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Phage Peptide Analysis

Phage Peptide Analysis. By Liza Lee. Contents. I. Naming the peptides and the pdb files II. Hydroxyapatite surface III. Adopted nomenclature for peptide and surface atoms

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Phage Peptide Analysis

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  1. Phage Peptide Analysis By Liza Lee

  2. Contents I. Naming the peptides and the pdb files II. Hydroxyapatite surface III. Adopted nomenclature for peptide and surface atoms IV. Brief guide on different graphs (residue-residue contact map, residue-surface contact map, and secondary structure plot) V. Analysis of each peptides Peptide 1 (pp1A, pp1B, pp1C) Peptide 2 (pp2A, pp2B, pp2C) Peptide 3 (pp3A, pp3B, pp3C) Peptide 4 (pp4A, pp4B, pp4C) VI. Summary

  3. I. Naming of the Peptides • I have named my pdbs in the following way and will be using the same convention throughout these slides. Peptide 1 (pp1) Sequence: AESSATQHVD Peptide 2 (pp2) Sequence: AESSSTASSD Peptide 3 (pp3) Sequence: ADSSTPSSTD Peptide 4 (pp4) Sequence: AGTNTSSADDD Peptide 5 (pp5) Sequence: AAASESTASDD Peptide 6 (pp6) Sequence: AGGTGDAMNMD To distinguish the charged residues, I often colored them: red=acidic, blue=basic residue • Hydroxyapatite (HAp) surfaces: A=(100), B=(010), and C=(001) faces HAp • Ex. aapp1A_0002.pdb contains Peptide 1 on (100) face of HAp (The two letters ‘aa’ infront of pp1A are meaningless). SolState_aapp1A_0002.pdb contains Peptide 1 on (100) face, and it is a precursor (folded in solution before docking to the surface) of aapp1A_0002.pdb

  4. II. Hydroxyapatite (HAp) Surface AESSATQHVD Monoclinic hydroxyapatite crystals were built using CrystalMaker. Appropriate cuts were made to expose flat a (001), b (010), and c (100) surfaces with approximately neutral (mixed charge) terminations. (Please ignore the parallelograms and its dimensions in front of the surfaces; it is irrelevant in our case)

  5. III. Adopted Nomenclature for the Peptide and Surface Atoms • This nomenclature applies to the ones in my pdbs and throughout these slides (and other files): • Backbone atoms are named the same way as in Protein Data Bank e.g. H from Ala-1 means amide hydrogen for residue 1, and HG from Ser means gamma hydrogen, the hydrogen at the hydroxyl group of serine’s side chain • Surface (HAp) atoms are named as follows: Ca2p = Calcium ion Hha = Hydrogen in the hydroxyl ion OHha = Oxygen in the hydroxyl ion Pha= Phosphorous in the phosphate ion OPha = Oxygen in the Phosphate ion

  6. IV. Brief guide on different graphs: • Residue-residue contact map • Residue-surface contact map • Secondary structure plot

  7. The x-axis and y-axis indicate residue numbers with corresponding one letter residue name on the opposite side. The residues are in “contact” if they are within 4 Å of each other. The frequency in which they are in contact (within the sample size) is denoted by the color gradient on the right. For example, from the figure on the left, we see that Ser-4 is in contact with Asp-10 about 57% of the time. Residue-Residue Contact Map

  8. The x-axis indicates peptide residue number with corresponding one letter residue name at the top of the map. The y-axis indicates how far a particular residue is away from the surface. The frequency in which a residue is a certain distance away from the surface is denoted by the color gradient on the right. For example, from the figure on the left, we see that Ser-3 is 2 Å away from the surface 62% of the time. Residue-Surface Contact Map

  9. The x-axis indicates peptide residue number, and the y-axis represents the frequency of secondary structure (Red=Helix, Green=Turn, and Blue=Other) adopted by the backbone at that residue position based on the phi-psi angles. For example, from the figure on the left, we see that the backbone conformation at Residue-1 is a helix 38% of the time and is a turn 40% of the time. Secondary Structure Plot

  10. IV. Data/Analysis:Peptide 1 AESSATQHVD

  11. pp1A Solution Adsorbed

  12. pp1A

  13. pp1A Solution Adsorbed

  14. pp1B Solution Adsorbed

  15. pp1B

  16. pp1B Solution Adsorbed

  17. pp1C Solution Adsorbed

  18. pp1C

  19. pp1C Solution Adsorbed

  20. IV. Data/Analysis:Peptide 2 AESSSTASSD

  21. pp2A Solution Adsorbed

  22. pp2A

  23. Solution Adsorbed pp2A

  24. pp2B Solution Adsorbed

  25. pp2B

  26. pp2B Solution Adsorbed

  27. pp2C Solution Adsorbed

  28. pp2C

  29. pp2C Solution Adsorbed

  30. IV. Data/Analysis:Peptide 3 ADSSTPSSTD

  31. pp3A Solution Adsorbed

  32. pp3A

  33. pp3A Solution Adsorbed

  34. pp3B Solution Adsorbed

  35. pp3B

  36. pp3B Solution Adsorbed

  37. pp3C Solution Adsorbed

  38. pp3C

  39. pp3C Solution Adsorbed

  40. IV. Data/Analysis:Peptide 4 AGTNTSSADDD

  41. pp4A Solution Adsorbed

  42. pp4A

  43. pp4A Solution Adsorbed

  44. pp4B Solution Adsorbed

  45. pp4B

  46. pp4B Solution Adsorbed

  47. pp4C Solution Adsorbed

  48. pp4C

  49. pp4C Solution Adsorbed

  50. V. Summary *Abbrev: SSplot, secondary structure plot; RRCM, residue-residue contact map; RSCM, residue-surface contact map

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