(511g) Influence of Backbone Hydrogen Bonding on the Stability of the WW Domain of the Protein Pin1

A detailed understanding of the thermal and chemical stability of proteins is crucial especially for protein engineering and the de-novo design of enzymes. An on-going debate in the biological community is the role of backbone hydrogen bonds for the protein stability [1]. In a recent study the effect of removing a hydrogen bond donor from the backbone of the 34-residue WW domain of the protein Pin1 was investigated by molecular dynamics (MD) in aqueous solution [2]. This three-stranded beta sheet fold is small enough to allow for substantial simulation time scales and is experimentally well characterized. The construction of so called amide-to-ester mutants allows to probe each of the 20 intramolecular hydrogen bonds experimentally [3] as well as computationally in terms of a relative stability of the mutant with respect to the wild type. It was found that a proper representation of the unfolded state conformations is essential for an adequate description. Since experiments and simulations agreed only for a subset of mutations, it is the aim of this work to systematically switch off or at least quantify the major simulation-related inaccuracies that could hamper better agreement. In particular this includes the finite simulation time, inadequate sampling, the representation of the unfolded state modelled by short peptides and the influence of protecting osmolytes like Trimethylamin-N-oxid (TMAO) present in the experiments. It is aimed for linking a residual discrepancy between experiment and simulation to either force field inaccuracies or uncertainties in the experimental measurements.

[1] G. D. Rose, P. J. Fleming, J. R. Banavar, A. Maritan, PNAS 103 (45) 2006, 16623–16633

[2] A. P. Eichenberger, W. F. van Gunsteren, S. Riniker, L. von Ziegler, N. Hansen, Biochim. Biophys. Acta 2015, 1850, 983–995

[3] S. Deechongkit, P. Dawson, J. Kelly, J. Am. Chem. Soc. 126 (51) 2004, 16762–16771