ArticleJournal of chemical theory and computation2024
The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics.
Article in Journal of chemical theory and computation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Molecular Modeling of the Pathogenetic Mechanisms of Neuropsychiatric Disorders.International journal of molecular sciences · 2026Review
- Proteins Inside the HSP60/HSP10 Fold Under a Constant Electric Field: Potential Implications for the Protein Folding Problem.International journal of molecular sciences · 2026Article
- Characterizing the Conformational Dynamics of the Ribose Transporter B Protein inJournal of chemical theory and computation · 2026Article
- Role of Water Models in Simulations of Ion Conduction in Potassium Channels.Journal of chemical theory and computation · 2026Article
- Cryo-EM structures of antibodies elicited by germline-targeting HIV MPER epitope scaffolds.Cell reports · 2026Article
- Structural basis of broad protection against influenza virus by human antibodies targeting the neuraminidase active site via a recurring motif in CDR H3.Nature communications · 2025Article
- In silico evolution of globular protein folds from random sequences.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Germline-encoded recognition of peanut underlies development of convergent antibodies in humans.Science translational medicine · 2025Article
- Umbrella Refinement of Ensembles-An Alternative View of Ensemble Optimization.Molecules (Basel, Switzerland) · 2025Article
- Challenges in simulating whole virus particles and how to fix them with the SIRAH force field.Biophysical reviews · 2025Review
- Predicting the conformational flexibility of antibody and T cell receptor complementarity-determining regions.Nature machine intelligence · 2025Article
- Use of AI-methods over MD simulations in the sampling of conformational ensembles in IDPs.Frontiers in molecular biosciences · 2025Review
- GRACE: Generative Redesign in Artificial Computational Enzymology.ACS synthetic biology · 2024Article
- Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents.Journal of chemical information and modeling · 2024Article
- Engineering of pH-dependent antigen binding properties for toxin-targeting IgG1 antibodies using light-chain shuffling.Structure (London, England : 1993) · 2024Article
- Simulation-driven design of stabilized SARS-CoV-2 spike S2 immunogens.Nature communications · 2024Article
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15 authors.
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Abstract
Protein folding is a fascinating, not fully understood phenomenon in biology. Molecular dynamics (MD) simulations are an invaluable tool to study conformational changes in atomistic detail, including folding and unfolding processes of proteins. However, the accuracy of the conformational ensembles derived from MD simulations inevitably relies on the quality of the underlying force field in combination with the respective water model. Here, we investigate protein folding, unfolding, and misfolding of fast-folding proteins by examining different force fields with their recommended water models, i.e., ff14SB with the TIP3P model and ff19SB with the OPC model. To this end, we generated long conventional MD simulations highlighting the perks and pitfalls of these setups. Using Markov state models, we defined kinetically independent conformational substates and emphasized their distinct characteristics, as well as their corresponding state probabilities. Surprisingly, we found substantial differences in thermodynamics and kinetics of protein folding, depending on the combination of the protein force field and water model, originating primarily from the different water models. These results emphasize the importance of carefully choosing the force field and the respective water model as they determine the accuracy of the observed dynamics of folding events. Thus, the findings support the hypothesis that the water model is at least equally important as the force field and hence needs to be considered in future studies investigating protein dynamics and folding in all areas of biophysics.
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