Summary.
The concentrations of free amino acids in plasma change coordinately and their profiles show distinctive features in various physiological conditions; however, their behavior can not always be explained by the conventional flow-based metabolic pathway network. In this study, we have revealed the interrelatedness of the plasma amino acids and inferred their network structure with threshold-test analysis and multilevel-digraph analysis methods using the plasma samples of rats which are fed diet deficient in single essential amino acid.
In the inferred network, we could draw some interesting interrelations between plasma amino acids as follows: 1) Lysine is located at the top control level and has effects on almost all of the other plasma amino acids. 2) Threonine plays a role in a hub in the network, which has direct links to the most number of other amino acids. 3) Threonine and methionine are interrelated to each other and form a loop structure.
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RH Allen SP Stabler DG Savage J Lindenbaum (1993) ArticleTitleMetabolic abnormalities in cobalamin (vitamin B12) and folate deficiency Faseb J 7 1344–1353 Occurrence Handle7901104 Occurrence Handle1:CAS:528:DyaK2cXns1SrtQ%3D%3D
IW Althaus JJ Chou AJ Gonzales MR Deibel KC Chou FJ Kezdy DL Romero PA Aristoff WG Tarpley F Reusser (1993a) ArticleTitleSteady-state kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-87201E J Biol Chem 268 6119–6124 Occurrence Handle1:CAS:528:DyaK3sXitVCktbo%3D
IW Althaus JJ Chou AJ Gonzales MR Deibel KC Chou FJ Kezdy DL Romero JR Palmer RC Thomas PA Aristoff et al. (1993b) ArticleTitleKinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-88204E Biochemistry 32 6548–6554 Occurrence Handle10.1021/bi00077a008 Occurrence Handle1:CAS:528:DyaK3sXltVynsbk%3D
IW Althaus AJ Gonzales JJ Chou DL Romero MR Deibel KC Chou FJ Kezdy L Resnick ME Busso AG So et al. (1993c) ArticleTitleThe quinoline U-78036 is a potent inhibitor of HIV-1 reverse transcriptase J Biol Chem 268 14875–14880 Occurrence Handle1:CAS:528:DyaK2cXksFagsw%3D%3D
R Banerjee CG Zou (2005) ArticleTitleRedox regulation and reaction mechanism of human cystathionine-beta-synthase: a PLP-dependent hemesensor protein Arch Biochem Biophys 433 144–156 Occurrence Handle15581573 Occurrence Handle10.1016/j.abb.2004.08.037 Occurrence Handle1:CAS:528:DC%2BD2cXhtVCgt7fK
E Borcsok RH Abeles (1982) ArticleTitleMechanism of action of cystathionine synthase Arch Biochem Biophys 213 695–707 Occurrence Handle6803676 Occurrence Handle10.1016/0003-9861(82)90600-2 Occurrence Handle1:CAS:528:DyaL38Xhtlykurk%3D
KC Chou (1981) ArticleTitleTwo new schematic rules for rate laws of enzyme-catalysed reactions J Theor Biol 89 581–592 Occurrence Handle7289637 Occurrence Handle10.1016/0022-5193(81)90030-8 Occurrence Handle1:CAS:528:DyaL3MXitVCnurs%3D
KC Chou (1989) ArticleTitleGraphic rules in steady and non-steady state enzyme kinetics J Biol Chem 264 12074–12079 Occurrence Handle2745429 Occurrence Handle1:CAS:528:DyaL1MXkslekt7o%3D
KC Chou (1990) ArticleTitleApplications of graph theory to enzyme kinetics and protein folding kinetics. Steady and non-steady-state systems Biophys Chem 35 1–24 Occurrence Handle2183882 Occurrence Handle10.1016/0301-4622(90)80056-D Occurrence Handle1:CAS:528:DyaK3cXhslCntro%3D
KC Chou WM Liu (1981) ArticleTitleGraphical rules for non-steady state enzyme kinetics J Theor Biol 91 637–654 Occurrence Handle10.1016/0022-5193(81)90215-0 Occurrence Handle1:CAS:528:DyaL3MXlsVKjtLo%3D
KC Chou FJ Kezdy F Reusser (1994) ArticleTitleKinetics of processive nucleic acid polymerases and nucleases Anal Biochem 221 217 Occurrence Handle7529005 Occurrence Handle10.1006/abio.1994.1405 Occurrence Handle1:CAS:528:DyaK2cXmt1Clt7k%3D
