4 papers · 1 filter
The folding mechanics of a knotted protein
Stefan Wallin, Konstantin B Zeldovich, Eugene I Shakhnovich
An increasing number of proteins are being discovered with a remarkable and somewhat surprising feature, a knot in their native structures. How the polypeptide chain is able to kno…
Sequence-based study of two related proteins with different folding behaviors
Giorgio Favrin, Anders Irbäck, Stefan Wallin
ZSPA-1 is an engineered protein that binds to its parent, the three-helix-bundle Z domain of staphylococcal protein A. Uncomplexed ZSPA-1 shows a reduced helix content and a meltin…
Two-state folding over a weak free-energy barrier
Giorgio Favrin, Anders Irbäck, Björn Samuelsson +1
We present a Monte Carlo study of a model protein with 54 amino acids that folds directly to its native three-helix-bundle state without forming any well-defined intermediate state…
Thermodynamics of alpha- and beta-structure formation in proteins
Anders Irbäck, Björn Samuelsson, Fredrik Sjunnesson +1
An atomic protein model with a minimalistic potential is developed and then tested on an alpha-helix and a beta-hairpin, using exactly the same parameters for both peptides. We fin…