Circular dichroism of aggregated deoxyhemoglobin S and the effect of amino acids.

It is well known that deoxyhemoglobin S (deoxy Hb S) aggregates at 37 °C and that it disaggregates at 1–5 °C. In this study solutions of pure Hb S at concentrations of 20–22 g/100 ml exhibit a normal circular dichroic spectrum in the range 250–650 nm at the temperature 1 °C. However, by the proper manipulation of the following parameters: temperatures of 1, 24 and 37 °C as well as the times required to change temperature and periods of maintaining at a certain temperature, five stages with different circular dichroic spectra can be produced. Not only the dichroic spectra of these stages are different but the kinetic behavior and stability of each of these stages are different. The evidence suggests that the mechanism of aggregation is similar to crystallization; that is, it exhibits a period of nucleation followed by growth. The overall kinetics of circular dichroic changes are described. At representative solution conditions the circular dichroic changes have been compared and found to parallel gel formation with pure Hb S. Also, the effect of certain anti-sickling amino acids (Sophianopoulos, A. J., et al. (1974) Clin. Biochem.7, 112–118) on the minimum Hb S concentration at which circular dichroic changes occur has been studied, and arginine chloride and arginine aspartate were found to raise this minimum concentration appreciably.     

Guanidination of Soluble Lysine-Rich Cyanophycin Yields a Homoarginine-Containing Polyamide

Soluble cyanobacterial granule polypeptide (CGP), especially that isolated from recombinant Escherichia coli strains, consists of aspartic acid, arginine, and a greater amount of lysine than that in insoluble CGP isolated from cyanobacteria or various other recombinant bacteria. In vitro guanidination of lysine side chains of soluble CGP with o-methylisourea (OMIU) yielded the nonproteinogenic amino acid homoarginine. The modified soluble CGP consisted of 51 mol% aspartate, 14 mol% arginine, and 35 mol% homoarginine. The complete conversion of lysine residues to homoarginine was confirmed by (i) nuclear magnetic resonance spectrometry, (ii) coupled liquid chromatography-mass spectrometry, and (iii) high-performance liquid chromatography. Unlike soluble CGP, this new homoarginine-containing polyamide was soluble only under acidic or alkaline conditions and was insoluble in water or at a neutral pH. Thus, it showed solubility behavior similar to that of the natural insoluble polymer isolated from cyanobacteria, consisting of aspartic acid and arginine only. Polyacrylamide gel electrophoresis revealed similar degrees of polymerization of the native (12- to 40-kDa) and modified (10- to 35-kDa) polymers. This study showed that the chemical structure and properties of a biopolymer could be changed by in vitro introduction of a new functional group after biosynthesis of the native polymer. In addition, the modified CGP could be digested in vitro using the cyanophycinase from Pseudomonas alcaligenes strain DIP1, yielding a new dipeptide consisting of aspartate and homoarginine.     

Rational design of pyridyl derivatives of vanillin for the treatment of sickle cell disease

Hypoxia-induced polymerization of sickle hemoglobin (Hb S) is the principal phenomenon that underlays the pathophysiology and morbidity associated with sickle cell disease (SCD). Opportunely, as an allosteric protein, hemoglobin (Hb) serves as a convenient and potentially critical druggable target. Consequently, molecules that prevent Hb S polymerization (Hb modifiers), and the associated erythrocyte sickling have been investigated–and retain significant interest–as a viable therapeutic strategy for SCD. This group of molecules, including aromatic aldehydes, form high oxygen affinity Schiff-base adducts with Hb S, which are resistant to polymerization. Here, we report the design and synthesis of novel potent antisickling agents (SAJ-009, SAJ-310 and SAJ-270) based on the pharmacophore of vanillin and INN-312, a previously reported pyridyl derivative of vanillin. These novel derivatives exhibited superior in vitro binding and pharmacokinetic properties compared to vanillin, which translated into significantly enhanced allosteric and antisickling properties. Crystal structure studies of liganded Hb in the R2 quaternary state in complex with SAJ-310 provided important insights into the allosteric and antisickling properties of this group of compounds. While these derivatives generally show similar in vitro biological potency, significant structure-dependent differences in their biochemical profiles would help predict the most promising candidates for successful in vivo pre-clinical translational studies and inform further structural modifications to improve on their pharmacologic properties.     

