Multifunnel Landscape of the Fold-Switching Protein RfaH-CTD.

Proteins such as the transcription factor RfaH can change biological function by switching between distinct three-dimensional folds. RfaH regulates transcription if the C-terminal domain folds into a double helix bundle and promotes translation when this domain assumes a β-barrel form. This fold-switch has been also observed for the isolated C-terminal domain, dubbed by us as RfaH-C-terminal domain (RfaH-CTD), and is studied here with a variant of the replica-exchange-with-tunneling approach recently introduced by us.

Simulating Protein Fold Switching by Replica Exchange with Tunneling.

Recent experiments suggest that an amino acid sequence encodes not only the native fold of a protein but also other forms that are essential for its function or are important during folding or association. These various forms populate a multifunnel folding and association landscape where mutations, changes in environment, or interaction with other molecules switch between the encoded folds. We introduce replica exchange with tunneling as a way to efficiently simulate switching between distinct folds of proteins and protein aggregates.

Replica-exchange-with-tunneling for fast exploration of protein landscapes.

While the use of replica-exchange molecular dynamics in protein simulations has become ubiquitous, its utility is limited in many practical applications. We propose to overcome some shortcomings that hold back its use in settings such as multi-scale or explicit solvent simulations by integrating ideas of hybrid MC/MD into the replica-exchange protocol. This Replica-Exchange-with-Tunneling method is tested by simulating the Trp-cage protein, a system often used in molecular biophysics for testing sampling techniques.

Mutations and seeding of amylin fibril-like oligomers.

Seeding a protein solution with preformed fibrils can dramatically enhance the growth rate of amyloids. As the seeds do not need to be of the same protein, seeding may account for the observed correlations between amyloid diseases. In an effort to understand better the molecular mechanisms behind cross seeding we have studied in silico the effect of mutations on the seeding of amylin fibrils.