| Predicting nitrogen and oxygen kinetic isotope effects of nitrate reduction by periplasmic dissimilatory nitrate reductase | |
| He YY(何雨旸)1; Zhang, Yining2; Zhang, Siting3,4; Liu, Yun2,4,5 | |
| Corresponding Author | He, Yuyang([email protected]) |
| Source Publication | GEOCHIMICA ET COSMOCHIMICA ACTA
 |
| 2021-01-15 | |
| Volume | 293Pages:224-239 |
| ISSN | 0016-7037 |
| Abstract | Kinetic isotope effect (KIE) reveals the transition state structure of an elementary reaction and can be predicted by quantum chemical calculation. Density Functional Theory calculation of an enzymatic reaction with large numbers of atoms is computationally prohibitive, especially if explicit solvent effect is considered. Cutoff method, which simplifies an entire molecule to a cluster around a target position, can simplify position-specific equilibrium isotope effect calculation for a large organic molecule. It should also be applicable to KIE calculation of an enzymatic reaction and allow us to introduce explicit solvent molecules to the system. If this treatment is feasible and trustable, it will provide an efficient method to estimate a number of KIEs produced by enzyme reactions. Obviously, its robustness must be tested. Here, using NO3- reduction by the active site of periplasmic dissimilatory nitrate reductase (Nap) in Rhodobacter sphaeroides as an example, we built 17 models to test the influence of cutoff size, implicit, and explicit solvent effects on KIE calculation. The results show that to estimate the KIE value of an enzymatic reaction accurately and efficiently, we can first simplify the reaction model to a cutoff model with 3 proximal bonds to the active position. Then, incorporating implicit-plus-explicit solvent models can simulate a reaction environment more realistically, which is necessary for accuracy. Our calculated lnKIE values for nitrate Nap reduction at 25 degrees C are -32.4 +/- 1.8 parts per thousand for N-15 and -20.9 +/- 0.4 parts per thousand for O-18, respectively, with a ln(18)KIE/ln(15) KIE ratio of 0.65 +/- 0.05. Although additional reservoir-transport processes need to be considered, our calculation results are consistent with calibrated isotope effects from laboratory experiments, suggesting that the transition state we calculated depicts the general reaction mechanism of NO3- reduction by Nap. (C) 2020 Elsevier Ltd. All rights reserved. |
| Keyword | Transition state theory Density functional theory Cutoff model Solvent effect Molybdenum enzyme |
| DOI | 10.1016/j.gca.2020.10.027 |
| Indexed By | SCI |
| Language | 英语 |
| WOS ID | WOS:000600550100012 |
| WOS Keyword | THEORETICAL CALCULATION ; CIS-DIHYDROXYLATION ; ENZYMATIC-REACTIONS ; ACTIVATED COMPLEX ; FRACTIONATION ; EQUILIBRIUM ; DENITRIFICATION ; MECHANISM ; MOLYBDENUM ; TUNGSTEN |
| WOS Research Area | Geochemistry & Geophysics |
| WOS Subject | Geochemistry & Geophysics |
| Funding Project | China Postdoctoral Science Foundation[2019M660811] ; strategic priority research program (B) of CAS[XDB41000000] ; strategic priority research program (B) of CAS[XDB18010100] ; Chinese NSF project[41773016] ; Chinese NSF project[41530210] |
| Funding Organization | China Postdoctoral Science Foundation ; strategic priority research program (B) of CAS ; Chinese NSF project |
| Classification | 一类 |
| Ranking | 1 |
| Contributor | He, Yuyang |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://dspace.imech.ac.cn/handle/311007/85898 |
| Collection | 高温气体动力学国家重点实验室 |
| Affiliation | 1.Chinese Acad Sci, Inst Mech, Beijing 100190, Peoples R China; 2.Chinese Acad Sci, Inst Geochem, State Key Lab Ore Deposit Geochem, Guiyang 550081, Peoples R China; 3.Chinese Acad Sci, Ctr Lunar & Planetary Sci, Inst Geochem, Guiyang 550081, Peoples R China; 4.Chinese Acad Sci Ctr Excellence Comparat Planetol, Hefei 230001, Peoples R China; 5.Chengdu Univ Technol, Coll Earth Sci, Int Ctr Planetary Sci, Chengdu 610059, Peoples R China |
| Recommended Citation GB/T 7714 | He YY,Zhang, Yining,Zhang, Siting,et al. Predicting nitrogen and oxygen kinetic isotope effects of nitrate reduction by periplasmic dissimilatory nitrate reductase[J]. GEOCHIMICA ET COSMOCHIMICA ACTA,2021,293:224-239.Rp_Au:He, Yuyang |
| APA | 何雨旸,Zhang, Yining,Zhang, Siting,&Liu, Yun.(2021).Predicting nitrogen and oxygen kinetic isotope effects of nitrate reduction by periplasmic dissimilatory nitrate reductase.GEOCHIMICA ET COSMOCHIMICA ACTA,293,224-239. |
| MLA | 何雨旸,et al."Predicting nitrogen and oxygen kinetic isotope effects of nitrate reduction by periplasmic dissimilatory nitrate reductase".GEOCHIMICA ET COSMOCHIMICA ACTA 293(2021):224-239. |
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| Jp2021060.pdf（1099KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | View Download | |
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