ArticleBiophysical journal2015
An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution.
Article in Biophysical journal, 2015. 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, 44 citations in OpenAlex.
- RNA polymerase II CTD Ser5 phosphorylation induces competing effects of expansion and compaction.Biophysical journal · 2026Article
- Energy-Based Coarse-Graining in Molecular Dynamics: A Flow-Based Framework without Data.Journal of chemical theory and computation · 2026Article
- Learning to evolve structural ensembles of unfolded and disordered proteins using experimental solution data.The Journal of chemical physics · 2023Article
- Conformational entropy limits the transition from nucleation to elongation in amyloid aggregation.Biophysical journal · 2022Article
- Configurational Entropy of Folded Proteins and Its Importance for Intrinsically Disordered Proteins.International journal of molecular sciences · 2021Article
- Recent Force Field Strategies for Intrinsically Disordered Proteins.Journal of chemical information and modeling · 2021Review
- Conformational Selection Mechanism Provides Structural Insights into the Optimization of APC-Asef Inhibitors.Molecules (Basel, Switzerland) · 2021Article
- Dissecting the role of glutamine in seeding peptide aggregation.Computational and structural biotechnology journal · 2021Article
- Force-Field Simulations of a Hydrated Lanreotide-Based Derivative: Hydration, Dynamics, and Numerical Evidence of Self-Assembly in Dimers.ACS omega · 2020Article
- Anomalous dynamics of water at the octopeptide lanreotide surface.RSC advances · 2020Article
- Physical Chemistry of the Protein Backbone: Enabling the Mechanisms of Intrinsic Protein Disorder.The journal of physical chemistry. B · 2020Review
- pH-Induced Changes in Polypeptide Conformation: Force-Field Comparison with Experimental Validation.The journal of physical chemistry. B · 2020Article
- Molecular dynamics simulations of an engineered T4 lysozyme exclude helix to sheet transition, and provide insights into long distance, intra-protein switchable motion.Protein science : a publication of the Protein Society · 2020Article
- Calmodulin-Calcineurin Interaction beyond the Calmodulin-Binding Region Contributes to Calcineurin Activation.Biochemistry · 2019Article
- Structural and dynamic studies reveal that the Ala-rich region of ataxin-7 initiates α-helix formation of the polyQ tract but suppresses its aggregation.Scientific reports · 2019Article
- Temperature-induced collapse of a disordered peptide observed by three sampling methods in molecular dynamics simulations.The Journal of chemical physics · 2018Article
- Femtosecond Hydration Map of Intrinsically Disordered α-Synuclein.Biophysical journal · 2018Article
- Force field development and simulations of intrinsically disordered proteins.Current opinion in structural biology · 2018Review
- High-Resolution Structures of the Amyloid-β 1-42 Dimers from the Comparison of Four Atomistic Force Fields.The journal of physical chemistry. B · 2017Article
- CHARMM36m: an improved force field for folded and intrinsically disordered proteins.Nature methods · 2017Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Polyglutamine (polyQ) peptides are a useful model system for biophysical studies of protein folding and aggregation, both for their intriguing aggregation properties and their own relevance to human disease. The genetic expansion of a polyQ tract triggers the formation of amyloid aggregates associated with nine neurodegenerative diseases. Several clearly identifiable and separable factors, notably the length of the polyQ tract, influence the mechanism of aggregation, its associated kinetics, and the ensemble of structures formed. Atomistic simulations are well positioned to answer open questions regarding the thermodynamics and kinetics of polyQ folding and aggregation. The additional, explicit representation of water permits deeper investigation of the role of solvent dynamics, and it permits a direct comparison of simulation results with infrared spectroscopy experiments. The generation of meaningful simulation results hinges on satisfying two essential criteria: achieving sufficient conformational sampling to draw statistically valid conclusions, and accurately reproducing the intermolecular forces that govern system structure and dynamics. In this work, we examine the ability of 12 biomolecular force fields to reproduce the properties of a simple, 30-residue polyQ peptide (Q30) in explicit water. In addition to secondary and tertiary structure, we consider generic structural properties of polymers that provide additional dimensions for analysis of the highly degenerate disordered states of the molecule. We find that the 12 force fields produce a wide range of predictions. We identify AMBER ff99SB, AMBER ff99SB*, and OPLS-AA/L to be most suitable for studies of polyQ folding and aggregation.
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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.