Average lifetimes of hydrogen bonds between Thr residues and water molecules.

<p>11 and 6 Thr residues are respectively classified as the ice-binding and non-ice-binding sites (a red dotted line).</p

Minimum distances between hydroxyl groups of different Thr residues as a function of time.

<p>Since the binding sites of TmAFP, TmAFP-m1, TmAFP-m2, and TmAFP-m3 respectively include 11, 7, 6, and 4 Thr residues, the minimum distance for each Thr residue is represented by different colors. Note that the neighboring residues should have the same minimum distance, and thus their values are often overlapped, as highlighted in TmAFP-m2 and TmAFP-m3.</p

Average diffusion coefficients (<i>D</i>) of TmAFP, TmAFP-m1, TmAFP-m2, and TmAFP-m3.

<p>Average diffusion coefficients were obtained by averaging those from three or five simulations. Error bars indicate standard errors calculated from the standard deviation of three or five samples (diffusion coefficients) with correction by multiplying a factor of 0.886 or 0.940, respectively [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198887#pone.0198887.ref063" target="_blank">63</a>].</p

List of simulations.

<p>List of simulations.</p

Distributions of minimum distances between hydroxyl groups of different Thr residues for all three or five simulations.

<p>Distributions of minimum distances between hydroxyl groups of different Thr residues for all three or five simulations.</p

Distances between the center of mass (COM) of TmAFP and its initial COM in the z-direction as a function of time.

<p>Since five simulations were performed for each force field, five values are represented with different colors, where black, red, green, blue, and yellow lines respectively correspond to systems 1, 2, 3, 4, and 5 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198887#pone.0198887.g002" target="_blank">Fig 2</a>.</p

Structures, dynamics, and hydrogen-bond interactions of antifreeze proteins in TIP4P/Ice water and their dependence on force fields - Fig 1

<p>Snapshots from the beginning (0 ns, left) to the end (120 ns, right) for the simulation of TmAFP in water. Green ribbons and blue lines respectively represent the backbone and Thr residues of TmAFP, while oxygen and hydrogen atoms of water are represented as red and white dots, respectively. TmAFP and the surrounding water (or ice) region are magnified (top), and the side and bottom views of TmAFP are depicted (bottom). The images were created using Visual Molecular Dynamics [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198887#pone.0198887.ref056" target="_blank">56</a>].</p

Diffusion coefficients (<i>D</i>) of TmAFP at the beginning (0~30 ns) and end (90~120 ns) of simulations.

<p>Error bars on points are obtained from standard errors of five <i>D</i> values from five simulations.</p

Average lifetimes of hydrogen bonds between ice-water interfaces and Thr residues on the ice-binding sites of TmAFP, TmAFP-m1, TmAFP-m2, and TmAFP-m3.

<p>Average lifetimes of hydrogen bonds between ice-water interfaces and Thr residues on the ice-binding sites of TmAFP, TmAFP-m1, TmAFP-m2, and TmAFP-m3.</p

Secondary structures (%) of TmAFP.

<p>Secondary structures (%) of TmAFP.</p