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Design, fabrication and molecular modeling of protein subunits for use in a novel hydrogel
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Text
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Title
Design, fabrication and molecular modeling of protein subunits for use in a novel hydrogel
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ETD_2194
Identifier
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http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.000051824
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eng
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theses
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Topic
Chemical and Biochemical Engineering
Subject
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(authority = ETD-LCSH)
Topic
Tissue engineering
Subject
(ID = SBJ-3);
(authority = ETD-LCSH)
Topic
Proteins
Abstract
Use of bioinspired, genetically engineered proteins in tissue engineering scaffolds represents a new opportunity for engineering these constructs. However, the production and rational modification of new, artificial proteins is hindered by significant gaps in knowledge regarding expression of artificial gene constructs in E. coli and their molecular modeling. This thesis focuses on the production of a novel hydrogel scaffold composed of four self-assembling protein modules and their rational modification using Molecular Dynamics (MD) simulations. Two of the modules are based on the ABA triblock copolymer design. In this triblock, a hydrophilic, random coiled region is flanked by 28 amino-acid α−helical endblocks. The purpose of these endblocks is to function as virtual crosslinkers and support network formation. The length of the endblocks can be changed by the addition of two unlinked, fiber-forming peptides and thus potentially alter the gelation and melting points of the hydrogel. We evaluate the efficacy of production of these endblocks by two separate expression strategies in E. coli and demonstrate their ability to form hydrogels. Furthermore, we analyze the Gibbs free energy of formation of oligomeric intermediates that arise early on during fibrillogenesis from the unlinked peptides using the MM/PBSA module of Amber 9. Thermodynamic data demonstrates changes in the primary structure of these peptides affect the stability of the intermediate that seeds fiber formation. This analysis also suggests a shift in the fiber forming mechanism from monomer addition to protofibril addition. We offer how this data can be used to improve interhelical interactions between endblocks and unlinked peptides and how to develop coarse-grain models of fiber formation.
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electronic resource
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xii, 116 p. : ill.
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Ph.D.
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Includes bibliographical references
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by Christopher Liam Gaughan
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Gaughan
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Christopher Liam
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1968-
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author
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Christopher Liam Gaughan
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Shreiber
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David
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chair
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Advisory Committee
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David Ira Shreiber
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Pedersen
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Henrik
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internal member
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Henrik Pedersen
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Roth
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Charles
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internal member
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Charles Roth
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Galliccio
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Emillio
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outside member
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Advisory Committee
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Emillio Galliccio
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Rutgers University
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degree grantor
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Graduate School - New Brunswick
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school
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2009
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2009-10
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xx
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Rutgers University Electronic Theses and Dissertations
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ETD
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Graduate School - New Brunswick Electronic Theses and Dissertations
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rucore19991600001
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NjNbRU
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doi:10.7282/T30C4VZ9
Genre
(authority = ExL-Esploro)
ETD doctoral
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Rights
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The author owns the copyright to this work
Copyright
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Copyright protected
Notice
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Availability
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Open
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Permission or license
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Gaughan
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Christopher
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Christopher Gaughan
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Rutgers University. Graduate School - New Brunswick
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Author Agreement License
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I hereby grant to the Rutgers University Libraries and to my school the non-exclusive right to archive, reproduce and distribute my thesis or dissertation, in whole or in part, and/or my abstract, in whole or in part, in and from an electronic format, subject to the release date subsequently stipulated in this submittal form and approved by my school. I represent and stipulate that the thesis or dissertation and its abstract are my original work, that they do not infringe or violate any rights of others, and that I make these grants as the sole owner of the rights to my thesis or dissertation and its abstract. I represent that I have obtained written permissions, when necessary, from the owner(s) of each third party copyrighted matter to be included in my thesis or dissertation and will supply copies of such upon request by my school. I acknowledge that RU ETD and my school will not distribute my thesis or dissertation or its abstract if, in their reasonable judgment, they believe all such rights have not been secured. I acknowledge that I retain ownership rights to the copyright of my work. I also retain the right to use all or part of this thesis or dissertation in future works, such as articles or books.
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