title: A computational investigation on the substrate preference of ten-eleven-translocation 2 (TET2).
abstract: TET proteins iteratively convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) in a Fe(ii)/α-ketoglutarate-dependent manner. Our previous biochemical studies revealed that TET proteins are more active on 5mC than on 5hmC and 5fC. However, the source of the substrate preference of TET proteins still remains largely elusive. Here, we investigated the substrate binding and catalytic mechanisms of oxidation reactions mediated by TET2 on different substrates through computational approaches. In accordance with previous experimental reports, our computational results suggest that TET2 can bind to different substrates with comparable binding affinities and the hydrogen abstraction step in the catalytic cycle acts as the rate-limiting step. Further structural characterization of the intermediate structures revealed that the 5-substitution groups on 5hmC and 5fC adopt an unfavorable orientation for hydrogen abstraction, which leads to a higher energy barrier for 5hmC and 5fC (compared to 5mC) and thus a lower catalytic efficiency. In summary, our mechanical insights demonstrate that substrate preference is the intrinsic property of TET proteins and our theoretical calculation results can guide further dry-lab or wet-lab studies on the catalytic mechanism of TET proteins as well as other Fe(ii)/α-ketoglutarate (KG)-dependent dioxygenases.
authors.affiliation: Drug Discovery and Design Centre, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. cluo@simm.ac.cn.
authors.forename: Junyan
authors.initials: J
authors.lastname: Lu
authors.affiliation: Fudan University Shanghai Cancer Centre, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China. xuyh@fudan.edu.cn and State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.
authors.forename: Lulu
authors.initials: L
authors.lastname: Hu
authors.affiliation: Fudan University Shanghai Cancer Centre, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China. xuyh@fudan.edu.cn.
authors.forename: Jingdong
authors.initials: J
authors.lastname: Cheng
authors.affiliation: Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Ave, Madison, WI 53706, USA.
authors.forename: Dong
authors.initials: D
authors.lastname: Fang
authors.affiliation: Drug Discovery and Design Centre, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. cluo@simm.ac.cn.
authors.forename: Chen
authors.initials: C
authors.lastname: Wang
authors.affiliation: Drug Discovery and Design Centre, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. cluo@simm.ac.cn.
authors.forename: Kunqian
authors.initials: K
authors.lastname: Yu
authors.affiliation: Drug Discovery and Design Centre, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. cluo@simm.ac.cn.
authors.forename: Hualiang
authors.initials: H
authors.lastname: Jiang
authors.affiliation: Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Ave, Madison, WI 53706, USA.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Cui
authors.affiliation: Fudan University Shanghai Cancer Centre, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China. xuyh@fudan.edu.cn and State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.
authors.forename: Yanhui
authors.initials: Y
authors.lastname: Xu
authors.affiliation: Drug Discovery and Design Centre, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. cluo@simm.ac.cn.
authors.forename: Cheng
authors.initials: C
authors.lastname: Luo
mesh_terms: D002384:Catalysis; D004268:DNA-Binding Proteins / Q000378:metabolism*; D049308:Dioxygenases; D010084:Oxidation-Reduction; D011518:Proto-Oncogene Proteins / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D004268:DNA-Binding Proteins; D011518:Proto-Oncogene Proteins; D049308:Dioxygenases; C541081:TET2 protein, human