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New Directions for Cu2+ Labeling of Biomolecules to Determine Structure, Conformation, and Flexibility

Jarvi, Austin Gamble (2021) New Directions for Cu2+ Labeling of Biomolecules to Determine Structure, Conformation, and Flexibility. Doctoral Dissertation, University of Pittsburgh. (Unpublished)

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In this thesis, we showcase several key applications of Cu2+ labeling in proteins and nucleic acids using electron paramagnetic resonance (EPR) spectroscopy. In proteins, the double histidine (dHis) motif is employed to coordinate a Cu2+ complex. With EPR, it is possible to measure nanoscale distances between two such sites. The dHis method produces distance measurements with a very narrow probability distribution, enabling precise structural assessment.
First, we provide optimal conditions to label a dHis motif with a Cu2+ complex in proteins, and a comprehensive overview of the factors that impact labeling efficiency. We show that dHis labeling is sensitive to the buffer used, and under optimal conditions, up to 80% of proteins can be doubly labeled – a substantial improvement over previous implementations. We demonstrate the power of the dHis method in the precise location of a native metal binding site within a protein. We show that the narrow distance distributions enable a high precision localization, even with very few measured constraints. Such principles can be extrapolated to protein-protein docking, quaternary structural assembly, substrate binding, and protein-DNA interactions. Additionally, we show that the dHis motif is uniquely suited to determine protein subunit orientations by performing distance measurements at high frequencies. Such orientational information is extracted from the Cu2+ center, and we show that the Cu2+ orientation is correlated to the protein subunit on which the dHis motif is applied. Finally, we take the characteristics behind the success of the dHis motif and apply them to peptide nucleic acids (PNA) to determine precise distance constraints between two site-specific Cu2+ labels. Combined with molecular dynamics simulations, we gain an atomistic insight into the structure and dynamics of the PNA duplex. Such work presents an efficient, precise method that provides detailed structural information regarding the nucleic acid, and may be applied to other systems such as DNA or RNA in the future. Overall, this body of work marks a significant advancement of Cu2+ labeling to determine relevant structural information in proteins and nucleic acids, while presenting clear methodologies to promote the widespread adoption of this technique within the scientific community.


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Item Type: University of Pittsburgh ETD
Status: Unpublished
CreatorsEmailPitt UsernameORCID
Jarvi, Austin Gamblearj51@pitt.eduarj51
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Committee ChairSaxena,
Committee MemberWaldeck,
Committee MemberHorne, W.
Committee MemberWang,
Date: 20 January 2021
Date Type: Publication
Defense Date: 19 November 2020
Approval Date: 20 January 2021
Submission Date: 1 December 2020
Access Restriction: No restriction; Release the ETD for access worldwide immediately.
Number of Pages: 190
Institution: University of Pittsburgh
Schools and Programs: Dietrich School of Arts and Sciences > Chemistry
Degree: PhD - Doctor of Philosophy
Thesis Type: Doctoral Dissertation
Refereed: Yes
Uncontrolled Keywords: EPR Spin-labeling dHis Copper PNA protein spectroscopy
Date Deposited: 20 Jan 2021 18:51
Last Modified: 20 Jan 2021 18:51


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