Theoretical design of a new chimeric protein for the treatment of breast cancer

Meysam Soleimani, Karim Mahnam, Hamid Mirmohammad-Sadeghi, Hojjat Sadeghi-Aliabadi, Ali Jahanian-Najafabadi


p28 and NRC peptides are two anticancer peptides with various mechanisms have shown to be effective against breast cancer. Therefore, it seems that construction of a chimeric protein containing the two peptides might cause synergistic cytotoxic effects. However, since the two peptides bear opposite charges, production of a chimeric protein in which the two moieties do not intervene each other is difficult. In this study, our goal was to find a suitable peptide linker for the new chimeric protein in a manner that none of the peptides intervene the other’s function. We selected some linkers with different characteristics and lengths and created a small library of the chimeric proteins harboring these linkers. Homology modeling and molecular dynamic simulation revealed that (PA)5P and (EAAAK)3 linkers can separate the p28 and NRC peptides effectively. Thus, the chimeric protein linked with (PA)5P or (EAAAK)3 linkers might show synergistic and stronger anticancer effects than the separate peptide moieties because they could exert their cytotoxic effects freely which is not influenced by the other part.

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Siegel R, Ma J, Zou Z, Jemal A. Cancer statistics. CA Cancer J Clin. 2014;64:9-29.

DeSantis C, Ma J, Bryan L, Jemal A. Breast cancer statistics, 2013. CA Cancer J Clin. 2014;64:52-62.

Tan M, Lan KH, Yao J, Lu CH, Sun M, Neal CL, et al. Selective inhibition of ErbB2-overexpressing breast cancer in vivo by a novel TAT-based ErbB2-targeting signal transducers and activators of transcription 3-blocking peptide. Cancer Res. 2006;66:3764-3772.

Craik DJ, Fairlie DP, Liras S, Price D. The future of peptide-based drugs. Chem Biol Drug Des. 2013;81:136-147.

Thundimadathil J. Cancer treatment using peptides: current therapies and future prospects. J Amino Acids.2012,2012:ID 967347.

Punj V, Bhattacharyya S, Saint-Dic D, Vasu C, Cunningham EA, Graves J, et al. Bacterial cupredoxin azurin as an inducer of apoptosis and regression in human breast cancer. Oncogene. 2004;23:2367-2378.

Yamada T, Fialho AM, Punj V, Bratescu L, Gupta TK, Chakrabarty AM. Internalization of bacterial redox protein azurin in mammalian cells: entry domain and specificity. Cell Microbiol. 2005;7:1418-1431.

Taylor BN, Mehta RR, Yamada T, Lekmine F, Christov K, Chakrabarty AM, et al. Noncationic peptides obtained from azurin preferentially enter cancer cells. Cancer Res. 2009;69:537-546.

Hilchie AL, Doucette CD, Pinto DM, Patrzykat A, Douglas S, Hoskin DW. Pleurocidin-family cationic antimicrobial peptides are cytolytic for breast carcinoma cells and prevent growth of tumor xenografts. Breast Cancer Res. 2011;13:R102.

Morash MG, Douglas SE, Robotham A, Ridley CM, Gallant JW, Soanes KH. The zebrafish embryo as a tool for screening and characterizing pleurocidin host-defense peptides as anti-cancer agents. Dis Model Mech. 2011;4:622-633.

Chen X, Zaro JL, Shen WC. Fusion protein linkers: property, design and functionality. Adv Drug Deliv Rev. 2013;65:1357-1369.

Wriggers W, Chakravarty S, Jennings PA. Control of protein functional dynamics by peptide linkers. Biopolymers. 2005;80:736-746.

Klein JS, Jiang S, Galimidi RP, Keeffe JR, Bjorkman PJ. Design and characterization of structured protein linkers with differing flexibilities. Protein Eng Des Sel. 2014;27:325-330.

George RA, Heringa J. An analysis of protein domain linkers: their classification and role in protein folding. Protein Eng. 2002;15:871-879.

