Single amino acid substitutions insn-glycerol-3-phosphate dehydrogenase allozymes fromDrosophila virilis

Summary The amino acid sequence was compared among the three allelic variants (allozymes) ofsn-glycerol-3-phosphate dehydrogenase inD. virilis, which are detected by one-dimensional electrophoresis. The GPDH^f variant was different from the GPDH^m by only one substitution of 68-lysine for asparagine; GPDH^s differed from GPDH^m by substitution of 127-glycine for arginine. No electrophoretically silent substitutions were found in a total of 352 amino acid residues.     

Evolutionary diversification of the mammalian defensins

Defensins are cysteine-rich cationic peptides that function in antimicrobial defense in both invertebrates and vertebrates. Three main groups of animal defensins are known: insect defensins; mammalian alpha-defensins and vertebrate beta-defensins. It has been difficult to determine whether these molecules are homologous or have independently evolved similar features, but overall the evidence favors a distant relationship. The best evidence of this relationship is structural, particularly from their overall three-dimensional structure and from the spacing of half-cystine residues involved in intra-chain disulfide bonds. Some evidence favors a closer relationship between vertebrate beta-defensins and insect defensins than between the two groups of vertebrate defensins. Examination of nucleotide substitutions between recently duplicated mammalian defensin genes shows that the rate of nonsynonymous (amino-acid-altering) substitution exceeds that of synonymous substitution in the region of the gene encoding the mature defensin. This highly unusual pattern of nucleotide substitution is evidence that natural selection has acted to diversify defensins at the amino acid level. The resulting rapid evolution explains why it is difficult to reconstruct the evolutionary history of these molecules.     

Folding and assembly defects of pyruvate dehydrogenase deficiency-related variants in the E1α subunit of the pyruvate dehydrogenase complex

The pyruvate dehydrogenase complex (PDC) bridges glycolysis and the citric acid cycle. In human, PDC deficiency leads to severe neurodevelopmental delay and progressive neurodegeneration. The majority of cases are caused by variants in the gene encoding the PDC subunit E1α. The molecular effects of the variants, however, remain poorly understood. Using yeast as a eukaryotic model system, we have studied the substitutions A189V, M230V, and R322C in yeast E1α (corresponding to the pathogenic variants A169V, M210V, and R302C in human E1α) and evaluated how substitutions of single amino acid residues within different functional E1α regions affect PDC structure and activity. The E1α A189V substitution located in the heterodimer interface showed a more compact conformation with significant underrepresentation of E1 in PDC and impaired overall PDC activity. The E1α M230V substitution located in the tetramer and heterodimer interface showed a relatively more open conformation and was particularly affected by low thiamin pyrophosphate concentrations. The E1α R322C substitution located in the phosphorylation loop of E1α resulted in PDC lacking E3 subunits and abolished overall functional activity. Furthermore, we show for the E1α variant A189V that variant E1α accumulates in the Hsp60 chaperonin, but can be released upon ATP supplementation. Our studies suggest that pathogenic E1α variants may be associated with structural changes of PDC and impaired folding of E1α.     

A comparison of pyridoxal 5'-phosphate dependent decarboxylase and transaminase enzymes at a molecular level.

Pyridoxal 5'-phosphate is a coenzyme for a number of enzymes which catalyse reactions at C alpha of amino acid substrates including transaminases, decarboxylases and serine hydroxymethyltransferase. Using the X-ray coordinates for a transaminase, aspartate aminotransferase, and the results of stereochemical and mechanistic studies for decarboxylases and serine hydroxymethyltransferase, an active-site structure for the decarboxylase group is constructed. The structure of the active-site is further refined through active-site pyridoxyllysine peptide sequence comparison and a 3-D catalytic mechanism for the L-alpha-amino acid decarboxylases is proposed. The chemistry of serine hydroxymethyltransferase is re-examined in the light of the proposed decarboxylase mechanism.     

A C-terminally elongated form of PHI from porcine intestine

A C-terminally elongated form of peptide histidine isoleucine amide (PHI) was isolated from porcine intestine based on its effect on cAMP production in IMR-32 cells. The structure was determined by amino acid sequence analysis of tryptic fragments and by mass spectrometry. The peptide has 42 amino acid residues like those described from human, rat and mouse, but the amino acid sequence of the C-terminal extension of pig PHI is unique. Unlike the other peptides, it has a C-terminal Ala and it differs at five positions from the human form and at six positions from the rat form, while the human and the rat forms differ by only two substitutions. To avoid confusion arising from different C-terminal residues, a unifying nomenclature is proposed: PHI-27 for the hormone and PHI-42 for the elongated product.     

