Fig 1.
Probe placement scheme and comparison to DEER data.
(A) A pool of 46 conformations of the MTSSL probe from the rotamer library are aligned to the backbone of residues K55 and K55’ of HIV-1 protease. The color code represent the Boltzmann weights of each rotamer, increasing from blue to red. (B) Electron-electron distance distribution for HIV-1 protease spin labeled at residues K55 and K55’. The blue line is the experimental data from Torbeev et al. [44] whereas the red line is the prediction using DEER-PREdict and a crystal structure of HIV-1 protease (PDB code 3BVB).
Fig 2.
Comparing experiments and simulations for HIV1-PR.
DEER distance distributions (A) and echo intensity curves (B) obtained by Torbeev et al. [44] from DEER experiments (blue), and calculated using DEER-PREdict from unbiased (orange) and RDC ensemble-biased MD simulations (red).
Fig 3.
Comparing experiments with simulations and structures of T4 lysozyme variants.
DEER distance distributions for probe positions (A) D89C–T109C and (B) T109C–N140C of the single (blue) and the triple variant (red). Solid lines are the experimental data by Lerch et al. [83], dotted lines are calculated from PDB codes and dashed lines are predictions from metadynamics (MTD) simulations by Wang and coworkers [80].
Fig 4.
Calculated and experimental PRE HSQC intensity ratios for the T17C, V36C, M46C, S65C and I86C mutants of ACBP.
Blue lines represent the experimental data [53], with the associated ±0.1 error shown by the blue shaded areas. Red lines represent intensity ratios calculated from PDB code 1NTI with τc = 2 ns, τt = 0.2 ns, td = 10 ms, R2 = 12.6 s−1.