New insights into the pathogenicity of TMEM165 variants using structural modeling based on AlphaFold 2 predictions

Area of Science:

• Biochemistry
• Structural Biology
• Genetics

Background:

• TMEM165 is a Golgi protein essential for manganese (Mn2+) transport, vital for glycosylation enzymes.
• Mutations in TMEM165 lead to Congenital Disorders of Glycosylation (CDG), impacting patient health.
• Previous topology predictions failed to clarify TMEM165 structure and mutation effects.

Purpose of the Study:

• To elucidate the 3D structure of TMEM165 using advanced modeling techniques.
• To understand how patient-derived and experimental mutations affect TMEM165 function.
• To provide a structural basis for Mn2+ transport and its role in glycosylation.

Main Methods:

• Utilized AlphaFold 2 for initial TMEM165 model construction.
• Refined the model using molecular dynamics simulations with lipids and water.
• Analyzed the structural impact of conserved motifs and specific mutations, like G>R304.

Main Results:

• Developed a refined 3D model of TMEM165 revealing a two-fold repeat structure.
• Identified a putative Mn2+ binding site formed by conserved motifs on the cytosolic side.
• Explained the functional impact of the G>R304 mutation and other mutations on TMEM165 transport.

Conclusions:

• The 3D TMEM165 model offers insights into Mn2+ transport mechanisms and CDG pathogenesis.
• Structural understanding aids in explaining mutation effects on TMEM165 function.
• The model provides a basis for comparing TMEM165 with related transporters in the CaCA2/UPF0016 family and LysE superfamily.