Molecular modeling of the C1q domain of otolin.

(A) The tertiary structures of Col10a1-C1q domain (green) and otolin-C1q domain (magenta) are nearly super-imposable. The modeled structure is consistent with the crystal structure of human COL10A1. Ca²⁺-binding residues are labeled and projected as sticks. (B) The surface of the otolin-C1q domain with temperature factors denoted in different colors. (C) Clustering of residues and the cationic surface of otolin-C1q domain. Residues are colored according to their electrical charges and hydrophobic nature. The nine key cationic residues are labeled and projected as sticks. (D) The protein backbone RMSD during 1ns simulation. After 400ps, the structure is stable. The 400–1000 ps range was used for computing the final structure. (E) The temperature factor (RMS fluctuation) of each residue. The residues with higher RMS fluctuation usually are exposed on molecule surface and may construct active sites. The Ca²⁺-binding residues in (A) are labeled.