Characterization of a glycoprotein in the cyst fluid of Cysticercus tenuicollis from the goat

Dixon S. N., Gibbons R., Parker Janice and Sellwood R. 1973. Characterization of a glycoprotein in the cyst fluid of Cysticercus tenuicollis from the goat. International Journal for Parasitology3:419–424. In the fluids of two tapeworm cysts from goats a prominent periodic acid- Schiff reagent staining protein was found on gel electrophoretograms. In one case serum proteins from the host were also observed. The glycoprotein has been isolated and found to contain about 7·7 per cent heterosaccharide consisting of glucose, galactose, mannose, fucose, neuraminic acid, glucosamine and an unidentified component. The amino acid portion is extremely rich in glutamic acid, aspartic acid, lysine and arginine. Its molecular weight is approximately 90,000. A small degree of heterogeneity was demonstrated by ultra-centrifugal analysis; this may be due to the presence of about 3 per cent of a glycosaminoglycan. In view of the high proportion of charged amino acids it is suggested that this glycoprotein, which appears to be derived from the parasite, functions as the osmotically active macromolecule in the cyst fluid maintaining the turgidity of the cyst.     

Hemoglobins Austin and Waco: two hemoglobins with substitutions in the alpha 1 beta 2 contact region.

Hemoglobins (Hbs) Austin and Waco were detected by their electrophoretic migration on cellulose acetate (pH 8.4) and citrate agar (pH 6.2). By these methods, both variants migrated between Hbs A and F. Globin chain analysis at pH 8.6 indicated that the mutant β chain of Hb Austin was faster moving than the β^A chain; however, the mutant chain of Hb Waco was indistinguishable from the β^A chain by this technique. The two variants were isolated by ion-exchange column chromatography. Sequence studies demonstrated a substitution of serine (Hb Austin) and lysine (Hb Waco) for arginine at position 40 in the β chain. These mutations involve an amino acid residue in the α₁β₂ contact region, which, before this report, had been considered invariant in all hemoglobin sequences. Hb Austin was found to exist as dimers when oxygenated and as tetramers when deoxygenated. The equilibrium constant (K_d) for the tetramer to dimer transition was approximately 300 × 10^?6m, as calculated from sedimentation velocity studies. This variant also had high oxygen affinity, a much reduced heme-heme interaction, and a normal Bohr effect. The functional properties of Hb Waco were similar to those of Hb A.     

Transport of arginine and aspartic Acid into isolated barley mesophyll vacuoles

The transport of arginine into isolated barley (Hordeum vulgare L.) mesophyll vacuoles was investigated. In the absence of ATP, arginine uptake was saturable with a K_m of 0.3 to 0.4 millimolar. Positively charged amino acids inhibited arginine uptake, lysine being most potent with a K_i of 1.2 millimolar. In the presence of free ATP, but not of its Mg-complex, uptake of arginine was drastically enhanced and a linear function of its concentration up to 16 millimolar. The nonhydrolyzable adenylyl imidodiphosphate, but no other nucleotide tested, could substitute for ATP. Therefore, it is suggested that this process does not require energy and does not involve the tonoplast ATPase. The ATP-dependent arginine uptake was strongly inhibited by p-chloromercuriphenylsulfonic acid. Furthermore, hydrophobic amino acids were inhibitory (I₅₀ phenylalanine 1 millimolar). Similar characteristics were observed for the uptake of aspartic acid. However, rates of ATP-stimulated aspartic acid transport were 10-fold lower as compared to arginine transport. Uptake of aspartate in the absence of ATP was negligible.     

Statistical evaluation of ways to analyze nonideal systems by sedimentation equilibrim

Three equations describing sedimentation equilibrium are examined and tested for their ability to analyze data. The testing procedure using simulated data is similar to that described previously (Holladay, L. A., and Sophianopoulos, A. J. (1972) J. Biol. Chem.247, 427–439) and used with another equation. The equations examined here are found to be of much less statistical reliability and of a more restricted range of application than the previously examined equation. The equation described previously, (Holladay, L. A., and Sophianopoulos, A. J. (1972) J. Biol. Chem.247, 427–439) is also used here to examine the conditions necessary to detect isodesmic systems of more than four components. The self-association of lysozyme reported previously (Sophianopoulos, A. J., and Van Holde, K. E. (1964) J. Biol. Chem.239, 2516–2524) is reexamined at pH 8.2, 0.15 ionic strength, and 13°C. The tentative conclusion is that the system is mainly a monomer-dimer, with a small, uncertain amount of tetramer possibly present. Under the above conditions the second virial coefficient, B, is estimated to lie in the range 0–4.4 × 10^?6 mole·dl·g^?2, the dimerization constant. K₂₁, lies in the range 2.3–2.7 × 10^?3m, and the tetramerdimer constant, K₄₂, is in the range 1.5–15 × 10^?3m.     

