Identification of Binding Motif of Anti-Freeze Protein using TIP4P-ice Water Model
Aritra Banerjee
Genome Science and Technology, Bredesen Center, University of Tennessee
This page shows visualizations of the binding motif of Tenebrio molitor antifreeze protein to the basal plane of ice.
Anti-freeze proteins bind to different planes of ice and prevent its growth. The binding of a protein to this flat ice surface can be studied by using molecular dynamics simulations. Form previous simulations (using single-site water model mW ), it is known Tenebrio molitor anti-freeze protein (TmAFP) binds to the basal and prismatic planes of ice via hydrogen bonding of the hydroxyl groups of the threonine residues by forming distinct anchored clathrate motifs. This anchored clathrate motif can be distinguished using CHILL+ algorithm. The question of whether all-atom TIP4P/Ice water model preserves this reported anchored-clathrate motif geometry for TmAFP is explored in this work.
Interactive Structures
Color Legend:
- protein = CPK element colors (C gray, N blue, O red, H white, S yellow)
- water = light blue, smaller spheres
- sodium ions = purple
References
1.Hudait, A., Odendahl, N., Qiu, Y., Paesani, F., & Molinero, V. (2018). Ice-nucleating and antifreeze proteins recognize ice through a diversity of anchored clathrate and ice-like motifs. Journal of the American Chemical Society, 140(14), 4905-4912
2.Nguyen, A. H., & Molinero, V. (2015). Identification of clathrate hydrates, hexagonal ice,cubic ice, and liquid water in simulations: The CHILL+ algorithm. The Journal of Physical Chemistry B, 119(29), 9369-9376.
posted: May 2026.
updated: May 2026.