Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulations -- Merchant et al. 104 (5): 1528 Data Supplement - HTML Page - index.htslp -- Proceedings of the National Academy of Sciences

Merchant et al. 10.1073/pnas.0607097104.

Supporting Information

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SI Text
SI Figure 8
SI Figure 9
SI Figure 10
SI Table 1
SI Table 2
SI Figure 11

SI Figure 8

Fig. 8. Effects of chain dynamics on the life-time: Gaussian chain without dynamics (black) (Eq. 6); with diffusion constant D = 16 Å²/ns from Buscaglia et al. (1) (red); with very rapid diffusion (D = 160 Å²/ns) (green), showing that an unphysically large value of the diffusion constant is required to easily detect the influence of polypeptide motion in the donor fluorescence decay. The donor fluorescence decays computed using Eq. 15 were convolved with the instrument response function, and the maximum values of each curve were normalized to unity.

1. Buscaglia M, Kubelka J, Eaton WA, Hofrichter J (2005) J Mol Biol 347:657-664.

SI Figure 9

Fig. 9. Distributions of end-to-end distance R as a function of denaturant concentration, calculated from all-atom simulations of protein L and CspTm in explicit aqueous urea solutions: 0.0 M (A), 2.1 M (B), 4.2 M (C), and 6.2 M (D). The red curves are fits of Gaussian-chain distributions to the calculated distributions.

SI Figure 10

Fig. 10. Distributions of radius of gyration R_g as a function of denaturant concentration calculated from all-atom simulations of protein L and CspTm in explicit aqueous urea solutions: 0.0 M (A), 2.1 M (B), 4.2 M (C), and 6.2 M (D).

SI Figure 11

Fig. 11. (A) FRET histograms for protein L at 4 M GdmCl for 1 ms (blue) and 2 ms (green) observation times counting only those bursts containing 25-35 photons. Events are defined by dividing trajectories into either 1- or 2-ms bins and accepting as events only those bins containing between 25 and 35 photons. Accepting all bins with at least 25 photons gives quantitatively similar results. The widths are insensitive to observation time, indicating that the source of the additional broadening is on a time scale much longer than 1 ms. (B) Distribution of FRET burst durations for protein L at 4 M GdmCl using the burst definition as defined in Materials and Methods. A wide distribution of burst durations are present and are sampled by the 1- and 2-ms binning.