Stimulation of Lysine Decarboxylase Production in Escherichia coli by Amino Acids and Peptides

A commercial hydrolysate of casein stimulated production of lysine decarboxylase (EC 4.1.1.18) by Escherichia coli B. Cellulose and gel chromatography of this hydrolysate yielded peptides which were variably effective in this stimulation. Replacement of individual, stimulatory peptides by equivalent amino acids duplicated the enzyme levels attained with those peptides. There was no indication of specific stimulation by any peptide. The peptides were probably taken up by the oligopeptide transport system of E. coli and hydrolyzed intracellularly by peptidases to their constituent amino acids for use in enzyme synthesis. Single omission of amino acids from mixtures was used to screen them for their relative lysine decarboxylase stimulating abilities. Over 100 different mixtures were evaluated in establishing the total amino acid requirements for maximal synthesis of lysine decarboxylase by E. coli B. A mixture containing all of the common amino acids except glutamic acid, aspartic acid, and alanine increased lysine decarboxylase threefold over an equivalent weight of casein hydrolysate. The nine most stimulatory amino acids were methionine, arginine, cystine, leucine, isoleucine, glutamine, threonine, tyrosine, and asparagine. Methionine and arginine quantitatively were the most important. A mixture of these nine was 87% as effective as the complete mixture. Several amino acids were inhibitory at moderate concentrations, and alanine (2.53 mM) was the most effective. Added pyridoxine increased lysine decarboxylase activity 30%, whereas other B vitamins and cyclic adenosine 5′-monophosphate had no effect.     

Isolation and properties of two allelic chymotrypsin inhibitors from the hemolymph of the silkworm,Bombyx mori

A chymotrypsin inhibitor, CI-1, and its co-dominant allelic counterpart CI-2, detectable in certain strains of Bombyx mori each as an electrophoretic band close to the origin, were purified from the larval hemolymph by using ion-exchange and affinity chromatography. CIs 1 and 2 were monomeric neutral proteins with a pI of 7.12 and 7.00 and an M_r of about 10,400 and 7900, respectively. Amino acid analysis showed that these inhibitors were rich in aspartic acid (or asparagine), glutamic acid (or glutamine) and lysine, but poor, or lacking, in valine, methionine, histidine and arginine. In the amino-terminal sequence, 14 out of 20 amino acid residues analyzed were common between CIs 1 and 2.     

Aspartic Acid 397 in Subunit B of the Na+-pumping NADH:Quinone Oxidoreductase from Vibrio cholerae Forms Part of a Sodium-binding Site,Is Involved in Cation Selectivity,and Affects Cation-binding Site Cooperativity

The Na⁺-pumping NADH:quinone complex is found in Vibrio cholerae and other marine and pathogenic bacteria. NADH:ubiquinone oxidoreductase oxidizes NADH and reduces ubiquinone, using the free energy released by this reaction to pump sodium ions across the cell membrane. In a previous report, a conserved aspartic acid residue in the NqrB subunit at position 397, located in the cytosolic face of this protein, was proposed to be involved in the capture of sodium. Here, we studied the role of this residue through the characterization of mutant enzymes in which this aspartic acid was substituted by other residues that change charge and size, such as arginine, serine, lysine, glutamic acid, and cysteine. Our results indicate that NqrB-Asp-397 forms part of one of the at least two sodium-binding sites and that both size and charge at this position are critical for the function of the enzyme. Moreover, we demonstrate that this residue is involved in cation selectivity, has a critical role in the communication between sodium-binding sites, by promoting cooperativity, and controls the electron transfer step involved in sodium uptake (2Fe-2S → FMN_C).     

A chiron approach towards the synthesis of 3-hydroxy lysine and its derivatives

A general and efficient route towards the synthesis of three derivatives of structurally and functionally important amino acid, lysine is reported. Chemoselective reduction of aldehydic functionality in C-3-azido conjugated aldehyde 4, under Luche condition, is the key step in the synthetic sequence. The lysine derivative, (2S,3R)-2,6-diazido-3-hydroxy-hex-4-ene-oic acid 9 could be used to prepare switch peptide using Staudinger reaction, while the unprotected (2S,3R)-2,6-diamino-3-hydroxy-hexanoic acid hydrochloride 10 is a proven reaction intermediate towards the synthesis of natural product (?)-Balanol.     

