Molecular Dynamics Study of Thymidine Phosphorylase from E. coli in the Apo Form and in Complexes with Substrates

Sidorov-Biryukov D. D.; Podshivalov D. D.; Timofeev V. I.; Zhukhlistova N. E.; Kuranova I. P.

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Molecular Dynamics Study of Thymidine Phosphorylase from E. coli in the Apo Form and in Complexes with Substrates

机译：APO形式中大肠杆菌胸苷磷酸化酶的分子动力学研究及基材复合物

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Models of E. coli thymidine phosphorylase in complexes with the substrates the complex with phosphate and the complex with phosphate and thymidine were obtained by molecular docking calculations. The influence of the substrates on domain movements in the dimeric thymidine phosphorylase molecule was probed by molecular dynamics simulations. The two subunits were shown to function asynchronously. In the thymidine phosphorylase/phosphate and thymidine phosphorylase/phosphate/thymidine complexes, phosphate is more weakly bound in the active site and moves away from the phosphate-binding site during the 60-ns trajectory, whereas thymidine remains in the active site but undergoes conformational changes.

机译：通过分子对接计算获得与基质与磷酸盐的复合物中络合物的大肠杆菌胸苷磷酸化酶的模型通过分子对接计算获得与磷酸盐和胸苷的复合物。通过分子动力学模拟探测了基材对二聚体胸苷磷酸化分子中的结构域移动的影响。两个亚基被示出异步起作用。在胸苷磷酸化酶/磷酸盐和胸苷磷酸化酶/磷酸盐/胸苷络合物中，磷酸盐在活性部位中更弱，在60-Ns轨迹期间远离磷酸盐结合位点移动，而胸苷留在活性位点，但经历一致性变化。

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《Crystallography reports》 |2019年第1期|共7页
作者
Sidorov-Biryukov D. D.; Podshivalov D. D.; Timofeev V. I.; Zhukhlistova N. E.; Kuranova I. P.;
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Russian Acad Sci Fed Sci Res Ctr Crystallog &

Photon Shubnikov Inst Crystallog Moscow 119333 Russia;

Russian Acad Sci Fed Sci Res Ctr Crystallog &

Photon Shubnikov Inst Crystallog Moscow 119333 Russia;

Russian Acad Sci Fed Sci Res Ctr Crystallog &

Photon Shubnikov Inst Crystallog Moscow 119333 Russia;

Russian Acad Sci Fed Sci Res Ctr Crystallog &

Photon Shubnikov Inst Crystallog Moscow 119333 Russia;

Russian Acad Sci Fed Sci Res Ctr Crystallog &

Photon Shubnikov Inst Crystallog Moscow 119333 Russia;

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正文语种 eng
中图分类晶体学;
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1. Molecular Dynamics Study of Thymidine Phosphorylase from E. coli in the Apo Form and in Complexes with Substrates [J] . Sidorov-Biryukov D. D., Podshivalov D. D., Timofeev V. I., Crystallography reports . 2019,第1期

机译：APO形式中大肠杆菌胸苷磷酸化酶的分子动力学研究及基材复合物
2. Substrate specificity of thymidine phosphorylase of E. coli: role of hydroxyl groups. [J] . Panova NG, Alexeev CS, Polyakov KM, Nucleosides, nucleotides and nucleic acids . 2008,第12期

机译：大肠杆菌胸苷磷酸化酶的底物特异性：羟基的作用。
3. Substrate specificity of E. coli uridine phosphorylase: evidences of high-syn conformation of the substrate [J] . Alexeev C., Polyakov K., Mikhailov S. The FEBS journal . 2016,第Suppla1期

机译：大肠杆菌尿苷磷酸化酶的底物特异性：底物的高syn构象的证据
4. An investigation of the energetics and conformations of polymer/substrate complexes studied with RRKM modeling, molecular dynamics and ion-mobility spectrometry [C] . Justin Renaud, Paul M. Mayer American Society for Mass Spectrometry Conference on Mass Spectrometry and Allied Topics . 2011

机译：用RRKM造型，分子动力学和离子迁移光谱研究研究高分子/底物络合物的能量和构象的研究
5. I:- Design, synthesis and study of nucleotide prodrugs. II:- Synthesis of 5-fluoro-6-[(2-aminoimidazol-1-yl)methyl]uracil (AIFU) and study of its mechanism of action as a thymidine phosphorylase inhibitor. III:- Design and synthesis of novel nucleotide analogs as alternative substrates for studying the mechanism of the thymidylate synthase-catalyzed reaction. [D] . Jain, Harsh Vardhan. 2010

机译：I：-核苷酸前药的设计，合成和研究。 II：5-氟-6-[（（2-氨基咪唑-1-基）甲基]尿嘧啶（AIFU）的合成及其作为胸苷磷酸化酶抑制剂的作用机理的研究。 III：-设计和合成新型核苷酸类似物作为研究底物胸苷酸合酶催化反应机理的替代底物。
6. A QM-MD simulation approach to the analysis of FRET processes in (bio)molecular systems. A case study: complexes of E. coli purine nucleoside phosphorylase and its mutants with formycin A [O] . M. Sobieraj, K. A. Krzyśko, A. Jarmuła, -1

机译：QM-MD模拟方法用于分析（生物）分子系统中的FRET过程。案例研究：大肠杆菌嘌呤核苷磷酸化酶及其突变体与甲霉素A的复合物
7. A QM-MD simulation approach to the analysis of FRET processes in (bio)molecular systems. A case study: complexes of E. coli purine nucleoside phosphorylase and its mutants with formycin A [O] . M. Sobieraj, K. A. Krzyśko, A. Jarmuła, 2015

机译：QM-MD模拟方法，用于分析（生物）分子系统中的FRET过程。案例研究：大肠杆菌嘌呤核苷磷酸化酶及其突变体与甲霉素A的复合物

Molecular Dynamics Study of Thymidine Phosphorylase from E. coli in the Apo Form and in Complexes with Substrates

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