Fig. 6
From: Novel pathogenic NPR2 variants in short stature patients and the therapeutic response to rhGH
Homology modeling and molecular dynamics simulation. (A) The three-dimensional structure was predicted by the HOPE online software. After the removal of the substrate, docking was carried out in standard docking mode. The figure displays an illustration of the protein (blue) and the ATP (stick model in wheat color). (B) Δ Vibrational Entropy Energy | Visual representation of variant: Amino acids are colored based on the vibrational entropy change of the variant. Blue represents a rigidification of structure. The red arrows point to a variant at position Leu527Phe. (C) The close-up view of the substrate binding pocket of ATP. (D) Binding pocket amino acid residue interaction patterns. The yellow dashed lines indicate hydrogen bonds between various amino acids in the binding pockets and ATP. The dotted burgundy line represents the salt bridge interaction. (D, E) Interaction prediction between amino acid residues: Wild-type and variant residues are represented as red sticks. These were placed alongside surrounding residues which were also involved in other types of interactions. Red arrows indicate altered intermolecular forces between amino acids. Hydrogen bonding is represented by a yellow dotted line. Hydrophobic bond interactions are represented as green dotted lines