Seung Joong Kim, Charles Dumont, Martin Gruebele Biophysical Journal

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Simulation-Based Fitting of Protein-Protein Interaction Potentials to SAXS Experiments Seung Joong Kim, Charles Dumont, Martin Gruebele Biophysical Journal Volume 94, Issue 12, Pages 4924-4931 (June 2008) DOI: 10.1529/biophysj.107.123240 Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 1 Method for extracting the protein-protein potential from SAXS data. In step 1, a protein ensemble of up to 100 molecules is simulated by Monte Carlo or molecular dynamics. In step 2, the exact x-ray scattering for the model ensemble is evaluated at each simulation snapshot. In step 3, the average x-ray scattering curve is obtained and compared with experimental data. In step 4, the interaction potential is adjusted by steepest descent for the next round of simulation. Biophysical Journal 2008 94, 4924-4931DOI: (10.1529/biophysj.107.123240) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 2 Scattering intensity versus magnitude of the scattering vector for λ6−85 (A) and fyn-SH3 (B). The lines going through the experimental data points are fits from Monte Carlo simulation. Biophysical Journal 2008 94, 4924-4931DOI: (10.1529/biophysj.107.123240) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 3 (A) Best-fit interaction potential for λ6−85 and fyn-SH3 (in 45% ethylene glycol buffer at −28°C). (B) Comparison of the MMC and analytical best-fit hard sphere plus Yukawa potentials for λ6−85. The greatest variation between the three λ6−85 shown is in D0. (MMC parameters: D0=35.5Å, δ=4.14Å, ɛ=1.65 kT0, and Rg=13.8Å; analytical: D0=37.8Å, δ=4.14Å (fixed), ɛ=1.71 kT0, and Rg=13.6Å). Biophysical Journal 2008 94, 4924-4931DOI: (10.1529/biophysj.107.123240) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 4 Experiment (circles with error bars) and molecular dynamics simulation (thick solid line) of the scattering intensity versus magnitude of the scattering vector for λ6−85 (A) and fyn-SH3 (B), confirming the quality of the parameter set obtained by MC modeling. The estimated 1σ sampling error we achieved in the MD simulations is indicated by the envelopes. (Insets) Native PDB structures for the protein fragments, as visualized with VMD (29). Biophysical Journal 2008 94, 4924-4931DOI: (10.1529/biophysj.107.123240) Copyright © 2008 The Biophysical Society Terms and Conditions