Substitution of the N-glycan function in glycosyltransferases by specific amino acids: ST3Gal-V as a model enzyme

The sialyltranferase ST3Gal-V transfers a sialic acid to lactosylceramide. We investigated the role of each of the N-glycans modifying mouse ST3Gal-V (mST3Gal-V) by measuring the in vitro enzyme activity of Chinese hamster ovary (CHO) cells transfected with ST3Gal-V cDNA or its mutants. By examining mutants of mST3Gal-V, in which each asparagine was replaced with glutamine (N180Q, N224Q, N334Q), we determined that all three sites are N-glycosylated and that each N-glycan is required for enzyme activity. Despite their importance, N-glycosylation sites in ST3Gal-V are not conserved among species. Therefore, we considered whether the function in the activity that is performed in mST3Gal-V by the N-glycan could be substituted for by specific amino acid residues selected from the ST3Gal-V of other species or from related sialyltransferases (ST3Gal-I, -II, -III, and -IV), placed at or near the glycosylation sites. To this end, we constructed a series of interspecies mutants for mST3Gal-V, specifically, mST3Gal-V-H177D-N180S (medaka or tetraodon type), mST3Gal-V-N224K (human type), and mST3Gal-V-T336Q (zebrafish type). The ST3Gal-V activity of these mutants was quite similar to that of the wild-type enzyme. Thus, we have demonstrated here that the N-glycans on mST3Gal-V are required for activity but can be substituted for specific amino acid residues placed at or near the glycosylation sites. We named this method SUNGA (substitution of N-glycan functions in glycosyltransferases by specific amino acids). Furthermore, we verified that the ST3Gal-V mutant created using the SUNGA method maintains its high activity when expressed in Escherichia coli thereby establishing the usefulness of the SUNGA method in exploring the function of N-glycans in vivo.     

The AAA amino acid list a mnemonic derivation of the structures and properties of the amino acids

A rhymed presentation of the amino acids, consisting of one line per amino acid, gives the structures of the amino acids, their nomenclature, abbreviations, pKs, basic chemistry, dietary requirements and the characteristics of the peptide bond.     

Determination of the specific activity of sheep plasma amino acids using high-performance liquid chromatography: comparison study between liquid scintillation counter and on-line flow-through detector

A method was developed for the determination of the specific activities of leucine and phenylalanine in plasma using a flow-through scintillation counter coupled with high-performance liquid chromatography components. Results were compared with those obtained from liquid scintillation counting. Differences in the specific activities of leucine and phenylalanine between the two methods were not statistically significant. We concluded that flow-through radioactivity detection can be used for quantitative amino acid assays. However, the minimum activity that can be detected may be prohibitively low in certain applications.     

Increased enantioselectivity in the enzymatic hydrolysis of amino acid esters in the ionic liquid 1-butyl-3-methyl-imidazolium tetrafluoroborate

The initial rate and enantioselectivity of enzymatic asymmetric hydrolysis of amino acid esters were examined in methylimidazolium-based ionic liquids with anions including tetrafluoroborate, chloride, bromide and bisulfate and in typical organic solvents. Papain displayed much higher enantioselectivity but lower activity in phosphate buffer solution of 1-butyl-3-methylimidazolium tetrafluoroborate BMIM·BF₄ than in other media tested (i.e. E=100, V ₀=0.21 mM min^-1 in BMIM·BF₄, E=2, V ₀=0.43 mM min^-1 in phosphate buffer, E=14-92, V ₀=0.22-0.25 mM min^-1 in organic solvents for D,L-phenylglycine methyl ester). The influence of BMIM·BF₄ on enzyme activity and enantioselectivity also varied with the substrate and the enzyme used. All of the enzymes assayed showed no activity or low enantioselectivity in the ILs with anions including chloride, bromide and bisulfate.     

