ArticleThe journal of physical chemistry. B2018
Computational Studies of Intrinsically Disordered Proteins.
Article in The journal of physical chemistry. B, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Survey of the Aβ-peptide structural diversity: molecular dynamics approaches.Biophysical reviews · 2024Review
- Application of artificial intelligence and machine learning techniques to the analysis of dynamic protein sequences.Proteins · 2024Article
- Molecular Mechanism of Nucleosome Recognition by the Pioneer Transcription Factor Sox.Journal of chemical information and modeling · 2023Article
- Exploring Structures and Dynamics of Protamine Molecules through Molecular Dynamics Simulations.ACS omega · 2022Article
- OCT4 interprets and enhances nucleosome flexibility.Nucleic acids research · 2022Article
- Histone tails cooperate to control the breathing of genomic nucleosomes.PLoS computational biology · 2021Article
- Folding and self-assembly of short intrinsically disordered peptides and protein regions.Nanoscale advances · 2021Review
- Significant compaction of H4 histone tail upon charge neutralization by acetylation and its mimics, possible effects on chromatin structure.Journal of molecular biology · 2021Article
- Development of Charge-Augmented Three-Point Water Model (CAIPi3P) for Accurate Simulations of Intrinsically Disordered Proteins.International journal of molecular sciences · 2020Article
- Nucleosomal DNA Dynamics Mediate Oct4 Pioneer Factor Binding.Biophysical journal · 2020Article
- Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins.Journal of chemical information and modeling · 2020Article
- Well-Balanced Force FieldJournal of chemical theory and computation · 2019Article
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Authors and funding
4 authors.
Funding
Abstract
Frequently elusive to experimental characterizations, intrinsically disordered proteins (IDPs) can be probed using molecular dynamics to provide detailed insight into their complex structure, dynamics, and function. However, previous computational studies were often found to disagree with experiment due to either force field biases or insufficient sampling. In this study, nine unstructured short peptides and the HIV-1 Rev protein were simulated and extended to microseconds to assess these limitations in IDP simulations. In short peptide simulations, a tested IDP-specific force field ff14IDPSFF outperforms its generic counterpart ff14SB as agreement of simulated NMR observables with experiment improves, though its advantages are not clear-cut in apo Rev simulations. It is worth noting that sampling is probably still not sufficient in the ff14SB simulations of apo Rev even if 10 ms have been collected. This indicates that enhanced sampling techniques would greatly benefit IDP simulations. Finally, detailed structural analyses of apo Rev conformations demonstrate different secondary structural preferences between ff14SB (helical) and ff14IDPSFF (random coil). A natural next step is to ask a more quantitative question: whether ff14SB is too ordered or ff14IDPSFF is too disordered in simulations of more complex IDPs such as Rev. This requires further quantitative analyses both experimentally and computationally.
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Registered trials
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