Zhao HL, Yao XQ, Xue C, Wang Y, Xiong XH, Liu ZM. Increasing the homogeneity, stability and activity of human serum albumin and interferon-alpha2b fusion protein by linker engineering. Protein Expr Purif. 2008;61:73-77.

Arai R, Ueda H, Kitayama A, Kamiya N, Nagamune T. Design of the linkers which effectively separate domains of a bifunctional fusion protein. Protein Eng. 2001;14:529-532.

Karplus M, Kuriyan J. Molecular dynamics and protein function. Proc Natl Acad Sci U S A.2005;102:6679-6685.

Mahnam K, Saffar B, Mobini-Dehkordi M, Fassihi A, Mohammadi A. Design of a novel metal bindingpeptide by molecular dynamics simulation to sequester Cu and Zn ions. Res Pharm Sci. 2014;9:69-82.

Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc. 2010;5:725-738.

Humphrey W, Dalke A, Schulten K. VMD: Visual molecular dynamics. J Mol Graph. 1996;14:33-38.

Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, et al. Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci. 2007;Chapter 2:Unit 29.

Eswar N, Eramian D, Webb B, Shen MY, Sali A. Protein structure modeling with MODELLER. Methods Mol Biol. 2008;426:145-159.

Lovell SC, Davis IW, Arendall WB3rd, de Bakker PI, Word JM, Prisant MG, et al. Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins. 2003;50:437-450.

Wiederstein M, Sippl MJ. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res. 2007;35:407-410.

Hooft RWW, Sander C, Vriend G. Objectively judging the quality of a protein structure from a Ramachandran plot. Comput Appl Biosci. 1997;13:425-430.

Pronk S, Pall S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics. 2013;29:845-854.

Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. GROMACS: fast, flexible, and free. J Comput Chem. 2005;26:1701-1718.

Darden T, York D, Pedersen L. Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. J Chem Phys. 1993;98:10089-10092.

Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys. 1984;81:3684-3690.

Hess B, Bekker H, Berendsen HJC, Fraaije JGEM. LINCS: A linear constraint solver for molecular simulations. J Comput Chem. 1997;18:1463-1472.

Chakravarty S, Godbole S, Zhang B, Berger S, Sanchez R. Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure. BMC Struct Biol. 2008;8:31.

Larsson P, Wallner B, Lindahl E, Elofsson A. Using multiple templates to improve quality of homology models in automated homology modeling. Protein Sci. 2008;17:990-1002.

Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23:2947-2948.

Karplus M, Kuriyan J. Molecular dynamics and protein function. Proc Natl Acad Sci U S A. 2005;102:6679-6685.

Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules. Nat Struct Biol. 2002;9:646-652.

Kumar S, Nussinov R. Close-range electrostatic interactions in proteins. Chembiochem. 2002;3:604-617.

Donald JE, Kulp DW, DeGrado WF. Salt bridges: geometrically specific, designable interactions. Proteins. 2011;79:898-915.

Barlow DJ, Thornton JM. Ion-pairs in proteins. J Mol Biol. 1983;168:867-885.

Holbrook JA, Tsodikov OV, Saecker RM, Record MT, Jr. Specific and non-specific interactions of integration host factor with DNA: thermodynamic evidence for disruption of multiple IHF surface salt-bridges coupled to DNA binding. J Mol Biol. 2001;310:379-401.

Ma L, Sundlass NK, Raines RT, Cui Q. Disruption and formation of surface salt bridges are coupled to DNA binding by the integration host factor: a computational analysis. Biochemistry. 2011;50: 266-275.

Williamson MP. The structure and function of proline-rich regions in proteins. Biochem J. 1994;297:249-260.

Boze H, Marlin T, Durand D, Perez J, Vernhet A, Canon F, et al. Proline-rich salivary proteins have extended conformations. Biophys J. 2010;99:656-665.

Saladino AC, Xu Y, Tang P. Homology modeling and molecular dynamics simulations of transmembrane domain structure of human neuronal nicotinic acetylcholine receptor. Biophys J.


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