KC Chou YD Cai WZ Zhong (2006) ArticleTitlePredicting networking couples for metabolic pathways of Arabidopsis EXCLI J 5 55–65
P Felig (1975) ArticleTitleAmino acid metabolism in man Annu Rev Biochem 44 933–955 Occurrence Handle1094924 Occurrence Handle10.1146/annurev.bi.44.070175.004441 Occurrence Handle1:CAS:528:DyaE2MXltFWnu7w%3D
P Ferenci F Wewalka (1978) ArticleTitlePlasma amino acids in hepatic encephalopathy J Neural Transm [Suppl] 14 87–94 Occurrence Handle1:CAS:528:DyaE1MXkvV2isL0%3D
E Holm O Sedlaczek E Grips (1999) ArticleTitleAmino acid metabolism in liver disease Curr Opin Clin Nutr Metab Care 2 47–53 Occurrence Handle10453330 Occurrence Handle10.1097/00075197-199901000-00009 Occurrence Handle1:CAS:528:DyaK1MXitVyitrc%3D
SY Hong DH Yang SK Chang (1998) ArticleTitleThe relationship between plasma homocysteine and amino acid concentrations in patients with end-stage renal disease J Ren Nutr 8 34–39 Occurrence Handle9724828 Occurrence Handle1:STN:280:DyaK1cvhtlahtw%3D%3D
FJ Jimenez Jimenez C Ortiz Leyba S Morales Menedez M Barros Perez J Munoz Garcia (1991) ArticleTitleProspective study on the efficacy of branched-chain amino acids in septic patients JPEN 15 252–261 Occurrence Handle1:STN:280:By6A38rjsF0%3D
M Kadowaki T Kanazawa (2003) ArticleTitleAmino acids as regulators of proteolysis J Nutr 133 2052S–2056S Occurrence Handle12771364 Occurrence Handle1:CAS:528:DC%2BD3sXksFeqsbw%3D
G Kapke L Davis (1976) ArticleTitleStereochemistry of the reaction of sheep liver threonine dehydratase. A nuclear magnetic resonance and optical rotatory dispersion study of its reaction pathway and products Biochemistry 15 3745–3749 Occurrence Handle986166 Occurrence Handle10.1021/bi00662a016 Occurrence Handle1:CAS:528:DyaE28XltFyksLw%3D
SR Kimball (2002) ArticleTitleRegulation of global and specific mRNA translation by amino acids J Nutr 132 883–886 Occurrence Handle11983807 Occurrence Handle1:CAS:528:DC%2BD38XjvFSns70%3D
P Kuzmic KY Ng TD Heath (1992) ArticleTitleMixtures of tight-binding enzyme inhibitors. Kinetic analysis by a recursive rate equation Anal Biochem 200 68–73 Occurrence Handle1595902 Occurrence Handle10.1016/0003-2697(92)90278-F Occurrence Handle1:CAS:528:DyaK38XhsVKlsLg%3D
SX Lin KE Neet (1990) ArticleTitleDemonstration of a slow conformational change in liver glucokinase by fluorescence spectroscopy J Biol Chem 265 9670–9675 Occurrence Handle2351663 Occurrence Handle1:CAS:528:DyaK3cXkt1SisLk%3D
Y Maki Y Takahashi Y Arikawa S Watanabe K Aoshima Y Eguchi T Ueda S Aburatani S Kuhara M Okamoto (2004) ArticleTitleAn integrated comprehensive workbench for inferring genetic networks: voyagene J Bioinform Comput Biol 2 533–550 Occurrence Handle15359425 Occurrence Handle10.1142/S0219720004000727 Occurrence Handle1:CAS:528:DC%2BD2MXpsVersbk%3D
Y Maki D Tominaga M Okamoto S Watanabe Y Eguchi (2001) ArticleTitleDevelopment of a system for the inference of large scale genetic networks Pac Symp Biocomput 6 446–458
JK Nicholson JC Lindon E Holmes (1999) ArticleTitle‘Metabonomics’: understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data Xenobiotica 29 1181–1189 Occurrence Handle10598751 Occurrence Handle10.1080/004982599238047 Occurrence Handle1:CAS:528:DyaK1MXns12ms7k%3D
Y Noguchi QW Zhang T Sugimoto Y Furuhata R Sakai M Mori M Takahashi T Kimura (2006) ArticleTitleNetwork analysis of plasma and tissue amino acids and the generation of an amino index for potential diagnostic use Am J Clin Nutr 83 513S–519S Occurrence Handle16470023 Occurrence Handle1:CAS:528:DC%2BD28Xhs1eisbg%3D
M Scarselli MG Padula A Bernini O Spiga A Ciutti R Leoncini D Vannoni E Marinello N Niccolai (2003) ArticleTitleStructure and function correlations between the rat liver threonine deaminase and aminotransferases Biochim Biophys Acta 1645 40–48 Occurrence Handle12535609 Occurrence Handle1:CAS:528:DC%2BD3sXjtFGrug%3D%3D
