Metabolism of Oxalate in Humans: A Potential Role Kynurenine Aminotransferase/Glutamine Transaminase/Cysteine Conjugate Betalyase Plays in Hyperoxaluria

Author(s): Qian Han*, Cihan Yang, Jun Lu, Yinai Zhang, Jianyong Li*.

Journal Name: Current Medicinal Chemistry

Volume 26 , Issue 26 , 2019

Abstract:

Hyperoxaluria, excessive urinary oxalate excretion, is a significant health problem worldwide. Disrupted oxalate metabolism has been implicated in hyperoxaluria and accordingly, an enzymatic disturbance in oxalate biosynthesis can result in the primary hyperoxaluria. Alanine-glyoxylate aminotransferase-1 and glyoxylate reductase, the enzymes involving glyoxylate (precursor for oxalate) metabolism, have been related to primary hyperoxalurias. Some studies suggest that other enzymes such as glycolate oxidase and alanine-glyoxylate aminotransferase-2 might be associated with primary hyperoxaluria as well, but evidence of a definitive link is not strong between the clinical cases and gene mutations. There are still some idiopathic hyperoxalurias, which require a further study for the etiologies. Some aminotransferases, particularly kynurenine aminotransferases, can convert glyoxylate to glycine. Based on biochemical and structural characteristics, expression level, and subcellular localization of some aminotransferases, a number of them appear able to catalyze the transamination of glyoxylate to glycine more efficiently than alanine glyoxylate aminotransferase-1. The aim of this minireview is to explore other undermining causes of primary hyperoxaluria and stimulate research toward achieving a comprehensive understanding of underlying mechanisms leading to the disease. Herein, we reviewed all aminotransferases in the liver for their functions in glyoxylate metabolism. Particularly, kynurenine aminotransferase-I and III were carefully discussed regarding their biochemical and structural characteristics, cellular localization, and enzyme inhibition. Kynurenine aminotransferase-III is, so far, the most efficient putative mitochondrial enzyme to transaminate glyoxylate to glycine in mammalian livers, which might be an interesting enzyme to look for in hyperoxaluria etiology of primary hyperoxaluria and should be carefully investigated for its involvement in oxalate metabolism.

Keywords: Hyperoxaluria, oxalate metabolism, aminotransferase, glyoxylate, kynurenine aminotransferase, kidney stone.

[1]
Asplin, J.R. Hyperoxaluric calcium nephrolithiasis. Endocrinol. Metab. Clin. North Am., 2002, 31(4), 927-949.
[http://dx.doi.org/10.1016/S0889-8529(02)00030-0]
[2]
Daudon, M.; Donsimoni, R.; Hennequin, C.; Fellahi, S.; Le Moel, G.; Paris, M.; Troupel, S.; Lacour, B. Sex- and age-related composition of 10 617 calculi analyzed by infrared spectroscopy. Urol. Res., 1995, 23(5), 319-326.
[http://dx.doi.org/10.1007/BF00300021]
[3]
Pearle, M.S.; Calhoun, E.; Curhan, G.C. Urolithiasis. Urologic Diseases in America; NIH Publication No. 07– 5512; DHHS, PHS, NIH, NIDDK., 2007, , 283-319.
[4]
Hiatt, R.A.; Dales, L.G.; Friedman, G.D.; Hunkeler, E.M. Frequency of urolithiasis in a prepaid medical care program. Am. J. Epidemiol., 1982, 115(2), 255-265.
[http://dx.doi.org/10.1093/oxfordjournals.aje.a113297]
[5]
Johnson, C.M.; Wilson, D.M.; O’Fallon, W.M.; Malek, R.S.; Kurland, L.T. Renal stone epidemiology: a 25-year study in Rochester, Minnesota. Kidney Int., 1979, 16(5), 624-631.
[http://dx.doi.org/10.1038/ki.1979.173]
[6]
Talati, J.J.; Hulton, S.A.; Garrelfs, S.F.; Aziz, W.; Rao, S.; Memon, A.; Nazir, Z.; Biyabani, R.; Qazi, S.; Azam, I.; Khan, A.H.; Ahmed, J.; Jafri, L.; Zeeshan, M. Primary hy-peroxaluria in populations of Pakistan origin: results from a literature review and two major registries. Urolithiasis, 2018, 46(2), 187-195.
[http://dx.doi.org/10.1007/s00240-017-0996-8]
[7]
Pearle, M.S.; Calhoun, E.A.; Curhan, G.C. Urologic diseases in America project: urolithiasis. J. Urol., 2005, 173(3), 848-857.
[http://dx.doi.org/10.1097/01.ju.0000152082.14384.d7]
[8]
Hyams, E.S.; Matlaga, B.R. Economic impact of urinary stones. Transl. Androl. Urol., 2014, 3(3), 278-283.
[9]
Luo, D.; Li, H.; Wang, K. Urolithiasis: Basic Science and Clinical Practice; Published by Springer London Ltd.: United Kingdom, 2012, pp. 53-59.
[10]
Zeng, Q.; He, Y. Age-specific prevalence of kidney stones in Chinese urban inhabitants. Urolithiasis, 2013, 41(1), 91-93.
[http://dx.doi.org/10.1007/s00240-012-0520-0]
[11]
Robertson, W.G.; Heyburn, P.J.; Peacock, M.; Hanes, F.A.; Swaminathan, R. The effect of high animal protein intake on the risk of calcium stone-formation in the urinary tract. Clin. Sci. (Lond.), 1979, 57(3), 285-288.
[http://dx.doi.org/10.1042/cs0570285]
[12]
Romero, V.; Akpinar, H.; Assimos, D.G. Kidney stones: a global picture of prevalence, incidence, and associated risk factors. Rev. Urol., 2010, 12(2-3), e86-e96.
[13]
Scales, C.D., Jr; Smith, A.C.; Hanley, J.M.; Saigal, C.S. Prevalence of kidney stones in the United States. Eur. Urol., 2012, 62(1), 160-165.
[http://dx.doi.org/10.1016/j.eururo.2012.03.052]
[14]
Joshi, V.S.; Parekh, B.B.; Joshi, M.J.; Vaidya, A.D. Inhibi-tion of the growth of urinary calcium hydrogen phosphate dihydrate crystals with aqueous extracts of Tribulus terrestris and Bergenia ligulata. Urol. Res., 2005, 33(2), 80-86.
[http://dx.doi.org/10.1007/s00240-004-0450-6]
[15]
Purdue, P.E.; Takada, Y.; Danpure, C.J. Identification of mutations associated with peroxisome-to-mitochondrion mis-targeting of alanine/glyoxylate aminotransferase in primary hyperoxaluria type 1. J. Cell Biol., 1990, 111(6 Pt 1), 2341-2351.
[http://dx.doi.org/10.1083/jcb.111.6.2341]
[16]
Holmes, R.P. Pharmacological approaches in the treatment of primary hyperoxaluria. J. Nephrol., 1998, 11(Suppl. 1), 32-35.
[17]
Liebow, A.; Li, X.; Racie, T.; Hettinger, J.; Bettencourt, B.R.; Najafian, N.; Haslett, P.; Fitzgerald, K.; Holmes, R.P.; Erbe, D.; Querbes, W.; Knight, J. An Investigational RNAi Therapeutic Targeting Glycolate Oxidase Reduces Oxalate Production in Models of Primary Hyperoxaluria. J. Am. Soc. Nephrol., 2017, 28(2), 494-503.
[http://dx.doi.org/10.1681/ASN.2016030338]
[18]
Han, Q.; Li, J.; Li, J. pH dependence, substrate specificity and inhibition of human kynurenine aminotransferase I. Eur. J. Biochem., 2004, 271(23-24), 4804-4814.
[http://dx.doi.org/10.1111/j.1432-1033.2004.04446.x]
[19]
Han, Q.; Robinson, H.; Cai, T.; Tagle, D.A.; Li, J. Biochem-ical and structural properties of mouse kynurenine ami-notransferase III. Mol. Cell. Biol., 2009, 29(3), 784-793.
[http://dx.doi.org/10.1128/MCB.01272-08]
[20]
Cooper, A.J. The role of glutamine transaminase K (GTK) in sulfur and alpha-keto acid metabolism in the brain, and in the possible bioactivation of neurotoxicants. Neurochem. Int., 2004, 44(8), 557-577.
[http://dx.doi.org/10.1016/j.neuint.2003.12.002]
[21]
Pinto, J.T.; Krasnikov, B.F.; Alcutt, S.; Jones, M.E.; Dorai, T.; Villar, M.T.; Artigues, A.; Li, J.; Cooper, A.J. Kynurenine aminotransferase III and glutamine transaminase L are identical enzymes that have cysteine S-conjugate β-lyase activity and can transaminate L-selenomethionine. J. Biol. Chem., 2014, 289(45), 30950-30961.
[http://dx.doi.org/10.1074/jbc.M114.591461]
[22]
Yang, C.; Zhang, L.; Han, Q.; Liao, C.; Lan, J.; Ding, H.; Zhou, H.; Diao, X.; Li, J. Kynurenine aminotransferase 3/glutamine transaminase L/cysteine conjugate beta-lyase 2 is a major glutamine transaminase in the mouse kidney. Biochem. Biophys. Rep., 2016, 8, 234-241.
[http://dx.doi.org/10.1016/j.bbrep.2016.09.008]
[23]
Danpure, C.J. In: The Molecular and Metabolic Bases of Inherited Disease; , 2001, pp. 3323-3367.
[24]
Sayer, J.A. The genetics of nephrolithiasis. Nephron, Exp. Nephrol., 2008, 110(2), e37-e43.
[http://dx.doi.org/10.1159/000151730]
[25]
Aronson, P.S. Essential roles of CFEX-mediated Cl(-)-oxalate exchange in proximal tubule NaCl transport and pre-vention of urolithiasis. Kidney Int., 2006, 70(7), 1207-1213.
[http://dx.doi.org/10.1038/sj.ki.5001741]
[26]
Coe, F.L.; Worcester, E.M.; Evan, A.P. Idiopathic hypercal-ciuria and formation of calcium renal stones. Nat. Rev. Nephrol., 2016, 12(9), 519-533.
[http://dx.doi.org/10.1038/nrneph.2016.101]
[27]
Danpure, C.J. Peroxisomal alanine:glyoxylate aminotransfer-ase and prenatal diagnosis of primary hyperoxaluria type 1. Lancet, 1986, 2(8516), 1168.
[http://dx.doi.org/10.1016/S0140-6736(86)90584-2]
[28]
Williams, H.E.; Smith, L.H. Jr L-glyceric aciduria. A new genetic variant of primary hyperoxaluria. N. Engl. J. Med., 1968, 278(5), 233-238.
[http://dx.doi.org/10.1056/NEJM196802012780502]
[29]
Cramer, S.D.; Ferree, P.M.; Lin, K.; Milliner, D.S.; Holmes, R.P. The gene encoding hydroxypyruvate reductase (GRHPR) is mutated in patients with primary hyperoxaluria type II. Hum. Mol. Genet., 1999, 8(11), 2063-2069.
[http://dx.doi.org/10.1093/hmg/8.11.2063]
[30]
Jiang, Z.; Asplin, J.R.; Evan, A.P.; Rajendran, V.M.; Ve-lazquez, H.; Nottoli, T.P.; Binder, H.J.; Aronson, P.S. Calci-um oxalate urolithiasis in mice lacking anion transporter Slc26a6. Nat. Genet., 2006, 38(4), 474-478.
[http://dx.doi.org/10.1038/ng1762]
[31]
Monico, C.G.; Weinstein, A.; Jiang, Z.; Rohlinger, A.L.; Cogal, A.G.; Bjornson, B.B.; Olson, J.B.; Bergstralh, E.J.; Milliner, D.S.; Aronson, P.S. Phenotypic and functional analysis of human SLC26A6 variants in patients with famili-al hyperoxaluria and calcium oxalate nephrolithiasis. Am. J. Kidney Dis., 2008, 52(6), 1096-1103.
