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Real Space Structural Real Space Structural Refinement Refinement in EMin EM
Houston Workshop
April 20, 2006
James Z. ChenJames Z. ChenGrigorieff Lab, HHMI at Brandeis University
Topics
Model-density docking
Ligand-receptor docking
Force-field-restrained EM docking
Application demo
Model-Density Docking
SITUS [Wriggers et al., 1999]
COAN [Volkmann & Hanein, 1999]
DOCKEM [Roseman, 2000]
EMFit [Rossmann et al., 2001]
Helixhunter & Foldhunter [Jiang et al., 2001]
RSRef [Chapman, 1995]
Ligand-Receptor Docking
Molecular Mechanics Force FieldsBond, angle, dihedral interactions
VDW, Coulomb, H-bond interactions
Environmental mean-fields
Molecular Interaction SimulationX-PLOR [Brünger, 1987]
DOCK and AutoDOCK [Olson et al., 1990]
VMD, FlexDock, FT-DOCK, and many more
Docking in EM
Why force-fieldsReduce DOF in low-resolution EM density map
Density matching ≠ realistic structure
Molecular complex modelingProtein-ligand docking prediction (CAPRI)
Density-guided homology modelingProtein folding prediction (CASP)
RSRef Methodology
( )2∑ −+=⊕atoms
calcobs bkE ρρ
**
*2**
2)2sin()(4)(
*
*
ddrd
rdddgQrhigh
low
d
dcalc π
ππρ ∫=
A resolution-dependant density calculation
RSMD Refinement
DynamicsDynamics
• Rigid-body MD• Torsion-angle MD• Cartesian-space MD• Energy minimization
E E ETOTAL CHEM= + ⊕.
EM Refinement Protocol
1. Rigid-body annotation
2. NCS restraints enforcement
3. Torsion-angle degree of freedom
4. Refinement via simulated annealing
Optimal Conformation
Crystal StructureCrystal StructureE(bond)=0.990 E(E(bond)=0.990 E(anglangl)=10.353 E()=10.353 E(torstors)=3.161 )=3.161 E(VDW )=E(VDW )=--208. E(PVDW)=0.3E+8 E(208. E(PVDW)=0.3E+8 E(rresrres)=167.0)=167.0
Manual AdjustmentManual AdjustmentE(bond)=0.975 E(E(bond)=0.975 E(anglangl)=10.397 E()=10.397 E(torstors)=3.169 )=3.169 E(VDW)=0.5E+7 E(PVDW)=0.3E+5 E(E(VDW)=0.5E+7 E(PVDW)=0.3E+5 E(rresrres)=161.0)=161.0
RSMD RefinementRSMD RefinementE(bond)=0.923 E(E(bond)=0.923 E(anglangl)=10.351 E()=10.351 E(torstors)=3.138 )=3.138 E(VDW )=E(VDW )=--191. E(PVDW)=191. E(PVDW)=--14.38 E(14.38 E(rresrres)=156.0)=156.0
The Road Ahead …
Density map & structureAtomic scattering v.s. electron scattering
Time-resolved dynamics study via EMConformational snapshots from EM experiments
Dynamics simulation to “connect the dots”
Interpretation of an EM refinementResolution, resolution, and resolution !!!
EM modeling from large, heterogeneous dataset