title: Integration of Inhibition Kinetics and Molecular Dynamics Simulations: A Urea-Mediated Folding Study on Acetaldehyde Dehydrogenase 1.
abstract: Understanding the mechanism of acetaldehyde dehydrogenase 1 (ALDH1) folding is important because this enzyme is directly involved in several types of cancers and other diseases. We investigated the urea-mediated unfolding of ALDH1 by integrating kinetic inhibition studies with computational molecular dynamics (MD) simulations. Conformational changes in the enzyme structure were also analyzed using intrinsic and 1-anilinonaphthalene-8-sulfonate (ANS)-binding fluorescence measurements. Kinetic studies revealed that the direct binding of urea to ALDH1 induces inactivation of ALDH1 in a manner of mixed-type inhibition. Tertiary structural changes associated with regional hydrophobic exposure of the active site were observed. The urea binding regions on ALDH1 were predicted by docking simulations and were partly shared with active site residues of ALDH1 and with interface residues of the oligomerization domain for tetramer formation. The docking results suggest that urea prevents formation of the ALDH1 normal shape for the tetramer state as well as entrance of the substrate into the active site. Our study provides insight into the structural changes that accompany urea-mediated unfolding of ALDH1 and the catalytic role associated with conformational changes.
authors.affiliation: Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, 314006, People's Republic of China.|School of Preclinical Medicine, Beijing University of Chinese Medicine, 11 Beisanhuan Dong Road, Beijing, 100029, People's Republic of China.
authors.forename: Yingying
authors.initials: Y
authors.lastname: Xu
authors.affiliation: Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, South Korea.|Department of Nanobiotechnology and Bioinformatics, University of Sciences and Technology, Daejeon, 305-350, South Korea.
authors.forename: Jinhyuk
authors.initials: J
authors.lastname: Lee
authors.affiliation: Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, 314006, People's Republic of China.
authors.forename: Zhi-Rong
authors.initials: ZR
authors.lastname: Lü
authors.affiliation: Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, 314006, People's Republic of China.
authors.forename: Hang
authors.initials: H
authors.lastname: Mu
authors.affiliation: School of Preclinical Medicine, Beijing University of Chinese Medicine, 11 Beisanhuan Dong Road, Beijing, 100029, People's Republic of China. zhangqian_beijing2014@hotmail.com.
authors.forename: Qian
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, 314006, People's Republic of China. parkyd@hotmail.com.|College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, People's Republic of China. parkyd@hotmail.com.
authors.forename: Yong-Doo
authors.initials: YD
authors.lastname: Park
mesh_terms: D000080924:Aldehyde Dehydrogenase 1 Family; D000817:Anilino Naphthalenesulfonates / Q000737:chemistry; D001665:Binding Sites; D020134:Catalytic Domain; D006801:Humans; D007527:Isoenzymes / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D017510:Protein Folding; D050697:Retinal Dehydrogenase / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism; D013050:Spectrometry, Fluorescence; D014508:Urea / Q000737:chemistry*
chemical_list: C515594:8-anilino-1-naphthalenesulfonic acid; D000817:Anilino Naphthalenesulfonates; D007527:Isoenzymes; D014508:Urea; D000080924:Aldehyde Dehydrogenase 1 Family; C510223:ALDH1A1 protein, human; D050697:Retinal Dehydrogenase
keywords: Acetaldehyde dehydrogenase 1; Inhibition; Kinetics; Molecular dynamics; Simulations; Urea