Data bank of three-dimensional structures of disaccharides,a tool to build 3-D structures of oligosaccharides

This work presents the first part of a database of conformations for all the disaccharide fragments that are found inN-glycans. The conformational study of the five disaccharides found in the oligo-mannose type are presented here. For each disaccharide, several possible conformations are described. A method is presented to obtain realistic models of oligosaccharides using molecular mechanic methods. Analysis of some possible conformations of the oligo-mannose type glycan Man₆-GlcNAc₂ is given as an illustration of the possibilities.On post-doctoral leave from CERMAV-CNRS, Grenoble, France     

Permeability of membranes to amino acids and modified amino acids: Mechanisms involved in translocation

Summary The amino acid permeability of membranes is of interest because they are one of the key solutes involved in cell function. Membrane permeability coefficients (P) for amino acid classes, including neutral, polar, hydrophobic, and charged species, have been measured and compared using a variety of techniques. Decreasing lipid chain length increased permeability slightly (5-fold), while variations in pH had only minor effects on the permeability coefficients of the amino acids tested in liposomes. Increasing the membrane surface charge increased the permeability of amino acids of the opposite charge, while increasing the cholesterol content decreased membrane permeability. The permeability coefficients for most amino acids tested were surprisingly similar to those previously measured for monovalent cations such as sodium and potassium (approximately 10^–12–10^–13 cm · s^–1). This observation suggests that the permeation rates for the neutral, polar and charged amino acids are controlled by bilayer fluctuations and transient defects, rather than partition coefficients and Born energy barriers. Hydrophobic amino acids were 10² more permeable than the hydrophilic forms, reflecting their increased partition coefficient values.External pH had dramatic effects on the permeation rates for the modified amino acid lysine methyl ester in response to transmembrane pH gradients. It was established that lysine methyl ester and other modified short peptides permeate rapidly (P = 10^–2 cm · s^–1) as neutral (deprotonated) molecules. It was also shown that charge distributions dramatically alter permeation rates for modified di-peptides. These results may relate to the movement of peptides through membranes during protein translocation and to the origin of cellular membrane transport on the early Earth.Abbreviations DCP dicetylphosphate - DMPC dimyristoyl phosphatidylcholine - EPC egg phosphatidylcholine - LUV large unilamellar vesicle - MLV multilamellar vesicle - PLM planar lipid membrane - SUV small unilamellar vesicle - pH transmembrane pH gradient     

Glycation research in amino acids: a place to call home

This is an introduction to a collection of review articles by leading investigators in the field of protein glycation research, see following articles in this issue. With this we launch a section of this journal now established for presentation of research results, reviews and commentaries on protein glycation and related topics. Glycation is the spontaneous, non-enzymatic reaction of protein with saccharides and saccharide derivatives. Although studied in the modern scientific era for over 100 years, its importance in the biology, medicine, food and nutrition, pharmacology and toxicology, and technological processing remains intriguingly undisclosed. In this section of amino acids, research on glycation is a qualifier for publication. Glycation research now has a place to call home.     

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.     

A survey of hydrogen bond geometries in the crystal structures of amino acids

An analysis of the geometries of the hydrogen bonds observed by neutron diffraction in thirt-two crystal structures of amino acids shows the following results. Of the 168 hydrogen bonds in the data set, 64 involve the zwitterion groups 

and $\text{C}$O₂. Another 18 are from

to sulphate or carbonyl oxygens. The majority, 46, of these

H … O bonds are three-centered (bifurcated). Nine are four-centered (trifurcated). The geometry in which the three-centered hydrogen bond involves both oxygens of the same carboxylate group is not especially favoured. When it does occur, one hydrogen bond is generally shorter and the other longer, than when the bonding involves oxygens on different carboxylate groups. The shortest hydrogen bonds are the OH … O $\text{C}$, from a carboxylic acid hydroxyl to a carboxylate oxygen, and NH … O$\text{C}$ when the nitrogen is the ring atom in histidine or proline. Carboxylate groups, on average, accept six hydrogen bonds, with no examples of less than four bonds. The reason for the large number of three-centered

H … O$\text{C}$ bonds is therefore a proton deficiency arising from the disparity between the tripled donor property of the

groups and the sextuple, on average, acceptor property of the carboxylate groups. There is good geometrical evidence for the existence of H … O and H … Cl^? hydrogen bonds, especially involving the hydrogen atoms on α-atoms.     