Studies on the conformation of secretin: The position of the helical stretch

An analog of the C-terminal tricosapeptide of secretin, with aspartic acid replacing glutamic acid in position 9 and lysine substituted for arginine in position 21, was prepared. The synthesis was carried out in solution by stepwise chain lengthening with the application of the in situ technique. The ord-cd spectra of this new analog closely resemble the spectra of the tricosapeptide with the unaltered secretin sequence and of the analog in which only arginine-21 was replaced by lysine and of secretin itself. The incorporation of aspartic acid instead of glutamic acid-9 resulted in an N-terminal sequence that has a consïderably reduced probability of assuming a helical conformation. The observation that the helix content remained unchanged adds support to a model of secretin in which the helical stretch is near the C-terminus. The role of an acidic residue in position 9 is also discussed.     

Rhipicephalus sanguineus: amino acid composition of egg shell

Acid hydrolysis of the protein fraction of a batch of egg shells of Rhipicephalus sanguineus was followed by determination of the amino acids in the hydrolysate. Using thin layer chromatography, the amino acids—lysine, arginine, aspartic acid, serine, glycine, glutamic acid, alanine, threonine, valine, tyrosine, isoleucine, and leucine were identified. Alkaline hydrolysis of the fraction followed by TLC revealed the presence of tryptophane. Chitin was revealed utilizing a chitosan test.     

Photosynthetic formation of the aspartate family of amino acids in isolated chloroplasts

The metabolism of ¹⁴C-labeled aspartic acid, diaminopimelic acid, malic acid and threonine by isolated pea (Pisum sativum L.) chloroplasts was examined. Light enhanced the incorporation of [¹⁴C] aspartic acid into soluble homoserine, isoleucine, lysine, methionine and threonine and protein-bound aspartic acid plus asparagine, isoleucine, lysine, and threonine. Lysine (2 millimolar) inhibited its own formation as well as that of homoserine, isoleucine and threonine. Threonine (2 millimolar) inhibited its own synthesis and that of homoserine but had only a small effect on isoleucine and lysine formation. Lysine and threonine (2 millimolar each) in combination strongly inhibited their own synthesis as well as that of homoserine. Radioactive [1,7-¹⁴C]diaminopimelic acid was readily converted into [¹⁴C]threonine in the light and its labeling was reduced by exogenous isoleucine (2 millimolar) or a combination of leucine and valine (2 millimolar each). The strong light stimulation of amino acid formation illustrates the point that photosynthetic energy is used in situ for amino acid and protein biosynthesis, not solely for CO₂ fixation.     

Synthesis and evaluation of novel neamine derivatives effectively targeting to RNA

Three new derivatives of neamine, 3 (NE), 6 (NEA) and 9 (NEL), were synthesized by connecting arginine or lysine to 5-hydroxyl group of neamine using ethylenediamine as a linker. The binding affinities of these derivatives to A site of 16S RNA and TAR RNA indicate that the modification on 5-hydroxyl of neamine by amino acid can enhance the binding affinity of neamine. Compound 9 (NEL) shows some antibacterial activities. These results demonstrate that modification on 5-hydroxyl group of neamine may provide a promising way for the development of potential candidates effectively targeting to RNAs.     

Interaction of arginine,lysine, and guanidine with surface residues of lysozyme: implication to protein stability

Additives are widely used to suppress aggregation of therapeutic proteins. However, the molecular mechanisms of effect of additives to stabilize proteins are still unclear. To understand this, we herein perform molecular dynamics simulations of lysozyme in the presence of three commonly used additives: arginine, lysine, and guanidine. These additives have different effects on stability of proteins and have different structures with some similarities; arginine and lysine have aliphatic side chain, while arginine has a guanidinium group. We analyze atomic contact frequencies to study the interactions of the additives with individual residues of lysozyme. Contact coefficient, quantified from contact frequencies, is helpful in analyzing the interactions with the guanidine groups as well as aliphatic side chains of arginine and lysine. Strong preference for contacts to the additives (over water) is seen for the acidic followed by polar and the aromatic residues. Further analysis suggests that the hydration layer around the protein surface is depleted more in the presence of arginine, followed by lysine and guanidine. Molecular dynamics simulations also reveal that the internal dynamics of protein, as indicated by the lifetimes of the hydrogen bonds within the protein, changes depending on the additives. Particularly, we note that the side-chain hydrogen-bonding patterns within the protein differ with the additives, with several side-chain hydrogen bonds missing in the presence of guanidine. These results collectively indicate that the aliphatic chain of arginine and lysine plays a critical role in the stabilization of the protein.     