[http://dx.doi.org/10.1053/j.ajkd.2008.07.041]
[32]
Heilberg, I.P.; Schor, N. Renal stone disease: Causes, eval-uation and medical treatment. Arq. Bras. Endocrinol. Metabol, 2006, 50(4), 823-831.
[http://dx.doi.org/10.1590/S0004-27302006000400027]
[33]
Auer, B.L.; Auer, D.; Rodgers, A.L. Relative hyperoxaluria, crystalluria and haematuria after megadose ingestion of vita-min C. Eur. J. Clin. Invest., 1998, 28(9), 695-700.
[http://dx.doi.org/10.1046/j.1365-2362.1998.00349.x]
[34]
Stapenhorst, L.; Hesse, A.; Hoppe, B. Hyperoxaluria after ethylene glycol poisoning. Pediatr. Nephrol., 2008, 23(12), 2277-2279.
[http://dx.doi.org/10.1007/s00467-008-0917-8]
[35]
Green, M.L.; Hatch, M.; Freel, R.W. Ethylene glycol induces hyperoxaluria without metabolic acidosis in rats. Am. J. Physiol. Renal Physiol., 2005, 289(3), F536-F543.
[http://dx.doi.org/10.1152/ajprenal.00025.2005]
[36]
Novak, M.A.; Roth, A.S.; Levine, M.R. Calcium oxalate retinopathy associated with methoxyflurane abuse. Retina, 1988, 8(4), 230-236.
[http://dx.doi.org/10.1097/00006982-198808040-00002]
[37]
Bardouri, M.; Neffati, F.; Trimeche, M.; Elhani, A.; Fadhel Najjar, M.; Sakly, R. Influence of hypercalcic and/or hy-peroxalic diet on calcium oxalate renal stone formation in rats. Scand. J. Urol. Nephrol., 2006, 40(3), 187-191.
[http://dx.doi.org/10.1080/00365590600621261]
[38]
Khan, S.R.; Glenton, P.A.; Byer, K.J. Dietary oxalate and calcium oxalate nephrolithiasis. J. Urol., 2007, 178(5), 2191-2196.
[http://dx.doi.org/10.1016/j.juro.2007.06.046]
[39]
Vaidyanathan, S.; von Unruh, G.E.; Watson, I.D.; Laube, N.; Willets, S.; Soni, B.L. Hyperoxaluria, hypocitraturia, hypo-magnesiuria, and lack of intestinal colonization by Oxalobac-ter formigenes in a cervical spinal cord injury patient with suprapubic cystostomy, short bowel, and nephrolithiasis. ScientificWorldJournal, 2006, 6, 2403-2410.
[http://dx.doi.org/10.1100/tsw.2006.373]
[40]
Sidhu, H.; Schmidt, M.E.; Cornelius, J.G.; Thamilselvan, S.; Khan, S.R.; Hesse, A.; Peck, A.B. Direct correlation between hyperoxaluria/oxalate stone disease and the absence of the gastrointestinal tract-dwelling bacterium Oxalobacter formi-genes: possible prevention by gut recolonization or enzyme replacement therapy. J. Am. Soc. Nephrol., 1999, 10(Suppl. 14), S334-S340.
[41]
Troxel, S.A.; Sidhu, H.; Kaul, P.; Low, R.K. Intestinal Oxa-lobacter formigenes colonization in calcium oxalate stone formers and its relation to urinary oxalate. J. Endourol., 2003, 17(3), 173-176.
[http://dx.doi.org/10.1089/089277903321618743]
[42]
Campieri, C.; Campieri, M.; Bertuzzi, V.; Swennen, E.; Matteuzzi, D.; Stefoni, S.; Pirovano, F.; Centi, C.; Ulisse, S.; Famularo, G.; De Simone, C. Reduction of oxaluria after an oral course of lactic acid bacteria at high concentration. Kidney Int., 2001, 60(3), 1097-1105.
[http://dx.doi.org/10.1046/j.1523-1755.2001.0600031097.x]
[43]
Coulter-Mackie, M.B. 4-Hydroxyproline metabolism and glyoxylate production: A target for substrate depletion in primary hyperoxaluria? Kidney Int., 2006, 70(11), 1891-1893.
[http://dx.doi.org/10.1038/sj.ki.5001987]
[44]
Knight, J.; Jiang, J.; Assimos, D.G.; Holmes, R.P. Hydrox-yproline ingestion and urinary oxalate and glycolate excre-tion. Kidney Int., 2006, 70(11), 1929-1934.
[http://dx.doi.org/10.1038/sj.ki.5001906]
[45]
Knight, J.; Holmes, R.P. Mitochondrial hydroxyproline me-tabolism: implications for primary hyperoxaluria. Am. J. Nephrol., 2005, 25(2), 171-175.
[http://dx.doi.org/10.1159/000085409]
[46]
Takayama, T.; Fujita, K.; Suzuki, K.; Sakaguchi, M.; Fujie, M.; Nagai, E.; Watanabe, S.; Ichiyama, A.; Ogawa, Y. Con-trol of oxalate formation from L-hydroxyproline in liver mi-tochondria. J. Am. Soc. Nephrol., 2003, 14(4), 939-946.
[http://dx.doi.org/10.1097/01.ASN.0000059310.67812.4F]
[47]
Krebs, H.A. Metabolism of amino-acids: Deamination of amino-acids. Biochem. J., 1935, 29(7), 1620-1644.
[http://dx.doi.org/10.1042/bj0291620]
[48]
Kawazoe, T.; Tsuge, H.; Pilone, M.S.; Fukui, K. Crystal structure of human D-amino acid oxidase: context-dependent variability of the backbone conformation of the VAAGL hy-drophobic stretch located at the si-face of the flavin ring. Protein Sci., 2006, 15(12), 2708-2717.
[http://dx.doi.org/10.1110/ps.062421606]
[49]
Molla, G.; Sacchi, S.; Bernasconi, M.; Pilone, M.S.; Fukui, K.; Polegioni, L. Characterization of human D-amino acid oxidase. FEBS Lett., 2006, 580(9), 2358-2364.
[http://dx.doi.org/10.1016/j.febslet.2006.03.045]
[50]
Baker, P.R.; Cramer, S.D.; Kennedy, M.; Assimos, D.G.; Holmes, R.P. Glycolate and glyoxylate metabolism in HepG2 cells. Am. J. Physiol. Cell Physiol., 2004, 287(5), C1359-C1365.
[http://dx.doi.org/10.1152/ajpcell.00238.2004]
[51]
Van Acker, K.J.; Eyskens, F.J.; Espeel, M.F.; Wanders, R.J.; Dekker, C.; Kerckaert, I.O.; Roels, F. Hyperoxaluria with hyperglycoluria not due to alanine:glyoxylate aminotransfer-ase defect: a novel type of primary hyperoxaluria. Kidney Int., 1996, 50(5), 1747-1752.
[http://dx.doi.org/10.1038/ki.1996.494]
[52]
Neuhaus, T.J.; Belzer, T.; Blau, N.; Hoppe, B.; Sidhu, H.; Leumann, E. Urinary oxalate excretion in urolithiasis and nephrocalcinosis. Arch. Dis. Child., 2000, 82(4), 322-326.
[http://dx.doi.org/10.1136/adc.82.4.322]
[53]
Monico, C.G.; Persson, M.; Ford, G.C.; Rumsby, G.; Milli-ner, D.S. Potential mechanisms of marked hyperoxaluria not due to primary hyperoxaluria I or II. Kidney Int., 2002, 62(2), 392-400.
[http://dx.doi.org/10.1046/j.1523-1755.2002.00468.x]
[54]
Salido, E.C.; Li, X.M.; Lu, Y.; Wang, X.; Santana, A.; Roy-Chowdhury, N.; Torres, A.; Shapiro, L.J.; Roy-Chowdhury, J. Alanine-glyoxylate aminotransferase-deficient mice, a model for primary hyperoxaluria that responds to adenoviral gene transfer. Proc. Natl. Acad. Sci. USA, 2006, 103(48), 18249-18254.
[http://dx.doi.org/10.1073/pnas.0607218103]
[55]
Williams, E.; Cregeen, D.; Rumsby, G. Identification and expression of a cDNA for human glycolate oxidase. Biochim. Biophys. Acta, 2000, 1493(1-2), 246-248.
[http://dx.doi.org/10.1016/S0167-4781(00)00161-5]
[56]
Jones, J.M.; Morrell, J.C.; Gould, S.J. Identification and characterization of HAOX1, HAOX2, and HAOX3, three human peroxisomal 2-hydroxy acid oxidases. J. Biol. Chem., 2000, 275(17), 12590-12597.
[http://dx.doi.org/10.1074/jbc.275.17.12590]
[57]
Danpure, C.J. Molecular etiology of primary hyperoxaluria type 1: new directions for treatment. Am. J. Nephrol., 2005, 25(3), 303-310.
[http://dx.doi.org/10.1159/000086362]
[58]
Vignaud, C.; Pietrancosta, N.; Williams, E.L.; Rumsby, G.; Lederer, F. Purification and characterization of recombinant human liver glycolate oxidase. Arch. Biochem. Biophys., 2007, 465(2), 410-416.
[http://dx.doi.org/10.1016/j.abb.2007.06.021]
[59]
Murray, M.S.; Holmes, R.P.; Lowther, W.T. Active site and loop 4 movements within human glycolate oxidase: implica-tions for substrate specificity and drug design. Biochemistry, 2008, 47(8), 2439-2449.
[http://dx.doi.org/10.1021/bi701710r]
[60]
Wanders, R.J.; van Roermund, C.W.; Griffioen, M.; Cohen, L. Peroxisomal enzyme activities in the human hepatoblasto-ma cell line HepG2 as compared to human liver. Biochim. Biophys. Acta, 1991, 1115(1), 54-59.
[http://dx.doi.org/10.1016/0304-4165(91)90011-5]
[61]
Takada, Y.; Mori, T.; Noguchi, T. The effect of vitamin B6 deficiency on alanine: glyoxylate aminotransferase isoen-zymes in rat liver. Arch. Biochem. Biophys., 1984, 229(1), 1-6.
[http://dx.doi.org/10.1016/0003-9861(84)90123-1]
[62]
Lee, I.S.; Muragaki, Y.; Ideguchi, T.; Hase, T.; Tsuji, M.; Ooshima, A.; Okuno, E.; Kido, R. Molecular cloning and se-quencing of a cDNA encoding alanine-glyoxylate ami-notransferase 2 from rat kidney. J. Biochem., 1995, 117(4), 856-862.
[http://dx.doi.org/10.1093/oxfordjournals.jbchem.a124787]
[63]
Veena, C.K.; Josephine, A.; Preetha, S.P.; Rajesh, N.G.; Varalakshmi, P. Mitochondrial dysfunction in an animal model of hyperoxaluria: a prophylactic approach with fu-coidan. Eur. J. Pharmacol., 2008, 579(1-3), 330-336.
[http://dx.doi.org/10.1016/j.ejphar.2007.09.044]
[64]
Donini, S.; Ferrari, M.; Fedeli, C.; Faini, M.; Lamberto, I.; Marletta, A.S.; Mellini, L.; Panini, M.; Percudani, R.; Polle-gioni, L.; Caldinelli, L.; Petrucco, S.; Peracchi, A. Recombi-nant production of eight human cytosolic aminotransferases and assessment of their potential involvement in glyoxylate metabolism. Biochem. J., 2009, 422(2), 265-272.
[http://dx.doi.org/10.1042/BJ20090748]
[65]
Su, A.I.; Cooke, M.P.; Ching, K.A.; Hakak, Y.; Walker, J.R.; Wiltshire, T.; Orth, A.P.; Vega, R.G.; Sapinoso, L.M.; Moqrich, A.; Patapoutian, A.; Hampton, G.M.; Schultz, P.G.; Hogenesch, J.B. Large-scale analysis of the human and mouse transcriptomes. Proc. Natl. Acad. Sci. USA, 2002, 99(7), 4465-4470.