Optimization of the formation of embedded multicellular spheroids of MCF-7 cells: How to reliably produce a biomimetic 3D model

To obtain a multicellular MCF-7 spheroid model to mimic the three-dimensional (3D) of tumors, the microwell liquid overlay (A) and hanging-drop/agar (B) methods were first compared for their technical parameters. Then a method for embedding spheroids within collagen was optimized. For method A, centrifugation assisted cells form irregular aggregates but not spheroids. For method B, an extended sedimentation period of over 24 h for cell suspensions and increased viscosity of the culture medium using methylcellulose were necessary to harvest a dense and regular cell spheroid. When the number was less than 5000 cells/drop, embedded spheroids showed no tight cores and higher viability than the unembedded. However, above 5000 cells/drop, cellular viability of embedded spheroids was not significantly different from unembedded spheroids and cells invading through the collagen were in a sun-burst pattern with tight cores. Propidium Iodide staining indicated that spheroids had necrotic cores. The doxorubicin cytotoxicity demonstrated that spheroids were less susceptible to DOX than their monolayer cells. A reliable and reproducible method for embedding spheroids using the hanging-drop/agarose method within collagen is described herein. The cell culture model can be used to guide experimental manipulation of 3D cell cultures and to evaluate anticancer drug efficacy.     

Role of organic acids in the formation of the ionic composition in developing glycophyte leaves

The ionic composition in the leaves of some glycophyte plants (Phaseolus vulgaris L., Lycopersicon esculentum L., and Amaranthus cruentus L.) was studied during leaf development. Plants were grown in a stationary hydroponic culture; a growth medium contained equimolar concentrations of inorganic ions (NO ₃ ^? , Cl^?, SO ₄ ^2? , H₂PO ₄ ^? , K⁺, Ca²⁺, Mg²⁺, and Na⁺) equal to 5 mg-equiv./l for each ion. In the juvenile leaf, the main ions were K⁺ and water-soluble anions of organic acids represented mainly by di-and tricarboxylic acids in kidney bean and tomato and oxalic acid in amaranth. An increase in the total amount of organic anions, coinciding with the accumulation of bivalent cations, was registered in leaves of glycophytes during their development. Mature and senescing leaves of tomato and kidney bean accumulated mainly di-and tricarboxylic acid salts with the prevalence of Ca²⁺ ions. In amaranth leaves, the formation of water-insoluble (acid-soluble) oxalate pool containing Ca²⁺ ions (mature leaves) or Ca²⁺ and Mg²⁺ ions (senescing leaves) was registered. The priority role of the metabolism of organic acids in the formation of the ionic composition of glycophyte leaves during their development is discussed. It is supposed that the species-specific ionic composition of glycophyte leaves at different developmental stages is due mainly to the pattern of carbon metabolism causing the accumulation either of di-and tricarboxylic acids or oxalic acid.     

Helix-Forming tendencies of amino acids depend on their sequence contexts: Tripeptides AFG and FAG show incipient β-bulge formation in their crystal structures

