Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents.
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 comput...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2015-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4430545?pdf=render |
| _version_ | 1818561186818424832 |
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| author | Hailey R Bureau Dale R Merz Eli Hershkovits Stephen Quirk Rigoberto Hernandez |
| author_facet | Hailey R Bureau Dale R Merz Eli Hershkovits Stephen Quirk Rigoberto Hernandez |
| author_sort | Hailey R Bureau |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-14T00:47:38Z |
| format | Article |
| id | doaj.art-1b9518ab1a0a462f92503e9c258407d6 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-14T00:47:38Z |
| publishDate | 2015-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-1b9518ab1a0a462f92503e9c258407d62022-12-21T23:24:01ZengPublic Library of Science (PLoS)PLoS ONE1932-62032015-01-01105e012703410.1371/journal.pone.0127034Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents.Hailey R BureauDale R MerzEli HershkovitsStephen QuirkRigoberto HernandezSteered 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.http://europepmc.org/articles/PMC4430545?pdf=render |
| spellingShingle | Hailey R Bureau Dale R Merz Eli Hershkovits Stephen Quirk Rigoberto Hernandez Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents. PLoS ONE |
| title | Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents. |
| title_full | Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents. |
| title_fullStr | Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents. |
| title_full_unstemmed | Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents. |
| title_short | Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents. |
| title_sort | constrained unfolding of a helical peptide implicit versus explicit solvents |
| url | http://europepmc.org/articles/PMC4430545?pdf=render |
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