A Computational Approach to Characterize the Protein S-Mer Tyrosine Kinase (PROS1-MERTK) Protein-Protein Interaction Dynamics

Abstract Protein S (PROS1) has recently been identified as a ligand for the TAM receptor MERTK, influencing immune response and cell survival. The PROS1–MERTK interaction plays a role in cancer progression, promoting immune evasion and metastasis in multiple cancers by fostering a tumor-supportive microenvironment. Despite its importance, limited structural insights into this interaction underscore the need for computational studies to explore their binding dynamics, potentially guiding targeted therapies. In this study, we investigated the PROS1–MERTK interaction using advanced computational analyses to support immunotherapy research. High-resolution structural models from ColabFold, an AlphaFold2 adaptation, provided a baseline structure, allowing us to examine the PROS1–MERTK interface with ChimeraX and map residue interactions through Van der Waals criteria. Molecular dynamics (MD) simulations were conducted in GROMACS over 100 ns to assess stability and conformational changes using RMSD, RMSF, and radius of gyration ( R g). The PROS1–MERTK interface was predicted to contain a heterogeneous mix of amino acid contacts, with lysine and leucine as frequent participants. MD simulations demonstrated prominent early structural shifts, stabilizing after approximately 50 ns with small conformational shifts occurring as the simulation completed. In addition, there are various regions in each protein that are predicted to have greater conformational fluctuations as compared to others, which may represent attractive areas to target to halt the progression of the interaction. These insights deepen our understanding of the PROS1–MERTK interaction role in immune modulation and tumor progression, unveiling potential targets for cancer immunotherapy.