THESIS
2017
xii, 55 pages : illustrations (chiefly color) ; 30 cm
Abstract
Biological molecules are complex molecules typically consisting of a few thousand atoms.
These molecules interact and undergo conformational change to perform biological function.
This thesis includes three projects that use computer modelling and simulations, with the aim
of predicting protein interactions, mechanism, and properties. To predict the interaction of
Transcription Factor IIB C-terminal domain (TFIIBc) and SSU72, we employ a combination
of molecular dynamics simulation with protein-protein docking. We have narrowed down the
possibilities to three models, ready for validation by experiment. This interaction will be
important for the understanding of gene-looping mechanism. The study of clamp domain
motion of bacterial RNA Polymerase aims to predict the mechanism of t...[
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Biological molecules are complex molecules typically consisting of a few thousand atoms.
These molecules interact and undergo conformational change to perform biological function.
This thesis includes three projects that use computer modelling and simulations, with the aim
of predicting protein interactions, mechanism, and properties. To predict the interaction of
Transcription Factor IIB C-terminal domain (TFIIBc) and SSU72, we employ a combination
of molecular dynamics simulation with protein-protein docking. We have narrowed down the
possibilities to three models, ready for validation by experiment. This interaction will be
important for the understanding of gene-looping mechanism. The study of clamp domain
motion of bacterial RNA Polymerase aims to predict the mechanism of transition from closed
clamp to open clamp. Using all-atom MD (aaMD) simulation and coarse-grained MD
simulations, we have found some insights on the reaction coordinate and the importance of
some regions on RNA Polymerase. Lastly, using aaMD simulation, we have shown the
difference in flexibility in the junction region of IQ5 and SAH of Myo7A.
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