iVEC Annual Symposium 2014
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.
iVEC Annual Symposium 2014
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
iVEC Annual Symposium 2014
Aim
• To predict the binding affinity of SOX2 to
DNA in the presence of OCT4.
iVEC Annual Symposium 2014
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.
iVEC Annual Symposium 2014
MM-PBSA/MM-GBSA
Image obtained from : http://sf.anu.edu.au/~vvv900/amber-tutorial/1cgh-ligand/mm-pbsa.html
iVEC Annual Symposium 2014
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.
iVEC Annual Symposium 2014
MM-PBSA/MM-GBSA
• Gsolv is different for MM-PBSA and MMGBSA:
• 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.
iVEC Annual Symposium 2014
Results
iVEC Annual Symposium 2014
Results
iVEC Annual Symposium 2014
Binding affinity of SOX2
Energy Component
VanderWaals (VDW)
Electrostatic (EEL)
EPB
EGB
Esurface
Enon-polar
Edispersion
Ggas (VDW+EEL)
Gsolvated
ΔG
MM-PBSA
Average
-205.5
-8324.7
8285
MM-GBSA
Average
-205.5
-8324.7
8348.1
-24.7
-132.7
263.4
-8530.2
8415.7
-114.5
-8530.2
8323.3
-206.824
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
iVEC Annual Symposium 2014
Binding affinity of SOX2
• VDW is the dominant interaction.
• Electrostatic and solvation terms do not
favour binding.
• Entropy (not completed)
iVEC Annual Symposium 2014
Truncated SOX2 (iPep)
• New MD simulations with truncated SOX2
protein.
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Average RMSD
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Future Work
• Constrain iPep
with respect to DNA.
• Finalize entropy calculations.
iVEC Annual Symposium 2014
Conclusion
• Interaction of SOX2 with DNA is dominated
by VDW interactions.
• MD simulations can be used to rationalize
DBD designs.
iVEC Annual Symposium 2014
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.
iVEC Annual Symposium 2014
Acknowledgements
• iVEC
• Curtin Biomolecular Modelling Group
• Supervisors Prof Ricardo Mancera, Dr. Neha
Gandhi and A/Prof Pilar Blancafort