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Understanding PLAPA: Phosphate Localization and Prediction Algorithm in Protein Modeling

This document delves into the PLAPA method for modeling phosphate localization and energy minimization in proteins. It outlines the step-by-step process including the surface generation tool usage, phosphate ball placement, energy calculations, and ranking of positions. The results showcase the evaluation of five test cases across different protein domains, highlighting challenges faced and modifications made to optimize outcomes. The future directions aim to explore unresolved examples and improve structural alignment methods for more accurate prediction and modeling of protein structures.

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Understanding PLAPA: Phosphate Localization and Prediction Algorithm in Protein Modeling

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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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