title: Determining the Energetics of Small β-Sheet Peptides using Adaptive Steered Molecular Dynamics.
abstract: Mechanically driven unfolding is a useful computational tool for extracting the energetics and stretching pathway of peptides. In this work, two representative β-hairpin peptides, chignolin (PDB: 1UAO ) and trpzip1 (PDB: 1LE0 ), were investigated using an adaptive variant of the original steered molecular dynamics method called adaptive steered molecular dynamics (ASMD). The ASMD method makes it possible to perform energetic calculations on increasingly complex biological systems. Although the two peptides are similar in length and have similar secondary structures, their unfolding energetics are quite different. The hydrogen bonding profile and specific residue pair interaction energies provide insight into the differing stabilities of these peptides and reveal which of the pairs provides the most significant stabilization.
authors.affiliation: Center for Computational and Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States.
authors.forename: Hailey R
authors.initials: HR
authors.lastname: Bureau
authors.affiliation: Center for Computational and Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States.
authors.forename: Eli
authors.initials: E
authors.lastname: Hershkovits
authors.affiliation: Kimberly-Clark Corporation , Atlanta, Georgia 30076-2199, United States.
authors.forename: Stephen
authors.initials: S
authors.lastname: Quirk
authors.affiliation: Center for Computational and Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States.
authors.forename: Rigoberto
authors.initials: R
authors.lastname: Hernandez
mesh_terms: D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*; D000072757:Protein Conformation, beta-Strand; D058767:Protein Unfolding; D011506:Proteins / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D009842:Oligopeptides; D010455:Peptides; D011506:Proteins; C539234:Trpzip2 protein; C506175:chignolin