ab initio modelling tutorial (part ii) - embl hamburg · ab initio tutorial (part ii) •ambimeter...
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Ab initio tutorial (part II)• Ambimeter
– model independent ambiguity score • Damclust
– alternative to Damaver• Gasbor (local & online)
– real/reciprocal space• Monsa (online)
– Nucleoprotein– Dimeric complex
• Dammin– limited search volume– anisometry restraint
EMBO Practical Course on Solution Scattering from Biological Macromolecules
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AMBIMETER: tool for Ambiguity AssessmentMap of renormalized scattering profiles from exhaustive set of shape topologies is employed to quantitatively evaluate the ambiguity of a small-angle-scattering curve
Map of SAXS profiles density
s*Rg1 2 3 4 5 6
lg(I/I0)
-1.6
-1.2
-0.8
-0.4
0.0
010 100 1000 10000
Extreme cases
Flat DiscRodSphere
18 Skeletons with identical SAXS curvesAMBIMETER is now a part of SASFLOW pipeline
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DamClust: Assessment of multimodality(has damaver & friends inside)
• Clustering of multiple SAS models– Discrepancies (distances) between
multiple models as criteria for grouping
– Normalized spatial deviation serves as a distance between heterogeneous models (e.g. bead models)
– R.m.s.d. is employed for those with atom-to-atom correspondence (e.g. rigid body models)
Creates the complete graph by iteratively joining the clusters (singles)
Selects the optimal threshold as a compromise between the number of clusters and averaged spread within the cluster
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EMBO Practical Course on Solution Scattering from Biological Macromolecules
Dummy Residues Model• Proteins typically consist of folded polypeptide
chains composed of amino acid residues• At a resolution of 0.5 nm each amino acid can be
represented as one entity (dummy residue)• In GASBOR a protein is represented by an
ensemble of K DRs those are– Identical– Have no ordinal
number– For simplicity are
centered at the Cαpositions
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EMBO Practical Course on Solution Scattering from Biological Macromolecules
ρ=0.334 e/A3
∆ρ=0.03 e/A3
Width=3A
n: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15Fib(n): 1 1 2 3 5 8 13 21 34 55 89 144 233 377 610 987
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EMBO Practical Course on Solution Scattering from Biological Macromolecules
MONSA (multiphase modelling)
• 1 phase = 1 component of a complex particle• For each phase, Rg, V and its scattering curve can be given• For each curve, contrast of each phase are specified
contrast variation and / or use of partial constructs
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Monsa case1: protein-RNA complex
EMBO Practical Course on Solution Scattering from Biological Macromolecules
252 AA protein (two domains)
67 nucleotides RNA
Three curves in total:
Free RNA
Complex
Free protein
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Monsa case2: dimeric compex• 172 AA (20kDa) and 538 AA (70 kDa) proteins• Dimerization via small one• Two-fold symmetry axis
EMBO Practical Course on Solution Scattering from Biological Macromolecules
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Dammin features missing in Dammif
• Specific (limited) search volume (sphere, ellipsoid, cylinder, parallelepiped, User supplied)
• Icosahedral and cubic symmetries• Anisometry restraint
EMBO Practical Course on Solution Scattering from Biological Macromolecules
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Anisometry (direction)
• both shapes are symmetric and extended
EMBO Practical Course on Solution Scattering from Biological Macromolecules