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Molecular Simulations of Alternate Frame Folding in Engineered Protein-Based Switches

Mills, Brandon Michael (2015) Molecular Simulations of Alternate Frame Folding in Engineered Protein-Based Switches. Master's Thesis, University of Pittsburgh. (Unpublished)

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Living organisms take advantage of proteins in order to carry out most of the biological tasks that keep them alive. Although most proteins do not drastically change shape, some behave as conformational switches: in response to an outside signal from its environment, the protein will shape-change to either an “on” or “off” position. These properties of conformational switches have motivated recent efforts towards the conversion of regular ligand binding proteins into novel switches for use as optical sensors and therapeutics. Here we seek to examine one such design that exhibits an intermolecular tug-of-war between two alternate frames of folding that can be made sensitive to calcium. The challenges of elucidating structural and mechanistic details from a partially unfolded protein have led us to consider coarse-grained simulation techniques. We plan to demonstrate that results from these simulations are in agreement with experimental data and can provide novel insight into the mechanisms of switching in this class of engineered proteins.


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Item Type: University of Pittsburgh ETD
Status: Unpublished
CreatorsEmailPitt UsernameORCID
Mills, Brandon Michaelbmm25@pitt.eduBMM25
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Committee ChairChong, Lillian Tltchong@pitt.eduLTCHONG
Committee MemberCoalson, Rob Dcoalson@pitt.eduCOALSON
Committee MemberGarrett-Roe, Seansgr@pitt.eduSGR
Date: 9 January 2015
Date Type: Publication
Defense Date: 4 December 2014
Approval Date: 9 January 2015
Submission Date: 5 December 2014
Access Restriction: No restriction; Release the ETD for access worldwide immediately.
Number of Pages: 45
Institution: University of Pittsburgh
Schools and Programs: Dietrich School of Arts and Sciences > Chemistry
Degree: MS - Master of Science
Thesis Type: Master's Thesis
Refereed: Yes
Uncontrolled Keywords: allostery; brownian dynamics; conformational change; alternate frame folding; molecular dynamics; molecular sensor; Go model; protein folding
Date Deposited: 09 Jan 2015 20:14
Last Modified: 15 Nov 2016 14:25


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