Vision in the ultraviolet

Sensitivity to ultraviolet light (UV) is achieved by photoreceptors in the eye that contain a class of visual pigments maximally sensitive to light at wavelengths <400 nm. It is widespread in the animal kingdom where it is used for mate choice, communication and foraging for food. UV sensitivity is not, however, a constant feature of the visual system, and in many vertebrate species, the UV-sensitive (UVS) pigment is replaced by a violet-sensitive (VS) pigment with maximal sensitivity between 410 and 435 nm. The role of protonation of the Schiff base-chromophore linkage and the mechanism for tuning of pigments into the UV is discussed in detail. Amino acid sequence analysis of vertebrate VS/UVS pigments indicates that the ancestral pigment was UVS, with loss of UV sensitivity occurring separately in mammals, amphibia and birds, and subsequently regained by a single amino acid substitution in certain bird species. In contrast, no loss of UV sensitivity has occurred in the UVS pigments of insects.     

Expansion of the bile acid pool changes the biliary transport characteristics of centrizonal hepatocytes

We investigated whether acinar differences in taurocholate transport are responsible for the increased maximal secretory rate observed after expansion of the bile acid pool. The bile acid pool was expanded by cholate feeding for four days. Periportal and centrizonal hepatocytes were then probed by ante- and retrograde liver perfusion, respectively. In control animals, secretory rate constant (alpha 1) averaged 0.439 +/- 0.123 and 0.104 +/- 0.035 min-1 during ante- and retrograde perfusion, respectively, in the absence of exogenous taurocholate. These values did not significantly change when taurocholate was infused. In cholate-fed animals, alpha 1 was comparable during antegrade perfusion but was significantly reduced (0.038 +/- 0.035, p less than 0.05) during retrograde perfusion in the absence of exogenous taurocholate, presumably owing to induction of cytosolic bile acid binding proteins. During loading with exogenous taurocholate, by contrast, alpha 1 was significantly accelerated (0.252 +/- 0.026; p less than 0.01) in centrizonal hepatocytes from bile-acid fed rats. Expansion of the bile acid pool is able to change the bile salt secretory characteristics of centrizonal hepatocytes toward those of periportal ones.     

Identification of 2 phosphorylated amino acids in chicken bone phosphoproteins]

Phosphoproteins of Chicken bone have been extracted by 0.5 M EDTA pH 7.5. Their amino acid composition was similar to that of phosphoproteins of other calcified tissues. The crude EDTA extract contained 80 to 90% proteins, only 70% of the total organic phosphorus was bound to the proteins. We have studied and identified two phosphorylated components. o-phosphoserine and o-phosphothreonine have been identified by amino acid analysis at pH 1.7 from a partial acid hydrolysate, and confirmed by the liberation of the parent amino acids after total hydrolysis. In addition, phosphorus was found equimolecular to both of them. The presence of these phosphorylated groups is important for an understanding of the role of these proteins in the mechanism of mineralization.     

Evolution of the arginase fold and functional diversity

Novel structural superfamilies can be identified among the large number of protein structures deposited in the Protein Data Bank based on conservation of fold in addition to conservation of amino acid sequence. Since sequence diverges more rapidly than fold in protein Evolution, proteins with little or no significant sequence identity are occasionally observed to adopt similar folds, thereby reflecting unanticipated evolutionary relationships. Here, we review the unique alpha/beta fold first observed in the manganese metalloenzyme rat liver arginase, consisting of a parallel eight-stranded beta-sheet surrounded by several helices, and its evolutionary relationship with the zinc-requiring and/or iron-requiring histone deacetylases and acetylpolyamine amidohydrolases. Structural comparisons reveal key features of the core alpha/beta fold that contribute to the divergent metal ion specificity and stoichiometry required for the chemical and biological functions of these enzymes.     

Possible involvement of protein kinase C in the stimulation of amino acid transport by phorbol ester,platelet-derived growth factor and A23187 in Swiss 3T3 cells

Summary Stimulation of amino acid transport induced by phorbol-12, 13-dibutyrate, platelet-derived growth factor or A23187 was not observed in cells lacking protein kinase C. On the other hand, stimulation of transport by epidermal growth factor or insulin was not affected. These results suggested that the stimulation of amino acid transport is mediated by at least two separate pathways.This work was supported in part by Grants-in-Aid for Scientific Research from the Ministry of Education, Science and Culture, and the Ministry of Health and Welfare of Japan.     

