ArticlePloS one2015
Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
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- Mechanism of Phosphate Release from Actin Filaments.bioRxiv : the preprint server for biology · 2024Article
- Molecular Mechanisms Underlying Medium-Chain Free Fatty Acid-Regulated Activity of the Phospholipase PlaF fromJACS Au · 2024Article
- Tertiary Plasticity Drives the Efficiency of Enterocin 7B Interactions with Lipid Membranes.The journal of physical chemistry. B · 2024Article
- Correlation between chemical denaturation and the unfolding energetics of Acanthamoeba actophorin.Biophysical journal · 2023Article
- Benchmarking Adaptive Steered Molecular Dynamics (ASMD) on CHARMM Force Fields.Chemphyschem : a European journal of chemical physics and physical chemistry · 2022Article
- Implementation of Telescoping Boxes in Adaptive Steered Molecular Dynamics.Journal of chemical theory and computation · 2022Article
- Demystifying DPP III Catalyzed Peptide Hydrolysis-Computational Study of the Complete Catalytic Cycle of Human DPP III Catalyzed Tynorphin Hydrolysis.International journal of molecular sciences · 2022Article
- Molecular dynamics study of the internalization of cell-penetrating peptides containing unnatural amino acids across membranes.Nanoscale advances · 2022Article
- Conserved FimH mutations in the globalComputational and structural biotechnology journal · 2022Article
- Energetics and structure of alanine-rich α-helices via adaptive steered molecular dynamics.Biophysical journal · 2021Article
- Insight into the drug resistance mechanisms of GS-9669 caused by mutations of HCV NS5B polymerase via molecular simulation.Computational and structural biotechnology journal · 2021Article
- Exploitation of dihydroorotate dehydrogenase (DHODH) and p53 activation as therapeutic targets: A case study in polypharmacology.The Journal of biological chemistry · 2020Article
- The relative stability of trpzip1 and its mutants determined by computation and experiment.RSC advances · 2020Article
- Mutational Analysis of Neuropeptide Y Reveals Unusual Thermal Stability Linked to Higher-Order Self-Association.ACS omega · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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