Protein Nucleic Acid Interactions

1. Protein Nucleic Acid Interactions September 28, 2006

2. Different types of recognition motifs • Helix turn helix • Homeodomains • Zinc finger • Leucine zipper • Winged helix • Beta ribbon

3. 1. Helix turn helixHTH • Most common DNA binding motif • Procaryotes • Found in hundreds of DNA binding proteins • Dimerization required for full activity • Sequences separated by approximately one turn of helix • Major groove contact to DNA • DNA sometimes bent

5. Proteins with HTH motif

6. Cro • HTH 2nd and 3rd helix • 17bp operator

7.  • 2 fold symmetry • Recognition helices 34 A apart • DNA slightly distorted

8. 434 • 4 helix cluster, 2,3 HTH • 34 A between recognition helices • Slight distortion

9. Comparison of 434 and  • Gln 33 H bonds to backbone • Gln 44 H bonds to adenine • Asn 52 H bonds to backbone

10. Relative orientation is different in different complexes

11. 2. Homeodomains • HTH in eukaryotes • 60 amino acids • Helix-loop-helix-turn-helix

12. DNA Binding • Helix 2 and 3 similar to HTH • Recognition helix (3) makes key contacts with major groove • Flexible arm in helix 1 contacts minor groove

13. 3. Zinc Finger •  • Hormone receptor • Gal4 • Loop sheet helix

14. a.  • Part of transcription regulatory proteins • 30 residue motif coordinating one zinc via 2 cysteines and 2 histidines

15. DNA binding of Zif268 • Monomer • Major groove • Finger bind to 3 base pair subsites

16. Different Zinc finger binding to DNA • Zn fingers all have similar structure • Different contacts to DNA • Arginine guanine contacts are common

17. b. Hormone receptor • Pseudosymmetric homo or heterodimer • 2 Zn coordinating modules • 1 Zn stabilizes DNA recognition helix, other Zn involved in dimer formation • Zn coordinated by 4 cysteines • Major groove contacts

18. c. Gal4 • Found in yeast transcriptional activators • 65 residue regions binds as dimer (C terminus) • 2 Zn coordinated by 6 cysteines (N terminus) • Major groove binder

19. d. Loop sheet helix • P53-transcriptional activator involved in tumor suppression • Zn coordinated by 3 cysteines and a histidine • Tetramer-5bp recognition helix one after another • Helix in major groove, loop in minor groove

20. 4. Leucine zipper • Dimer (homo or hetero) • Two a helices wound around one another • Grip DNA like a clothespin

21. GCN4 • Yeast transcriptional activator • Coiled coil packing of helices (knobs in hole) • homodimer

22. AP-1 Fos Jun • heterodimer

23. 5. Winged helix • Compact  structure • 2 wings, 3 helices and 3 strands • Helix 3 is recognition helix

24. HNF 3

25. 6. Beta ribbon group proteins • Bind via  structures • Major groove binding in ribbon helix helix family • Minor groove binding in DNA benders and TATA box binding proteins

26. Beta ribbon proteins

27. Arc repressor • Homodimer • Monomer has pair of helices connected by  sheet •  sheet recognizes bases in major groove

28. Integration host factor • Beta sheets binds in minor groove • Pseudosymmetric • 180 degree bend in DNA

29. TATA binding protein • Specifically recognize AT rich DNA seqeunces • 8 stranded  sheet binds to DNA • Hydrophobic side chains intercalate in minor groove • DNA kinked

30. References http://www.acsu.buffalo.edu/~koudelka/Bio522_coursepage.html

31. Systematic Studies

32. Questions • What features characterize the DNA-binding site of a protein? • How do proteins induce conformational changes in the DNA structures they bind?

33. Datasets • Two datasets selected from the NDB/PDB • 21 B-DNA structures • uncomplexed • unmodified • resolution range 1.4 Å-2.5Å • 26 protein-DNA complexes

34. Dataset Selection NDB/PDB Query “Protein/DNA <3.0” 132 Protein-DNA complexes 5 Unclassified 7 Single Helix NDB Classification 3 Quadruple Helix 117 Double Helix Full atom records 110 Protein-DNA complexes Pairwise structure comparisons using SSAP 110 Protein-DNA complexes grouped in 26 protein structure families Select family representative 26 Protein-DNA complexes nonhomologous by protein

35. DNA-Binding Sites on Proteins Computational analysis of • Size (ASA) • Packing • Polarity • Hydrogen Bonding • Bridging Water Molecules • Residue Propensities

36. Comparisons of Residue Propensities Propensity

37. Protein and DNA Interaction Footprints Single headed binding proteins

38. Schematics of Protein-DNA Complexes Single Headed Proteins PU 1 ETS-domain Endonuclease V P53 Tumor Suppressor Paired Domain

39. Protein and DNA Interaction Footprints Double headed binding proteins

40. Schematics of Protein-DNA Complexes Double Headed Proteins MyoD bHLH GCN4-bZIP bound to ATF/CREB l repressor- operator GAL4 CAP Glucocorticoid PurR Bovine Papillomarvirus Arc repressor- operator gd resolvase RAP1 IHF Metj

41. Protein and DNA Interaction Footprints Enveloping binding proteins

42. Schematics of Protein-DNA Complex EcoRV endonuclease EcoRI endonuclease HhaL Methyltransferase Endonuclease BamHI NFkB Enveloping Proteins Zif268 Zinc Finger PvuII endonuclease Yeast TBP/TATA box Hin Recombinase

43. Measuring DNA Distortion (superposition onto canonical B-DNA) rmsd = 3Å rmsd = 10Å rmsd = 22Å  repressor  resolvase integration host factor

44. 1ihf 1erl 1tsr 1igr 206l 1hci 1pvl 1bdl 1nfk 1glu 1rva 1ytb 1par 1gdt 1ber 1d29 1aay 1vas 1pnv 126d 252d 243d 1cgc 1d56 196d 167d 1d23 1d65 250d 1d49 1d98 119d 287d 194d 1d66 1dn9 1bna 2dgc 1pue 1lmb 5dnb 2bop 3mht 1oma 1mdy 1bhm 1pdm Distortion in protein-bound and unbound DNA RMSD DNA fitted to 40bp B-DNA PDB Code