Disease-causing mutations in proteins: structural analysis of the CYP1B1 mutations causing primary congenital glaucoma in humans

Abstract

In this communication, we report an in-depth structure-based analysis of the human CYP1b1 protein carrying disease-causing mutations that are discovered in patients suffering from primary congenital glaucoma (PCG). The "wild-type" and the PCG mutant structures of the human CYP1b1 protein obtained from comparative modeling were subjected to long molecular dynamics simulations with an intention of studying the possible impact of these mutations on the protein structure and hence its function. Analysis of time evolution as well as time averaged values of various structural properties--especially of those of the functionally important regions: the heme binding region, substrate binding region, and substrate access channel--gave some insights into the possible structural characteristics of the disease mutant and the wild-type forms of the protein. In a nutshell, compared to the wild-type the core regions in the mutant structures are associated with subtle but significant changes, and the functionally important regions seem to adopt such structures that are not conducive for the wild-type-like functionality.

FIGURE 1

Sequence alignment of CYP1b1 (residues 50–527) with 1OG2 template (residues 30–490). The α-helices (boxed regions) are named in alphabetical order (A–L). The β-strands (boxed regions) are named using the sheet number (S1–S5) in which they occur followed by the strand number. The CHR and HBL regions are also represented by boxed regions. The nomenclature for secondary structures was adopted from the nomenclature generally followed in CYP1b1 literature especially from Akarsu et al. (4). Minor helices are indicated with a prime (A′, B′, F′, G′, and K′).

FIGURE 2

Trajectories of the overall Cα RMSDs (in angstroms) (black line) of the WT and MT structures with respect to the starting structure over 30,000 ps MD simulation. The x axis represents the simulation time in picoseconds. The y axis represents RMSD in angstrom units. Gray lines indicate the Cα RMSD trajectories calculated for only the secondary structures. This figure was prepared using XMGRACE (50) (http://plasmagate.weizmann.ac.il/Grace).

FIGURE 3

Residue-wise RMSF (in angstroms) profiles of Cα atoms of the WT and MT structures computed after stabilization of the RMSD trajectories. The x axis represents the residue number. The y axis represents RMSF in angstrom units. The bars at the bottom of the figure indicate the location of α-helices (black) and β-strands (gray). This figure was prepared using XMGRACE.