Aims and Goals
The unifying goal of the proposed research is to clarify the role of biomolecular flexibility across a large range of time and length scales and, in doing so, improve the current state of understanding of the target biological processes as well as of the underlying conceptual frameworks.
In parallel, this project aims to maintain momentum in developing the computational life sciences platform at the RBI, as well as to ensure continued scientific excellence and international recognition of the project team.
We can also identify a number of more specific goals, designed to contribute to realization of the overall aim. These goals can be grouped within the following work packages.
WP1 – Peptides and spectroscopy
In the context of short peptide-based systems and protein fragments, we plan to clarify the nature of excited state dynamics and reveal its connection to molecular flexibility (Task 1.1). Strongly related is the role of Task 1.2, which is to elaborate the connection between the ground state structural ensemble of flexible peptides and their Circular Dichroism (CD) spectra, and develop its potential application as an environmental probe.
WP2 – Protein structure and flexibility
Here we will upscale the systems of interest to deepen our understanding of molecular flexibility in whole proteins. A key experimental method in this respect is H/D exchange (HDX). We will attempt to develop a robust mathematical analysis of HDX data to provide an improved tool for measuring molecular flexibility in these and related systems (Task 2.1).
WP3 – Enzyme related transformations
Further increasing the level of complexity, we will study different dimensions of the connection between flexibility and chemical transformations, specifically in the context of enzyme function. Pyruvate Formate-Lyase will serve as a model to clarify the effects of chemical changes in the active site on molecular flexibility (Task 3.1). The GDH systems will be used to establish flexibility-based differences between the mutase and eliminase families and the B12-dependent and B12-independent enzymes. The related reduction of ribonucleotides will be used to investigate molecular flexibility in the context of chemical evolution (Task 3.2). Finally, we aim to investigate retinal photoisomerization in order to connect excited state dynamics and ground state molecular flexibility (Task 3.3).