Investigation of changes in structure and thermodynamic of spruce budworm antifreeze protein under subfreezing temperature

Abstract

The aim of this theoretical work is to investigate of the changes in structure and thermodynamics of spruce budworm antifreeze protein (sbAFP) at low temperatures by using molecular dynamics simulation. The aqueous solution will form ice crystal network under the vaguely hexagonal shape at low temperature and fully represented the characteristics of hydrophobic interaction. Like ice crystal network, the cyclohexane region (including cyclohexane molecules) have enough of the characteristics of hydrophobic interaction. Therefore, in this research the cyclohexane region will be used as a representation of ice crystal network to investigate the interactions of sbAFP and ice crystal network at low temperature. The activity of sbAFP in subfreezing environment, therefore, can be clearly observed via the changes of the hydrophobic (cyclohexane region) and hydrophilic (water region) interactions. The obtained results from total energies, hydrogen bond lifetime correlation C(t), radial distribution function, mean square deviation and snapshots of sbAFP complexes indicated that sbAFP has some special changes in structure and interaction with water and cyclohexane regions at 278 K, as being transition temperature point of water molecules in sbAFP complex at low temperatures, which is more structured and support the experimental observation that the sbAFP complex becomes more rigid as the temperature is lowered.

WITHDRAWN: Structural analysis, molecular dynamics simulation and thermodynamic modification of the antifreeze protein type IV mutant under subfreezing temperatures

“…Hence, this occurrence holds signi cant potency as a result of the hydrogen bonds formed between the ice/water and the residues, ultimately dictating the effectiveness of the antifreeze proteins' functionality (Duboue and Laage 2014). Moreover, the prevention of ice formation relies on the presence of AFP covering the surface of the ice interface that is exposed to water (Nguyen and Le 2017). The IBS in AFPs has been acknowledged as being hydrophobic and made up of numerous hydrogen bonds (Garnham et al 2011).…”

“…Additionally, through molecular dynamics simulation, it has been observed that the hydrophobic IBS within AFPs rearranges water molecules into a structure resembling ice. (Nguyen and Le, 2017).…”

Ice-nucleating proteins are activated by low temperatures to control the structure of interfacial water

“…For ice-active proteins these effects could be more pronounced because studies of INPs and related AFP β-helices have shown that for this class of proteins all of these factors are affected by temperature. For example, it has been shown that their hydration 52 and lateral protein interactions 53 change significantly when decreasing the temperature close to the water melting point. The protein–water interface of INPs has also been observed to become less dynamic at lower temperatures 28 .…”

The Ice Nucleating Protein InaZ is Activated by Low Temperature

“…Studies of INpros and related AFP β-helices have shown that all these factors can be affected by temperature changes. For example, it has been shown that hydration 57,58 and lateral protein interactions 58 change significantly when lowering the temperature close to the water melting point. The protein-water interface has also been observed to become less dynamic at lower temperatures.…”