TITLE:
Correctness and accuracy of template-based modeled single chain fragment variable (scFv) protein anti-breast cancer cell line (MCF-7)
AUTHORS:
Elham O. Mahgoub, Ahmed Bolad
KEYWORDS:
Single Chain Fragment Variable; Homology Modeling; SWISS-MODEL; Insight II; Model
JOURNAL NAME:
Open Journal of Genetics,
Vol.3 No.3,
August
28,
2013
ABSTRACT: Multiple sequence alignments
can be used in the template-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 databases, 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 template-based structures
are enhanced by using the evaluation methods Verify3D, ERRAT and Ramchandran
plotting, which measure the error in the residues. In the results, 100% of the
light-chain residues 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 evaluation method showed large numbers of residues in the favoured areas in both
chains; these findings demonstrated that all of the chosen templates were the
best candidates.