Molecular modelling of novel ADCY3 variant predicts a molecular target for tackling obesity

Abstract

Severe early‑onset obesity is mainly attributed to single gene variations of the hypothalamic leptin‑melanocortin system, which is critical for controlling the balance between appetite and energy expenditure. Adenylate cyclase 3 (ADCY3), a transmembrane enzyme localized in primary neuronal cilia, is a key genetic candidate, which appears to have an essential role in regulating body weight. The present study aimed to identify ADCY3 genetic variants in severely obese young patients of Greek‑Cypriot origin by genomic sequencing. Apart from previously reported variants, the novel and probably pathogenic variant c.349T>A, causing a p.Leu117Met substitution within one of the two pseudo‑symmetric halves of the transmembrane part of the protein, was reported. Molecular modelling analysis used to delineate bonding interactions within the mutated protein structure strongly suggested a change in interactive forces and energy levels affecting the pseudo‑twofold symmetry of the transmembrane domain of the protein and probably its catalytic function. These results support the involvement of ADCY3 in the pathology of the disease and point towards the requirement of defining protein function and evaluating the clinical significance of the detected variants.

Keywords: ADCY3; body mass index; molecular modelling; obesity; variants.

Figure 1

Molecular modelling of ADCY3 in an explicit lipid bilayer, in an effort to depict the structural arrangement of ADCY3 in the membrane. The transmembrane and the outer membrane parts of ADCY3 are presented alongside the position of the amino acid position 117. Upper panel: Left, the wild-type ADCY3 model positioned in the lipid bilayer with all-atom representation; right, with ribbon representation. Middle panel: Bottom view of the positioned model of ADCY3 in the lipid bilayer. Lower panel: Left, bottom view of the wild-type ADCY3 model in the lipid bilayer (Leu117 shown in green space fill representation); right, bottom view of the mutant ADCY3 model (p.Leu117Met) in the lipid bilayer (Met117 displayed in orange space fill representation). ADCY3, adenylate cyclase 3.

Figure 2

Modelling of ADCY3 in the explicit lipid bilayer solvated in a water periodic box for the molecular dynamics simulations. (A) A cube-periodic box solvation system for the full molecular system (left) and the ADCY3 model positioned in the lipid bilayer (right). (B) Close-up view of the ADCY3 model and lipid bilayer solvated in the water periodic system during the molecular dynamics simulations. ADCY3, adenylate cyclase 3.

Figure 3

Identification of a probably pathogenic novel p.Leu117Met ADCY3 variant. The sequence electropherogram of the novel ADCY3 p.Leu117Met variant and the schematic representation of the ADCY3 gene and protein with the novel p.Leu117Met variant are displayed. ADCY3, adenylate cyclase 3.

Figure 4

Molecular modelling of wild-type ADCY3 (on the left) and the ADCY3 variant c.349T>A/p.Leu117Met. Upper panel: The wild-type ADCY3 model with Leu117. Lower panel: The mutant ADCY3 model with the p.Leu117Met substitution. Note the position of the 117 amino acid (in spacefill representation) and the difference between wild-type and mutant. The latter induces a slight bend to the middle of the α-helix where it is located. ADCY3, adenylate cyclase 3.

Figure 5

Molecular interactions 2D diagram. (A) 2D interaction diagram for the wild-type leucine residue at position 117 of the ADCY3 model. (B) 2D interaction diagram for the mutant methionine residue at position 117 of the ADCY3 model. Interactions are presented according to the conventions of the embedded interaction legend. ADCY3, adenylate cyclase 3.

Figure 6

Membrane topology of the adenylate cyclase 3 transmembrane protein determined using the Protter tool (https://wlab.ethz.ch/protter/start/). Mutations located in the coding region are indicated, including the p.Ile117Met mutation identified in the present study.