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Biophysics and Thermodynamics A pproaches for Modeling and Testing NF- B Binding S ites

Marcin Pacholczyk , Silesian University of Technology. Biophysics and Thermodynamics A pproaches for Modeling and Testing NF- B Binding S ites . Physics-based Laws of Physics – electrostatics, van der Waals, molecular flexibility, geometry of hydrogen bonds

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Biophysics and Thermodynamics A pproaches for Modeling and Testing NF- B Binding S ites

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  1. Marcin Pacholczyk, Silesian University of Technology Biophysics and Thermodynamics Approaches for Modeling and Testing NF-B Binding Sites

  2. Physics-based • Laws of Physics – electrostatics, van der Waals, molecular flexibility, geometry of hydrogen bonds • Computationally intensive, some effects difficult to model (desolvation) • Knowledge-based • Relatively simple, based on observation • Training set! PhysicsvsKnowledge– basedpotentials

  3. Physics-BasedPotential Poisson-Boltzmann equation + Lenard-Jonespotential

  4. Knowledge-BasedStatisticalPotential Gibbs energy  probability of „correctness” Robertson and Varani 2007

  5. Knowledge-BasedStatisticalPotential Probability of individualatomiccontact P(C) – Bayesianprior of observingnative-like protein-DNA complex – set to 1. Robertson and Varani 2007

  6. Knowledge-BasedStatisticalPotential Probabilityfunction Continousdijismapped to a set of discretedistancebinsb0, b1, … , bnwithdistancecutoffs db0, db1, … , dbn A countisassigned to biifdbi-1 dij < dbi 3 Å, 4 Å, 5 Å, 6 Å, 7 Å, 8 Å, 9 Å, 10 Å Robertson and Varani 2007

  7. Knowledge-BasedStatisticalPotential Marginaldistribution NC – totalnumber of observedcontactsbetweeninterfaceatoms of alltypes, atalldistancesinthetraining set Training set – NucleicAcidDatabasendbserver.rutgers.edu Robertson and Varani 2007

  8. Computation of the PWMs Threemembers of theNF-Bfamily of TF p50p50 homodimer (1NFK) p50RelB heterodimer (2V2T) p50p65 heterodimer (1VKX) Complexeswith DNA fragments DNA chainsweremutated(MMTSB – MultiscaleModelingTools for StructuralBiology) one basepairateach step (backbonefixed) Almanova et al. 2010

  9. Computation of the PWMs Threemembers of theNF-Bfamily of TF p50p50 homodimer (1NFK) p50RelB heterodimer (2V2T) p50p65 heterodimer (1VKX) Complexeswith DNA fragments (PDB) Almanova et al. 2010

  10. NF-Bfamily p50p50 p50p65 p50RelB

  11. Computation of the PWMs DNA chainsweremutated(MMTSB – MultiscaleModelingTools for StructuralBiology) one basepairateach step (backbonefixed) 4N + R • All weights w(i, u) in the PWMpredicted by solving the linear equation: • X is a vector of 4N dimensions of the estimated weights • Ais a binary matrix of dimensions (4N, 4N + R), with all random DNA sequences whose free binding energy was computed. • The free binding energy vectorb consists of 4N + Rvalues obtained with the protein-DNA scoring procedure

  12. Almanova et al. 2010

  13. p50p50 p50RelB p50p65 TRANSFAC V$NFKAPPAB_01

  14. Comparison Relativeentropy Almanova et al. 2010

  15. 69 human genes regulated by NF-B with 124 promoter sequences (TRANSPRO) Experimentally confirmed 31 out of 124 promoters belonging to 25 genes Matrix scan with Match on 58 confirmed binding sites Comparison Bindingsitediscovery Almanova et al. 2010

  16. Comparison Almanova et al. 2010

  17. Comparison AUC Almanova et al. 2010

  18. Implementation http://cogangs.biobase.de/3dtf/

  19. Discovery ofnovel NF-B binding sites • Investigation of postranslational modificationslikeRelA Ser276phosphorylation (Nowak et al. 2008) Conclusions It is possible to compute PWMs which perform comparably to the ones derived from experimental data (TRANSFAC) Thermodynamicbasedmodels of transcriptionalregulationincludingSynergisticActivation, CooperativeBinding and Short-RangeRepression (He et al. 2010)

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