[http://dx.doi.org/10.1073/pnas.012025199]
[66]
Mortazavi, A.; Williams, B.A.; McCue, K.; Schaeffer, L.; Wold, B. Mapping and quantifying mammalian transcrip-tomes by RNA-Seq. Nat. Methods, 2008, 5(7), 621-628.
[http://dx.doi.org/10.1038/nmeth.1226]
[67]
Foster, L.J.; de Hoog, C.L.; Zhang, Y.; Zhang, Y.; Xie, X.; Mootha, V.K.; Mann, M. A mammalian organelle map by protein correlation profiling. Cell, 2006, 125(1), 187-199.
[http://dx.doi.org/10.1016/j.cell.2006.03.022]
[68]
Perkins, M.N.; Stone, T.W. An iontophoretic investigation of the actions of convulsant kynurenines and their interaction with the endogenous excitant quinolinic acid. Brain Res., 1982, 247(1), 184-187.
[http://dx.doi.org/10.1016/0006-8993(82)91048-4]
[69]
Guidetti, P.; Okuno, E.; Schwarcz, R. Characterization of rat brain kynurenine aminotransferases I and II. J. Neurosci. Res., 1997, 50(3), 457-465.
[http://dx.doi.org/10.1002/(SICI)1097-4547(19971101)50:3<457:AID-JNR12>3.0.CO;2-3]
[70]
Okuno, E.; Schmidt, W.; Parks, D.A.; Nakamura, M.; Schwarcz, R. Measurement of rat brain kynurenine ami-notransferase at physiological kynurenine concentrations. J. Neurochem., 1991, 57(2), 533-540.
[http://dx.doi.org/10.1111/j.1471-4159.1991.tb03783.x]
[71]
Schwarcz, R.; Pellicciari, R. Manipulation of brain kynurenines: glial targets, neuronal effects, and clinical op-portunities. J. Pharmacol. Exp. Ther., 2002, 303(1), 1-10.
[http://dx.doi.org/10.1124/jpet.102.034439]
[72]
Han, Q.; Li, J.; Li, J. pH dependence, substrate specificity and inhibition of human kynurenine aminotransferase I. Eur. J. Biochem., 2004, 271(23-24), 4804-4814.
[http://dx.doi.org/10.1111/j.1432-1033.2004.04446.x]
[73]
Okuno, E.; Du, F.; Ishikawa, T.; Tsujimoto, M.; Nakamura, M.; Schwarcz, R.; Kido, R. Purification and characterization of kynurenine-pyruvate aminotransferase from rat kidney and brain. Brain Res., 1990, 534(1-2), 37-44.
[http://dx.doi.org/10.1016/0006-8993(90)90109-O]
[74]
Baran, H.; Okuno, E.; Kido, R.; Schwarcz, R. Purification and characterization of kynurenine aminotransferase I from human brain. J. Neurochem., 1994, 62(2), 730-738.
[http://dx.doi.org/10.1046/j.1471-4159.1994.62020730.x]
[75]
Du, F.; Schmidt, W.; Okuno, E.; Kido, R.; Köhler, C.; Schwarcz, R. Localization of kynurenine aminotransferase immunoreactivity in the rat hippocampus. J. Comp. Neurol., 1992, 321(3), 477-487.
[http://dx.doi.org/10.1002/cne.903210313]
[76]
Du, F.; Williamson, J.; Bertram, E.; Lothman, E.; Okuno, E.; Schwarcz, R. Kynurenine pathway enzymes in a rat model of chronic epilepsy: immunohistochemical study of activated glial cells. Neuroscience, 1993, 55(4), 975-989.
[http://dx.doi.org/10.1016/0306-4522(93)90312-4]
[77]
Roberts, R.C.; Du, F.; McCarthy, K.E.; Okuno, E.; Schwarcz, R. Immunocytochemical localization of kynurenine aminotransferase in the rat striatum: a light and electron microscopic study. J. Comp. Neurol., 1992, 326(1), 82-90.
[http://dx.doi.org/10.1002/cne.903260107]
[78]
Kapoor, R.; Okuno, E.; Kido, R.; Kapoor, V. Immuno-localization of kynurenine aminotransferase (KAT) in the rat medulla and spinal cord. Neuroreport, 1997, 8(16), 3619-3623.
[http://dx.doi.org/10.1097/00001756-199711100-00039]
[79]
Tamburin, M.; Mostardini, M.; Benatti, L. Kynurenine ami-notransferase I (KATI) isoform gene expression in the rat brain: an in situ hybridization study. Neuroreport, 1999, 10(1), 61-65.
[http://dx.doi.org/10.1097/00001756-199901180-00012]
[80]
Kapoor, R.; Lim, K.S.; Cheng, A.; Garrick, T.; Kapoor, V. Preliminary evidence for a link between schizophrenia and NMDA-glycine site receptor ligand metabolic enzymes, d-amino acid oxidase (DAAO) and kynurenine aminotransfer-ase-1 (KAT-1). Brain Res., 2006, 1106(1), 205-210.
[http://dx.doi.org/10.1016/j.brainres.2006.05.082]
[81]
Cooper, A.J.; Pinto, J.T.; Krasnikov, B.F.; Niatsetskaya, Z.V.; Han, Q.; Li, J.; Vauzour, D.; Spencer, J.P. Substrate specificity of human glutamine transaminase K as an ami-notransferase and as a cysteine S-conjugate beta-lyase. Arch. Biochem. Biophys., 2008, 474(1), 72-81.
[http://dx.doi.org/10.1016/j.abb.2008.02.038]
[82]
Lash, L.H.; Nelson, R.M.; Van Dyke, R.A.; Anders, M.W. Purification and characterization of human kidney cytosolic cysteine conjugate beta-lyase activity. Drug Metab. Dispos., 1990, 18(1), 50-54.
[83]
Okuno, E.; Nakamura, M.; Schwarcz, R. Two kynurenine aminotransferases in human brain. Brain Res., 1991, 542(2), 307-312.
[http://dx.doi.org/10.1016/0006-8993(91)91583-M]
[84]
Perry, S.J.; Schofield, M.A.; MacFarlane, M.; Lock, E.A.; King, L.J.; Gibson, G.G.; Goldfarb, P.S. Isolation and ex-pression of a cDNA coding for rat kidney cytosolic cysteine conjugate beta-lyase. Mol. Pharmacol., 1993, 43(5), 660-665.
[85]
Mosca, M.; Cozzi, L.; Breton, J.; Speciale, C.; Okuno, E.; Schwarcz, R.; Benatti, L. Molecular cloning of rat kynurenine aminotransferase: identity with glutamine trans-aminase K. FEBS Lett., 1994, 353(1), 21-24.
[http://dx.doi.org/10.1016/0014-5793(94)01003-X]
[86]
Abraham, D.G.; Cooper, A.J. Cloning and expression of a rat kidney cytosolic glutamine transaminase K that has strong sequence homology to kynurenine pyruvate aminotransfer-ase. Arch. Biochem. Biophys., 1996, 335(2), 311-320.
[http://dx.doi.org/10.1006/abbi.1996.0512]
[87]
Malherbe, P.; Alberati-Giani, D.; Köhler, C.; Cesura, A.M. Identification of a mitochondrial form of kynurenine ami-notransferase/glutamine transaminase K from rat brain. FEBS Lett., 1995, 367(2), 141-144.
[http://dx.doi.org/10.1016/0014-5793(95)00546-L]
[88]
Alberati-Giani, D.; Malherbe, P.; Köhler, C.; Lang, G.; Kief-er, V.; Lahm, H.W.; Cesura, A.M. Cloning and characteriza-tion of a soluble kynurenine aminotransferase from rat brain: identity with kidney cysteine conjugate beta-lyase. J. Neurochem., 1995, 64(4), 1448-1455.
[http://dx.doi.org/10.1046/j.1471-4159.1995.64041448.x]
[89]
Perry, S.; Harries, H.; Scholfield, C.; Lock, T.; King, L.; Gibson, G.; Goldfarb, P. Molecular cloning and expression of a cDNA for human kidney cysteine conjugate beta-lyase. FEBS Lett., 1995, 360(3), 277-280.
[http://dx.doi.org/10.1016/0014-5793(95)00123-Q]
[90]
Cooper, J.L.; Meister, A. Isolation and properties of highly purified glutamine transaminase. Biochemistry, 1972, 11(5), 661-671.
[http://dx.doi.org/10.1021/bi00755a001]
[91]
Cooper, A.J.; Meister, A. Isolation and properties of a new glutamine transaminase from rat kidney. J. Biol. Chem., 1974, 249(8), 2554-2561.
[92]
Yu, P.; Li, Z.; Zhang, L.; Tagle, D.A.; Cai, T. Characteriza-tion of kynurenine aminotransferase III, a novel member of a phylogenetically conserved KAT family. Gene, 2006, 365, 111-118.
[http://dx.doi.org/10.1016/j.gene.2005.09.034]
[93]
Claros, M.G.; Vincens, P. Computational method to predict mitochondrially imported proteins and their targeting se-quences. Eur. J. Biochem., 1996, 241(3), 779-786.
[http://dx.doi.org/10.1111/j.1432-1033.1996.00779.x]
[94]
Wiggins, J.E.; Goyal, M.; Sanden, S.K.; Wharram, B.L.; Shedden, K.A.; Misek, D.E.; Kuick, R.D.; Wiggins, R.C. Podocyte hypertrophy, “adaptation,” and “decompensation” associated with glomerular enlargement and glomerulosclero-sis in the aging rat: prevention by calorie restriction. J. Am. Soc. Nephrol., 2005, 16(10), 2953-2966.
[http://dx.doi.org/10.1681/ASN.2005050488]
[95]
Rossi, F.; Han, Q.; Li, J.; Li, J.; Rizzi, M. Crystal structure of human kynurenine aminotransferase I. J. Biol. Chem., 2004, 279(48), 50214-50220.
[http://dx.doi.org/10.1074/jbc.M409291200]
[96]
Han, Q.; Gao, Y.G.; Robinson, H.; Li, J. Structural insight into the mechanism of substrate specificity of aedes kynurenine aminotransferase. Biochemistry, 2008, 47(6), 1622-1630.
[http://dx.doi.org/10.1021/bi701800j]
[97]
Chou, K.C.; Elrod, D.W. Bioinformatical analysis of G-protein-coupled receptors. J. Proteome Res., 2002, 1(5), 429-433.
[http://dx.doi.org/10.1021/pr025527k]
[98]
Chou, K.C.; Watenpaugh, K.D.; Heinrikson, R.L. A model of the complex between cyclin-dependent kinase 5 and the activation domain of neuronal Cdk5 activator. Biochem. Biophys. Res. Commun., 1999, 259(2), 420-428.
[http://dx.doi.org/10.1006/bbrc.1999.0792]
[99]
Zhang, J.; Luan, C.H.; Chou, K.C.; Johnson, G.V. Identifica-tion of the N-terminal functional domains of Cdk5 by molec-ular truncation and computer modeling. Proteins, 2002, 48(3), 447-453.
[http://dx.doi.org/10.1002/prot.10173]
[100]
Pielak, R.M.; Schnell, J.R.; Chou, J.J.; Harrison, S.C. Mech-anism of drug inhibition and drug resistance of influenza A M2 channel. Proc. Natl. Acad. Sci. USA, 2009, 106(18), 7379-7384.
[http://dx.doi.org/10.1073/pnas.0902548106]
[101]
Chou, K.C. Molecular therapeutic target for type-2 diabetes. J. Proteome Res., 2004, 3(6), 1284-1288.
[http://dx.doi.org/10.1021/pr049849v]
[102]
Huang, R.B.; Du, Q.S.; Wang, C.H.; Chou, K.C. An in-depth analysis of the biological functional studies based on the NMR M2 channel structure of influenza A virus. Biochem. Biophys. Res. Commun., 2008, 377(4), 1243-1247.
[http://dx.doi.org/10.1016/j.bbrc.2008.10.148]
[103]
Chou, K.C.; Wei, D.Q.; Zhong, W.Z. Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS. Biochem. Biophys. Res. Commun., 2003, 308(1), 148-151.
