A coarse-grained molecular dynamics study on primary ciliary dyskinesia-related protein dynein axonemal intermediate chain 1 (DNAI1)

Abstract

Primary ciliary dyskinesia (PCD) is a rare heterogeneous genetic disorder resulting from impaired axonemal protein structures and function in cilia. Some PCD-related mutations locate on the DNAI1 gene. It codes for the dynein axonemal intermediate chain 1 (DNAI1) protein. Mutations in DNAI1 are reported to cause loss of axonemal outer dynein arm (ODA), hence, an immotile cilium. This study computationally predicted the structural and functional effects of mutations (G515S, A538T, and V408M) reported by clinical studies. Homology modeling and a 15-µs coarse-grained molecular dynamics (CGMD) simulation were employed. CGMD was done using GROMACS version 5.0.4. Biophysical properties such as principal component analysis (PCA), root-mean-squared deviation (RMSD), radius of gyration (Rg), and B-factor were analyzed. PCA revealed that V408M’s global motion is entirely different. It is hypothesized that this is due to the mutation site being both part of a conserved block and a WD domain. Also, relative RMSD and Rg are not significantly different making these values insufficient to infer ciliary immotility. B-factor analysis, however, reveals that mutants became highly fluctuating. Interestingly, sites near the mutation became less fluctuating than in the wild-type, while causing higher fluctuations in regions of the N (residues 100-300) and C termini (residues 301-699). A portion of the N terminus, residues 261-298, is reported to code for an LC7 binding site. LC7 is found in Chlamydomonas reinhardtii’s ODA, and functions as a protein carrier during assembly of axonemal structures. LC7 homologs in humans are identified as DNCL2A and DNCL2B, which are discovered to associate with the sperm flagellum. Moreover, the C-terminus is known as heavy chain (HC) binding site. HCs are the force-generating components of dynein arms. It is surmised that these highly fluctuating regions may reduce the DNAI1’s binding affinity for the two proteins; hence, nondeliverance of the DNAI1 to the developing cilium, or absence of force-generating components. These may then explain loss of outer dynein arms resulting in an immotile cilium.