Solvation Layer of Antifreeze Proteins Analyzed with a Markov State Model

Abstract

Three structurally very different antifreeze proteins (AFPs) are studied, addressing the question as to what extent the hypothesized preordering-binding mechanism is still relevant in the second solvation layer of the protein and beyond. Assuming a two-state model of water, the solvation layers are analyzed with the help of molecular dynamics simulations together with a Markov state model, which investigates the local tedrahedrality of the water hydrogen-bond network around a given water molecule. It has been shown previously that this analysis can discriminate the high-entropy, high-density state of the liquid (HDL) from its more structured low-density state (LDL). All investigated proteins, regardless of whether they are an AFP or not, have a tendency to increase the amount of HDL in their second solvation layer. The ice binding site (IBS) of the antifreeze proteins counteracts that trend, with either a hole in the HDL layer or a true excess of LDL. The results correlate to a certain extent with recent experiments, which have observed ice-like vibrational (VSFG) spectra for the water atop the IBS of only a subset of antifreeze proteins. It is concluded that the preordering-binding mechanism indeed seems to play a role but is only part of the overall picture.

Antifreeze Proteins and Their Practical Utilization in Industry, Medicine, and Agriculture

“…Recently, screening and bioinformatics tools were effective and accurate to analyze the diverse types of AFPs. For instance, the hydration structure of AFPs could be analyzed by random tool modeling [30,31], meanwhile the AFPs salvation layer could be analyzed by molecular dynamic (MD) simulations [32]. Additionally, there are some user-friendly website servers that could analyze the secondary structures and easily predict their structural models [33].…”