Computational Study of Differences between Antifreeze Activity of Type-III Antifreeze Protein from Ocean Pout and Its Mutant

Abstract

The antifreeze activity of a type-III antifreeze protein (AFP) expressed in ocean pout (Zoarces americanus) is compared with that of a specific mutant (T18N) using all-atom molecular dynamics simulations. The antifreeze activity of the mutant is only 10% of the wild-type AFP. The results from this simulation study revealed the following insights into the mechanism of antifreeze action by type-III AFPs. The AFP gets adsorbed to the advancing ice front due to its hydrophobic nature. A part of the hydrophobicity is caused by the presence of clathrate structure of water molecules near the ice-binding surface (IBS). The mutation in the AFP disrupts this structure and thereby reduces the ability of the mutant to adsorb to the ice–water interface leading to the loss of antifreeze activity. The mutation, however, has no effect on the ability of the adsorbed protein to bind to the growing ice phase. Simulations also revealed that all surfaces of the protein can bind to the ice phase, although the IBS is the preferred surface.

Detailed Analysis of the Ice Surface after Binding of an Insect Antifreeze Protein and Correlation with the Gibbs–Thomson Equation

“…An important aspect regarding the binding behavior is the interaction strength between the protein and the ice surface. “AFPs that adsorb strongly will have higher surface concentrations and a larger thermal hysteresis gap” (Kumari et al 2020, page 2444) . The simulative determination of this interaction strength proves to be difficult, since the dynamic of the ice surface has a non-negligible influence on the adsorption of the protein.…”

“…Therefore, it would be desirable to be able to determine this binding strength unambiguously. Kumari et al also proposed a new method to compare the adsorption behavior of different AFPs or toward different ice crystal planes . This method should be evaluated in more detail.…”

“…"AFPs that adsorb strongly will have higher surface concentrations and a larger thermal hysteresis gap" (Kumari et al 2020, page 2444). 43 The simulative determination of this interaction strength proves to be difficult, since the dynamic of the ice surface has a nonnegligible influence on the adsorption of the protein. This in turn depends on the force field and the water model used.…”

“…Kumari et al also proposed a new method to compare the adsorption behavior of different AFPs or toward different ice crystal planes. 43 This method should be evaluated in more detail. In combination with other MD simulations, this could provide further insights into the functioning of AFPs and molecules with similar properties.…”

Energetics and J-coupling constants for Ala, Gly, and Val peptides demonstrated using ABEEM polarizable force field in vacuo and an aqueous solution

“…Considering the molecular scale from monomer to multibody, every amino acid is equipped with intrinsic behaviour, sequence behaviour, and environmental behaviour. [102][103][104][105] The intrinsic behaviour of amino acids involves the collection of conformational and energetic characteristics, which is the basis for the other two behaviours, and can be inherited and extended traceably. The dipeptides that have been blocked were chosen for investigation to observe their intrinsic behaviour.…”