Molecular models of Chionodraco hamatus IgM transmembrane region

Membrane-bound immunoglobulin M (IgM) participates to the assembly of the B cell receptor (BCR). IgM consists of two μ heavy chains crossing the cell membrane and two light chains. The μ chain region traversing the lipid bilayer (TM region) is highly conserved among species and contains a universal motif for antigen receptors that is important for BCR assembly and function. We analysed the TM region of Igμ from the Antarctic teleost Chionodraco hamatus, belonging to the Channichthyidae family. Its membrane μ chain is particularly interesting because generated by an unusual mRNA splicing mechanism. We determined the complete nucleotide sequence of C. hamatus membrane μ chain and analyzed the deduced amino acid sequence encoded by the TM exons. Using different computational methods, we predicted the length andthe polarity of the α-helical region crossing the cell membrane, and build a molecular model of the C. hamatus μ chain TM region, using the H helix of the photosynthetic reaction center of Rhodobacter sphaeroides as template. The stability of the model was investigated by molecular dynamics (MD) simulations. Models of a TM homodimer were also obtained by performing MD simulations using two copies of the helix, at a 14-16 Å distance between the centers of mass and in different orientations, as starting model. The obtained structures were related to the available experimental data collected on IgM TM region of different species.