Research Article

Improved scFv Anti-HIV-1 p17 Binding Affinity Guided from the Theoretical Calculation of Pairwise Decomposition Energies and Computational Alanine Scanning

Figure 4

Histograms reporting the calculated pairwise decomposition energy which negative numbers in mean highly favorable binding and the relative decomposition energy from the computational alanine scanning mutagenesis experiments compared to wild type of scFv with p17.1. The total bar height reflects the relative binding free energies of each amino acid in CDRs loops with wild type of scFv anti-p17 whose mutation to alanine by alanine scanning mutagenesis. The negative numbers indicated the preference for alanine mutation. Pairwise decomposition analysis 2 ns was extracted from 500 snapshots from 1.5–2 ns whereas the analysis 10 ns was from 500 snapshots from 5–10 ns simulations.
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