Molecular modeling and scFv78-TEM1 docking

Amino acid sequences of TEM1 and scFv78 were each taken as query sequences for similarity search against the Protein Data Bank (PDB) at www.pdb.org [23]. Similarity searches were performed using FASTA in an effort to identify homologous proteins of known structure for use as structure templates for model construction [24]. Structure-based sequence alignment between the template and the query sequences was generated using Molecular Operating Environment (MOE) software (Molecular Computing Group Inc. version 2011.10) with default parameters [25]. A 3D structural model of the query sequence was then created based on such alignment using the homology model tool in MOE. Docking of the 3D structural model of either human or murine TEM1 to the scFv78 structural model was performed using the protein–protein docking software ZDOCK (version2.3) [26]. Hydrogen atoms were removed from both structures, and the standard parameters from the uniCHARMM file were used for all atoms in both structures. ZDOCK searches all possible binding modes in the translational and rotational space between the two proteins and evaluates each position using an energy-based scoring function. The scoring function is composed of IFACE statistical potential, shape complementarity and electrostatics. The docking complex with the best fit with the experimental data was reported.