Computational protocol: Revisiting antibody modeling assessment for CDR-H3 loop

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[…] Our CDR-H3 loop target sequence is A(H93)R(H94)G(H95)R(H96)L(H97)R(H98)R(H99)G(H100)G(H100a)Y(H100b)F(H100c)D(H101)Y(H102) from the monoclonal antibody A52, where the characters in parentheses are the residue numbers by Chothia's scheme (; ) and by North's CDR definition (). The crystal structure of A52 (PDBID 4m61, ), which contains two similar Fab domains, was obtained from the Protein Data Bank (), and the Fab domain of chains A and B was used for modeling. The initial structure of the CDR-H3 loop was taken from our previous model (), which had been built with the MODELLER program (), followed by energy minimization with the myPresto/cosgene program (). This structure, named joaAb10m3.pdb, is available at the AMA-II Web site (http://www.3dabmod.com). The other part of the antibody structure was exactly the same as the X-ray crystal structure. The rest of the Fab domain other than the Fv domain was deleted, in order to reduce the computational costs. The dangling bonds corresponding to the C-termini of the heavy and light chains were capped by N-methyl groups. After modeling, the system consisted of 232 residues, GluH1-SerH113 (total 120 residues) in the heavy chain and AsnL1-LysL107 (total 112 residues) in the light chain. The residue IDs are indicated by Chothia's definition, and the total residue numbers are described in parentheses. A rectangular water box with dimensions of 54 × 61 × 67 Å3 was placed around the antibody. Sodium and chloride ions were added to neutralize the system and to achieve a physiological concentration (100 mM). The final system consisted of 20 265 atoms (3547 antibody atoms, 5 sodium ions, 15 chloride ions, and 5566 TIP3P water molecules). The force field parameters for the antibody, ions, and water molecules were derived from the AMBER ff99SB force field (; ), the halide monovalent ion parameters (), and the flexible TIP3P water model (), respectively. The 500 steps of conjugated gradient energy minimizations (i) with positional restraints on the heavy atoms of the solute using a force constant of 1.0 kcal / (mol Å2), (ii) with positional restraints on the backbone heavy atoms of the solute using a force constant of 1.0 kcal / (mol Å2), and (iii) without restraints, were executed sequentially. Next, the system was equilibrated for 500 ps by Berendsen's NPT (constant Number of particles, Pressure and Temperature) algorithm () at 300 K and 1bar, using the Particle Mesh Ewald method () with a damping factor α = 0.35 Å−1 for the electrostatic interactions and a time step of 0.5 fs. Here, the positions of the heavy atoms of the antibody were restrained with a force constant of 1.0 kcal / (mol Å2). After the NPT simulation, the cell dimensions were equilibrated to 51.4 × 59.6 × 63.9 Å3. The myPresto/cosgene program () was used for the energy minimizations and the NPT simulation. […]

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