PB Soeters JE Fischer (1976) ArticleTitleInsulin, glucagon, aminoacid imbalance, and hepatic encephalopathy Lancet 2 880–882 Occurrence Handle62115 Occurrence Handle10.1016/S0140-6736(76)90541-9 Occurrence Handle1:STN:280:CSiD3szkvVw%3D
SP Stabler J Lindenbaum DG Savage RH Allen (1993) ArticleTitleElevation of serum cystathionine levels in patients with cobalamin and folate deficiency Blood 81 3404–3413 Occurrence Handle8507876 Occurrence Handle1:STN:280:ByyB1czmvFc%3D
I Tudor I Tanase-Mogos E Tanasie E Badescu M Rascanu (1976) ArticleTitleA study of aminoacidemia and aminoaciduria in epileptic children Neurol Psychiatr (Bucur) 14 277–282 Occurrence Handle1:STN:280:CSiC2M%2FksV0%3D
M Wang JS Yao ZD Huang ZJ Xu GP Liu HY Zhao XY Wang J Yang YS Zhu KC Chou (2005) ArticleTitleA new nucleotide-composition based fingerprint of SARS-CoV with visualization analysis Med Chem 1 39–47 Occurrence Handle16789884 Occurrence Handle10.2174/1573406053402505
A Watanabe T Higashi T Sakata H Nagashima (1984) ArticleTitleSerum amino acid levels in patients with hepatocellular carcinoma Cancer 54 1875–1882 Occurrence Handle6090002 Occurrence Handle10.1002/1097-0142(19841101)54:9<1875::AID-CNCR2820540918>3.0.CO;2-O Occurrence Handle1:STN:280:BiqD3c7nvFA%3D
A Watanabe N Takei S Hayashi H Nagashima (1983) ArticleTitleSerum neutral amino acid concentrations in cirrhotic patients with impaired carbohydrate metabolism Acta Med Okayama 37 381–384 Occurrence Handle6353875 Occurrence Handle1:STN:280:BiuD38%2Fls1E%3D
F Watanabe Y Nakano (1999) ArticleTitle[Vitamin B12] Nippon Rinsho 57 2205–2210 Occurrence Handle10540863 Occurrence Handle1:STN:280:DC%2BD3c%2FgvVektQ%3D%3D
X Xiao S Shao Y Ding Z Huang X Chen KC Chou (2005a) ArticleTitleAn application of gene comparative image for predicting the effect on replication ratio by HBV virus gene missense mutation J Theor Biol 235 555–565 Occurrence Handle10.1016/j.jtbi.2005.02.008 Occurrence Handle1:CAS:528:DC%2BD2MXltVelt7c%3D
X Xiao S Shao Y Ding Z Huang X Chen KC Chou (2005b) ArticleTitleUsing cellular automata to generate image representation for biological sequences Amino Acids 28 29–35 Occurrence Handle10.1007/s00726-004-0154-9 Occurrence Handle1:CAS:528:DC%2BD2MXhsVKqs70%3D
X Xiao S Shao Y Ding Z Huang KC Chou (2006a) ArticleTitleUsing cellular automata images and pseudo amino acid composition to predict protein subcellular location Amino Acids 30 49–54 Occurrence Handle10.1007/s00726-005-0225-6 Occurrence Handle1:CAS:528:DC%2BD28XhsFCksrk%3D
X Xiao SH Shao KC Chou (2006b) ArticleTitleA probability cellular automaton model for hepatitis B viral infections Biochem Biophys Res Commun 342 605–610 Occurrence Handle10.1016/j.bbrc.2006.01.166 Occurrence Handle1:CAS:528:DC%2BD28XhvVehsLg%3D
CH Yeang HC Mak S McCuine C Workman T Jaakkola T Ideker (2005) ArticleTitleValidation and refinement of gene-regulatory pathways on a network of physical interactions Genome Biol 6 R62 Occurrence Handle15998451 Occurrence Handle10.1186/gb-2005-6-7-r62 Occurrence Handle1:CAS:528:DC%2BD2MXmvFehsrc%3D
CT Zhang KC Chou (1996) ArticleTitleAn analysis of base frequencies in the anti-sense strands corresponding to the 180 human protein coding sequences Amino Acids 10 253–262 Occurrence Handle10.1007/BF00807327 Occurrence Handle1:CAS:528:DyaK28XkslKms7Y%3D
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Shikata, N., Maki, Y., Noguchi, Y. et al. Multi-layered network structure of amino acid (AA) metabolism characterized by each essential AA-deficient condition. Amino Acids 33, 113–121 (2007). https://doi.org/10.1007/s00726-006-0412-0
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DOI: https://doi.org/10.1007/s00726-006-0412-0