNA-free myosin by dialysis yields very long filaments or ribbons (greater than 5 micrometer, 30--60 nm wide) in which the myosin may be packed diagonally across the filament, similar to the "side-polar" aggregates formed by other nonmuscle myosins and by smooth muscle myosin (Craig R, Megerman J: J Cell Biol 75:990, 1977; Hinssen H, D'Haese J, Small JV, Sobieszek A: J Ultrastruct Res 64:282, 1978). Slow precipitation of myosin with copurified RNA generates linear filaments with repeat intervals of 290 and 650 nm. Other polyanions were tested for their effects on myosin aggregation. Total RNA and ribosomal RNA from Dictyostelium, when added to RNA-free myosin, also induced the extensive linear aggregation seen with the copurified RNA/myosin complex, although higher concentrations of RNA were required to obtain quantitatively the same effect. DNA and heparin were also effective inducers of linear aggregation, whereas homopolymers of nucleotides and of acidic or basic amino acids were poorly effective.

Dictyostelium↗
PubMed2004

A combination of different mass spectroscopic techniques for the analysis of dynamic changes of histone modifications.

The N-terminal tails of the histones are subject to many enzyme-mediated post-translational modifications, such as lysine acetylation, lysine and arginine methylation, serine phosphorylation, poly-ADP ribosylation and the attachment of the small peptide ubiquitin. These modifications, singly or in combination, are thought to generate an epigenetic code that specifies different patterns of gene activity. We present a detailed study on the mapping of histone post-translational modifications using a combination of matrix-assisted laser desorption/ionization-time of flight and electrospray ionization tandem mass spectrometry analysis of peptides generated by protease cleavage of individual histones isolated from different developmental stages. Due to their high content in basic amino acid residues and in order to be able to quantitatively compare two different samples we developed a chemical derivatization protocol. This strategy enabled us to determine the primary sequence of the peptides and to unambiguously assign specific modifications. This method is generally applicable to histone samples from various sources and can be used to study changes of modification patterns during early embryonic development or tissue differentiation and regeneration.

Amino Acid Sequence↗
PubMed2004

Oligopeptide-mediated acceleration of amyloid fibril formation of amyloid beta(Abeta) and alpha-synuclein fragment peptide (NAC).

The effects of oligopeptides on the secondary structures of Abeta and NAC, a fragment of alpha-synuclein protein, were studied by circular dichroism (CD) spectra. The effects of oligopeptides on the amyloid fibril formation were also studied by fluorescence spectra due to thioflavine-T. The oligopeptides were composed of a fragment of Abeta or NAC and were interposed by acidic or basic amino acid residues. The peptide, Ac-ELVFFAKK-NH2, which involved a fragment Leu-Val-Phe-Phe-Ala at Abeta(17-21), had no effect on the secondary structures of Abeta(1-28) in 60% or 90% trifluoroethanol (TFE) solutions at both pH 3.2 and pH 7.2. However, it showed pronounced effects on the secondary structure of Abeta(1-28) at pH 5.4. The Ac-ELVFFAKK-NH2 reduced the alpha-helical content, while it increased the beta-sheet content of Abeta(1-28). In phosphate buffer solutions at pH 7.0, Ac-ELVFFAKK-NH2 had little effect on the secondary structures of Abeta(1-28). However, it accelerated amyloid fibril formation when monitored by fluorescence spectra due to thioflavine-T. On the other hand, LPFFD, a peptide known as a beta-sheet breaker, caused neither an appreciable extent of change in the secondary structure nor amyloid fibril formation in the same buffer solution. The peptide, Ac-ETVK-NH2, which involved a fragment Thr-Val at NAC(21-22), had no effect on the secondary structure of NAC in 90% TFE and in isotonic phosphate buffer. However, Ac-ETVK-NH2 in water with small amounts of NaN3 and hexafluoroisopropanol greatly increased the beta-sheet content of NAC after standing the solution for more than 1 week. Interestingly, in this solution. Ac-ETVK-NH2, accelerated the fibril formation of NAC. It was concluded that an oligopeptide that involves a fragment of amyloidogenic proteins could be a trigger for the formation of amyloid plaques of the proteins even when it had little effect on the secondary structures of the proteins as monitored by CD spectra for a short incubation time.

Amino Acid Sequence↗
PubMed1986

The sensitivity of isoelectric focusing and electrophoresis in the detection of sequence differences in proteins.

Fourteen myoglobins of known sequence were examined by isoelectric focusing with and without urea. The 14 sequences formed six distinct mobility classes on gels without urea and three classes on those with urea. For these proteins, isoelectric focusing provides no advantage over single, nonequilibrium, nondenaturing gels in the total number of distinguishable mobility classes. Only major charge differences, resulting from the changes in the total numbers of acidic and basic amino acids, can be detected on gels with urea, indicating that denaturation by urea alters proteins so that small differences in ionization are eliminated.

Amino Acid Sequence↗
PubMed1986

Chemosensory stimuli in feeding behavior of the leech Hirudo medicinalis.

The involvement of chemotherapy stimuli in the feeding behavior of the blood-sucking leech Hirudo medicinalis was investigated using a behavioral feeding test in which test solutions were encased in a highly permeable membrane and presented to the leech. Whole human blood or plasma at ambient temperature elicited the complete sequence of feeding behavior: probing, attachment, biting and ingestion. Spring water, 300 mM sucrose, or dialyzed plasma did not elicit any of these responses. Spring water warmed to 38 degrees C elicited probing and transient attachment but not ingestion. Thus, appropriate chemical stimuli were necessary for complete feeding behavior. A chemically defined artificial blood mix, containing the major components of low molecular weight found in blood, elicited all aspects of leech feeding behavior. Eliminating either NaCl or arginine from the mix resulted in complete loss of effectiveness. Moreover, a solution containing only NaCl (150 mM) and arginine (90 microM) was also an effective feeding stimulus. Thus, appropriate chemical stimuli are sufficient for complete feeding behavior. Neither NaCl nor arginine alone induced feeding although NaCl alone elicited probing. Sensory detection of blood was localized to a region of the dorsal lip that contains structures composed of ciliated, bipolar neurons, which are likely candidates as chemoreceptors. Surgical ablation of this region of the skin resulted in complete loss of ability to alert to, orient toward and ingest blood, while sham-operated controls fed normally. Substitution with other ions revealed specificity, with respect to both the cation and the anion, in the response to NaCl. Of the inorganic and organic cations tested, only Li+ substituted effectively for Na+. Of the inorganic and organic anions tested, only Br- was as effective as Cl-. Thus, the requirement for NaCl in leech feeding represents more than simply an ionic strength requirement or a requirement for Na+ ions and bears similarities to the chemosensory detection of NaCl in other species. Substitution with other amino acids and analogues for arginine revealed marked specificity in the feeding response to this compound as well. D-arginine at concentrations of up to 1000-fold greater than the effective threshold for L-arginine did not elicit ingestion, nor did other common L-amino acids, including the other basic amino acids histidine and lysine. Of the arginine analogues tested, only homoarginine and canavanine (in which all three functional groups of arginine are unchanged) were effective feeding stimulants.

Animals↗