title: Peptide folding in the presence of interacting protein crowders.
abstract: Using Monte Carlo methods, we explore and compare the effects of two protein crowders, BPTI and GB1, on the folding thermodynamics of two peptides, the compact helical trp-cage and the β-hairpin-forming GB1m3. The thermally highly stable crowder proteins are modeled using a fixed backbone and rotatable side-chains, whereas the peptides are free to fold and unfold. In the simulations, the crowder proteins tend to distort the trp-cage fold, while having a stabilizing effect on GB1m3. The extent of the effects on a given peptide depends on the crowder type. Due to a sticky patch on its surface, BPTI causes larger changes than GB1 in the melting properties of the peptides. The observed effects on the peptides stem largely from attractive and specific interactions with the crowder surfaces, and differ from those seen in reference simulations with purely steric crowder particles.
authors.affiliation: Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden.
authors.forename: Anna
authors.initials: A
authors.lastname: Bille
authors.affiliation: Jülich Supercomputing Centre, Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany.
authors.forename: Sandipan
authors.initials: S
authors.lastname: Mohanty
authors.affiliation: Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden.
authors.forename: Anders
authors.initials: A
authors.lastname: Irbäck
mesh_terms: D000818:Animals; D007611:Aprotinin / Q000737:chemistry; D003198:Computer Simulation; D006801:Humans; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D018080:Receptors, GABA-B / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D010455:Peptides; D018080:Receptors, GABA-B; D007611:Aprotinin