Comparative genomics, molecular evolution and computational modeling of ALDH1B1 and ALDH2

Marchitti, 2008, Non-P450 aldehyde oxidizing enzymes: the aldehyde dehydrogenase superfamily, Expert Opin. Drug. Metab. Toxicol., 4, 697, 10.1517/17425255.4.6.697 Hsu, 1988, Genomic structure of the human mitochondrial aldehyde dehydrogenase gene, Genomics, 2, 57, 10.1016/0888-7543(88)90109-7 Wang, 2002, Effects of aldehyde dehydrogenase-2 genetic polymorphisms on metabolism of structurally different aldehydes in human liver, Drug Metab. Dispos., 30, 69, 10.1124/dmd.30.1.69 Ohta, 2004, Mitochondrial ALDH2 deficiency as an oxidative stress, Ann. N. Y. Acad. Sci., 1011, 36, 10.1196/annals.1293.004 Yoshida, 1985, Molecular abnormality and cDNA cloning of human aldehyde dehydrogenases, Alcohol, 2, 103, 10.1016/0741-8329(85)90024-2 Goedde, 1987, Polymorphism of aldehyde dehydrogenase and alcohol sensitivity, Enzyme, 37, 29, 10.1159/000469239 Higuchi, 1992, The relationship between low Km aldehyde dehydrogenase phenotype and drinking behavior in Japanese, J. Stud. Alcohol, 53, 170, 10.15288/jsa.1992.53.170 Cook, 2005, Associations of ALDH2 and ADH1B genotypes with response to alcohol in Asian Americans, J. Stud. Alcohol, 66, 196, 10.15288/jsa.2005.66.196 Chen, 2009, Pharmacokinetic and pharmacodynamic basis for overcoming acetaldehyde-induced adverse reaction in Asian alcoholics, heterozygous for the variant ALDH2∗2 gene allele, Pharmacogenet. Genomics, 19, 588, 10.1097/FPC.0b013e32832ecf2e Wang, 1996, Heterotetramers of human liver mitochondrial (class 2) aldehyde dehydrogenase expressed in Escherichia coli. A model to study the heterotetramers expected to be found in Oriental people, J. Biol. Chem., 271, 31172, 10.1074/jbc.271.49.31172 Hsu, 1991, Cloning and characterization of a new functional human aldehyde dehydrogenase gene, J. Biol. Chem., 266, 12257, 10.1016/S0021-9258(18)98890-3 Stagos, 2010, Aldehyde dehydrogenase 1B1: molecular cloning and characterization of a novel mitochondrial acetaldehyde-metabolizing enzyme, Drug Metab. Dispos., 38, 1679, 10.1124/dmd.110.034678 Chen, 2011, Aldehyde dehydrogenase 1B1 (ALDH1B1) is a potential biomarker for human colon cancer, Biochem. Biophys. Res. Commun., 405, 173, 10.1016/j.bbrc.2011.01.002 Klyosov, 1996, Possible role of liver cytosolic and mitochondrial aldehyde dehydrogenases in acetaldehyde metabolism, Biochemistry, 35, 4445, 10.1021/bi9521093 Johnsen, 1992, Clinical responses in relation to blood acetaldehyde levels, Pharmacol. Toxicol., 70, 41, 10.1111/j.1600-0773.1992.tb00423.x Husemoen, 2008, The association of ADH and ALDH gene variants with alcohol drinking habits and cardiovascular disease risk factors, Alcohol. Clin. Exp. Res., 32, 1984 Linneberg, 2010, Genetic determinants of both ethanol and acetaldehyde metabolism influence alcohol hypersensitivity and drinking behaviour among Scandinavians, Clin. Exp. Allergy, 40, 123, 10.1111/j.1365-2222.2009.03398.x Endo, 2009, Metabolic remodeling induced by mitochondrial aldehyde stress stimulates tolerance to oxidative stress in the heart, Circ. Res., 105, 1118, 10.1161/CIRCRESAHA.109.206607 Karolchik, 2007, Comparative genomic analysis using the UCSC genome browser, Methods Mol. Biol., 395, 17, 10.1007/978-1-59745-514-5_2 D. Thierry-Mieg, J. Thierry-Mieg, AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome. Biol. 7 Suppl. 