DOI: 10.5061/dryad.7wm37pvz4
title: Data for: Molecular docking simulation of FMP or N-FMP and FAPα

description: 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.
description: <strong>1.5 Docking Analysis</strong><strong>. </strong>The X-ray structure of FAPα (PDB code 1Z68) is obtained from the Protein following Data Bank (http://www.rcsb.org/pdb). 3D structures of FMP and N-FMP are obtained and energetically optimized by ChemDraw 3D software. The MolAICal software package is used to process and save FAPα, FMP, and N-FMP in PDBQT molecular format. FAPα is the definition of a crystal ligand in the active pocket of molecular docking. Take x = 39.84 Å, y = 0.221 Å, and z = 59.383 Å as the center coordinate of the FAPα active pocket box, and the size of the grid box is set to 30 Å. The detained operations are as follows: <strong>1.5.1 Software Requirement </strong> 1) MolAICal: https://molaical.github.io 2) UCSF Chimera: https://www.cgl.ucsf.edu/chimera <strong>1.5.2 Prepare the Receptor Protein</strong> The X-ray structure of FAPα (PDB code 1Z68) was obtained from the protein following data bank (http://www.rcsb.org/pdb). Save the file in 1Z68.pdb format. <strong>1.5.3 Prepare the Ligand Molecule</strong> 3D structures of FMP and N-FMP are obtained and energetically optimized by ChemDraw 3D software. FMP and N-FMP are saved in the format of FMP.pdb and N-FMP.pdb. using the MolAICal software. <strong>1.5.4 Convert the Receptor and Ligand to PDBQT Format</strong> The CD command is used to switch to the folder where the receptor and ligand are located, following using the following command to get the PDBQT format of the receptor and ligand: Receptor: #&gt; MolAICal-xxx\molaical.exe -dock receptor -i 1Z68.pdb Ligand: #&gt; MolAICal-xxx\molaical.exe -dock ligand -i FMP (or N-FMP).pdb MolAICal-xxx indicates the folder where the MolAICal software is stored. <strong>1.5.5 Determine Box Size and Center Through UCSF Chimera</strong> UCSF Chimera software is used to open the 1Z68.pdb and FMP (or N-FMP).pdb files. Using UCSF Chimera Software Tools: Tools--&gt; Surface/Binding Analysis--&gt; Autodock Vina In the dialog box, the receptor selects 1Z68.pdb and the ligand selects FMP (or N-FMP).pdb. Fill in "39.840, 0.221, 59.383" at the center coordinates, and fill in 30 for the box size. <strong>1.5.6 Prepare Configuration Files</strong> The final configuration file is set to: out = all.pdbqt cpu = 4 receptor = 1Z68.pdbqt center_x = 39.840 center_y = 0.221 center_z = 59.383 size_x = 30 size_y = 30 size_z = 30 num_modes = 10 Save the file as conf.txt <strong>1.5.7 Molecular Docking</strong> MolAICalD from MolAICal package is used for molecular docking of receptor and ligand: #&gt; MolAICal-xxx\molaicald --config conf.txt --ligand FMP (or N-FMP).pdbqt <strong>1.5.8 Result Processing</strong> At the end of the simulation, the results are split into individual molecules: #&gt; MolAICal-xxx\molaical.exe -tool pdbqt -i all.pdbqt -o ./ Individual molecules are named 1.pdbqt, 2.pdbqt, or 3.pdbqt, etc. 1.pdbqt, 2.pdbqt or 3.pdbqt can be checked directly through Pymol or UCSF Chimera software. The above operations are carried out in the window system using MolAICal and UCSF Chimera software.
description:  Software
 requirement 1) MolAICal: https://molaical.github.io 2) UCSF Chimera: https://www.cgl.ucsf.edu/chimera