Correctness and accuracy of template-based modeled single chain fragment variable (scFv) protein anti-breast cancer cell line (MCF-7)

Abstract

Multiple sequence alignments can be used in the tem- plate-based modelling of protein structures to build fragment-based assembly models. Therefore, useful functional information on the 3D structure of the anti-MCF-7 scFv protein can be obtained using available bioinformatics tools. This paper utilises several commonly-used bioinformatics tools and da- tabases, including BLAST (Basic Local Alignment Search Tool), GenBank, PDB (Protein Data Bank), KABAT numbering and SWISS-MODEL, to gain specific functional insights into the anti-MCF-7 scFv protein and the assembly of single-chain fragment variable (scFv) antibodies, which consist of a variable heavy chain (VH) and a variable light chain (VL) connected by the linker (Gly4-Ser)3. The linker has been built as a loop structure using the Insight II software. The accuracy of the loop structure has been evaluated using Root Mean Square Deviation (RMSD). The accuracies of the VL and VH tem- plate-based structures are enhanced by using the evaluation methods Verify3D, ERRAT and Ram- chandran plotting, which measure the error in the residues. In the results, 100% of the light-chain resi- dues scored above 0.2, whereas 88.5% of the heavy- chain residues’ scored above 0.15 in the Verify3D evaluation method. Meanwhile, using ERRAT, the alignments of both chains scored more than 70% in space. Additionally, the Ramchandran plot evalua- tion method showed large numbers of residues in the favoured areas in both chains; these findings demon- strated that all of the chosen templates were the best candidates.