Transcript DaGrancharov_slides

Investigation of Binding Affinity
of hIFN-gamma Mutated Forms
with the Rosetta Suite of
Programs
Damyan Grancharov1, Peicho Petkov1, Elena Lilkova1,
Nevena Ilieva2, Leandar Litov1
Faculty of Physics, Sofia University “St. Kliment Ohridski”, Sofia,
Bulgaria
Institute for Nuclear Research and Nuclear Energy, Bulgarian Academy of
Sciences, Sofia, Bulgaria
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Overview
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hIFN-γ and suppressing its abnormal
biological activity
Protein docking with Rosetta
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Algorithm
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Scoring functions
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hIFN-γ study with Rosetta
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Conclusions
hIFN-γ
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Powerful immunomodulator;
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Autoimmune diseases due to abnormal expression;
Suppression of biological activity
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Competitive binding of the hIFN-γR;
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Mutated analogs of the native hIFN-γ that:
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Interrupt the signal transduction pathway;
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Preserve binding ability;
12 mutated analogs out of 100 were selected;
Preservation of 3D structure = preservation of
binding ability;
Protein docking is needed to test such a
hypothesis!
Rosetta docking
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Imitates the binding process in real life;
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Low resolution search:
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Centroid representation;
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500 random perturbations of the current conformation;
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Low res scoring function;
High resolution calculation:
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All atom representation;
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High res scoring function;
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50 perturbations of random displacement and side-chain
optimization;
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Minimization;
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Acceptance via Metropolis criterion;
High resolution calculation
concept
Scoring function (1)
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Low resolution scoring function:
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Chemical terms:
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Spair – accounts for pairwise coupling of amino acids;
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Senv – accounts for the environment of amino acids;
Structural terms:
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Scontact – “reward” term for VdW attractive interaction;
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Sbump – “penalty” term for VdW repulsive interaction;
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Salign – term to account for additional biological information;
Scoring functions (2)
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High resolution scoring function:
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S – scoring function terms;
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w – weights.
Scoring functions (3)
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Satr – attractive Van der Waals interaction;
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Srep – repulsive Van der Waals interaction;
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Ssol – accounts for the presence of an implicit solvent;
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Ssasa – accounts for the solvent accessible surface area;
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Shb – accounts for the presence of hydrogen bonds;
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Sdun – accounts for rotamer probabilities;
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Spair – accounts for pairwise coupling of amino acids;
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Selec – electrostatic interaction, divided into short and long
ranged, attractive and repulsive;
hIFN-γ study with Rosetta
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For the sake of testing the algorithm:
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Native hIFN-γ was used;
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“Blind prediction” protocol was used:
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Partners were randomized;
50000 models were generated;
Results plotted: Score vs RMSD;
Best model passed on to refinement;
Refinement run:
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1000 model were generated;
In the Score vs RMSD plot a “funnel” appeared;
Blind prediction results
Refinement run results
Predicted structure
RMSD 0,74 Å
Conclusions
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Close-to-native conformations can be
obtained, paying the cost of extensive search:
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Native hIFN-γ with receptor complex
reproduced within 0,74 Å;
All 12 mutated forms will enter only a
refinement procedure:
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To be adjusted within the funnel in free
energy space, encountered for the native
hIFN-γ;
Thank You
for
Your Attention!
Back-up slides
Metropolis acceptance criterion
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Probability to go from state j to state i:
Table of weights