Development of Biomolecular Analysis methods for 2D-IR Spectroscopy
Lead Research Organisation:
University of York
Department Name: Chemistry
Abstract
The aim of this PhD programme is to continue the development of 2-dimensional infrared spectroscopy tools and data analysis methods, using fundamental dynamic data to inform construction of analytical technologies. Experimental methods will utilise the STFC-Central Laser Facility ULTRA laser systems. We will seek to build on previous collaborative work towards scientific understanding of binding small molecules to proteins and DNA while advancing the capability of UK national facilities. The project is in 3 strands:
Strand 1: High throughput 2D-IR spectroscopy of biomolecular complexes
This strand will develop the use of high throughput 2D-IR methods for observing small molecule binding to proteins. This will extend recent work on DNA-binding systems to the spectroscopically more complex and subtle problem of protein-drug binding. In particular, we will target the use of 2D-IR to report on changes in protein dynamics and intramolecular vibrational coupling upon drug binding, linking spectral observables to biological function or physical phenomena such as binding constants.
Strand 2: Real time measurements of biomolecular interactions.
This strand will develop modified T-jump IR and T-jump 2D-IR spectroscopy-based strategies that allow observation of dynamic non-equilibrium responses of biomolecules to steps in temperature, but extend them to allow combined heating/cooling experiments. These will be used to observe examples of dynamic biomolecular structure change in solution both during the initial perturbation but also upon relaxation, giving new access to the process of location of the binding site by the ligand and so direct observation of mechanisms such as induced fit or conformational selection. We will begin with melting/rebinding of double stranded DNA or RNA as test systems including ligand binding events, but progress towards experiments that can probe protein secondary structure change and ligand binding, potentially drawing on key systems from Strand 1.
This strand will apply the cutting edge laser equipment of the CLF to advance our understanding of dynamic behaviour of biological molecules in solution.
Strand 3: This ambitious final stage will combine the results of Strand 1 and 2 by developing measurements of protein-DNA binding, initially at equilibrium but potentially under dynamic conditions.
Strand 1: High throughput 2D-IR spectroscopy of biomolecular complexes
This strand will develop the use of high throughput 2D-IR methods for observing small molecule binding to proteins. This will extend recent work on DNA-binding systems to the spectroscopically more complex and subtle problem of protein-drug binding. In particular, we will target the use of 2D-IR to report on changes in protein dynamics and intramolecular vibrational coupling upon drug binding, linking spectral observables to biological function or physical phenomena such as binding constants.
Strand 2: Real time measurements of biomolecular interactions.
This strand will develop modified T-jump IR and T-jump 2D-IR spectroscopy-based strategies that allow observation of dynamic non-equilibrium responses of biomolecules to steps in temperature, but extend them to allow combined heating/cooling experiments. These will be used to observe examples of dynamic biomolecular structure change in solution both during the initial perturbation but also upon relaxation, giving new access to the process of location of the binding site by the ligand and so direct observation of mechanisms such as induced fit or conformational selection. We will begin with melting/rebinding of double stranded DNA or RNA as test systems including ligand binding events, but progress towards experiments that can probe protein secondary structure change and ligand binding, potentially drawing on key systems from Strand 1.
This strand will apply the cutting edge laser equipment of the CLF to advance our understanding of dynamic behaviour of biological molecules in solution.
Strand 3: This ambitious final stage will combine the results of Strand 1 and 2 by developing measurements of protein-DNA binding, initially at equilibrium but potentially under dynamic conditions.
Organisations
People |
ORCID iD |
| Neil Hunt (Primary Supervisor) | |
| Clement Howe (Student) |