Free amino acid composition of the intestinal contents,intestinal cells and hemolymph ofPhilosamia cynthia larvae

Summary Free amino acid composition of the intestinal contents, intestinal cells and hemolymph has been determined in larvae of the mothPhilosamia cynthia. From the hemolymph/lumen concentration ratio, an active transport could be inferred for neutral and basic amino acids. The values of cell/lumen and hemolymph/cell ratios suggested that the active step in the transport mechanism could be localized at the luminal pole of the enterocyte for neutral amino acids (except aromatic amino acids) and at the basolateral pole of the enterocyte for basic amino acids (except arginine).This work was supported by grants from Italian Consiglio Nazionale delle Ricerche and from Ministero della Pubblica Istruzione, Rome. The authors are indebted to Prof. V. Capraro for helpful discussion.     

A new solid-phase synthesis of porcine vasoactive intestinal peptide using Nα-9-fluorenylmethyloxycarbonyl amino acids

Summary The solid-phase synthesis of an octacosapeptide amide corresponding to the amino acid sequence of porcine vasoactive intestinal peptide (VIP) is described. No final treatment with strong, anhydrous acid was employed, since the use of base-labile 9-fluorenylmethyloxycarbonyl amino acids bearing tert-butyl based side chain protection enabled the peptide chain assembly to be performed on p-benzyloxybenzyl amine resin, which was cleaved from the whole peptide amide at the end of the synthesis by diluted trifluoroacetic acid.     

Antimutagenic unusual amino acids from plants

Five unusual amino acids were identified as antimutagens against spontaneous mutation of Salmonella typhimurium TA100: L-azetidine-2-carboxylic acid (1) from Liliaceae plants, alpha-(methylenecyclopropyl)glycine (2) from Litchi chinensis seeds, and 2-amino-4-methylhex-5-ynoic acid (3), hypoglycin A (4), and (2S,4R)-2-amino-4-hydroxyhept-6-ynoic acid (5) from Euphoria longana seeds. The absolute stereochemistry of 5 was determined by its chiral synthesis from L-allylglycine, proving that 5 is the C-4 epimer of the amino acid previously isolated from dried longan seeds.     

Buffalo α S1-casein; its terminal residues and amino acid composition

Summary BuffaloaS₁-casein was treated with carboxypeptidase-A to determine the C-terminal amino acid residue, which was — leucine-tryptophan. The Sakaguchi reagent was used to confirm arginine as the N-terminal amino acid. The colored p-phenylazophenyl thiohydantions of tryptophan and arginine released from C- and N-terminals respectively were quantitatively estimated and from this molecular weights of buffaloaS₁ casein were calculated and found to be 26,300 and 26,100 respectively.Acknowledgment. We are thankful to Prof. B. K. Bachhawat, Indian Institute of Chemical Biology, for encouragement. We also thank Prof. S. K. Mukherjee, Bose Institute, for amino acid analysis. Part of this work was completed when the authors were at the University of Kalyani, West Bengal.     

Absorption of protein in the early postoperative period in chronic conscious dogs

Postoperative alterations in amino acid exchange across the intestinal tract and in the capacity for protein absorption were investigated in a chronic canine model. Changes in postoperative splanchnic amino acid exchange consisted of a temporary decrease of total splanchnic amino acid release, including a significant reduction in alanine production, and an increase in glutamine consumption. Contrary to results under stable metabolic conditions, branched chain amino acids were also taken up by the intestine in the early postoperative period. The changes in postoperative amino acid exchange were not, however, reflected by a corresponding alteration in protein transport capacity. The absorptive capacity for a protein hydrolysate remained stable during the early postoperative period.     

Hypotensive activity of histidine-containing analogues of C-terminal hexapeptide of substance P

Four new hexapeptide analogues of C-terminal Substance P fragment with increased solubility in aqueous solutions are described. The peptides contain histidine in positions 6, 8, 9 and 10, respectively. The effect of the structural changes on the hypotensive activity and antigenic properties of analogues was compared. It was found that substitution of amino acid residues in various positions in the C-terminal hexapeptide of Substance P resulted in different effects on the hypotensive and antigenic properties, respectively. Only the [His6] SP6-11 analogue had an unchanged antigenic structure when compared with the C-terminal region of Substance P, but it showed an almost total loss of hypotensive activity. The [His9] SP6-11 analogue retained 50% of the hypotensive activity of the C-terminal hexapeptide but showed a markedly reduced expression of the antigenic epitope localized in this region of Substance P.     

