title: Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents.
abstract: Steered Molecular Dynamics (SMD) has been seen to provide the potential of mean force (PMF) along a peptide unfolding pathway effectively but at significant computational cost, particularly in all-atom solvents. Adaptive steered molecular dynamics (ASMD) has been seen to provide a significant computational advantage by limiting the spread of the trajectories in a staged approach. The contraction of the trajectories at the end of each stage can be performed by taking a structure whose nonequilibrium work is closest to the Jarzynski average (in naive ASMD) or by relaxing the trajectories under a no-work condition (in full-relaxation ASMD--namely, FR-ASMD). Both approaches have been used to determine the energetics and hydrogen-bonding structure along the pathway for unfolding of a benchmark peptide initially constrained as an α-helix in a water environment. The energetics are quite different to those in vacuum, but are found to be similar between implicit and explicit solvents. Surprisingly, the hydrogen-bonding pathways are also similar in the implicit and explicit solvents despite the fact that the solvent contact plays an important role in opening the helix.
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 of America.
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 of America.
authors.forename: Dale R
authors.initials: DR
authors.lastname: Merz
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 of America.
authors.forename: Eli
authors.initials: E
authors.lastname: Hershkovits
authors.affiliation: Kimberly-Clark Corporation, Atlanta, GA 30076-2199, United States of America.
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 of America.
authors.forename: Rigoberto
authors.initials: R
authors.lastname: Hernandez
mesh_terms: D000595:Amino Acid Sequence; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D058767:Protein Unfolding; D012997:Solvents / Q000737:chemistry*; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D010455:Peptides; D012997:Solvents; D014867:Water