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Molecular engineering of DNA-binding domains to recognise and modify cancer genomes

Molecular engineering of DNA-binding domains to recognise and modify cancer genomes. Yu Jie Kan Curtin University. Supervisors: Prof Ricardo L. Mancera, Curtin University, A/Prof Pilar Blancafort, UWA. Introduction.

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Molecular engineering of DNA-binding domains to recognise and modify cancer genomes

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  1. Molecular engineering of DNA-binding domains to recognise and modify cancer genomes Yu Jie KanCurtin University Supervisors: Prof Ricardo L. Mancera, Curtin University, A/Prof Pilar Blancafort, UWA.

  2. Introduction • Highly specific DNA-binding domains (DBDs) can be engineered and used for cancer gene sequence recognition. • DBDs can be used to improve selectivity and penetration of existing cancer drugs via conjugation. • Engineering of DBDs may be facilitated by molecular dynamics (MD) simulation. Reference: Chen, Y., et al. (2008) J. Bio Chem, 283(26), 17969-17978

  3. Aim • To predict the binding affinity of SOX2 to DNA in the presence of OCT4.

  4. Approach • MD simulations were run with Amber 12 in explicit solvent at 300K. • Two stage equilibration: 0.5 ns of heating and 0.5 ns of density equilibration followed by 9 ns production. • Ten repetitions.

  5. MM-PBSA/MM-GBSA Image obtained from : http://sf.anu.edu.au/~vvv900/amber-tutorial/1cgh-ligand/mm-pbsa.html

  6. MM-PBSA/MM-GBSA • ΔGBind = GAB - GA - GB • Individual GX = EMM + Gsolv - TSMM • EMM = Ebond + Eangle + Etors + Evdw + Eelec • Gsolv is the calculated solvation free energy • -TSMM is the solute entropy Reference: Hayes, Joseph M. and Georgios Archontis. (2012) Molecular dynamics. InTech, Rijeka, Kroatien.

  7. MM-PBSA/MM-GBSA • Gsolv is different for MM-PBSA and MM-GBSA: • Gsolv for MM-PBSA= EPB+ Enon-polar+ Edispersion • Gsolv for MM-GBSA = EGB+ Esurface Reference: Hayes, Joseph M. and Georgios Archontis. (2012) Molecular dynamics. InTech, Rijeka, Kroatien.

  8. Results

  9. Results

  10. Binding affinity of SOX2 Energies are in kcal/mol. • ΔG(GB)= -206.824 kcal/mol • ΔG(PB)= -114.502 kcal/mol • Electrostatic/solvation = Gsolv + EEL • MM-GBSA: -1.4 kcal/mol • MM-PBSA: 91 kcal/mol

  11. Binding affinity of SOX2 • VDW is the dominant interaction. • Electrostatic and solvation terms do not favour binding. • Entropy (not completed)

  12. Truncated SOX2 (iPep) • New MD simulations with truncated SOX2 protein.

  13. Average RMSD

  14. Future Work • Constrain iPep with respect to DNA. • Finalize entropy calculations.

  15. Conclusion • Interaction of SOX2 with DNA is dominated by VDW interactions. • MD simulations can be used to rationalize DBD designs.

  16. References Chen, Y., Shi, L., Zhang, L., Li, R., Liang, J., Yu, W., ... & Shang, Y. (2008). The molecular mechanism governing the oncogenic potential of SOX2 in breast cancer. Journal of Biological Chemistry, 283(26), 17969-17978. Hayes, Joseph M., and Georgios Archontis. (2012). "MM-GB (PB) SA calculations of protein-ligand binding free energies." Molecular dynamics–studies of synthetic and biological macromolecules. InTech, Rijeka, Kroatien. Reményi, A., Lins, K., Nissen, L. J., Reinbold, R., Schöler, H. R., & Wilmanns, M. (2003). Crystal structure of a POU/HMG/DNA ternary complex suggests differential assembly of Oct4 and Sox2 on two enhancers. Genes & development, 17(16), 2048-2059.

  17. Acknowledgements • iVEC • Curtin Biomolecular Modelling Group • Supervisors Prof Ricardo Mancera, Dr. Neha Gandhi and A/Prof Pilar Blancafort

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