[http://dx.doi.org/10.1016/S0006-291X(03)01342-1]
[104]
Chou, K.C.; Jones, D.; Heinrikson, R.L. Prediction of the tertiary structure and substrate binding site of caspase-8. FEBS Lett., 1997, 419(1), 49-54.
[http://dx.doi.org/10.1016/S0014-5793(97)01246-5]
[105]
Zhou, G.P.; Troy, F.A. II NMR study of the preferred membrane orientation of polyisoprenols (dolichol) and the impact of their complex with polyisoprenyl recognition se-quence peptides on membrane structure. Glycobiology, 2005, 15(4), 347-359.
[http://dx.doi.org/10.1093/glycob/cwi016]
[106]
Okuno, E.; Minatogawa, Y.; Nakamura, M.; Kamoda, N.; Nakanishi, J.; Makino, M.; Kido, R. Crystallization and char-acterization of human liver kynurenine--glyoxylate ami-notransferase. Identity with alanine--glyoxylate aminotrans-ferase and serine--pyruvate aminotransferase. Biochem. J., 1980, 189(3), 581-590.
[http://dx.doi.org/10.1042/bj1890581]
[107]
Thompson, J.S.; Richardson, K.E. Isolation and characteriza-tion of an L-alanine: glyoxylate aminotransferase from hu-man liver. J. Biol. Chem., 1967, 242(16), 3614-3619.
[108]
Liepman, A.H.; Olsen, L.J. Alanine aminotransferase homo-logs catalyze the glutamate:glyoxylate aminotransferase reac-tion in peroxisomes of Arabidopsis. Plant Physiol., 2003, 131(1), 215-227.
[http://dx.doi.org/10.1104/pp.011460]
[109]
Han, Q.; Li, J. Comparative characterization of Aedes 3-hydroxykynurenine transaminase/alanine glyoxylate transam-inase and Drosophila serine pyruvate aminotransferase. FEBS Lett., 2002, 527(1-3), 199-204.
[http://dx.doi.org/10.1016/S0014-5793(02)03229-5]
[110]
Han, Q.; Kim, S.R.; Ding, H.; Li, J. Evolution of two alanine glyoxylate aminotransferases in mosquito. Biochem. J., 2006, 397(3), 473-481.
[http://dx.doi.org/10.1042/BJ20060469]
[111]
Schlösser, T.; Gätgens, C.; Weber, U.; Stahmann, K.P. Ala-nine: glyoxylate aminotransferase of Saccharomyces cere-visiae-encoding gene AGX1 and metabolic significance. Yeast, 2004, 21(1), 63-73.
[http://dx.doi.org/10.1002/yea.1058]
[112]
Birdsey, G.M.; Lewin, J.; Holbrook, J.D.; Simpson, V.R.; Cunningham, A.A.; Danpure, C.J. A comparative analysis of the evolutionary relationship between diet and enzyme target-ing in bats, marsupials and other mammals. Proc. Biol. Sci., 2005, 272(1565), 833-840.
[http://dx.doi.org/10.1098/rspb.2004.3011]
[113]
Birdsey, G.M.; Lewin, J.; Cunningham, A.A.; Bruford, M.W.; Danpure, C.J. Differential enzyme targeting as an evolutionary adaptation to herbivory in carnivora. Mol. Biol. Evol., 2004, 21(4), 632-646.
[http://dx.doi.org/10.1093/molbev/msh054]
[114]
Holbrook, J.D.; Danpure, C.J. Molecular basis for the dual mitochondrial and cytosolic localization of alanine:glyoxylate aminotransferase in amphibian liver cells. J. Biol. Chem., 2002, 277(3), 2336-2344.
[http://dx.doi.org/10.1074/jbc.M107047200]
[115]
Danpure, C.J. Variable peroxisomal and mitochondrial tar-geting of alanine: glyoxylate aminotransferase in mammalian evolution and disease. BioEssays, 1997, 19(4), 317-326.
[http://dx.doi.org/10.1002/bies.950190409]
[116]
Watts, R.W. Alanine glyoxylate aminotransferase deficiency: biochemical and molecular genetic lessons from the study of a human disease. Adv. Enzyme Regul., 1992, 32, 309-327.
[http://dx.doi.org/10.1016/0065-2571(92)90024-T]
[117]
Danpure, C.J.; Jennings, P.R.; Leiper, J.M.; Lumb, M.J.; Oatey, P.B. Targeting of alanine: glyoxylate aminotransferase in normal individuals and its mistargeting in patients with primary hyperoxaluria type 1. Ann. N. Y. Acad. Sci., 1996, 804, 477-490.
[http://dx.doi.org/10.1111/j.1749-6632.1996.tb18638.x]
[118]
Sethi, S.K.; Waterham, H.R.; Sharma, S.; Sharma, A.; Hari, P.; Bagga, A. Primary hyperoxaluria type 1 with a novel mutation. Indian J. Pediatr., 2009, 76(2), 215-217.
[http://dx.doi.org/10.1007/s12098-008-0187-2] [PMID: 18810341]
[119]
Coulter-Mackie, M.B.; Lian, Q.; Applegarth, D.A.; Toone, J.; Waters, P.J.; Vallance, H. Mutation-based diagnostic test-ing for primary hyperoxaluria type 1: survey of results. Clin. Biochem., 2008, 41(7-8), 598-602.
[http://dx.doi.org/10.1016/j.clinbiochem.2008.01.018]
[120]
Williams, E.; Rumsby, G. Selected exonic sequencing of the AGXT gene provides a genetic diagnosis in 50% of patients with primary hyperoxaluria type 1. Clin. Chem., 2007, 53(7), 1216-1221.
[http://dx.doi.org/10.1373/clinchem.2006.084434]
[121]
Leumann, E.; Hoppe, B. Primary hyperoxaluria type 1: is genotyping clinically helpful? Pediatr. Nephrol., 2005, 20(5), 555-557.
[http://dx.doi.org/10.1007/s00467-005-1813-0]
[122]
Danpure, C.J. Molecular aetiology of primary hyperoxaluria type 1. Nephron, Exp. Nephrol., 2004, 98(2), e39-e44.
[http://dx.doi.org/10.1159/000080254]
[123]
Monico, C.G.; Rossetti, S.; Olson, J.B.; Milliner, D.S. Pyri-doxine effect in type I primary hyperoxaluria is associated with the most common mutant allele. Kidney Int., 2005, 67(5), 1704-1709.
[http://dx.doi.org/10.1111/j.1523-1755.2005.00267.x]
[124]
Dindo, M.; Oppici, E.; Dell’Orco, D.; Montone, R.; Cellini, B. Correlation between the molecular effects of mutations at the dimer interface of alanine-glyoxylate aminotransferase leading to primary hyperoxaluria type I and the cellular re-sponse to vitamin B6. J. Inherit. Metab. Dis., 2018, 41(2), 263-275.
[http://dx.doi.org/10.1007/s10545-017-0105-8]
[125]
M’dimegh, S.; Omezzine, A.; Hamida-Rebai, M.B.; Aqua-viva-Bourdain, C.; M’barek, I.; Sahtout, W.; Zellama, D.; Souche, G.; Achour, A.; Abroug, S.; Bouslama, A. Identifi-cation of a novel AGXT gene mutation in primary hyperox-aluria after kidney transplantation failure. Transpl. Immunol., 2016, 39, 60-65.
[http://dx.doi.org/10.1016/j.trim.2016.08.008]
[126]
M’Dimegh, S.; Aquaviva-Bourdain, C.; Omezzine, A.; M’Barek, I.; Souche, G.; Zellama, D.; Abidi, K.; Achour, A.; Gargah, T.; Abroug, S.; Bouslama, A. A novel mutation in the AGXT gene causing primary hyperoxaluria type I: geno-type-phenotype correlation. J. Genet., 2016, 95(3), 659-666.
[http://dx.doi.org/10.1007/s12041-016-0676-4]
[127]
Kontani, Y.; Kaneko, M.; Kikugawa, M.; Fujimoto, S.; Tamaki, N. Identity of D-3-aminoisobutyrate-pyruvate ami-notransferase with alanine-glyoxylate aminotransferase 2. Biochim. Biophys. Acta, 1993, 1156(2), 161-166.
[http://dx.doi.org/10.1016/0304-4165(93)90131-Q]
[128]
Ogawa, T.; Kimoto, M.; Sasaoka, K. Dimethylarg-inine:pyruvate aminotransferase in rats. Purification, proper-ties, and identity with alanine:glyoxylate aminotransferase 2. J. Biol. Chem., 1990, 265(34), 20938-20945.
[129]
Cooper, A.J.; Krasnikov, B.F.; Okuno, E.; Jeitner, T.M. L-alanine-glyoxylate aminotransferase II of rat kidney and liver mitochondria possesses cysteine S-conjugate beta-lyase ac-tivity: a contributing factor to the nephrotoxici-ty/hepatotoxicity of halogenated alkenes? Biochem. J., 2003, 376(Pt 1), 169-178.
[http://dx.doi.org/10.1042/bj20030988]
[130]
Okuno, E.; Minatogawa, Y.; Kido, R. Co-purification of alanine-glyoxylate aminotransferase with 2-aminobutyrate aminotransferase in rat kidney. Biochim. Biophys. Acta, 1982, 715(1), 97-104.
[http://dx.doi.org/10.1016/0304-4165(82)90054-X]
[131]
Noguchi, T.; Fujiwara, S. Identification of mammalian ami-notransferases utilizing glyoxylate or pyruvate as amino ac-ceptor. Peroxisomal and mitochondrial asparagine ami-notransferase. J. Biol. Chem., 1988, 263(1), 182-186.
[132]
Noguchi, T.; Okuno, E.; Takada, Y.; Minatogawa, Y.; Okai, K.; Kido, R. Characteristics of hepatic alanine-glyoxylate aminotransferase in different mammalian species. Biochem. J., 1978, 169(1), 113-122.
[http://dx.doi.org/10.1042/bj1690113]
[133]
Rowsell, E.V.; Snell, K.; Carnie, J.A.; Al-Tai, A.H. Liver-L-alanine-glyoxylate and L-serine-pyruvate aminotransferase activities: an apparent association with gluconeogenesis. Biochem. J., 1969, 115(5), 1071-1073.
[http://dx.doi.org/10.1042/bj1151071]
[134]
Shao, L.; Vawter, M.P. Shared gene expression alterations in schizophrenia and bipolar disorder. Biol. Psychiatry, 2008, 64(2), 89-97.
[http://dx.doi.org/10.1016/j.biopsych.2007.11.010]
[135]
Taylor, S.W.; Fahy, E.; Zhang, B.; Glenn, G.M.; Warnock, D.E.; Wiley, S.; Murphy, A.N.; Gaucher, S.P.; Capaldi, R.A.; Gibson, B.W.; Ghosh, S.S. Characterization of the human heart mitochondrial proteome. Nat. Biotechnol., 2003, 21(3), 281-286.
[http://dx.doi.org/10.1038/nbt793]
[136]
Jadhao, S.B.; Yang, R.Z.; Lin, Q.; Hu, H.; Anania, F.A.; Shuldiner, A.R.; Gong, D.W. Murine alanine aminotransfer-ase: cDNA cloning, functional expression, and differential gene regulation in mouse fatty liver. Hepatology, 2004, 39(5), 1297-1302.
[http://dx.doi.org/10.1002/hep.20182]
[137]
Rajamohan, F.; Nelms, L.; Joslin, D.L.; Lu, B.; Reagan, W.J.; Lawton, M. cDNA cloning, expression, purification, distribution, and characterization of biologically active canine alanine aminotransferase-1. Protein Expr. Purif., 2006, 48(1), 81-89.
[http://dx.doi.org/10.1016/j.pep.2005.12.009]
[138]
Liu, L.; Zhong, S.; Yang, R.; Hu, H.; Yu, D.; Zhu, D.; Hua, Z.; Shuldiner, A.R.; Goldstein, R.; Reagan, W.J.; Gong, D.W. Expression, purification, and initial characterization of human alanine aminotransferase (ALT) isoenzyme 1 and 2 in High-five insect cells. Protein Expr. Purif., 2008, 60(2), 225-231.
