2D-NMR and molecular dynamics analysis of the Torpedo californica acetylcholine receptor alpha 67-76 fragment and of its [Ala76]-analogue.

The alpha 67-76 fragment (Trp67-Asn68-Pro69-Ala70-Asp71-Tyr72 -Gly73-Gly74- Ile75-Lys76) of the Torpedo californica acetylcholine receptor (AChR) is selectively recognized by antibodies against the main immunogenic region of the AChR. The antibody binding capacity of its [Ala76]-analogue is usually higher than that of the natural fragment. A conformational analysis of these two decapeptides has been carried out in Me2SO by 2D-NMR and molecular dynamics using the SYBYL and BIOGROMOS programs. The natural sequence presents the most numerous and strongest NOE connectivities and is accordingly less flexible than the [Ala76]-analogue. Due to the flexible orientation of the side chains in both peptides, the NOE backbone side chain and side chain-side chain connectivities have not been introduced as distance constraints in the molecular dynamics calculations. It appeared that the N-terminal heptapeptide in both sequences assumes two very similar folded conformations, whereas the Ala substitution induces conformational flexibility in the C-terminal tripeptide sequence. The most flexible [Ala76]-analogue is the most tightly bound to the monoclonal mAb6 anti-AChR antibody, and the transferred NOEs from the bound to the free peptide in D2O reveal some similarity with the intrinsic NOEs for the free natural sequence in Me2SO, suggesting that the bound conformation of the [Ala76]-analogue could not be very different from that of the free natural fragment.