Dresden 2014 – scientific programme

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BP: Fachverband Biologische Physik

BP 28: Protein structure and dynamics II

BP 28.3: Talk

Wednesday, April 2, 2014, 15:45–16:00, HÜL 386

Determining the protein folding core: an experimental and computational approach — •Jack Heal, Claudia Blindauer, Robert Freedman, and Rudolf Römer — University of Warwick, Coventry, England, CV4 7AL

The protein folding problem has been a prevalent concern of structural biology for more than 50 years. We study the folding process by identifying an experimental 'folding core' through hydrogen-deuterium exchange NMR (HDX) as well as a computationally determined folding core based on a combination of coarse-grained simulations using the software FRODA and rigidity analysis using FIRST. We test whether such rapid methods can reliably predict the results of HDX experiments. Our experimental system is Cyclophilin A (CypA), an enzyme that helps proteins to fold. It also binds to and aids the function of the immunosuppressant drug cyclosporin A (CsA) as well as binding to the HIV-1 capsid protein. We characterise the protein and its interaction with CsA using circular dichroism and fluorescence spectroscopy in addition to HDX experiments. From the set of slowly exchanging residues we establish the HDX folding core for both the unbound CypA and the CypA-CsA complex. We are able to improve upon the prediction from the established method of FIRST by using FRODA in combination with normal mode analysis. To accomplish this, we introduce a method of tracking the surface-exposure of backbone N-H atoms through the simulation. In this way, we are in the process of designing computationally undemanding methods that can predict the results of sophisticated experiments characterising ligand binding.