1. BL5203 Molecular Recognition & Interaction Section D: Molecular Modeling. Chen Yu Zong Department of Computational Science National University of Singapore Singapore 119260

2. Second Part Computer modeling of molecular interaction.

3. Forces Involved in Molecular Interactions More info on the web More info on the web –Bond stretch –Bond angle bending –Torsion (bond rotation) –Hydrogen bonding –van der Waals interactions –Electrostatic interactions –Empirical solvation free energy V =  bond 1/2K b (r-r eq ) 2 + Sangle ½ K  (  -  eq ) 2 +  torsions 1/2 V n [ 1 + cos(n  -  ') ] +  H bonds [ V 0 (1-e -a(r-r0) ) 2 - V 0 ] +  non bonded [ A ij /r ij 12 - B ij /r ij 6 + q i q j /  r r ij ] +  atoms i  i A i

4. Conformation optimization for molecular interaction Molecular Mechanics Approach:

5. Other Approaches: Molecular dynamics. Time-dependent motion trajectory based on laws of classical physics. Advantage: "Accurate" dynamics. Disadvantage: Short-time event only. Application: "All purpose", most widely used approach. Curr. Opin. Struct. Biol. 6, 232 (1996).

6. Other Approaches: Stochastic Dynamics. Solvent represented by frictional and stochastic forces. Advantage: Large scale motions, simplified treatment. Disadvantage: Limited applicability. Application: Protein transport, Domain motion, side-chain swing. Ann. Rev. Biochem 53, 263 (1983)

7. Other Approaches: Simplified Model Dynamics. Simplified structure or forces (e.g. HP lattice, spin glass model). Advantage: Long time and large scale dynamics. Disadvantage: Loss of important features. Application: Protein folding, mechanical models, solitons. Proc. Natl. Acad. Sci. USA 90, 1942 (1993); 89, 4918 (1992)

8. Other Approaches: Energy Landscape Along Motion Pathways. Generation of motion pathways by bond rotations. Molecular mechanics energy analysis. Advantage: Complete motion trajectories. Disadvantage: Limited to “straightforward” motions. Application: DNA base opening, base flipping motions. Phys. Rev. EPhys. Rev. E62, 1133-1137 (2000).

9. Molecular Dynamics: Basic Assumptions: Atoms interact with each other by empirical forces. Their motions governed by Newton's law.

10. Molecular Dynamics: Basic Equations: Forces = bond stretch + angle bending + torsion angle distortion + hydrogen bonding + van de Waals + electrostatic forces + hydrophobic + other solvent interactions Newton's law: Forces = mass x acceleration (F=ma)

11. Molecular Dynamics: Initial conditions at time t: r(t), v(t-dt/2) Atomic trajectory at t+dt: a(t) = F(r(t))/m v(t+dt/2) = v(t-dt/2) + a(t) dt r(t+dt) = r(t) + v(t+dt/2) dt

12. Simulation of open "back door" in acetylcholinesterase: Science 263, 1276 (1994) Why interested in this protein? Key role in signal control in nervous system. Target of Chinese natural product (Qian Ceng Ta). Nature Struct. Biol. 4, 57-62 (1997)

13. Simulation of open "back door" in acetylcholinesterase: Science 263, 1276 (1994) Special features: Active site is in a deep and narrow gorge. Strong electrostatic force attracts substrate into the gorge.

14. Simulation of open "back door" in acetylcholinesterase: Science 263, 1276 (1994) Question: How can a substrate and water escape from the active site?

15. Pathways for Functionally Important Motions DNA base flipping mechanism: –Enzyme induced?. –Enzyme captures a transiently opened base? X-ray crystallogaphy: –Structural information on both end of pathway. –The intermediate path remains unclear Curr. Opin. Struct. Biol. 7, 103 (1997) Cell 82, 9 (1995)

16. Mechanism of base flipping Scenario I: Protein induced flipping? Major groove blocked by enzyme, minor groove pathway? May explain why flipped base orients towards minor groove.. Cell 76, 357-369 (1994) Cell 82, 9-12 (1995)

17. Mechanism of base flipping Scenario II: Enzyme recognises and traps a transiently flipped base? Structure 2, 79 (1994). Base pair life time comparable to methyltransferase reaction time. All modelling studies consistently show base opens via major groove, yet to show how minor groove opening is possible. Proc. Natl. Acad. Sci. USA. 85, 7231 (1988) J. Biomol. Struct. Dyn. 15, 765 (1998)

18. Objective: –Major groove or minor groove pathway? Enzyme-captured or enzyme-induced flipping? Flipping motion and pathway modelling: –Identification of key rotatable bonds whose motions constructive to flipping. –Modelling of collective rotations of all bonds. Energy cost of motion. –Energy barrier along pathway computed by standard force fields. Testing Scenarios by Molecular Modelling

19. Modelling Strategy Phys. Rev. EPhys. Rev. E62, 1133-1137 (2000).

20. Modelling Strategy

21. Modelling Results on DNA Base Flipping

22. Energy Barrier for Base Flipping Phys. Rev. EPhys. Rev. E62, 1133-1137 (2000).

23. Maximum Extent of Base Flipping Along Both Grooves System NDB ID Flipped D major d minor Base (A) (A) Hhal Mtase GATAGCGCTATC PDEB08C1811.894.87 HhaI MTase CCATGCGCTGAC PDEB123C1812.253.23 Hhal Mtase GTCAGCGCATGG PD0017A1811.374.42 HeaIII Mtase ACCAGCAGGCCACCAGTG PDEB19C1012.011.23 B-form CCGGCGGCCGG BDL039C512.132.13 B-form CGCGAATTCGCG BDL001A514.171.47 B-form ACCGGCGCACA BDL035 C7 12.18 2.02 Phys. Rev. EPhys. Rev. E62, 1133-1137 (2000).