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Approaches to studying peptide aggregation, polymorphism and thermodynamics
Descriptive
TitleInfo
Title
Approaches to studying peptide aggregation, polymorphism and thermodynamics
Name
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Mushnoori
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Srinivas Chakravarthy
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1989-
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Srinivas Chakravarthy Mushnoori
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author
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Dutt
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Meenakshi
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Meenakshi Dutt
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Advisory Committee
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chair
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Masanori
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Masanori Hara
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Advisory Committee
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internal member
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Jha
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Shantenu
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Shantenu Jha
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Advisory Committee
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internal member
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Olson
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Wilma
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Wilma Olson
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Advisory Committee
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outside member
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Rutgers University
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degree grantor
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School of Graduate Studies
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theses
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ETD doctoral
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2020
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2020-10
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English
Abstract
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Harnessing the self-assembly of peptide sequences has demonstrated great promise in the domain of creating high precision shape-tunable biological materials. The unique properties of peptides allow for a building blocks approach to materials design. In this proposal, self-assembly of mixed systems encompassing two peptide sequences with identical hydrophobic regions and distinct polar segments is investigated. The two peptide sequences are diphenylalanine and phenylalanine-asparagine-phenylalanine. The dissertation aims to examine the impact of molecular composition (i.e, the total peptide concentration and the relative tripeptide concentration) on the morphology of the self-assembled hybrid biological material. We report a rich polymorphism in the assemblies of these peptides and explain the relationship between peptide sequence, concentration and the morphology of the supramolecular assembly. We discuss three techniques to explore the phase space of this morphological diversity: Classical Coarse Grained Molecular Dynamics (CGMD), Replica Exchange Molecular Dynamics (REMD), and a hybrid Workflows/Machine Learning framework for Targeted Design of Supramolecular Assemblies, which we have called PACE: Pipelines for Automation of Compliance-based Elimination. Classical CGMD establishes the polymorphism in the phase space, REMD sheds light on the thermodynamics of assembly and helps determine the most likely thermodynamic states, and the PACE framework provides a workflow to automate the simulation, detection and screening of configurations that can target specific morphologies.
Subject
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Topic
Peptides
Subject
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Topic
Chemical and Biochemical Engineering
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Rutgers University Electronic Theses and Dissertations
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ETD_11226
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1 online resource (xii, 56 pages) : illustrations
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Ph.D.
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Includes bibliographical references
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School of Graduate Studies Electronic Theses and Dissertations
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rucore10001600001
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Identifier
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doi:10.7282/t3-nm38-rb79
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Rights
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The author owns the copyright to this work.
RightsHolder
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Name
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Mushnoori
GivenName
Srinivas
Role
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Permission or license
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2020-09-28 14:20:23
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Srinivas Mushnoori
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Rutgers University. School of Graduate Studies
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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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2020-10-31
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2021-10-31
Detail
Access to this PDF has been restricted at the author's request. It will be publicly available after October 31st, 2021.
Copyright
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Copyright protected
Availability
Status
Open
Reason
Permission or license
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