Objective: To investigate the distribution of antigenic sites in two human NR1a polypeptides related to activation of N-methyl-D-aspartate receptor (NMDAR) and their physicochemical properties.
Methods: The amino acid sequences of two polypeptides, P1, a region containing 151 amino acid residues preceding the first transmembrane domain of the human NR1a, and P2 with 144 residues following the third transmembrane domain, were obtained from protein database by GOLDKEY software (4.0 version). Four parameters including Hopp-Woods and Kyte hydrophilicity, Janin accessibility, Karplus-Schulz flexibility, and Welling antigenicity were used to determine the antigenic sites, and Prosite programme and Chou-Fasman method were employed to analyze their related sequence motifs and the secondary structures. Finally, comparison of the comprehensive predictions with some of the available experimental information was made.
Results: There were about six and seven antigenic sites containing 8 approximately 15 residues in the P1 and P2 polypeptides respectively. The antigenic sites in P1 were mainly located in the amino terminal, but the ones in P2 were dispersed rather uniformly. Many sites in P2 polypeptide including some residues in its initial part, the amino terminal, showed higher hydrophilicity, accessibility, and antigenicity than those in P1. In addition, P1 and P1 were also different in the primary and secondary structure. P1 contained more cysteine residues and was rich in random coils, while P2 contained more aromatic residues and exhibited mainly helical structures.
Conclusion: Both human NR1a polypeptides related to activation of NMDA receptor, P1 and P2, have a certain amount of antigenic sites. Compared with P1, P2 may be of higher antigenicity, and may be more easily used as a molecular target in immunization intervention to control the activation of NMDAR.