pI as a Potential Factor Influencing Evolutionary Residue Selection and Structural Stability Among Junctional Adhesion Molecules

Abstract

ObjectiveJunctional adhesion molecules (JAMs) are a family of conserved proteins involved in immune regulation and cell adhesion. In this study, we investigate the evolutionary and structural dynamics among three paralogs in Homo sapiens, which share similar tertiary structures but differ in isoelectric points (pI) (JAM-B: 9.23, JAM-A: 8.09, JAM-C: 7.53). MethodsBy integrating residue conservation, partial correlation, network centrality, pathogenicity analyses, and evolutionary molecular dynamics in various pH (6.5-10.5) conditions, we explore how these proteins have functionally and evolutionary diversified. ResultsPartial correlation-conservation analysis identified JAM-B functions as an evolutionary hub. Network analyses further highlighted Lys and Cys residues in JAM-B as central evolutionary residues. Negatively charged and hydrophobic residues (Tyr, Val, Asp) were conserved at lower-pI (JAM-C). AlphaMissense profiling revealed that acidic->basic mutations exhibit significantly lower pathogenicity scores, particularly in JAM-A and JAM-B. In dynamics simulations, root-mean-square-deviation (RMSD) profiles revealed a pI-stability relationship: JAM-B, the highest-pI paralog, remained stable across pH levels, while JAM-A and JAM-C displayed V-shaped pH-dependent deviations (JAM-A at pH 8.0, JAM-C at pH 8.5). Dynamics-aware evolutionary analyses identified key residues combining high evolutionary conservation with pH-sensitive fluctuations: JAM-A at Gln66, JAM-B at Gln36 and Val57, and JAM-C at several basic residues (Lys97, Arg108, Arg123, Arg191). ConclusionTogether, these results demonstrate that pI is influencing evolutionary residue selection and pH-dependent structural dynamics. Our integrated evolutionary-dynamics framework provides mechanistic insight into paralog diversification and offering a foundation for targeted mutagenesis or therapeutic modulation of pH-sensitive adhesion processes.