Identification and characterisation of two allelic forms of human alcohol dehydrogenase 2

The human alcohol dehydrogenase system is comprised of multiple forms that catalyse the oxidation/reduction of a large variety of alcohols and aldehydes. A transition that results in an Ile308Val substitution was identified in the human ADH2 gene by single-strand conformation polymorphism analysis. Screening a Swedish population revealed that Val308 was the most frequent allele (73%), and site-directed mutagenesis was used to obtain both allelozymes, which were expressed in Escherichia coli for characterisation. Thermostability was assayed by activity measurements and circular dichroism spectroscopy. The results showed that the 308Val substitution decreases protein stability, as compared to the Ile308 variant, an effect also demonstrated during prolonged storage. Ethanol, octanol, 12-hydroxydodecanoic acid and all-trans retinol were used as model substrates and, generally, slightly higher Km values were observed with Val at position 308. Finally, homology modelling, from mouse ADH2, further supported the decreased stability of the Val308 variant and located position 308 in the subunit interface of the molecule and in the vicinity of the active-site pocket entrance. In conclusion, the Ile308Val substitution represents a novel functional polymorphism within the human alcohol dehydrogenase gene cluster that may affect the metabolism of ethanol and other substrates.     

Structural characterization of two papaya chitinases, a family GH19 of glycosyl hydrolases

Two chitinases, able to use tetra-N-acetylglucosamine, chitin and chitosan as substrates, were characterized after purification from Carica papaya latex. The complete amino acid sequence of the major form and about 40% of the minor one were determined through proteolytic digestions and mass spectroscopy analysis. Sequencing demonstrated that both papaya chitinases are members of the family 19 of glycosyl hydrolases (GH19). Based on the known 3-D structures of other members of family GH19, it was expected that papaya chitinases would adopt all-alpha structures. However, circular dichroism and infrared spectroscopy indicated, for the papaya chitinases, a content of 15–20% of extended structures besides the expected 40% of alpha helices. Since the fully sequenced papaya chitinase contains a large number of proline residues the possibility that papaya chitinase contains polyproline II stretches was examined in the context of their resistance against proteolytic degradation. Received 11 July 2006; received after revision 13 October 2006; accepted 25 October 2006     

Resculpting the binding pocket of APC superfamily LeuT-fold amino acid transporters

Amino acid transporters are essential components of prokaryote and eukaryote cells, possess distinct physiological functions, and differ markedly in substrate specificity. Amino acid transporters can be both drug targets and drug transporters (bioavailability, targeting) with many monogenic disorders resulting from dysfunctional membrane transport. The largest collection of amino acid transporters (including the mammalian SLC6, SLC7, SLC32, SLC36, and SLC38 families), across all kingdoms of life, is within the Amino acid-Polyamine-organoCation (APC) superfamily. The LeuT-fold is a paradigm structure for APC superfamily amino acid transporters and carriers of sugars, neurotransmitters, electrolytes, osmolytes, vitamins, micronutrients, signalling molecules, and organic and fatty acids. Each transporter is specific for a unique sub-set of solutes, specificity being determined by how well a substrate fits into each binding pocket. However, the molecular basis of substrate selectivity remains, by and large, elusive. Using an integrated computational and experimental approach, we demonstrate that a single position within the LeuT-fold can play a crucial role in determining substrate specificity in mammalian and arthropod amino acid transporters within the APC superfamily. Systematic mutation of the amino acid residue occupying the equivalent position to LeuT V104 titrates binding pocket space resulting in dramatic changes in substrate selectivity in exemplar APC amino acid transporters including PAT2 (SLC36A2) and SNAT5 (SLC38A5). Our work demonstrates how a single residue/site within an archetypal structural motif can alter substrate affinity and selectivity within this important superfamily of diverse membrane transporters.     

The effect of dietary amino acids on the growth of tumors

Summary In C3H mice, a direct dose response relationship between tumor growth and dietary amino acid is seen for fibrosarcoma and mammary carcinoma, extending over a range the lower limit of which is defined by the minimum amino acid requirements, and the upper limit by the amino acid level found in most stock diets.Supported by Medical Research Council of Canada.