ArticlePloS one2018
Structures, dynamics, and hydrogen-bond interactions of antifreeze proteins in TIP4P/Ice water and their dependence on force fields.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed, 31 citations in OpenAlex.
- Protein Confinement Decouples Dynamical Heterogeneity from Structural Preordering in Supercooled Monolayer Water.JACS Au · 2025Article
- Understanding pectin cross-linking in plant cell walls.Communications biology · 2025Article
- Structural investigation, computational analysis, and theoretical cryoprotectant approach of antifreeze protein type IV mutants.European biophysics journal : EBJ · 2024Article
- Biophysical assessment of amantadine and SDS surfactant mixture onto boron nitride nanotube: a molecular dynamics investigation.Journal of molecular modeling · 2023Article
- Mechanistic elucidation of freezing-induced surface decomposition of aluminum oxyhydroxide adjuvant.iScience · 2022Article
- The role of structural order in heterogeneous ice nucleation.Chemical science · 2022Article
- Dynamic motions of ice-binding proteins in livingBiochemistry and biophysics reports · 2022Article
- The atomistic details of the ice recrystallisation inhibition activity of PVA.Nature communications · 2021Article
- Sampling of the conformational landscape of small proteins with Monte Carlo methods.Scientific reports · 2020Article
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Authors and funding
1 author at 1 institution in 1 country.
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Abstract
Tenebrio molitor antifreeze protein (TmAFP) was simulated with growing ice-water interfaces at a realistic melting temperature using TIP4P/Ice water model. To test compatibility of protein force fields (FFs) with TIP4P/Ice water, CHARMM, AMBER, and OPLS FFs were applied. CHARMM and AMBER FFs predict more β-sheet structure and lower diffusivity of TmAFP at the ice-water interface than does OPLS FF, indicating that β-sheet structure is important for the TmAFP-interface binding and antifreeze activity. In particular, CHARMM FF more clearly distinguishes the strengths of hydrogen bonds in the ice-binding and non-ice-binding sites of TmAFP than do other FFs, in agreement with experiments, implying that CHARMM FF can be a reasonable choice to simulate proteins with TIP4P/Ice water. Simulations of mutated TmAFPs show that for the same density of Thr residues, continuous arrangement of Thr with the distance of 0.4~0.6 nm induces the higher extent of antifreeze activity than does intermittent arrangement of Thr with larger distances. These findings suggest the choice of CHARMM FF for AFP-TIP4P/Ice simulations and help explain the relationship between Thr-residue arrangement and antifreeze activity.
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