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. 2006 Feb 3;90(8):2718–2730. doi: 10.1529/biophysj.105.073304

FIGURE 2.

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 Inline graphic, 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).

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