MOESM2 of Structure and application of antifreeze proteins from Antarctic bacteria

Additional file 2: Figure S2. Ramachandran plot analysis of the dihedral angles PSI (ψ) and PHI (ɸ) of the generated models for (a) afp5A, (b) gu3A and (c) gu3B obtained by RAMPAGE. The three plots show favorable positioning of amino acids for the different models generated

MOESM1 of Structure and application of antifreeze proteins from Antarctic bacteria

Additional file 1: Figure S1. Multiple sequence alignment between the DUF3494 domains of the identified antifreeze proteins gu3A, gu3B and afp5A. Asterisks (*) indicate positions with fully conserved residues; colons (:) indicate conservation of residues with strong similar properties; periods (.) indicate conservation of weakly similar residues. Alignment was performed using ClustalW

MM-GBSA Binding Free energy results.

<p>MM-GBSA Binding Free energy results.</p

Snapshots of the last conformation of Dendrimer- DNA complexes, taken at 180 ns of MD simulations.

<p>a) PAMAM-Arg and b) PAMAM-Lys.</p

Details of the molecular systems reported in this article.

<p>Details of the molecular systems reported in this article.</p

Time evolution of the radius of gyration (R_gyr) of DNA, dendrimer and the dendrimer-DNA complex for a) PAMAM-Lys and b) PAMAM-Arg.

<p>Time evolution of the radius of gyration (R_gyr) of DNA, dendrimer and the dendrimer-DNA complex for a) PAMAM-Lys and b) PAMAM-Arg.</p

Distance between center of mass (COM) of DNA and dendrimers as a function of time.

<p>PAMAM-Arg shows a shorter distance to DNA towards the end of MD simulations.</p

van der Waals interactions (expressed in percentages) established between each amino acid type and bases, sugar and phosphate DNA groups.

<p>Percentages were normalized considering the total number of van der Waals interactions found in protein-dsDNA complexes.</p

Contribution of each nitrogenous base to the interaction with Arginine/Lysine terminal groups of the dendrimers.

<p>100% corresponds to the total number of contacts established only with bases of DNA (not including interaction with sugar or phosphate groups).</p

Hydrogen-bond interactions (expressed in percentages) established between amino acid type and each DNA base (Adenine, Guanine, Cytosine, Thymine).

<p>Percentages were normalized considering the total number of hydrogen-bond interactions established only with bases found in protein-dsDNA complexes.</p