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The role of shape readout in protein – DNA interactions

The role of shape readout in protein – DNA interactions. Ana Carolina Dantas 1 st year student. 03/25/2011. Introduction Methods Fis and p53 Future Work. Protein – DNA interactions. How is DNA binding specificity achieved?

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The role of shape readout in protein – DNA interactions

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  1. The role of shape readout in protein – DNA interactions Ana Carolina Dantas 1st year student 03/25/2011

  2. Introduction • Methods • Fisand p53 • Future Work

  3. Protein – DNA interactions • How is DNA binding specificity achieved? • How are proteins that share similar regions responsible for specific functions? • How does a protein bind to DNA sequences with different affinities?

  4. Protein-DNA specificity Rohs et al., Annu Rev Biochem, 2010

  5. Hox protein example • Family of transcription factors involved in embryonic segmentation • Scr binds to DNA • ExdDNA-bound cofactor Joshi et al., Cell, 2007

  6. Hox protein example Joshi et al., Cell, 2007

  7. Hox protein example Joshi et al., Cell, 2007

  8. Methods • Curves calculates helical parameters • DelPhi calculates electrostatic potential Roll

  9. Fis protein

  10. Fis protein

  11. R248 R273 R175 G245 R282 R249 1 393 100 300 DNA binding domain Transactivation domain (20-60) Oligomerization domain (320-360) Regulatory domain (363-393) p53 • Tumor suppressor protein • DNA binding half sites: RRRCWWGYYY (R=A,G; W=A,T; Y=C,T) They can be separated up to 20bp

  12. Comparison between the two p53 tetramers Kitayner et al., NSMB 2010 Chen et al., Structure 2010

  13. Hoogsteen base pairs Honig & Rohs, Nature, 2011

  14. Comparison between DNA sequences Kitayner et al., Nat StructMol Bio, 2010

  15. Minor groove contacting argininesShape Readout Kitayner et al., Nat StructMolBiol, 2010

  16. Future Directions • Analyze how DNA shape affects protein-DNA interactions • Binding affinity of Dorsal-ventral transcription factors • Identify SNPs that affect protein binding

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