[http://dx.doi.org/10.1016/j.pep.2008.04.006]
[139]
Strecker, H.J. Purification and Properties of Rat Liver Orni-thine Delta-Transaminase. J. Biol. Chem., 1965, 240, 1225-1230.
[140]
Tamaki, N.; Kubo, K.; Aoyama, H.; Funatsuka, A. Inhibitory effect of 6-azauracil on purified rabbit liver 4-aminobutyrate aminotransferase. J. Biochem., 1983, 93(4), 955-959.
[http://dx.doi.org/10.1093/oxfordjournals.jbchem.a134250]
[141]
Han, Q.; Robinson, H.; Cai, T.; Tagle, D.A.; Li, J. Biochem-ical and structural characterization of mouse mitochondrial aspartate aminotransferase, a newly identified kynurenine aminotransferase-IV. Biosci. Rep., 2011, 31(5), 323-332.
[http://dx.doi.org/10.1042/BSR20100117]
[142]
Leeson, P.D.; Iversen, L.L. The glycine site on the NMDA receptor: Structure-activity relationships and therapeutic po-tential. J. Med. Chem., 1994, 37(24), 4053-4067.
[http://dx.doi.org/10.1021/jm00050a001]
[143]
Stone, T.W.; Perkins, M.N. Actions of excitatory amino acids and kynurenic acid in the primate hippocampus: a pre-liminary study. Neurosci. Lett., 1984, 52(3), 335-340.
[http://dx.doi.org/10.1016/0304-3940(84)90184-8]
[144]
Birch, P.J.; Grossman, C.J.; Hayes, A.G. Kynurenic acid antagonises responses to NMDA via an action at the strych-nine-insensitive glycine receptor. Eur. J. Pharmacol., 1988, 154(1), 85-87.
[http://dx.doi.org/10.1016/0014-2999(88)90367-6]
[145]
Pereira, E.F.; Hilmas, C.; Santos, M.D.; Alkondon, M.; Maelicke, A.; Albuquerque, E.X. Unconventional ligands and modulators of nicotinic receptors. J. Neurobiol., 2002, 53(4), 479-500.
[http://dx.doi.org/10.1002/neu.10146]
[146]
Hilmas, C.; Pereira, E.F.; Alkondon, M.; Rassoulpour, A.; Schwarcz, R.; Albuquerque, E.X. The brain metabolite kynurenic acid inhibits alpha7 nicotinic receptor activity and increases non-alpha7 nicotinic receptor expression: physio-pathological implications. J. Neurosci., 2001, 21(19), 7463-7473.
[http://dx.doi.org/10.1523/JNEUROSCI.21-19-07463.2001]
[147]
Alkondon, M.; Pereira, E.F.; Yu, P.; Arruda, E.Z.; Almeida, L.E.; Guidetti, P.; Fawcett, W.P.; Sapko, M.T.; Randall, W.R.; Schwarcz, R.; Tagle, D.A.; Albuquerque, E.X. Target-ed deletion of the kynurenine aminotransferase ii gene reveals a critical role of endogenous kynurenic acid in the regulation of synaptic transmission via alpha7 nicotinic receptors in the hippocampus. J. Neurosci., 2004, 24(19), 4635-4648.
[http://dx.doi.org/10.1523/JNEUROSCI.5631-03.2004]
[148]
Stone, T.W. Kynurenic acid blocks nicotinic synaptic trans-mission to hippocampal interneurons in young rats. Eur. J. Neurosci., 2007, 25(9), 2656-2665.
[http://dx.doi.org/10.1111/j.1460-9568.2007.05540.x]
[149]
Han, Q.; Cai, T.; Tagle, D.A.; Li, J. Structure, expression, and function of kynurenine aminotransferases in human and rodent brains. Cell. Mol. Life Sci., 2010, 67(3), 353-368.
[http://dx.doi.org/10.1007/s00018-009-0166-4]
[150]
Notarangelo, F.M.; Pocivavsek, A. Elevated kynurenine pathway metabolism during neurodevelopment: Implications for brain and behavior Neuropharmacology, 2017. 112(Pt B), 275-285.
[http://dx.doi.org/10.1016/j.neuropharm.2016.03.001] [PMID: 26944732]
[151]
Colombari, E.; Sato, M.A.; Cravo, S.L.; Bergamaschi, C.T.; Campos, R.R., Jr; Lopes, O.U. Role of the medulla oblonga-ta in hypertension. Hypertension, 2001, 38(3 Pt 2), 549-554.
[http://dx.doi.org/10.1161/01.HYP.38.3.549]
[152]
Salimi Elizei, S.; Poormasjedi-Meibod, M.S.; Wang, X.; Kheirandish, M.; Ghahary, A. Kynurenic acid downregulates IL-17/1L-23 axis in vitro. Mol. Cell. Biochem., 2017, 431(1-2), 55-65.
[http://dx.doi.org/10.1007/s11010-017-2975-3]
[153]
Kwok, J.B.; Kapoor, R.; Gotoda, T.; Iwamoto, Y.; Iizuka, Y.; Yamada, N.; Isaacs, K.E.; Kushwaha, V.V.; Church, W.B.; Schofield, P.R.; Kapoor, V. A missense mutation in kynurenine aminotransferase-1 in spontaneously hyperten-sive rats. J. Biol. Chem., 2002, 277(39), 35779-35782.
[http://dx.doi.org/10.1074/jbc.C200303200]
[154]
Wang, Y.; Liu, H.; McKenzie, G.; Witting, P.K.; Stasch, J.P.; Hahn, M.; Changsirivathanathamrong, D.; Wu, B.J.; Ball, H.J.; Thomas, S.R.; Kapoor, V.; Celermajer, D.S.; Mellor, A.L.; Keaney, J.F., Jr; Hunt, N.H.; Stocker, R. Kynurenine is an endothelium-derived relaxing factor produced during in-flammation. Nat. Med., 2010, 16(3), 279-285.
[http://dx.doi.org/10.1038/nm.2092]
[155]
Han, Q.; Cai, T.; Tagle, D.A.; Li, J. Thermal stability, pH dependence and inhibition of four murine kynurenine ami-notransferases. BMC Biochem., 2010, 11, 19.
[http://dx.doi.org/10.1186/1471-2091-11-19]
[156]
Han, Q.; Robinson, H.; Cai, T.; Tagle, D.A.; Li, J. Structural insight into the inhibition of human kynurenine aminotrans-ferase I/glutamine transaminase K. J. Med. Chem., 2009, 52(9), 2786-2793.
[http://dx.doi.org/10.1021/jm9000874]
[157]
Wilmore, D.W. Glutamine and the gut. Gastroenterology, 1994, 107(6), 1885-1886.
[http://dx.doi.org/10.1016/0016-5085(94)90836-2]
[158]
Kaiser, L.G.; Schuff, N.; Cashdollar, N.; Weiner, M.W. Age-related glutamate and glutamine concentration changes in normal human brain: 1H MR spectroscopy study at 4 T. Neurobiol. Aging, 2005, 26(5), 665-672.
[http://dx.doi.org/10.1016/j.neurobiolaging.2004.07.001]
[159]
Newsholme, P.; Procopio, J.; Lima, M.M.; Pithon-Curi, T.C.; Curi, R. Glutamine and glutamate--their central role in cell metabolism and function. Cell Biochem. Funct., 2003, 21(1), 1-9.
[http://dx.doi.org/10.1002/cbf.1003]
[160]
Saito, K.; Fujigaki, S.; Heyes, M.P.; Shibata, K.; Takemura, M.; Fujii, H.; Wada, H.; Noma, A.; Seishima, M. Mecha-nism of increases in L-kynurenine and quinolinic acid in re-nal insufficiency. Am. J. Physiol. Renal Physiol., 2000, 279(3), F565-F572.
[http://dx.doi.org/10.1152/ajprenal.2000.279.3.F565]
[161]
Cooper, A.J.L.; Dorai, T.; Dorai, B.; Krasnikov, B.F.; Li, J.; Hallen, A.; Pinto, J.T. Role of glutamine transaminases in nitrogen, sulfur, selenium, and 1-carbon metabolism. Glutam. Clin. Nutr., 2015, 37-54.
[162]
Cooper, A.J.; Kuhara, T. α-Ketoglutaramate: an overlooked metabolite of glutamine and a biomarker for hepatic encepha-lopathy and inborn errors of the urea cycle. Metab. Brain Dis., 2014, 29(4), 991-1006.
[http://dx.doi.org/10.1007/s11011-013-9444-9]
[163]
Peng, M.; Falk, M.J.; Haase, V.H.; King, R.; Polyak, E.; Selak, M.; Yudkoff, M.; Hancock, W.W.; Meade, R.; Saiki, R.; Lunceford, A.L.; Clarke, C.F.; Gasser, D.L. Primary co-enzyme Q deficiency in Pdss2 mutant mice causes isolated renal disease. PLoS Genet., 2008, 4(4)e1000061
[http://dx.doi.org/10.1371/journal.pgen.1000061]
[164]
Zhou, G.P.; Troy, F.A. II NMR studies on how the binding complex of polyisoprenol recognition sequence peptides and polyisoprenols can modulate membrane structure. Curr. Protein Pept. Sci., 2005, 6(5), 399-411.
[http://dx.doi.org/10.2174/138920305774329377]
[165]
Zhou, G.P.; Troy, F.A. II Characterization by NMR and molecular modeling of the binding of polyisoprenols and polyisoprenyl recognition sequence peptides: 3D structure of the complexes reveals sites of specific interactions. Glycobiology, 2003, 13(2), 51-71.
[http://dx.doi.org/10.1093/glycob/cwg008]
[166]
Zhou, G.P.; Troy, F.A. 2-D NMR analyses reveals a specific interaction between polyisoprenols (PIs) and the polyiso-prenol recognition sequences (PIRS) in model membranes. Glycoconj. J., 1995, 12, 434.
[167]
OuYang, B.; Xie, S.; Berardi, M.J.; Zhao, X.; Dev, J.; Yu, W.; Sun, B.; Chou, J.J. Unusual architecture of the p7 chan-nel from hepatitis C virus. Nature, 2013, 498(7455), 521-525.
[http://dx.doi.org/10.1038/nature12283]
[168]
Berardi, M.J.; Shih, W.M.; Harrison, S.C.; Chou, J.J. Mito-chondrial uncoupling protein 2 structure determined by NMR molecular fragment searching. Nature, 2011, 476(7358), 109-113.
[http://dx.doi.org/10.1038/nature10257]
[169]
Dev, J.; Park, D.; Fu, Q.; Chen, J.; Ha, H.J.; Ghantous, F.; Herrmann, T.; Chang, W.; Liu, Z.; Frey, G.; Seaman, M.S.; Chen, B.; Chou, J.J. Structural basis for membrane anchor-ing of HIV-1 envelope spike. Science, 2016, 353(6295), 172-175.
[http://dx.doi.org/10.1126/science.aaf7066]
[170]
Schnell, J.R.; Zhou, G.P.; Zweckstetter, M.; Rigby, A.C.; Chou, J.J. Rapid and accurate structure determination of coiled-coil domains using NMR dipolar couplings: applica-tion to cGMP-dependent protein kinase Ialpha. Protein Sci., 2005, 14(9), 2421-2428.
[http://dx.doi.org/10.1110/ps.051528905]
[171]
Schnell, J.R.; Chou, J.J. Structure and mechanism of the M2 proton channel of influenza A virus. Nature, 2008, 451(7178), 591-595.
[http://dx.doi.org/10.1038/nature06531]
[172]
Sharma, A.K.; Zhou, G.P.; Kupferman, J.; Surks, H.K.; Christensen, E.N.; Chou, J.J.; Mendelsohn, M.E.; Rigby, A.C. Probing the interaction between the coiled coil leucine zipper of cGMP-dependent protein kinase Ialpha and the C terminus of the myosin binding subunit of the myosin light chain phosphatase. J. Biol. Chem., 2008, 283(47), 32860-32869.
