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IRENE Conference
- 1. Industrial Strength QM/MM: Computa8onal high throughput screening of enzyme ac8vity in enzyme mutants Jan H. Jensen, Mar$n Hediger, Luca De Vico, Kasper Primdal, Allan Svendsen, Werner Besenma=er Department of Chemistry University of Copenhagen Slides at: h=p://Fnyurl.com/bsqbojf MarFn R. Hediger, Luca De Vico, Allan Svendsen, Werner Besenma=er, Jan H. Jensen “A ComputaFonal Methodology to Screen AcFviFes of Enzyme Variants” PLoS ONE, submi=ed. h=p://arxiv.org/abs/1203.2950
- 2. Slides at: h=p://Fnyurl.com/bsqbojf Industrial enzyme design High-‐through put screening of 100s of mutants IdenFfies promising candidates for further study ComputaFonal predicFon: Homology modeling QSAR (QM or QM/MM too slow and lacks automaFon) IdenFfies promising candidates for further study Further study: 20-‐50 mutants Goal Automated predicFon of barrier height for enzymaFc reacFon within 24 hr using < 10 cores IdenFfies promising candidates for further study
- 3. Methods PM6 implemented in Mopac2009 (MOZYME) Automated mutant builder (PYMOL) Barrier from adiabaFc mapping Applica$on Increase amidase acFvity in an estarase (CalB) MarFn R. Hediger, Luca De Vico, Allan Svendsen, Werner Besenma=er, Jan H. Jensen “A ComputaFonal Methodology to Screen AcFviFes of Enzyme Variants” PLoS ONE, submi=ed.
- 4. PM6 is good enough
- 5. PM6 and MOZYME MOZYME = PM6 computed with MOZYME PM6 = PM6//MOZYME MOZYMEReortho = MOZYME//MOZYME
- 6. PM6/MOZYME is fast enough 55 aa MOPAC2009 No parallelized
- 7. PM6/MOZYME is fast enough OpFmizaFon Single point
- 10. Future Direc$ons Whole protein COSMO solvaFon More automaFzaFon Be=er sampling Complete scan of single mutants Single -‐> double -‐> triple mutants PM6 in GAMESS Linear scaling PM6 PM6/PCM interface AlternaFves to adiabaFc mapping Beyond PM6: EFMO
- 11. Blurring the boundary between linear scaling QM, QM/MM and polarizable force fields The Effec@ve Fragment Molecular Orbital Method Jan H. Jensen, Casper Steinmann, Mikael Wistoi Ibsen, Kasper Thoie University of Copenhagen Dmitri Fedorov AIST, Japan Casper Steinmann, Dmitri G. Fedorov, and Jan H. Jensen “ The EffecFve Fragment Molecular Orbital Method: A Merger of the Fragment Molecular Orbital and EffecFve Fragment PotenFal Methods” Journal of Physical Chemistry A 2010, 114, 8705-‐8712 Casper Steinmann, Dmitri G. Fedorov, and Jan H. Jensen “ The EffecFve Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds” PLoS ONE, submi=ed. h=p://arxiv.org/abs/1202.4935 11
- 12. The Effec$ve Fragment Molecular Orbital (EFMO) method Using ideas from the EffecFve Fragment PotenFal (EFP) and the Fragment Molecular Orbital (FMO) method 12
- 13. The Effec$ve Fragment Molecular Orbital (EFMO) method (Using ideas from the EffecFve Fragment PotenFal (EFP) method) Monomer SCF in the gas phase Extract mulFpoles and dipole polarizability 13
- 14. The Effec$ve Fragment Molecular Orbital (EFMO) method (Using ideas from the EffecFve Fragment PotenFal (EFP) method) Many-‐body polariza$on Computed classically using induced dipoles for enFre system 14
- 15. The Effec$ve Fragment Molecular Orbital (EFMO) method (Using ideas from the EffecFve Fragment PotenFal (EFP) method) Coulomb and Non-‐Coulomb effects dimer SCF in the gas phase 15
- 16. The Effec$ve Fragment Molecular Orbital (EFMO) method (Using ideas from the EffecFve Fragment PotenFal (EFP) method) Coulomb effects Computed using staFc mulFpoles 16
- 17. MP2 (DFT doesn’t scale well) + 0 17
- 18. Covalent Fragmenta$on (ElectrostaFc screening crucial) 18
- 19. Implemented in GAMESS With gradients Trp cage (20 residues) 2 residues/fragment EFMO FMO2 Error in energy -‐4.3 6.4 kcal/mol MP2/6-‐31G(d) gradient 314 409 minutes 20 cores (most Fme spent in MP2 dimers) 19
- 20. QM/”MM” PCM Large parts of MM region oien frozen = Requires only monomer gas phase calculaFons for that region = Very fast 20
- 21. To Do Flexible EFP/Polarizable “Force Field” covalent dimers ∑ (E ) N E EFMO = ∑ EI0 + 0 IJ − EI0 − EJ − EIJ 0 POL I IJ ( ) N + ∑ EIJ + EIJ /CT + EIJ + Etot ES XR Disp POL IJ Important miscellanea EFMO GUI: FRAGIT (Mikael Ibsen) TS search algorithms (Kasper Thoie) 21
- 22. Funding: EU (IRENE collab program) Thank You! Ques$ons? Slides at: h=p://Fnyurl.com/bsqbojf 22