Many of the theoretical methods used for predicting the occurrence of α-helices in peptides are based on the helical preferences of amino acid monomer residues. In order to check whether the helix-forming tendencies are based on helical preferences of monomers only or also on their sequence contexts, we synthesized permuted sequences of the tripeptides GAP, GAV, and GAL that formed crystalline helices with near α-helical conformation. The tripeptides AFG and FAG formed good crystals. The x-ray crystallographic studies of AFG and FAG showed that though they contain the same amino acids as GAF but in different sequences, they do not assume a helical conformation in the solid state. On the other hand, AFG and FAG, which contain the same amino acids but in a different sequence, exhibit nearly the same backbone torsion angles corresponding to an incipient formation of a β-bulge, and exhibit nearly identical unit cells and crystal structures. Based on these results, it appears that the helix-forming tendencies of amino acids depend on the sequence context in which it occurs in a polypeptide. The synthetic peptides AFG (L -Ala-L -Phe-Gly) and FAG (L -Phe-L -Ala-Gly), C₁₄H₁₉N₃O₄, crystallize in the orthorhombic space group P2₁2₁2₁, with a = 5. 232(1), b = 14. 622(2), c = 19. 157(3) Å, D_x = 1.329 g cm^?3, Z = 4, R = 0.041 for 549 reflections for AFG, and with a = 5. 488(2), b = 14.189 (1), c = 18.562(1) Å, D_x = 1.348 g cm^?3, Z = 4, R = 0.038 for 919 reflections for FAG. Unlike the other tripeptides GAF, GGV, GAL, and GAI, the crystals of AFG and FAG do not contain water molecule, and the molecules of AFG or FAG do not show the helical conformation. The torsion angles at the backbone of the peptide are ψ₁ = 144. 5(5)°; ?₂, ψ₂ = ?98.1(6)°, ?65.2(6)° ?₃, ψ₁₃, ψ₃₁ = 154.1(6)°, ?173.6(6)°, 6.9(8)° for AFG; and ψ₁ = 162.6(3)°; ?₂, ψ₂ = ?96.7(4)°, ?46.3(4)°; ?₃, ψ₁₃, ψ₃₁ = 150.1(3)°, ?168.7(3)°, 12.2(5)° for FAG. The conformation angles (? ψ) for residues 2 and 3 for both AFG and FAG show incipient formation of an β-bulge. © 1993 John Wiley & Sons, Inc.     

Binding of thyroglobulin to bovine thyroid membranes. Role of specific amino acids in receptor recognition

Bovine thyroglobulin was treated with increasing ratios of succinic anhydride, trinitrobenzene sulfonic acid, tetranitromethane, and N-acetylimidazole in an attempt to assess the role of lysine or tyrosine residues in binding to thyroid membrane receptors. Extensive succinylation results in dissociation to 12 S thyroglobulin with retention of a considerable portion of the three-dimensional structure. Only 25% of the lysine residues can be modified by trinitrophenylation without affecting inter-subunit interactions. Succinylation as well as trinitrophenylation increases the affinity of thyroglobulin for the membrane receptor by a factor of 2. The binding of thyroglobulin to the membrane was reduced after nitration of 30% of the tyrosyl residues with tetranitromethane. O-Acetylation of 40-70% of the tyrosyl residues by N-acetylimidazole nearly abolished the ability of thyroglobulin to bind to the membrane. Removal of the O-acetyl group with hydroxylamine restored the binding properties. The results indicate that tyrosyl residues play an important role in thyroglobulin interactions with thyroid membranes.     

Growth responses of Neisseria gonorrhoeae auxotypes to required amino acids and bases in liquid medium

Neisseria gonorrhoeae strains can be grouped or differentiated (auxotyped) by their requirements for none, or any one or more of proline, uracil, hypoxanthine, and citrulline or ornithine. Most strains were readily assessed because they responded with growth or no growth on each defined auxanographic medium. Other strains gave indeterminate responses on agar and the reasons were not obvious. Liquid growth studies for quantifying the usual responses showed that yields of appropriate N. gonorrhoeae auxotrophs were proportional to replacement concentrations of any one of these amino acids or bases, of methionine, or of cysteine plus cystine. This type of response, where log growth rates and lag times were unaffected, is proposed as the basis for defining (simple) auxotrophy in gonococci. The formula of the defined medium was improved by increasing proline, uracil, and hypoxanthine beyond limiting concentrations, and decreasing citrulline or ornithine, and cysteine plus cystine. Fatty acid--free bovine albumin was used to ensure homogeneous growth in liquid media. In agar, it was superior to starch for the nonnutritive protective effect required by many strains.