[http://dx.doi.org/10.1074/jbc.M804916200]
[173]
Oxenoid, K.; Dong, Y.; Cao, C.; Cui, T.; Sancak, Y.; Markhard, A.L.; Grabarek, Z.; Kong, L.; Liu, Z.; Ouyang, B.; Cong, Y.; Mootha, V.K.; Chou, J.J. Architecture of the mitochondrial calcium uniporter. Nature, 2016, 533(7602), 269-273.
[http://dx.doi.org/10.1038/nature17656]
[174]
Wang, J.F.; Chou, K.C. Insights from modeling the 3D structure of New Delhi metallo-β-lactamse and its binding in-teractions with antibiotic drugs. PLoS One, 2011, 6(4)e18414
[http://dx.doi.org/10.1371/journal.pone.0018414]
[175]
Ma, Y.; Wang, S.Q.; Xu, W.R.; Wang, R.L.; Chou, K.C. Design novel dual agonists for treating type-2 diabetes by targeting peroxisome proliferator-activated receptors with core hopping approach. PLoS One, 2012, 7(6)e38546
[http://dx.doi.org/10.1371/journal.pone.0038546]
[176]
Li, X.B.; Wang, S.Q.; Xu, W.R.; Wang, R.L.; Chou, K.C. Novel inhibitor design for hemagglutinin against H1N1 in-fluenza virus by core hopping method. PLoS One, 2011, 6(11)e28111
[http://dx.doi.org/10.1371/journal.pone.0028111]
[177]
Liao, Q.H.; Gao, Q.Z.; Wei, J.; Chou, K.C. Docking and molecular dynamics study on the inhibitory activity of novel inhibitors on epidermal growth factor receptor (EGFR). Med. Chem., 2011, 7(1), 24-31.
[http://dx.doi.org/10.2174/157340611794072698]
[178]
Chou, K.C.; Tomasselli, A.G.; Heinrikson, R.L. Prediction of the tertiary structure of a caspase-9/inhibitor complex. FEBS Lett., 2000, 470(3), 249-256.
[http://dx.doi.org/10.1016/S0014-5793(00)01333-8]
[179]
Wang, S.Q.; Du, Q.S.; Huang, R.B.; Zhang, D.W.; Chou, K.C. Insights from investigating the interaction of oseltamivir (Tamiflu) with neuraminidase of the 2009 H1N1 swine flu virus. Biochem. Biophys. Res. Commun., 2009, 386(3), 432-436.
[http://dx.doi.org/10.1016/j.bbrc.2009.06.016]
[180]
Wang, J.F.; Wei, D.Q.; Lin, Y.; Wang, Y.H.; Du, H.L.; Li, Y.X.; Chou, K.C. Insights from modeling the 3D structure of NAD(P)H-dependent D-xylose reductase of Pichia stipitis and its binding interactions with NAD and NADP. Biochem. Biophys. Res. Commun., 2007, 359(2), 323-329.
[http://dx.doi.org/10.1016/j.bbrc.2007.05.101]
[181]
Chou, K.C. Insights from modeling the 3D structure of DNA-CBF3b complex. J. Proteome Res., 2005, 4(5), 1657-1660.
[http://dx.doi.org/10.1021/pr050135+]
[182]
Chou, K-C. Insights from modeling the tertiary structure of human BACE2. J. Proteome Res., 2004, 3(5), 1069-1072.
[http://dx.doi.org/10.1021/pr049905s]
[183]
Chou, K.C. Coupling interaction between thromboxane A2 receptor and alpha-13 subunit of guanine nucleotide-binding protein. J. Proteome Res., 2005, 4(5), 1681-1686.
[http://dx.doi.org/10.1021/pr050145a]
[184]
Chou, K.C. Insights from modelling the 3D structure of the extracellular domain of alpha7 nicotinic acetylcholine recep-tor. Biochem. Biophys. Res. Commun., 2004, 319(2), 433-438.
[http://dx.doi.org/10.1016/j.bbrc.2004.05.016]
[185]
Chou, K.C. Insights from modeling three-dimensional struc-tures of the human potassium and sodium channels. J. Proteome Res., 2004, 3(4), 856-861.
[http://dx.doi.org/10.1021/pr049931q]
[186]
Wang, J.F.; Chou, K.C. Insights into the mutation-induced HHH syndrome from modeling human mitochondrial orni-thine transporter-1. PLoS One, 2012, 7(1)e31048
[http://dx.doi.org/10.1371/journal.pone.0031048]
[187]
Chou, K.C. Structural bioinformatics and its impact to bio-medical science. Curr. Med. Chem., 2004, 11(16), 2105-2134.
[http://dx.doi.org/10.2174/0929867043364667]
[188]
Zhou, G.P. Predictions and determinations of protein and peptide structures. Protein Pept. Lett., 2011, 18(10), 964-965.
[http://dx.doi.org/10.2174/092986611796378738]
[189]
Huang, R.B.; Cheng, D.; Liao, S.M.; Lu, B.; Wang, Q.Y.; Xie, N.Z.; Troy Ii, F.A.; Zhou, G.P. The Intrinsic Relation-ship Between Structure and Function of the Sialyltransferase ST8Sia Family Members. Curr. Top. Med. Chem., 2017, 17(21), 2359-2369.
[http://dx.doi.org/10.2174/1568026617666170414150730]
[190]
Zhou, G.P. The structural determinations of the leucine zip-per coiled-coil domains of the cGMP-dependent protein ki-nase Iα and its interaction with the myosin binding subunit of the myosin light chains phosphase. Protein Pept. Lett., 2011, 18(10), 966-978.
[http://dx.doi.org/10.2174/0929866511107010966]
[191]
Zhou, G.P. The disposition of the LZCC protein residues in wenxiang diagram provides new insights into the protein-protein interaction mechanism. J. Theor. Biol., 2011, 284(1), 142-148.
[http://dx.doi.org/10.1016/j.jtbi.2011.06.006]
[192]
Zhou, G.P.; Huang, R.B. The pH-triggered conversion of the PrP(c) to PrP(sc.). Curr. Top. Med. Chem., 2013, 13(10), 1152-1163.
[http://dx.doi.org/10.2174/15680266113139990003]
[193]
Zhou, G.P. Mission of randomness. Virulence, 2013, 4(8), 669-670.
[http://dx.doi.org/10.4161/viru.27136]
[194]
Zhou, G.P.; Huang, R.B.; Troy, F.A. II 3D structural con-formation and functional domains of polysialyltransferase ST8Sia IV required for polysialylation of neural cell adhe-sion molecules. Protein Pept. Lett., 2015, 22(2), 137-148.
[http://dx.doi.org/10.2174/0929866521666141019192221]
[195]
Zhou, G.P. Editorial: Current progress in structural bioin-formatics of protein-biomolecule interactions. Med. Chem., 2015, 11(3), 216-217.
[http://dx.doi.org/10.2174/1573406411666141229162618]
[196]
Zhou, G.P.; Chen, D.; Liao, S.; Huang, R.B. Recent Pro-gresses in Studying Helix-Helix Interactions in Proteins by Incorporating the Wenxiang Diagram into the NMR Spec-troscopy. Curr. Top. Med. Chem., 2016, 16(6), 581-590.
[http://dx.doi.org/10.2174/1568026615666150819104617]
[197]
Xiao, X.; Min, J.L.; Lin, W.Z.; Liu, Z.; Cheng, X.; Chou, K.C. iDrug-Target: Predicting the interactions between drug compounds and target proteins in cellular networking via benchmark dataset optimization approach. J. Biomol. Struct. Dyn., 2015, 33(10), 2221-2233.
[http://dx.doi.org/10.1080/07391102.2014.998710]
[198]
Xiao, X.; Min, J.L.; Wang, P.; Chou, K.C. iCDI-PseFpt: identify the channel-drug interaction in cellular networking with PseAAC and molecular fingerprints. J. Theor. Biol., 2013, 337(47), 71-79.
[http://dx.doi.org/10.1016/j.jtbi.2013.08.013]
[199]
Xiao, X.; Min, J.L.; Wang, P.; Chou, K.C. iGPCR-drug: A web server for predicting interaction between GPCRs and drugs in cellular networking. PLoS One, 2013, 8(8)e72234
[http://dx.doi.org/10.1371/journal.pone.0072234]
[200]
Min, J-L.; Xiao, X.; Chou, K-C. A web server for identify-ing the interaction between enzymes and drugs in cellular networking. BioMed Res. Int., 2013, 2013, 2314-6133.
[http://dx.doi.org/10.1155/2013/701317]
[201]
Fan, Y.N.; Xiao, X.; Min, J.L.; Chou, K.C. iNR-Drug: Pre-dicting the interaction of drugs with nuclear receptors in cel-lular networking. Int. J. Mol. Sci., 2014, 15(3), 4915-4937.
[http://dx.doi.org/10.3390/ijms15034915]
[202]
Wang, J.F.; Chou, K.C. Insights from studying the mutation-induced allostery in the M2 proton channel by molecular dy-namics. Protein Eng. Des. Sel., 2010, 23(8), 663-666.
[http://dx.doi.org/10.1093/protein/gzq040]
[203]
Fan, Y-N.; Xiao, X.; Min, J-L.; Chou, K-C. iNR-Drug: pre-dicting the interaction of drugs with nuclear receptors in cel-lular networking. Int. J. Mol. Sci., 2014, 15(3), 4915-4937.
[http://dx.doi.org/10.3390/ijms15034915]
[204]
Chou, K.C. Pseudo Amino Acid Composition and its Appli-cations in Bioinformatics, Proteomics and System Biology. Curr. Proteomics, 2009, 6(4), 262-274.
[http://dx.doi.org/10.2174/157016409789973707]
[205]
Chou, K.C. An Unprecedented Revolution in Medicinal Chemistry Driven by the Progress of Biological Science. Curr. Top. Med. Chem., 2017, 17(21), 2337-2358.
[http://dx.doi.org/10.2174/1568026617666170414145508]
[206]
Sabooh, M.F.; Iqbal, N.; Khan, M.; Khan, M.; Maqbool, H.F. Identifying 5-methylcytosine sites in RNA sequence us-ing composite encoding feature into Chou’s PseKNC. J. Theor. Biol., 2018, 452, 1-9.
[http://dx.doi.org/10.1016/j.jtbi.2018.04.037]
[207]
Ju, Z.; Wang, S.Y. Prediction of citrullination sites by incor-porating k-spaced amino acid pairs into Chou’s general pseudo amino acid composition. Gene, 2018, 664, 78-83.
[http://dx.doi.org/10.1016/j.gene.2018.04.055]
[208]
Feng, P.; Yang, H.; Ding, H.; Lin, H.; Chen, W.; Chou, K.C. iDNA6mA-PseKNC: Identifying DNA N 6 -methyladenosine sites by incorporating nucleotide physico-chemical properties into PseKNC. Genomics, 2019, 111(1), 96-102.
[http://dx.doi.org/10.1016/j.ygeno.2018.01.005] [PMID: 29360500]
[209]
Chen, W.; Feng, P.; Yang, H.; Ding, H.; Lin, H.; Chou, K.C. iRNA-3typeA: identifying 3-types of modification at RNA’s adenosine sites. Mol. Ther. Nucleic Acids, 2018, 1(11), 468-474.
[http://dx.doi.org/10.1016/j.omtn.2018.03.012]
[210]
Xu, Y.; Wang, Z.; Li, C.; Chou, K.C. iPreny-PseAAC: identify C-terminal cysteine prenylation sites in proteins by in-corporating two tiers of sequence couplings into PseAAC. Med. Chem., 2017, 13(6), 544-551.
