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. 2013 Oct 24;9(10):e1003277. doi: 10.1371/journal.pcbi.1003277

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© 2013 Bhattacherjee, Wallin

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

PMC Copyright notice

As a quantitative test of the all-atom model [36] used in this work, we calculate binding free energies, , for the protein PSD95 and 9 different peptide sequences. The values were obtained from protein-peptide binding simulations performed separately for each PSD95-peptide pair according to our previous protocol [35], [36] (see also Methods) and using Equation 2. The peptide sequences considered are derived from KKETEV (black diamond) and are either -variants, KKETE-[I/L/M/F/A/T], (black diamonds) or -variants, KKE[S/C]EV (red circles). All simulations were performed at and standard errors were estimated from 10 independent runs. Experimental binding free energies, , are taken from Ref. [46]. Both and values are shown relative to the weakest binding peptide. The solid line represents the best linear fit, exluding KKECEV, and the correlation coefficient is .

Inline graphic — As a quantitative test of the all-atom model [36] used in this work, we calculate binding free energies, , for the protein PSD95 and 9 different peptide sequences. The values were obtained from protein-peptide binding simulations performed separately for each PSD95-peptide pair according to our previous protocol [35], [36] (see also Methods) and using Equation 2. The peptide sequences considered are derived from KKETEV (black diamond) and are either -variants, KKETE-[I/L/M/F/A/T], (black diamonds) or -variants, KKE[S/C]EV (red circles). All simulations were performed at and standard errors were estimated from 10 independent runs. Experimental binding free energies, , are taken from Ref. [46]. Both and values are shown relative to the weakest binding peptide. The solid line represents the best linear fit, exluding KKECEV, and the correlation coefficient is .