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Dryad

Data for: Molecular docking simulation of FMP or N-FMP and FAPα

Data files

Apr 11, 2023 version files 4.97 MB

Abstract

The data proves that a longer self-immolative linker of FMP improves the probe responsivity toward FAPα. To uncover the underlying mechanism, theoretical molecular docking simulation is further carried out to elucidate the different FAPα responsivity towards FMP and N-FMP by MolAICal 1.3. The X-ray crystal structure of FAPα from the Protein Data Bank (PDB code 1Z68) is used. 3D structures of FMP and N-FMP are obtained and energetically optimized by a ChemDraw 3D software. After molecular docking, FMP presents a strong hydrogen bond between the peptide substrate of the probe and FAPα residues at the site of Val540, Ser548, Gln547, Gly542, and Ser546 in the active pocket. By contrast, N-FMP shows relatively weak hydrogen bond interaction with only one site of FAPα at the Gln547 residue in the active pocket. The theoretical simulations indicate that the higher affinity of FAPα towards FMP and thus promotes the enzymatic cleavage efficiency relative to N-FMP, which is consistent well with the experimental results. Therefore, both theoretical simulations and experimental results confirm that FMP with the longer self-immolative linker has superior enzymatic kinetics for FAPα.