SLC4A11 Three-Dimensional Homology Model Rationalizes Corneal Dystrophy-Causing Mutations

Abstract

We studied the structural effects of point mutations of a membrane protein that cause genetic disease. SLC4A11 is a membrane transport protein (OH /H /NH /H O) of basolateral corneal endothelium, whose mutations cause some cases of congenital hereditary endothelial dystrophy and Fuchs endothelial corneal dystrophy. We created a three-dimensional homology model of SLC4A11 membrane domain, using Band 3 (SLC4A1) crystal structure as template. The homology model was assessed in silico and by analysis of mutants designed on the basis of the model. Catalytic pathway mutants p.Glu675Gln, p.His724Arg, and p.His724Ala impaired SLC4A11 transport. p.Ala720Leu, in a region of extended structure of the proposed translocation pore, failed to mature to the cell surface. p.Gly509Lys, located in an open region at the core domain/gate domain interface, had wild-type level of transport function. The molecular phenotype of 37 corneal dystrophy-causing point mutants was rationalized, based on their location in the homology model. Four map to the substrate translocation pathway, 25 to regions of close transmembrane helix packing, three to the dimeric interface, and five lie in extramembraneous loops. The model provides a view of the spectrum of effects of disease mutations on membrane protein structure and provides a tool to analyze pathogenicity of additional newly discovered SLC4A11 mutants.

Molecular phenotype of SLC4A11 missense mutants: Setting the stage for personalized medicine in corneal dystrophies

“…What patterns emerge when examining the molecular phenotypes of 54 corneal dystrophy‐causing SLC4A11 point mutants (Figures and )? The topology model (Figure ) illustrates the folding of SLC4A11 on the basis of structural homology with the SLC4 protein family member AE1 (SLC4A1, Band 3) (Arakawa et al., ; Badior et al., ). Strikingly, intracellular‐retained mutants are enriched in the plane of the lipid bilayer (20 out of 27), whereas outside the bilayer only six out of 22 cause ER retention (Figure A).…”

“…Molecular phenotype of SLC4A11 mutants mapped onto topology model. Topology model of SLC4A11 based on SLC4A11 homology model (Badior et al., ). Boxes represent transmembrane segment and each circle represent one SLC4A11 amino acid whose single letter code is indicated.…”

“…SLC4A11 is a two‐domain protein, with a 374 amino acid cytoplasmic domain and a 517 amino acid membrane domain (Vilas, Morgan, Loganathan, Quon, & Casey, ). A homology model for SLC4A11 membrane domain (Badior, Alka, & Casey, ), on the basis of the SLC4A1 crystal structure (Arakawa et al., ), predicts the membrane domain to have 14 transmembrane segments. SLC4A11 is a member of the SLC4 family of bicarbonate transport proteins (Alka & Casey, ).…”

“…SLC4A11 is a member of the SLC4 family of bicarbonate transport proteins (Alka & Casey, ). The crystal structure for SLC4A1 (Band 3/ AE1) provides a model for the folding of other SLC4 members, which was used to develop a homology model for SLC4A11 (Badior et al., ). Although other SLC4 proteins are bicarbonate transporters, there is no evidence that SLC4A11 has this role (Loganathan, Schneider, Morgan, Deitmer, & Casey, ).…”

“…The link between SLC4A11 and corneal dystrophy has been studied. Many SLC4A11 mutants, when heterologously expressed in HEK293 or Madin‐Darby canine kidney (MDCK) cells, are retained in the endoplasmic reticulum (ER), likely because of misfolding and recognition by ER quality control apparatus (Badior et al., ; Loganathan & Casey, ; Soumittra et al., ; Vithana et al., ; Vithana et al., ). Failure to reach the cell surface explains disease symptoms in this case.…”