[http://dx.doi.org/10.2174/1573406413666170419150052]
[211]
Qiu, W.R.; Sun, B.Q.; Xiao, X.; Xu, D.; Chou, K.C. iPhos-PseEvo: Identifying Human Phosphorylated Proteins by In-corporating Evolutionary Information into General PseAAC via Grey System Theory. Mol. Inform., 2017, 36(5-6)
[http://dx.doi.org/10.1002/minf.201600010]
[212]
Qiu, W.R.; Jiang, S.Y.; Xu, Z.C.; Xiao, X.; Chou, K.C. iR-NAm5C-PseDNC: identifying RNA 5-methylcytosine sites by incorporating physical-chemical properties into pseudo dinucleotide composition. Oncotarget, 2017, 8(25), 41178-41188.
[http://dx.doi.org/10.18632/oncotarget.17104]
[213]
Qiu, W.R.; Jiang, S.Y.; Sun, B.Q.; Xiao, X.; Cheng, X.; Chou, K.C. iRNA-2methyl: identify RNA 2′-O-methylation sites by incorporating sequence-coupled effects into general PseKNC and ensemble classifier. Med. Chem., 2017, 13(8), 734-743.
[http://dx.doi.org/10.2174/1573406413666170623082245]
[214]
Liu, L.M.; Xu, Y.; Chou, K.C. iPGK-PseAAC: identify lysine phosphoglycerylation sites in proteins by incorporat-ing four different tiers of amino acid pairwise coupling in-formation into the general PseAAC. Med. Chem., 2017, 13(6), 552-559.
[http://dx.doi.org/10.2174/1573406413666170515120507]
[215]
Ju, Z.; He, J.J. Prediction of lysine crotonylation sites by incorporating the composition of k-spaced amino acid pairs into Chou’s general PseAAC. J. Mol. Graph. Model., 2017, 77, 200-204.
[http://dx.doi.org/10.1016/j.jmgm.2017.08.020]
[216]
Feng, P.; Ding, H.; Yang, H.; Chen, W.; Lin, H.; Chou, K.C. iRNA-PseColl: Identifying the Occurrence Sites of Different RNA Modifications by Incorporating Collective Effects of Nucleotides into PseKNC. Mol. Ther. Nucleic Acids, 2017, 7(C), 155-163.
[http://dx.doi.org/10.1016/j.omtn.2017.03.006]
[217]
Xu, Y.; Chou, K.C. Recent Progress in Predicting Posttrans-lational Modification Sites in Proteins. Curr. Top. Med. Chem., 2016, 16(6), 591-603.
[http://dx.doi.org/10.2174/1568026615666150819110421]
[218]
Qiu, W.R.; Xiao, X.; Xu, Z.C.; Chou, K.C. iPhos-PseEn: identifying phosphorylation sites in proteins by fusing differ-ent pseudo components into an ensemble classifier. Oncotarget, 2016, 7(32), 51270-51283.
[http://dx.doi.org/10.18632/oncotarget.9987]
[219]
Qiu, W.R.; Sun, B.Q.; Xiao, X.; Xu, Z.C.; Chou, K.C. iPTM-mLys: identifying multiple lysine PTM sites and their different types. Bioinformatics, 2016, 32(20), 3116-3123.
[http://dx.doi.org/10.1093/bioinformatics/btw380]
[220]
Qiu, W.R.; Sun, B.Q.; Xiao, X.; Xu, Z.C.; Chou, K.C. iHyd-PseCp: Identify hydroxyproline and hydroxylysine in pro-teins by incorporating sequence-coupled effects into general PseAAC. Oncotarget, 2016, 7(28), 44310-44321.
[http://dx.doi.org/10.18632/oncotarget.10027]
[221]
Liu, Z.; Xiao, X.; Yu, D.J.; Jia, J.; Qiu, W.R.; Chou, K.C. pRNAm-PC: Predicting N(6)-methyladenosine sites in RNA sequences via physical-chemical properties. Anal. Biochem., 2016, 497, 60-67.
[http://dx.doi.org/10.1016/j.ab.2015.12.017]
[222]
Jia, J.; Zhang, L.; Liu, Z.; Xiao, X.; Chou, K.C. pSumo-CD: predicting sumoylation sites in proteins with covariance dis-criminant algorithm by incorporating sequence-coupled ef-fects into general PseAAC. Bioinformatics, 2016, 32(20), 3133-3141.
[http://dx.doi.org/10.1093/bioinformatics/btw387]
[223]
Jia, J.; Liu, Z.; Xiao, X.; Liu, B.; Chou, K.C. iCar-PseCp: identify carbonylation sites in proteins by Monte Carlo sam-pling and incorporating sequence coupled effects into general PseAAC. Oncotarget, 2016, 7(23), 34558-34570.
[http://dx.doi.org/10.18632/oncotarget.9148]
[224]
Jia, J.; Liu, Z.; Xiao, X.; Liu, B.; Chou, K.C. pSuc-Lys: Pre-dict lysine succinylation sites in proteins with PseAAC and ensemble random forest approach. J. Theor. Biol., 2016, 394, 223-230.
[http://dx.doi.org/10.1016/j.jtbi.2016.01.020]
[225]
Jia, J.; Liu, Z.; Xiao, X.; Liu, B.; Chou, K.C. iSuc-PseOpt: Identifying lysine succinylation sites in proteins by incorpo-rating sequence-coupling effects into pseudo components and optimizing imbalanced training dataset. Anal. Biochem., 2016, 497, 48-56.
[http://dx.doi.org/10.1016/j.ab.2015.12.009]
[226]
Chen, W.; Tang, H.; Ye, J.; Lin, H.; Chou, K.C. iRNA-PseU: Identifying RNA pseudouridine sites. Mol. Ther. Nucleic Acids, 2016, 5(7)e332
[227]
Qiu, W.R.; Xiao, X.; Lin, W.Z.; Chou, K.C. iUbiq-Lys: pre-diction of lysine ubiquitination sites in proteins by extracting sequence evolution information via a gray system model. J. Biomol. Struct. Dyn., 2015, 33(8), 1731-1742.
[http://dx.doi.org/10.1080/07391102.2014.968875]
[228]
Chou, K.C. Impacts of bioinformatics to medicinal chemistry. Med. Chem., 2015, 11(3), 218-234.
[http://dx.doi.org/10.2174/1573406411666141229162834]
[229]
Chen, W.; Ding, H.; Zhou, X.; Lin, H.; Chou, K-C. iRNA (m6A)-PseDNC: Identifying N6-methyladenosine sites us-ing pseudo dinucleotide composition. Anal. Biochem., 2018, 3, 2697.
[http://dx.doi.org/10.1016/j.ab.2018.09.002]
[230]
Zhang, J.; Zhao, X.; Sun, P.; Ma, Z. PSNO: predicting cyste-ine S-nitrosylation sites by incorporating various sequence-derived features into the general form of Chou’s PseAAC. Int. J. Mol. Sci., 2014, 15(7), 11204-11219.
[http://dx.doi.org/10.3390/ijms150711204]
[231]
Xu, Y.; Wen, X.; Wen, L.S.; Wu, L.Y.; Deng, N.Y.; Chou, K.C. iNitro-Tyr: prediction of nitrotyrosine sites in proteins with general pseudo amino acid composition. PLoS One, 2014, 9(8)e105018
[http://dx.doi.org/10.1371/journal.pone.0105018]
[232]
Xu, Y.; Wen, X.; Shao, X.J.; Deng, N.Y.; Chou, K.C. iHyd-PseAAC: predicting hydroxyproline and hydroxylysine in proteins by incorporating dipeptide position-specific propen-sity into pseudo amino acid composition. Int. J. Mol. Sci., 2014, 15(5), 7594-7610.
[http://dx.doi.org/10.3390/ijms15057594]
[233]
Qiu, W.R.; Xiao, X.; Lin, W.Z.; Chou, K.C. iMethyl-PseAAC: identification of protein methylation sites via a pseudo amino acid composition approach. BioMed Res. Int., 2014, 2014(12)947416
[http://dx.doi.org/10.1155/2014/947416]
[234]
Jia, C.; Lin, X.; Wang, Z. Prediction of protein S-nitrosylation sites based on adapted normal distribution bi-profile Bayes and Chou’s pseudo amino acid composition. Int. J. Mol. Sci., 2014, 15(6), 10410-10423.
[http://dx.doi.org/10.3390/ijms150610410]
[235]
Xu, Y.; Shao, X.J.; Wu, L.Y.; Deng, N.Y.; Chou, K.C. pLoc-mPlant: predict subcellular localization of multi-location plant proteins by incorporating the optimal GO information into general PseAAC. Mol. Biosyst., 2017, 13(9), 1722-1727.
[236]
Xu, Y.; Ding, J.; Wu, L.Y.; Chou, K.C. iSNO-PseAAC: predict cysteine S-nitrosylation sites in proteins by incorpo-rating position specific amino acid propensity into pseudo amino acid composition. PLoS One, 2013, 8(2)e55844
[http://dx.doi.org/10.1371/journal.pone.0055844]
[237]
Xie, H.L.; Fu, L.; Nie, X.D. Using ensemble SVM to identi-fy human GPCRs N-linked glycosylation sites based on the general form of Chou’s PseAAC. Protein Eng. Des. Sel., 2013, 26(11), 735-742.
[http://dx.doi.org/10.1093/protein/gzt042]
[238]
Chen, W.; Feng, P.M.; Lin, H.; Chou, K.C. iSS-PseDNC: Identifying splicing sites using pseudo dinucleotide composi-tion. BioMed Res. Int., 2014, 2014(2)623149
[http://dx.doi.org/10.1155/2014/623149]
[239]
Qiu, W.R.; Sun, B.Q.; Xiao, X.; Xu, Z.C.; Jia, J.H.; Chou, K.C. iKcr-PseEns: Identify lysine crotonylation sites in his-tone proteins with pseudo components and ensemble classifi-er. Genomics, 2018, 110(5), 239-246.
[http://dx.doi.org/10.1016/j.ygeno.2017.10.008]
[240]
Khan, Y.D.; Rasool, N.; Hussain, W.; Khan, S.A.; Chou, K.C. iPhosT-PseAAC: Identify phosphothreonine sites by incorporating sequence statistical moments into PseAAC. Anal. Biochem., 2018, 550, 109-116.
[http://dx.doi.org/10.1016/j.ab.2018.04.021]
[241]
Chen, W.; Feng, P.; Ding, H.; Lin, H.; Chou, K.C. iRNA-Methyl: Identifying N(6)-methyladenosine sites using pseu-do nucleotide composition. Anal. Biochem., 2015, 490, 26-33.
[http://dx.doi.org/10.1016/j.ab.2015.08.021]
[242]
Chou, K.C. Some remarks on protein attribute prediction and pseudo amino acid composition. J. Theor. Biol., 2011, 273(1), 236-247.
[http://dx.doi.org/10.1016/j.jtbi.2010.12.024]
[243]
Chen, W.; Lin, H.; Chou, K.C. Pseudo nucleotide composi-tion or PseKNC: An effective formulation for analyzing ge-nomic sequences. Mol. Biosyst., 2015, 11(10), 2620-2634.
[http://dx.doi.org/10.1039/C5MB00155B]
[244]
Xiao, X.; Cheng, X.; Chen, G.; Mao, Q.; Chou, K.C. pLocmGpos: Predict subcellular localization of Gram-positive bacterial proteins by quasi-balancing training dataset and PseAAC. Genomics, 2018. pii: S0888-7543(18), 30260-X.
[245]
Chou, K-C.; Cheng, X.; Xiao, X. pLoc_bal-mHum: Predict subcellular localization of human proteins by PseAAC and quasi-balancing training dataset. Genomics, 2018, 888, 7543.
[http://dx.doi.org/10.1016/j.ygeno.2018.08.007]
[246]
Cheng, X.; Xiao, X.; Chou, K-C. pLoc_bal-mGneg: Predict subcellular localization of Gram-negative bacterial proteins by quasi-balancing training dataset and general PseAAC. J. Theor. Biol., 2018, 22, 5193.
[http://dx.doi.org/10.1016/j.jtbi.2018.09.005]
[247]
Cheng, X.; Lin, W.Z.; Xiao, X.; Chou, K.C. pLoc_bal-mAnimal: Predict subcellular localization of animal proteins by balancing training dataset and PseAAC. Bioinformatics, 2019, 35(3), 398-406.
