OJGen  Vol.3 No.3 , September 2013
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 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.
Cite this paper: Mahgoub, E. and Bolad, A. (2013) Correctness and accuracy of template-based modeled single chain fragment variable (scFv) protein anti-breast cancer cell line (MCF-7). Open Journal of Genetics, 3, 183-194. doi: 10.4236/ojgen.2013.33021.

[1]   Chua, K.H., et al. (2006) Bioinformatics in molecular immunology laboratories demonstrated: Modeling an anti-CMV scFv antibody. Bioinformation, 1, 118-120.

[2]   Blundell, T.L. and Srinivasan, N. (1996) Symmetry, stability, and dynamics of multidomain and multicomponent protein systems. Proceedings of National Academy of Sciences of the USA, 93, 14243-14248. doi:10.1073/pnas.93.25.14243

[3]   Katchalski, K., Katzir, E., Shariv. I., et al. (1992) Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques. Proceedings of National Academy of Sciences of the USA, 89, 2195-2199.

[4]   Wu, S. and Zhang, Y. (2009) Chapter 11: Protein structure prediction. In: D. Edwards, et al., Eds., Bioinformatics: Tools and Applications, Springer Science+Business Media, LLC, Berlin, 225-242.

[5]   Janin, J., Henrick, K., Moult, J., et al. (2003) A critical assessment of predicted interactions. Proteins: Structure, Function, and Bioinformatics, 52, 2-9. doi:10.1002/prot.10381

[6]   Ramachandran, G.N., Ramakrishnan, C. and Sasisekharan, V. (1963) Stereochemistry of polypeptide chain configurations. Journal of Molecular Biology, 7, 95-99. doi:10.1016/S0022-2836(63)80023-6

[7]   Eisenberg, D., Lüthy, R. and Bowie, J.U. (1997) VERIFY3D: Assessment of protein models with three-dimensional profile. Methods in Enzymology, 277, 396-404. doi:10.1016/S0076-6879(97)77022-8

[8]   Sanchez, R. and Sali, A. (1998) Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proceedings of National Academy of Sciences of the USA, 95, 13597-13602. doi:10.1073/pnas.95.23.13597

[9]   Dlakic, M. (2002) A model of the replication fork blocking protein Fob1p based on the catalytic core domain of retroviral integrates protein. Protein Science, 11, 1274-1277.

[10]   Marti-Renom, M.A., Stuart, A.C., Fiser, A., et al. (2000) Comparative protein structure modeling of genes and genomes. Annual Review of Biophysics and Biomolecular Structure, 29, 291-325. doi:10.1146/annurev.biophys.29.1.291

[11]   Madhusudhan, M.S., et al. (2006) Variable gap penalty for protein sequence-structure alignment. Protein Engineering, Design and Selection, 19, 129-133. doi:10.1093/protein/gzj005

[12]   Sanchez, R., Pieper, U., Melo, F., et al. (2000) Protein structure modeling for structural genomics. Nature Structural Biology, 7, 986-990.

[13]   Colovos, C. and Yeates, T.O. (1993) Verification of protein structures: Patterns of non-bonded atomic interactions. Protein Science, 2, 1511-1519. doi:10.1002/pro.5560020916

[14]   Hatem, R., Pierre, B., Elie, E., et al. (2005) Structural and functional analysis of the C-terminal STAS (sulfate transporter and anti-sigma antagonist) domain of the Arabidopsis thaliana sulfate transporter SULTR. The Journal of Biological Chemistry, 280, 15976-15983.

[15]   Fiser, A., Sanchez, R., Melo, F., et al. (2001) Comparative protein structure modeling. In: Becker, O.M., Ed., Computational Biochemistry and Biophysics, Marcel Dekker, New York, 275-312.

[16]   Bowie, J.U., Luthy, R. and Eisenberg, D. (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science, 253, 164-170. doi:10.1126/science.1853201

[17]   Lüthy, R., Bowie, J.U. and Eisenberg, D. (1992) Assessment of protein models with three-dimensional profiles. Nature, 356, 83-85. doi:10.1038/356083a0

[18]   Tyndall, D.A., Linda, A., Fothergill-Gilmore, P., et al. (2000) Crystal structure of a thermostable lipase from Bacillus stearohermophilus P1. Journal of Molecular Biology, 323, 859-869.

[19]   Bernstein, F.C., Koetzle, T.F., Williams, J.B., et al. (1977) Protein data bank: A computer-based archival file for macromolecular structures. Journal of Molecular Biology, 112, 535-542. doi:10.1016/S0022-2836(77)80200-3

[20]   DeBartolo, J., Colubri, A., Jha, A.K., et al. (2009) Mimicking the folding pathway to improve homology free protein structure prediction. Proceedings of National Academy of Sciences of the USA, 106, 3734-3739.

[21]   Laskowski, R.A., Moss, D.S. and Thornton, J.M. (1993) Main-chain bond lengths and bond angles in protein structures. Journal of Molecular Biology, 231, 1049-1067.

[22]   Vriend, G. (1990) WHATIF: A molecular modeling and drug design program. Journal of Molecular Graphics, 8, 52-56. doi:10.1016/0263-7855(90)80070-V

[23]   Ryan, D., Xiaotao, Q., Rosemarie, S., et al. (2011) Relative packing groups in template-based structure prediction: Cooperative effects of true positive constraints. Journal of Computational Biology, 18, 17-26.