Michael S. Lee, Mark A. Olson Biophysical Journal

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Presentation transcript:

Calculation of Absolute Protein-Ligand Binding Affinity Using Path and Endpoint Approaches Michael S. Lee, Mark A. Olson Biophysical Journal Volume 90, Issue 3, Pages 864-877 (February 2006) DOI: 10.1529/biophysj.105.071589 Copyright © 2006 The Biophysical Society Terms and Conditions

Figure 1 One-dimensional potential of mean force for pulling BUQ out of the FKBP binding pocket using GB-SA and hybrid explicit/implicit solvent models. See Theory and Methods sections for simulation details. Solid line indicates a hybrid solvent and dashed line signifies GB-SA implicit solvent. Arbitrary vertical shifts of each curve were manually adjusted so that the perceived asymptotic values of the PMF are located near 0. Biophysical Journal 2006 90, 864-877DOI: (10.1529/biophysj.105.071589) Copyright © 2006 The Biophysical Society Terms and Conditions

Figure 2 One-dimensional potential of mean force for pulling FK506 out of the FKBP binding pocket using GB-SA and hybrid solvent models. See Fig. 1 for legend and details. Biophysical Journal 2006 90, 864-877DOI: (10.1529/biophysj.105.071589) Copyright © 2006 The Biophysical Society Terms and Conditions

Figure 3 Distribution of modes for normal mode and quasiharmonic vibration calculations for the FKBP-BUQ complex. Harmonic modes (thin line) are shown for one complex structure from the RD4 calculation. Quasiharmonic modes (thick line) were obtained from the 1.5-ns production run of the GB-SA complex simulation. Frequency bins start at 1cm−1 and exponentially increase with a multiplier of 1.1. Biophysical Journal 2006 90, 864-877DOI: (10.1529/biophysj.105.071589) Copyright © 2006 The Biophysical Society Terms and Conditions

Figure 4 Contribution to free entropy values from harmonic/quasiharmonic modes. See Fig. 3 for legend and details. Biophysical Journal 2006 90, 864-877DOI: (10.1529/biophysj.105.071589) Copyright © 2006 The Biophysical Society Terms and Conditions