title: Enhanced Wang Landau sampling of adsorbed protein conformations.
abstract: Using computer simulations to model the folding of proteins into their native states is computationally expensive due to the extraordinarily low degeneracy of the ground state. In this paper, we develop an efficient way to sample these folded conformations using Wang Landau sampling coupled with the configurational bias method (which uses an unphysical "temperature" that lies between the collapse and folding transition temperatures of the protein). This method speeds up the folding process by roughly an order of magnitude over existing algorithms for the sequences studied. We apply this method to study the adsorption of intrinsically disordered hydrophobic polar protein fragments on a hydrophobic surface. We find that these fragments, which are unstructured in the bulk, acquire secondary structure upon adsorption onto a strong hydrophobic surface. Apparently, the presence of a hydrophobic surface allows these random coil fragments to fold by providing hydrophobic contacts that were lost in protein fragmentation.
authors.affiliation: Department of Chemical Engineering, Columbia University, New York, New York 10027, USA.
authors.forename: Mithun
authors.initials: M
authors.lastname: Radhakrishna
authors.forename: Sumit
authors.initials: S
authors.lastname: Sharma
authors.forename: Sanat K
authors.initials: SK
authors.lastname: Kumar
mesh_terms: D000327:Adsorption; D000465:Algorithms; D057927:Hydrophobic and Hydrophilic Interactions; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013499:Surface Properties
chemical_list: D011506:Proteins