FIGURE 2.
Schematics of the soft balls used to probe the SecY complex. Although protein atoms will start to feel a ball at center-of-mass distance , at a center-of-mass distance Rh + σ, EBP is ε, which is specified to be 1 kcal/mol in our simulations, where the outmost part of such a ball is fairly soft, that volume should be easily accessible to protein atoms. We use Rh + σ as the effective ball radius (denoted R in the text).