https://doi.org/10.1140/epjb/e2006-00036-x
Unfolding designable structures
Physics Department, Rutherford Building, McGill University, 3600 rue University, Montreal Quebec, H3A 2T8, Canada
Corresponding authors: a diasc@physics.mcgill.ca - b grant@physics.mcgill.ca
Received:
17
October
2005
Revised:
25
November
2005
Published online:
8
February
2006
Among an infinite number of possible folds, nature has chosen only about 1000 distinct folds to form protein structures. Theoretical studies suggest that selected folds are intrinsically more designable than others; these selected folds are unusually stable, a property called the designability principle. In this paper we use the 2D hydrophobic-polar lattice model to classify structures according to their designability, and Langevin dynamics to account for their time evolution in the presence of shear flow. We demonstrate that, among all possible folds, the more designable ones are easier to unfold due to their large number of surface-core bonds.
PACS: 87.15.-v – Biomolecules: structure and physical properties / 87.15.Aa – Theory and modeling; computer simulation / 87.15.By – Structure and bonding / 87.15.He – Dynamics and conformational changes
© EDP Sciences, Società Italiana di Fisica, Springer-Verlag, 2006
