Research Paper Volume 12, Issue 4 pp 3516—3557

Adaptive selection in the evolution of programmed cell death-1 and its ligands in vertebrates

Figure 1. (A) Molecular structure of PD1 and Conserved domain analysis of PD1 protein. (B) Showing the MSA of the 20 most homologous proteins to PD1 (obtained with a BLAST+ search against the PDBAA database). Known secondary structure elements are displayed for all aligned sequences. Alternate residues are highlighted by gray. Identical and similar residues are boxed in red and yellow, respectively. (C) Location of positively selected amino acid sites identified PD1 conserved Ig domain. The crystal structure of human PD1 was used as a reference sequence and positively selected sites were drawn onto the crystal structure using Phyre tool (http://www.sbg.bio.ic.ac.uk/phyre2/html). Two residues identified under selection fall in the immunoglobulin-like domain containing the ligand-binding site. The sites which fall in the region identified as the ligand-binding site and another cluster in a region immediately following the signal sequence.