[http://dx.doi.org/10.1093/bioinformatics/bty628]
[248]
Cheng, X.; Xiao, X.; Chou, K.C. pLoc-mHum: predict sub-cellular localization of multi-location human proteins via gen-eral PseAAC to winnow out the crucial GO information. Bioinformatics, 2018, 34(9), 1448-1456.
[http://dx.doi.org/10.1093/bioinformatics/btx711]
[249]
Cheng, X.; Xiao, X.; Chou, K.C. pLoc-mGneg: Predict subcellular localization of Gram-negative bacterial proteins by deep gene ontology learning via general PseAAC. Genomics, 2017. S0888-7543(17), 30102-7.
[250]
Cheng, X.; Xiao, X.; Chou, K.C. pLoc-mEuk: Predict sub-cellular localization of multi-label eukaryotic proteins by ex-tracting the key GO information into general PseAAC. Genomics, 2018, 110(1), 50-58.
[http://dx.doi.org/10.1016/j.ygeno.2017.08.005]
[251]
Xiao, X.; Cheng, X.; Su, S.; Mao, Q.; Chou, K-C. pLoc-mGpos: incorporate key gene ontology information into gen-eral PseAAC for predicting subcellular localization of Gram-positive bacterial proteins. Nat. Sci., 2017, 9(09), 330.
[http://dx.doi.org/10.4236/ns.2017.99032]
[252]
Cheng, X.; Zhao, S.G.; Lin, W.Z.; Xiao, X.; Chou, K.C. pLoc-mAnimal: predict subcellular localization of animal pro-teins with both single and multiple sites. Bioinformatics, 2017, 33(22), 3524-3531.
[http://dx.doi.org/10.1093/bioinformatics/btx476]
[253]
Cheng, X.; Xiao, X.; Chou, K-C. pLoc-mPlant: predict sub-cellular localization of multi-location plant proteins by incor-porating the optimal GO information into general PseAAC. Mol. Biosyst., 2017, 13(9), 1722-1727.
[http://dx.doi.org/10.1039/C7MB00267J]
[254]
Cheng, X.; Xiao, X.; Chou, K.C. pLoc-mVirus: Predict sub-cellular localization of multi-location virus proteins via incor-porating the optimal GO information into general PseAAC. Gene, 2017, 13(9), 1722-1727.
[http://dx.doi.org/10.1016/j.gene.2017.07.036]
[255]
Cheng, X.; Zhao, S.G.; Xiao, X.; Chou, K.C. iATC-mISF: A multi-label classifier for predicting the classes of anatomical therapeutic chemicals. Bioinformatics, 2017, 33(3), 341-346.
[http://dx.doi.org/10.1093/bioinformatics/btx387]
[256]
Chou, K.C. Some remarks on predicting multi-label attributes in molecular biosystems. Mol. Biosyst., 2013, 9(6), 1092-1100.
[http://dx.doi.org/10.1039/c3mb25555g]
[257]
Cai, L.; Huang, T.; Su, J.; Zhang, X.; Chen, W.; Zhang, F.; He, L.; Chou, K.C. Implications of newly identified brain eQTL genes and their interactors in schizophrenia. Mol. Ther. Nucleic Acids, 2018, 12, 433-442.
[http://dx.doi.org/10.1016/j.omtn.2018.05.026]
[258]
Feng, P.M.; Chen, W.; Lin, H.; Chou, K.C. iHSP-PseRAAAC: Identifying the heat shock protein families us-ing pseudo reduced amino acid alphabet composition. Anal. Biochem., 2013, 442(1), 118-125.
[http://dx.doi.org/10.1016/j.ab.2013.05.024]
[259]
Liu, B.; Yang, F.; Huang, D.S.; Chou, K.C. iPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC. Bioinformatics, 2018, 34(1), 33-40.
[http://dx.doi.org/10.1093/bioinformatics/btx579]
[260]
Liu, B.; Weng, F.; Huang, D.S.; Chou, K.C. iRO-3wPseKNC: identify DNA replication origins by three-window-based PseKNC. Bioinformatics, 2018, 34(18), 3086-3093.
[http://dx.doi.org/10.1093/bioinformatics/bty312]
[261]
Zhang, Z.D.; Liang, K.; Li, K.; Wang, G.Q.; Zhang, K.W.; Cai, L.; Zhai, S.T.; Chou, K.C. Chlorella vulgaris induces apoptosis of human non-small cell lung carcinoma (NSCLC) cells. Med. Chem., 2017, 13(6), 560-568.
[http://dx.doi.org/10.2174/1573406413666170510102024]
[262]
Wang, J.; Yang, B.; Revote, J.; Leier, A.; Marquez-Lago, T.T.; Webb, G.; Song, J.; Chou, K.C.; Lithgow, T. POS-SUM: a bioinformatics toolkit for generating numerical se-quence feature descriptors based on PSSM profiles. Bioinformatics, 2017, 33(17), 2756-2758.
[http://dx.doi.org/10.1093/bioinformatics/btx302]
[263]
Su, Q.; Lu, W.; Du, D.; Chen, F.; Niu, B.; Chou, K.C. Pre-diction of the aquatic toxicity of aromatic compounds to tet-rahymena pyriformis through support vector regression. Oncotarget, 2017, 8(30), 49359-49369.
[http://dx.doi.org/10.18632/oncotarget.17210]
[264]
Niu, B.; Zhang, M.; Du, P.; Jiang, L.; Qin, R.; Su, Q.; Chen, F.; Du, D.; Shu, Y.; Chou, K.C. Small molecular floribun-diquinone B derived from medicinal plants inhibits acetylcho-linesterase activity. Oncotarget, 2017, 8(34), 57149-57162.
[http://dx.doi.org/10.18632/oncotarget.19169]
[265]
Liu, B.; Yang, F.; Chou, K.C. 2L-piRNA: A two-layer en-semble classifier for identifying PIWI-interacting RNAS and their function. Mol. Ther. Nucleic Acids, 2017, 7(C), 267-277.
[http://dx.doi.org/10.1016/j.omtn.2017.04.008]
[266]
Liu, B.; Wu, H.; Zhang, D.; Wang, X.; Chou, K.C. Pse-Analysis: a python package for DNA/RNA and protein/pep-tide sequence analysis based on pseudo components and ker-nel methods. Oncotarget, 2017, 8(8), 13338-13343.
[http://dx.doi.org/10.18632/oncotarget.14524]
[267]
Liu, B.; Wu, H.; Chou, K.C. Pse-in-One 2.0: An improved package of web servers for generating various modes of pseudo components of dna, rna, and protein sequences. Nat. Sci., 2017, 9(4), 67-91.
[http://dx.doi.org/10.4236/ns.2017.94007]
[268]
Du, Q.S.; Wang, S.Q.; Xie, N.Z.; Wang, Q.Y.; Huang, R.B.; Chou, K.C. 2L-PCA: a two-level principal component ana-lyzer for quantitative drug design and its applications. Oncotarget, 2017, 8(41), 70564-70578.
[http://dx.doi.org/10.18632/oncotarget.19757]
[269]
Cheng, X.; Zhao, S.G.; Xiao, X.; Chou, K.C. iATC-mHyb: A hybrid multi-label classifier for predicting the classification of anatomical therapeutic chemicals. Oncotarget, 2017, 8(35), 58494-58503.
[http://dx.doi.org/10.18632/oncotarget.17028]
[270]
Chen, W.; Feng, P.; Yang, H.; Ding, H.; Lin, H.; Chou, K.C. iRNA-AI: identifying the adenosine to inosine editing sites in RNA sequences. Oncotarget, 2017, 8(3), 4208-4217.
[http://dx.doi.org/10.18632/oncotarget.13758]
[271]
Lin, H.; Deng, E.Z.; Ding, H.; Chen, W.; Chou, K.C. iPro54-PseKNC: A sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition. Nucleic Acids Res., 2014, 42(21), 12961-12972.
[http://dx.doi.org/10.1093/nar/gku1019]
[272]
Yang, H.; Qiu, W.R.; Liu, G.; Guo, F.B.; Chen, W.; Chou, K.C.; Lin, H. iRSpot-Pse6NC: Identifying recombination spots in Saccharomyces cerevisiae by incorporating hexamer composition into general PseKNC. Int. J. Biol. Sci., 2018, 14(8), 883-891.
[http://dx.doi.org/10.7150/ijbs.24616]
[273]
Liu, B.; Wang, S.; Long, R.; Chou, K.C. iRSpot-EL: Identify recombination spots with an ensemble learning approach. Bioinformatics, 2017, 33(1), 35-41.
[http://dx.doi.org/10.1093/bioinformatics/btw539]
[274]
Qiu, W.R.; Xiao, X.; Chou, K.C. iRSpot-TNCPseAAC: Identify recombination spots with trinucleotide composition and pseudo amino acid components. Int. J. Mol. Sci., 2014, 15(2), 1746-1766.
[http://dx.doi.org/10.3390/ijms15021746]
[275]
Chen, W.; Feng, P.M.; Lin, H.; Chou, K.C. iRSpot-PseDNC: identify recombination spots with pseudo dinu-cleotide composition. Nucleic Acids Res., 2013, 41(6)e68
[http://dx.doi.org/10.1093/nar/gks1450]
[276]
Nadvi, N.A.; Salam, N.K.; Park, J.; Akladios, F.N.; Kapoor, V.; Collyer, C.A.; Gorrell, M.D.; Church, W.B. High resolu-tion crystal structures of human kynurenine aminotransfer-ase-I bound to PLP cofactor, and in complex with aminooxy-acetate. Protein Sci., 2017, 26(4), 727-736.
[http://dx.doi.org/10.1002/pro.3119]
[277]
Wlodawer, A.; Dauter, Z.; Porebski, P.J.; Minor, W.; Stan-field, R.; Jaskolski, M.; Pozharski, E.; Weichenberger, C.X.; Rupp, B. Detect, correct, retract: How to manage incorrect structural models. FEBS J., 2018, 285(3), 444-466.
[http://dx.doi.org/10.1111/febs.14320]
[278]
Jacobs, K.R.; Castellano-Gonzalez, G.; Guillemin, G.J.; Lovejoy, D.B. Major Developments in the design of inhibi-tors along the kynurenine pathway. Curr. Med. Chem., 2017, 24(23), 2471-2495.
[http://dx.doi.org/10.2174/0929867324666170502123114]
[279]
Akladios, F.N.; Nadvi, N.A.; Park, J.; Hanrahan, J.R.; Ka-poor, V.; Gorrell, M.D.; Church, W.B. Design and synthesis of novel inhibitors of human kynurenine aminotransferase-I. Bioorg. Med. Chem. Lett., 2012, 22(4), 1579-1581.
[http://dx.doi.org/10.1016/j.bmcl.2011.12.138]
[280]
Cooper, A.J.; Krasnikov, B.F.; Niatsetskaya, Z.V.; Pinto, J.T.; Callery, P.S.; Villar, M.T.; Artigues, A.; Bruschi, S.A. Cysteine S-conjugate β-lyases: important roles in the metabo-lism of naturally occurring sulfur and selenium-containing compounds, xenobiotics and anticancer agents. Amino Acids, 2011, 41(1), 7-27.
[http://dx.doi.org/10.1007/s00726-010-0552-0]
[281]
Katayama, R.; Nagata, S.; Iida, H.; Yamagishi, N.; Yamashi-ta, T.; Furuhama, K. Possible role of cysteine-S-conjugate β-lyase in species differences in cisplatin nephrotoxicity. Food Chem. Toxicol., 2011, 49(9), 2053-2059.
[http://dx.doi.org/10.1016/j.fct.2011.05.017]


Rights & PermissionsPrintExport Cite as

Article Details

VOLUME: 26
ISSUE: 26
Year: 2019
Page: [4944 - 4963]
Pages: 20
DOI: 10.2174/0929867326666190325095223
Price: $58

Article Metrics

PDF: 19
HTML: 2