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  4. HIGH-PRESSURE SMALL-ANGLE X-RAY SCATTERING AND THE MOLECULAR MECHANISM OF ALLOSTERIC COMMUNICATION IN ASPARTATE TRANSCARBAMOYLASE

HIGH-PRESSURE SMALL-ANGLE X-RAY SCATTERING AND THE MOLECULAR MECHANISM OF ALLOSTERIC COMMUNICATION IN ASPARTATE TRANSCARBAMOYLASE

File(s)
Miller_cornellgrad_0058F_14720.pdf (44.7 MB)
Permanent Link(s)
http://doi.org/10.7298/zbwp-9p14
https://hdl.handle.net/1813/117164
Collections
Cornell Theses and Dissertations
Author
Miller, Robert
Abstract

High-Pressure Small-Angle X-ray Scattering: Recent discoveries have illustrated a significant portion of earth’s biosphere, potentially as large as 80%, exists under conditions of extreme pressure (>10 MPa or 100 atm) yet the biological mechanisms of adaptation to life under such conditions is poorly understood. Moreover, pressure is a unique thermodynamic variable and therefore provides a powerful biophysical lens into protein structure, stability, ligand binding events, and other biophysical processes. This thesis presents important advancements in high-pressure small-angle X-ray scattering (HP-SAXS), focusing on the development of novel instrumentation and methodologies to probe biomolecular structures under extreme pressure conditions. Two experimental configurations will be discussed: (1) a so-called static HP-cell capable of data acquisition at pressures up to 400 MPa with high reproducibility and minimal background interference and (2) a chromatography-coupled SAXS system capable of reaching pressures of 100 MPa over a pressure range of approximately 4-ß55 °C. These configurations utilize modern material design, such as diamond windows and corrosion-resistant alloys, optimizing reproducible structural measurements of biological materials particularly for non-expert users. This work significantly expands the capacity of HP-SAXS to investigate pressure-dependent structural changes, contributing to the understanding of molecular adaptation in extreme environments and enhancing biophysical methodologies for broader applications in structural biology. Aspartate transcarbamoylase: For nearly seven decades, aspartate transcarbamoylase (ATCase) from Escherichia coli, a heterododecamer comprising two catalytic trimers and three regulatory dimers, has been a classical model for enzyme allostery. Despite extensive research, the precise molecular mechanism of allosteric regulation by nucleotides has remained elusive. In this work, we provide a comprehensive biochemical and structural characterization of E. coli ATCase, revealing novel insights into its allosteric regulation. Using activity assays, SAXS, cryo-EM, and crystallography, we demonstrate that ATCase generally follows a two-state model in response to substrate binding, from a T (inactive) to R-state (active), but exhibits distinct R-state ensembles depending on the identity of the bound nucleotides. Remarkably, ATP and GTP induce a novel conformational intermediate that expands the enzyme in the absence of both substrates, bypassing the energy-intensive T-to-R transition and decoupling the catalytic trimers. This discovery challenges the classical Monod-Wyman-Changeux (MWC) model and uncovers a sophisticated regulatory mechanism ensuring balanced nucleotide synthesis. Our findings not only resolve longstanding questions but also provide novel insight into the molecular mechanism of allosteric regulation in E. coli ATCase.

Description
326 pages
Date Issued
2024-12
Keywords
Allostery
•
Aspartate Transcarbamoylase
•
ATCase
•
Cryo-EM
•
PDB
•
SAXS
Committee Chair
Ando, Nozomi
Committee Member
Crane, Brian
Cerione, Richard
Degree Discipline
Chemistry and Chemical Biology
Degree Name
Ph. D., Chemistry and Chemical Biology
Degree Level
Doctor of Philosophy
Rights
Attribution 4.0 International
Rights URI
https://creativecommons.org/licenses/by/4.0/
Type
dissertation or thesis
Link(s) to Catalog Record
https://newcatalog.library.cornell.edu/catalog/16921969

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