Carbohydrases and phytase with rice bran,effects on amino acid digestibility and energy use in broiler chickens

Protein sources from cereals are used in broiler diets, usually in order to reduce feeding costs. However, their efficient use in poultry diets is limited by the level of fiber whose compounds are resistant to digestion in the small intestine; due to this sugars are not digested by endogenous poultry enzymes. The aim of this study was to determine the effect of multi-carbohydrase (MC) and phytase (Phy) on the total retention of nutrients, retention of apparent metabolizable energy corrected for nitrogen (AME_N) (trial 1) and apparent and standardized ileal digestibility of amino acids (trial 2) of rice bran (RB). A total of 245-day-old male broilers (Cobb 500) was distributed at 21-day-old in a completely randomized design in a 2 × 2 + 1 (0 and 200 mg/kg MC; 0 and 50 mg/kg Phy, and basal diet – BD) factorial arrangement of treatments, to give seven replicates and seven birds per replicate. The BD based on corn (trial 1) and cornstarch and casein (trial 2) was used only to determine the coefficients of retention of nutrients and energy, and coefficients of digestibility of amino acids of the RB. The test diets were made by mixing BD and RB 7 : 3 wt/wt basis. There was interaction (P<0.05) between MC × Phy for DM, nitrogen and AMEN, retention and no interaction (P>0.05) for ash, calcium, phosphorous and NDF was observed. Enzymes interacted (P<0.05) on standardized ileal digestibility of arginine, histidine, leucine, methionine, phenylalanine, threonine, valine, aspartic acid, glutamic acid, proline and serine. Dietary combination of MC and Phy resulted in higher (P<0.05) standardized digestibility of arginine, histidine, methionine and threonine relative to single enzyme supplementation or control diet without enzymes. Enzyme isolated inclusions in the diets improved (P<0.05) standardized digestibility of methionine. The supplementation of carbohydrases and Phy in RB will improve the nitrogen, energy and amino acids utilization for broiler chickens.     

Cerato-ulmin—a wilting toxin of Dutch elm disease fungus

Cerato-ulmin, a toxin produced by Ceratocystis ulmi, the causal agent of Dutch elm disease, has been characterized as a small protein (128 residues) with a MW of ca 13000. The protein has a high content of cystine, proline, leucine, serine and aspartic acid/asparagine; it is low in histidine, lysine, arginine, isoleucine, phenylalanine and tyrosine and does not contain cysteine, methionine, or tryptophan. The amino acid sequence of the N-terminal region is: H₂N-Ala-Asp-Ser-Tyr-Asp-Pro-Cys-Thr-Gly-Leu-Leu-Gln-Lys-Ser-Pro-Gln-Cys-Cys-Asp-Thr-Asp-Ile-Leu-Gly-Val-Ser-Asp-Leu-Asp-Cys-. Toxic symptoms similar to those of Dutch elm disease can be elicited by cerato-ulmin in white elm shoot cuttings (Ulmus americana L.).     

Regulation of lysine transport by feedback inhibition in Saccharomyces cerevisiae.

A steady-state level of about 240 nmol/mg (dry wt) occurs during lysine transport in Saccharomyces cerevisiae. No subsequent efflux of the accumulated amino acid was detected. Two transport systems mediate lysine transport, a high-affinity, lysine-specific system and an arginine-lysine system for which lysine exhibits a lower affinity. Preloading with lysine, arginine, glutamic acid, or aspartic acid inhibited lysine transport activity; preloading with glutamine, glycine, methionine, phenylalanine, or valine had little effect; however, preloading with histidine stimulated lysine transport activity. These preloading effects correlated with fluctuations in the intracellular lysine and/or arginine pool: lysine transport activity was inhibited when increases in the lysine and/or arginine pool occurred and was stimulated when decreases in the lysine and/or arginine pool occurred. After addition of lysine to a growing culture, lysine transport activity was inhibited more than threefold in one-third of the doubling time of the culture. These results indicate that the lysine-specific and arginine-lysine transport systems are regulated by feedback inhibition that may be mediated by intracellular lysine and arginine.