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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 By Liza Lee
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
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
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)
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
IV. Brief guide on different graphs: • Residue-residue contact map • Residue-surface contact map • Secondary structure plot
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
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
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
pp1A Solution Adsorbed
pp1A Solution Adsorbed
pp1B Solution Adsorbed
pp1B Solution Adsorbed
pp1C Solution Adsorbed
pp1C Solution Adsorbed
pp2A Solution Adsorbed
Solution Adsorbed pp2A
pp2B Solution Adsorbed
pp2B Solution Adsorbed
pp2C Solution Adsorbed
pp2C Solution Adsorbed
pp3A Solution Adsorbed
pp3A Solution Adsorbed
pp3B Solution Adsorbed
pp3B Solution Adsorbed
pp3C Solution Adsorbed
pp3C Solution Adsorbed
pp4A Solution Adsorbed
pp4A Solution Adsorbed
pp4B Solution Adsorbed
pp4B Solution Adsorbed
pp4C Solution Adsorbed
pp4C Solution Adsorbed
V. Summary *Abbrev: SSplot, secondary structure plot; RRCM, residue-residue contact map; RSCM, residue-surface contact map