ArticlePloS one2017
Effects of forcefield and sampling method in all-atom simulations of inherently disordered proteins: Application to conformational preferences of human amylin.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 34 citations in OpenAlex.
- Impact of Stabilizing Osmolytes on the Conformational Dynamics of Human and Rat Islet Amyloid Polypeptides.Proteins · 2026Article
- Exploring 2D Graphene-Based Nanomaterials for Biomedical Applications: A Theoretical Modeling Perspective.Small science · 2025Article
- Survey of the Aβ-peptide structural diversity: molecular dynamics approaches.Biophysical reviews · 2024Review
- Review
- Influence of force field choice on the conformational landscape of rat and human islet amyloid polypeptide.Proteins · 2023Article
- Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma.Biophysics reviews · 2022Review
- Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations.Communications biology · 2021Article
- Microcanonical insights into the physicochemical stability of the coformulation of insulin with amylin analogues.Journal of molecular modeling · 2021Article
- Assessing the Direct Binding of Ark-Like E3 RING Ligases to Ubiquitin and Its Implication on Their Protein Interaction Network.Molecules (Basel, Switzerland) · 2020Article
- Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Synergistic long-range effects of mutations underlie aggregation propensities of amylin analogues.Journal of molecular modeling · 2019Article
- Application of molecular dynamics simulations to design a dual-purpose oligopeptide linker sequence for fusion proteins.Journal of molecular modeling · 2018Article
- Effects of Size and Functionalization on the Structure and Properties of Graphene Oxide Nanoflakes: An in Silico Investigation.ACS omega · 2018Article
- Characterisation of the Structure and Oligomerisation of Islet Amyloid Polypeptides (IAPP): A Review of Molecular Dynamics Simulation Studies.Molecules (Basel, Switzerland) · 2018Review
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3 authors at 1 institution in 1 country.
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Abstract
Although several computational modelling studies have investigated the conformational behaviour of inherently disordered protein (IDP) amylin, discrepancies in identifying its preferred solution conformations still exist between various forcefields and sampling methods used. Human islet amyloid polypeptide has long been a subject of research, both experimentally and theoretically, as the aggregation of this protein is believed to be the lead cause of type-II diabetes. In this work, we present a systematic forcefield assessment using one of the most advanced non-biased sampling techniques, Replica Exchange with Solute Tempering (REST2), by comparing the secondary structure preferences of monomeric amylin in solution. This study also aims to determine the ability of common forcefields to sample a transition of the protein from a helical membrane bound conformation into the disordered solution state of amylin. Our results demonstrated that the CHARMM22* forcefield showed the best ability to sample multiple conformational states inherent for amylin. It is revealed that REST2 yielded results qualitatively consistent with experiments and in quantitative agreement with other sampling methods, however far more computationally efficiently and without any bias. Therefore, combining an unbiased sampling technique such as REST2 with a vigorous forcefield testing could be suggested as an important step in developing an efficient and robust strategy for simulating IDPs.
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