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Title:Modification and regulation of biomolecules in vitro and in silico
Author(s):Chao, Shu-Han
Director of Research:Gruebele, Martin; Aksimentiev, Aleksei
Doctoral Committee Chair(s):Tajkhorshid, Emad
Doctoral Committee Member(s):Kuhlman, Thomas
Department / Program:Physics
Discipline:Physics
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:Ph.D.
Genre:Dissertation
Subject(s):DNA sequencing
molecular dynamics
nanopore
coarsed-grained model
double-nanopore
protein folding
PEGylation
thermal denaturation
Temperature Jump
Abstract:The focus in functional and dynamics studies of biomolecules, such as protein or DNA, has been very much on their own structures and energy landscapes. However, in real biological systems, biomolecules are usually modified or regulated by several external factors, including surface coating, hydration condition, and local environment. For example, by covalently coupling a Poly(ethylene glycol) (PEG) on a protein surface, the stability of the host protein could be largely enhanced. This method, called PEGylation, has been widely used in pharmaceutical industry to protect protein drugs and increase their circulation life-time since the 1990s. However, the mechanism of protein-PEG interaction is yet to be understood. On the other hand, in developing one of the advanced DNA sequencing techniques --- nanopore sequencing, different mechanisms have been introduced to the nanopore system to regulate the conformation and motion of DNA molecules, attempting to achieve a better signal-to-noise ratio in reading DNA sequence. This dissertation aims to study the above two topics from both experiments and molecular dynamics simulations. The first part focuses on developing nanopore sequencing techniques. We have developed a method combining continuum modeling results of a nano-scale system and a coarse-grained DNA model to study the DNA translocation through a nanopore in a device scale. We use this method to develop advanced DNA sequencing techniques, including plasmonic nanopore and double nanopores. Both of them show great potential as novel approaches for DNA sequencing. The protein-PEG interaction is addressed in the second part. We show that the conjugated PEG affects the thermodynamic stability and local structure of the host protein WW domain, but not that of Lambda repressor. A reoccurring and cooperative folding of a PEG molecule onto the protein surface is revealed by molecular dynamics simulations. Specific PEG-binding motifs on the protein surface are identified.
Issue Date:2016-12-01
Type:Thesis
URI:http://hdl.handle.net/2142/95604
Rights Information:Copyright 2016 Shu-Han Chao
Date Available in IDEALS:2017-03-01
Date Deposited:2016-12


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