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PLAPA

PLAPA. Phosphate Localization And Prediction Algorithm. How does it work?. Generates a surface using Matt’s surface generation tool in PLOP Places a phosphate “ball” of -2 charge at each point Minimizes the position of the ball Calculates energy

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PLAPA

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  1. PLAPA Phosphate Localization And Prediction Algorithm

  2. How does it work? • Generates a surface using Matt’s surface generation tool in PLOP • Places a phosphate “ball” of -2 charge at each point • Minimizes the position of the ball • Calculates energy • Ranks all positions and chooses the lowest energy point – no averages among points

  3. What Have I Done? • Used five test cases to evaluate different strategies • 1gxc – FHA domain • 1g6g – FHA domain • 1fpr – SH2 domain • 1bm2 – SH2 domain • 1een – SH2 domain

  4. FHA Domain

  5. What Have I Done? • Started by using a phosphate ball • This did not work at either of the trial radii of 1.4, 2.0, and 3.0 A, or the OPLSAA phosphate radius of 4.83 A • Why?? (All following examples with 1BM2 only, Native is always BLUE, Decoy RED)

  6. Radius vs Distance from Native Post Minimization Distance from Native Radius of Sphere in A

  7. Energy of Native vs Decoy at Different Radii Energy in Kcals Radius of Sphere in A

  8. Energy of Native vs Decoy After Subtraction of LJ Energy in Kcals Radius of Sphere in A

  9. Energy of Native vs Decoy Using only Electrostatics Energy in Kcals Radius of Sphere in A

  10. Another Issue, 1G6G

  11. 1G6G Fix • Added capping group (ACE) • Lowest energy moved to within 5 A of native phosphate position in native vs decoy trials

  12. Final Output for 1BM2 Energy in Kcals Distance from Native in A

  13. Distance from Native with Minimization in GB and in vacuum

  14. Future Directions • Investigate the two examples that are not working, haven’t had time due to CASP…

  15. CASP Target T0196 Possible Elongation Factor from Pyrococcus furiosus

  16. Initial Alignment * Poly His at the beginning of a sequence is usually a His tag…

  17. Secondary Structure Prediction With and Without His Tag

  18. Superposition on 1JNY

  19. Ok, so it doesn’t quite match • Genomic search – is it only a piece? • Bacterial gene prediction • Operon search (functional proteins are grouped onto operons in prokaryotes) • Similar operons = more sequences for the alignment • It’s a real protein…

  20. Structural Alignment • Schrodinger Structural Alignment Tool • ~jacobson/bin/dinger/utilities/structalign pdb1 pdb2 pdbN • Must use PDB files with only one chain • ~jacobson/bin/dinger/utilities/getpdb pdbID:chain (CAPS) • BUGS • Rotation matrix a bit screwy for some pdbs • Some of your pdbs will appear in alignment but will not appear as files at the end of the run • This can be fixed by creating a .fasta file with the structural alignment, loading into chimera, and aligning the structures

  21. Structural Alignment • Whole protein structural alignment performed with CE and Schrodinger • CE provided a good alignment, but output pdb file useless since the other domains influenced position • Schrodinger script could not handle this • Domain only alignment based on sequence alignment • CE could not do this • Schrodinger could…with bugs

  22. Domain Alignment

  23. Domain Alignment

  24. Domain Alignment without 1KJZ

  25. Domain Alignment without 1KJZ

  26. Interlude • Here is where I bitch about how chimera crashed my system about 5 times so I downloaded the linux version, in which I could not figure out how to change the background to white…so its black.

  27. No Gaps: 1B23, 1MJ1, 1AIP

  28. One Gap: 1DG1, 1D2E, 1EFC

  29. Two Gaps: 1JNY, 1F60

  30. Different Partial Templates Different Full Templates

  31. Alignment

  32. All Models

  33. No Gaps: 1B23, 1MJ1, 1AIP

  34. One Gap: 1DG1, 1D2E, 1EFC

  35. Two Gaps: 1JNY, 1F60

  36. Two Lowest Energy Models

  37. 1JNY and 1B23 structures

  38. Further Directions • Build longer models • Look over surface of final model to see whether there is a hydrophobic patch for helix packing • Get your suggestions…

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