Document Type

Dissertation

Date of Degree

Spring 2016

Degree Name

PhD (Doctor of Philosophy)

Degree In

Chemistry

First Advisor

Claudio J. Margulis

Abstract

This thesis focuses mainly on the consequences that single mutations have on structural, functional and energetic aspects of the protein cyanovirin-N. In order to estimate the free energy of single mutations, we have applied thermodynamics integration and Bennett acceptance ratio techniques. Replica exchange molecular dynamics has been applied to accelerate simulations for complicated scenarios. Our studies suggest that certain single mutations may be promising to improve binding affinity to Manα1→2Manα but we also learned that the simplistic view of a strong hydrogen bond correlating to a high binding affinity may not always be correct. Finally, we explored in detail the widely used mutation P51G for its impact on protein rigidity at the very important hinge region as well as for its possible effect on glycan binding.

Keywords

binding affinity, computational simulations, cyanovirin-N, mutations, structure

Pages

xii, 113

Bibliography

103-113

Copyright

Copyright 2016 Zhen Li

Included in

Chemistry Commons

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