molecular replacement and model-building using distant homology models as templates
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Molecular replacement and model-building using distant homology models as templates. ACA Trueblood Award Lecture July 24, 2013 Honolulu, Hawaii. Tom Terwilliger Los Alamos National Laboratory. Kenneth Trueblood 1920-1998. - PowerPoint PPT PresentationTRANSCRIPT
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Molecular replacement and model-building using distant homology
models as templatesACA Trueblood Award Lecture
July 24, 2013Honolulu, Hawaii
Tom TerwilligerLos Alamos National
LaboratoryKenneth Trueblood
1920-1998
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The challenge: Crystal structure determination from a distant homology model
Search model too different from target to find its location by molecular replacement
Correctly-placed model too different from target to yield useful electron density maps
The problems:
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The challenge: Crystal structure determination from a distant homology model
Homology modeling before molecular replacement
Modeling with density at early stages of structure rebuilding
Solutions using Rosetta:
DiMaio et al. (2011). Improving molecular replacement by density and energy guided protein structure optimization. Nature 473, 540-543
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Complementarity of PHENIX and Rosetta model-building
Crystallographic model-building
(PHENIX)
Interpretation of patterns of density
Density search for regular secondary structure
3-residue fragment library
Fit to density
Structure-factor likelihood refinement target
Structure-modeling (Rosetta)
Creating physically plausible models
Ab-initio modeling or homology modeling
3- and 9-residue libraries
Rosetta force field (optional density term)
Rosetta force field (optional density term)
Characteristic
Optimization
Model-buildingapproach
Fragment libraries
Model-building target
Refinement target
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Generating improved homology models for molecular
replacement with Rosetta
ag9603NMR model, 100% identity
1.7 Å data
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NMR model of of ag9603
NMR model(CC to final map: 0.17)
Final model
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Typical Rosetta model of of ag9603
Final model
Rosetta model 791(CC to final map: 0.27)
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Best Rosetta model of of ag9603
Final model
Best Rosetta model for
ag9603(CC to
model map: 0.34)
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Improving models with Rosetta using density
Density fit as part of optimization targetModeling segments not in template
Comparison with simulated annealing
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Rosetta models vs SA models
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Integrating Rosetta modeling in Phenix
phenix.mr_rosetta
Molecular replacementRebuilding with Rosetta
Rebuilding with phenix.autobuild
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mr_rosetta example: HP3342, 22% identity template, 3.2 Å data, B=87 A2
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hp3342, 22% identity
template (1vgy),
3.2 Å data
Density- modified map
based on 1vgy
Yellow: final modelBlue:
template (1vgy)
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MR_rosetta example: hp3342
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hp3342, 22% identity
template (1vgy),
3.2 Å data
Density- modified map
based on 1vgy
Yellow: final modelBlue:
template (1vgy)
Pink: Highest-scoring
Rosetta model
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hp3342, 22% identity
template (1vgy),
3.2 Å data
Density- modified map
based on Rosetta model
Yellow: final modelBlue:
template (1vgy)
Pink: Highest-scoring
Rosetta model
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hp3342, 22% identity
template (1vgy),
3.2 Å data
Density- modified map
based on Rosetta model
Yellow: final model
Green: autobuild
model
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HP3342, 22% identity template, 3.2 Å data, R/Rfree=0.34/0.41 B=87 A2
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mr_rosetta example II: XMRV, 30% identity template (2hs1), 2.0 Å data
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XMRV, 30% identity
template, 2.0 Å data
Density- modified map
based on 2hs1
Yellow: final modelBlue:
template (2hs1)
Pink: Highest-scoring
Rosetta model
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MR_rosetta example: XMRV
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XMRV, 30% identity
template, 2.0 Å data
Density- modified map
based on 2hs1
Yellow: final modelBlue:
template (2hs1)
Red: Highest-scoring
Rosetta model
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XMRV, 30% identity
template, 2.0 Å data
Density- modified map from Rosetta
model
Yellow: final modelBlue:
template (2hs1)
Red: Highest-scoring
Rosetta model
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XMRV, 30% identity
template, 2.0 Å data
Density- modified map from Rosetta
model
Yellow: final modelBlue:
template (2hs1)
Purple: Relaxed
Rosetta model
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XMRV, 30% identity
template, 2.0 Å data
Density- modified map
from autobuild
Yellow: final modelBlue:
template (2hs1)
Green: autobuild
model
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XMRV, 30% identity
template, 2.0 Å data
Density- modified map
from autobuild
Yellow: final modelBlue:
template (2hs1)
Green: autobuild
model
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Structure determination of cab55348 (using template supplied by user)
1.9 A, 28% sequence identity (AutoMR alone fails with R/Rfree=0.47/0.53)
MR model: blue, Final model: green
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MR model : blue Final model: pink
Rosetta models cycle 1: greenSample Rosetta
models in cycles 1 and
2,
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MR model : blue Final model: pink
Map from refined MR modelRebuilding in a poor section of
the starting model
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MR model : blue Final model: pink Rosetta models cycle 1: green
Map from refined MR modelRebuilding in a poor section of
the starting model
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MR model : blue Final model: pink
Best-scoring Rosetta model cycle 1: yellow Map from refined MR modelRebuilding in a poor section of
the starting model
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MR model : blue Final model: pink Rosetta models cycle 2: yellow
AutoBuild Map from cycle 1Rebuilding in a poor section of
the starting model
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AutoBuild model cycle 2
Map CC: 0.78 R/Rfree = 0.26/0.31 Rebuilding in a poor section of
the starting model
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mr_rosetta rebuilding starting with placed templates
structure dmin % ident ncs Free Rtemplate
(Structural genomics structures)
ag9603a 1.7 100 2 0.27 NMR model
cab55348 1.9 31 1 0.23 Unpublished structure
xmrv 2.0 30 2 0.34 HIV protease
fk4430 2.1 22 1 0.29 Nudix hydrolase (MCSG)
thiod 2.1 22/15 1 0.30Thioredoxin;protein disulfide
isomerase
bfr258e 2.2 19 2 0.28 Glutathione-S-transferase
niko 2.5 27 2 0.31 Carboxyvinyltransferase (RIKEN)
estan 2.5 18 1 0.25 Alpha-amylase
fj6376 2.7 21 4 0.30Domain of unknown function 364
(JCSG)
pc02153 2.8 29 1 0.44 Prephanate dehydrogenase (NYSGC)
pc0265 2.9 29 2 0.39 Xanthine dehydrogenase
tirap 3.0 22 1 0.42 MYD88 (NMR model, NESG)
hp3342 3.2 20 1 0.42Succinyl diaminopimelate
desuccinylase (SGX)
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The challenge: Crystal structure determination from a distant homology model
Morphing (distortion) of the template using a density map to make it more like the target
structure
Another solution:
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ag9603; approximate NMR model as template
in pink
Related structures often have high local similarity
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XMRV PR, 30% identity template (2hs1) in blue
Related structures often have high local similarity
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cab55348
32% identical template (Cip2) in blue
Related structures often have high local similarity