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Title: Simulation of biochemical reaction and biophysical process
Author: Huang, Xin
ISNI:       0000 0001 3583 3051
Awarding Body: Queen's University of Belfast
Current Institution: Queen's University Belfast
Date of Award: 2008
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The density functional theory (DFT) and molecular mechanics (MM) are used to study biochemical reactions and biophysical processes. The mechanism of DNA backbone hydrolysis by specific enzyme is studied. It is found that the Mg2 + cation can polarize the breaking P-O bond while a histidine acts as both the stabilizer and activator of the attacking water. Moreover, the water dissociation and formation ofnew bond should be coinstantaneous. In order to understand the nitrosylation ~f target thiol group in cells, we study oxygen-dependent thiol nitrosylating pathway. A general trend of the mixed pathway is found. Different intermediate (N203 or N02) can perform the nitrosylation of the target thiol group. Water can diminish the N20 3pathway through hydrolyzing N20 3, but it is capable of enhancing the effect of agent N02. Selectivity of target thiol is also studied. By this means, the thiol group which. is the easiest to accept the NO group would be nitrosylated rather than others. Aiming to further understanding of the fidelity transformation during the process in which tRNA is bound to aminoacyl-tRNA synthetases (aaRS), the mechanism is studied using molecular mechanics calculations. The effects of anticodon, positive arginines and crucial alanine site are analysed. The binding sequence is outlined. The fidelity of genetics information in DNA replication is studied by DFT and molecular mechanics. We find that the correct nucleotide insertion has nothing to do with'its complementary part, but determined by nearby essential residues. The match base pair can allow the residue to be fully positioned in the reactive pocket. Thus a new mechanism of DNA replication is proposed: it is the match base pair induced hydrophobic domain that determines the fidelity in the reaction.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available