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Computational Studies of Mutually Exclusive Folding in a Two-Domain Molecular Switch

Mills, Brandon Michael (2009) Computational Studies of Mutually Exclusive Folding in a Two-Domain Molecular Switch. Undergraduate Thesis, University of Pittsburgh. (Unpublished)

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Enzymatic proteins have their activity tightly regulated, often via conformational switching (shape-changing) events which can turn them on or off in a reversible fashion. A change in shape at one location on a protein can induce a change at another location. The Loh Group at SUNY Medical School has engineered a model system for studying such changes in molecular switches by inserting a guest protein (ubiquitin) into a host (barnase). The two protein domains undergo a thermodynamic tug-of-war that is concluded by the mechanically induced unfolding (and deactivation) of one domain. It has been experimentally shown that through changes in environmental conditions or the addition of effector molecules, the unfolded domain can refold by unfolding its competitor. Methodologies for the design of engineered switches may be used to design novel biological sensors and therapeutics.However, it is difficult to obtain structural information for these molecular switches due to their partially unfolded nature. Therefore, we have conducted atomistic and coarse-grained simulations in order to gain structural insight into mutually exclusive folding. To our knowledge, the simulations described in this thesis document are the first at any level of structural detail to show that the folding of one protein domain can drive the unfolding of another.


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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Status: Unpublished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 MemberZuckerman, Daniel Mddmmzz@pitt.eduDDMMZZ
Committee MemberKuntz, Irwin
Committee MemberBrodsky, Jeffrey Ljbrodsky@pitt.eduJBRODSKY
Date: 22 May 2009
Date Type: Completion
Defense Date: 8 April 2009
Approval Date: 22 May 2009
Submission Date: 14 May 2009
Access Restriction: No restriction; Release the ETD for access worldwide immediately.
Institution: University of Pittsburgh
Schools and Programs: Dietrich School of Arts and Sciences > Chemistry
David C. Frederick Honors College
Degree: BPhil - Bachelor of Philosophy
Thesis Type: Undergraduate Thesis
Refereed: Yes
Uncontrolled Keywords: allostery; brownian dynamics; conformational change; domain insertion; mechanically induced unfolding; molecular dynamics; molecular sensor; Go model; protein folding
Other ID:, etd-05142009-164530
Date Deposited: 10 Nov 2011 19:44
Last Modified: 15 Nov 2016 13:43


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