title: Folding 19 proteins to their native state and stability of large proteins from a coarse-grained model.
abstract: We develop an intermediate resolution model, where the backbone is modeled with atomic resolution but the side chain with a single bead, by extending our previous model (Proteins (2013) DOI: 10.1002/prot.24269) to properly include proline, preproline residues and backbone rigidity. Starting from random configurations, the model properly folds 19 proteins (including a mutant 2A3D sequence) into native states containing β sheet, α helix, and mixed α/β. As a further test, the stability of H-RAS (a 169 residue protein, critical in many signaling pathways) is investigated: The protein is stable, with excellent agreement with experimental B-factors. Despite that proteins containing only α helices fold to their native state at lower backbone rigidity, and other limitations, which we discuss thoroughly, the model provides a reliable description of the dynamics as compared with all atom simulations, but does not constrain secondary structures as it is typically the case in more coarse-grained models. Further implications are described.
authors.affiliation: Department of Physics and Astronomy, Iowa State University, Ames, Iowa, 50011.
authors.forename: Abhijeet
authors.initials: A
authors.lastname: Kapoor
authors.forename: Alex
authors.initials: A
authors.lastname: Travesset
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D006153:Guanosine Diphosphate; D056004:Molecular Dynamics Simulation; D017510:Protein Folding; D055550:Protein Stability; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D011506:Proteins; D006153:Guanosine Diphosphate
keywords: GPUs; coarse graining; molecular dynamics; proteins; secondary structure; α helices; β sheets