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Combined approaches to map protein-ligand interactions using NMR and X-ray crystallography

Anthonyrajah, Erin Shamini (2018) Combined approaches to map protein-ligand interactions using NMR and X-ray crystallography. Doctor of Philosophy (PhD) thesis, University of Kent,. (KAR id:77160)

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Abstract

Understanding protein interactions with modulators, signalling molecules or inhibitors can give information about ligand binding sites, ligand interaction topology and allosteric regulation at an atomic level, which is key for the design of novel inhibitors and protein molecules. Many techniques in-vitro have been developed and utilised including X-ray crystallography, nuclear magnetic resonance (NMR), electron microscopy, mass spectrometry etc... Further advances in these biophysical techniques and combining the information from the different techniques are still required to provide detailed insights into the structure and function of proteins and relate these to the physiological environment.

Seven novel liganded BRD4-BD1 crystal structures and NMR assignments are presented in this thesis. The pair of triple resonance experiments HNCA, HN(CO)CA, HNCACB, HN(CO)CACB for BRD4-BD1 led to the sequential backbone assignment of 1HN, 15N, 13Cα and 13Cβ nuclei. Major chemical shift differences ranging above 0.3 ppm were observed for the residues W81, V87, D88, A89, N93, L94, I146, A150, L158 and K160 with the ligand BTB 07004. This chemical shift mapping was in agreement with the binding site in the

BRD4-BD1 crystal structures, particularly for the residues W81, V87, L94, Y97, C136, Y139, N140 and I146.

The thesis confirms that combining X-ray crystallography and NMR leads to an advanced understanding of ligand interaction sites in proteins. This could be used for generating accurate topology maps of ligand-binding sites of any proteins with specific ligands, known as the "Group Epitope Mapping" (GEM) in the future and be extended to novel proteins.

Item Type: Thesis (Doctor of Philosophy (PhD))
Thesis advisor: Brown, Dr David
Uncontrolled keywords: X-ray Crystallography Nuclear Magnetic Resonance Protein Ligand Biding Sites
Divisions: Divisions > Division of Natural Sciences > School of Biosciences
SWORD Depositor: System Moodle
Depositing User: System Moodle
Date Deposited: 08 Oct 2019 13:10 UTC
Last Modified: 26 Feb 2021 10:26 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/77160 (The current URI for this page, for reference purposes)
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