Feb 26 2025
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This option uses the same methodology as the effect of mutation on Protein-Protein interaction except that backbone in the peptide is flexible.
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Step 1 Read in your PDB structure. In this example we will use PDB 1
tp5 and select V425 in the peptide (b chain).
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Step 2 In this example we will choose to see the effect of mutation of Val > Leu. Enter the letter of the chain for the interacting part 1 (peptide) and part 2 (protein). In addition you can choose:
- Scan Peptide Sequence This option will try a single residue side-chain mutation at each position in the peptide.
- Scan Pocket Surface This option will try a single residue side-chain mutation at each position in the protein that is in contact with the peptide.
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Step 3 The simulation will run in the background and may take a while to finish if the option "all" or "Scan Sequence" is selected.
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Step 4 A message dialog box will let you know when your simulation has finished.
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Step 5 A table reporting the free energy change in peptide will be displayed (ddG kcal/mol). Double click a row of the table to load and display the mutated structure.
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How to interpret the results:
- ddG > 0: The mutation increases the free energy of folding, making the peptide binding less favorable.
- ddG < 0: The mutation decreases the free energy of folding, making the folded state more favorable.
- ddG ≈ 0: Suggests the mutation has little to no effect on peptide binding compared to wild type.
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