1 (2006) S12 11–14. Hempel, 1985, Mitochondrial aldehyde dehydrogenase from human liver. Primary structure, differences in relation to the cytosolic enzyme, and functional correlations, Eur. J. Biochem., 153, 13, 10.1111/j.1432-1033.1985.tb09260.x Stewart, 1996, Distribution of messenger RNAs for aldehyde dehydrogenase 1, aldehyde dehydrogenase 2, and aldehyde dehydrogenase 5 in human tissues, J. Investig. Med., 44, 42 Chang, 1994, Cloning and characterization of the gene encoding mouse mitochondrial aldehyde dehydrogenase, Gene, 148, 331, 10.1016/0378-1119(94)90708-0 Thompson, 1994, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res., 22, 4673, 10.1093/nar/22.22.4673 Steinmetz, 1997, Structure of mitochondrial aldehyde dehydrogenase: the genetic component of ethanol aversion, Structure, 5, 701, 10.1016/S0969-2126(97)00224-4 Larson, 2007, Structural and functional consequences of coenzyme binding to the inactive asian variant of mitochondrial aldehyde dehydrogenase: roles of residues 475 and 487, J. Biol. Chem., 282, 12940, 10.1074/jbc.M607959200 Moore, 1998, Sheep liver cytosolic aldehyde dehydrogenase: the structure reveals the basis for the retinal specificity of class 1 aldehyde dehydrogenases, Structure, 6, 1541, 10.1016/S0969-2126(98)00152-X Brooks, 1983, Charmm – a program for macromolecular energy, minimization, and dynamics calculations, J. Comput. Chem., 4, 187, 10.1002/jcc.540040211 Feig, 2004, Recent advances in the development and application of implicit solvent models in biomolecule simulations, Curr. Opin. Struct. Biol., 14, 217, 10.1016/j.sbi.2004.03.009 Chen, 2002, Docking unbound proteins using shape complementarity, desolvation, and electrostatics, Proteins, 47, 281, 10.1002/prot.10092 Pierce, 2007, ZRANK: reranking protein docking predictions with an optimized energy function, Proteins, 67, 1078, 10.1002/prot.21373 Jackson, 2011, Update on the aldehyde dehydrogenase gene (ALDH) superfamily, Hum. Genomics, 5, 283, 10.1186/1479-7364-5-4-283 Lu, 2012, Profiling of gene duplication patterns of sequenced teleost genomes: evidence for rapid lineage-specific genome expansion mediated by recent tandem duplications, BMC Genomics, 13, 246, 10.1186/1471-2164-13-246 Zhou, 1995, Proteolysis prevents in vivo chimeric fusion protein import into yeast mitochondria. Cytosolic cleavage and subcellular distribution, J. Biol. Chem., 270, 16689, 10.1074/jbc.270.28.16689 Yu, 2007, Analysis of the role of retrotransposition in gene evolution in vertebrates, BMC Bioinformatics, 8, 308, 10.1186/1471-2105-8-308 Cordaux, 2009, The impact of retrotransposons on human genome evolution, Nat. Rev. Genet., 10, 691, 10.1038/nrg2640 McCarrey, 1996, Analysis of the cDNA and encoded protein of the human testis-specific PGK-2 gene, Dev. Genet., 19, 321, 10.1002/(SICI)1520-6408(1996)19:4<321::AID-DVG5>3.0.CO;2-B Uechi, 2002, Functional second genes generated by retrotransposition of the X-linked ribosomal protein genes, Nucleic Acids Res., 30, 5369, 10.1093/nar/gkf696 Dahl, 1990, A testis-specific form of the human pyruvate dehydrogenase E1 alpha subunit is coded for by an intronless gene on chromosome 4, Genomics, 8, 225, 10.1016/0888-7543(90)90275-Y