ArticleJournal of chemical theory and computation2012
Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides.
Article in Journal of chemical theory and computation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Advanced computational approaches to understand protein aggregation.Biophysics reviews · 2024Review
- Hybrid resolution molecular dynamics simulations of amyloid proteins interacting with membranes.Methods (San Diego, Calif.) · 2022Article
- An Overview of Several Inhibitors for Alzheimer's Disease: Characterization and Failure.International journal of molecular sciences · 2021Review
- Diverse Aggregation Kinetics Predicted by a Coarse-Grained Peptide Model.The journal of physical chemistry. B · 2021Article
- The Martini Model in Materials Science.Advanced materials (Deerfield Beach, Fla.) · 2021Article
- Building Minimalist Models for Functionalized Metal Nanoparticles.Frontiers in molecular biosciences · 2019Article
- Insight into the Self-Assembling Properties of Peptergents: A Molecular Dynamics Simulation Study.International journal of molecular sciences · 2018Article
- Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments.Chemical Society reviews · 2018Review
- Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.Biochimica et biophysica acta · 2016Review
- Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunits.The Journal of chemical physics · 2015Article
- Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.The Journal of membrane biology · 2015Review
- Exploring the sequence space for (tri-)peptide self-assembly to design and discover new hydrogels.Nature chemistry · 2015Article
- Tunable Coarse Graining for Monte Carlo Simulations of Proteins via Smoothed Energy Tables: Direct and Exchange Simulations.Journal of chemical theory and computation · 2014Article
- Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.The journal of physical chemistry. B · 2014Article
- Assembly of Nsp1 nucleoporins provides insight into nuclear pore complex gating.PLoS computational biology · 2014Article
- Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the MARTINI coarse-grained force field.Journal of chemical theory and computation · 2013Article
- Effects of flanking loops on membrane insertion of transmembrane helices: a role for peptide conformational equilibrium.The journal of physical chemistry. B · 2013Article
- Molecular basis for the dissociation dynamics of protein A-immunoglobulin G1 complex.PloS one · 2013Article
- Optimization of an elastic network augmented coarse grained model to study CCMV capsid deformation.PloS one · 2013Article
- The role of molecular simulations in the development of inhibitors of amyloid β-peptide aggregation for the treatment of Alzheimer's disease.ACS chemical neuroscience · 2012Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present an extension of the coarse-grained MARTINI model for proteins and apply this extension to amyloid- and elastin-like peptides. Atomistic simulations of tetrapeptides, octapeptides, and longer peptides in solution are used as a reference to parametrize a set of pseudodihedral potentials that describe the internal flexibility of MARTINI peptides. We assess the performance of the resulting model in reproducing various structural properties computed from atomistic trajectories of peptides in water. The addition of new dihedral angle potentials improves agreement with the contact maps computed from atomistic simulations significantly. We also address the question of which parameters derived from atomistic trajectories are transferable between different lengths of peptides. The modified coarse-grained model shows reasonable transferability of parameters for the amyloid- and elastin-like peptides. In addition, the improved coarse-grained model is also applied to investigate the self-assembly of β-sheet forming peptides on the microsecond time scale. The octapeptides SNNFGAIL and (GV)(4) are used to examine peptide aggregation in different environments, in water, and at the water-octane interface. At the interface, peptide adsorption occurs rapidly, and peptides spontaneously aggregate in favor of stretched conformers resembling β-strands.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.