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Title: Development and application of AMBER molecular mechanics force field for herbicide interaction in plants
Author: Khanna, Tarun
ISNI:       0000 0004 8504 5944
Awarding Body: Imperial College London
Current Institution: Imperial College London
Date of Award: 2018
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Photosystem II is a popular target for herbicides like Terbutryn. These herbicides inhibit the electron transport chain in Photosystem II by replacing the plastoquinone molecule from the QB binding site. In this thesis all atom molecular dynamics simulations were used to get insights into this electron transport chain. The major contributions of this thesis are (a) a well-tested and most complete AMBER molecular mechanics force field of the cofactors and the non-standard amino acids associated with the Photosystem II complex. (b) AMBAT- AMBER based Membrane Builder and Analysis Tool, for setting up and analysing lipid-membrane based simulations. AMBAT is distributed as a part of AmberTools 18. (c) Correlation of the dynamic properties of plastoquinone and plastoquinol molecules (electron carrier molecules in Photosystem II) with their biological function. The dynamic properties were found to be consistent with the previous experimentally reported values. (d) All atom molecular dynamics simulations of Photosystem II, with the focus to understand the electron transport reaction at the QB binding site (mobile plastoquinone binding site in Photosystem II). The major findings of these simulations are (i) different binding poses of plastoquinone molecule as it undergoes double reduction (ii) the structural changes to the plastoquinone molecule (in terms of translation, rotation and twisting of the plastoquinone head) during the electron transport reaction, and (iii) the role of local protein structure in the plastoquinone double reduction. These results agreed with the crystal structure investigation. The major differences between the Photosystem II simulations reported in this thesis and other all-atom simulations of the system reported in the literature are (1) well tested molecular mechanics force field of the cofactors associated with Photosystem II complex (2) a large computational time, with the total simulation time of around 35 times that of the previously published all atom simulation for this system (3) preservation of the structurally and functionally important internal lipid environment and the water molecules (possible through AMBAT).
Supervisor: Gould, Ian ; Barter, Laura ; Kidley, Nathan Sponsor: European Commission
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral