Volume 111, Issue 11, Pages 2368-2376 (December 2016) High-Resolution Mapping of a Repeat Protein Folding Free Energy Landscape  Martin J. Fossat, Thuy P. Dao, Kelly Jenkins, Mariano Dellarole, Yinshan Yang, Scott A. McCallum, Angel E. Garcia, Doug Barrick, Christian Roumestand, Catherine A. Royer  Biophysical Journal  Volume 111, Issue 11, Pages 2368-2376 (December 2016) DOI: 10.1016/j.bpj.2016.08.027 Copyright © 2016 Biophysical Society Terms and Conditions

Figure 1 Ribbon diagram of the crystal structure of the leucine-rich repeat protein pp32 (PDB: 2JE0) (16). The N-terminal cap is shown in yellow, the first repeat is colored in red, the second in green, the third in blue, the fourth in purple, the fifth in brown, and the C-terminal cap in cyan. The major cavity is displayed in gray. The cavity was visualized using the software HOLLOW (34) with a grid of 0.25 Å and a probe radius of 1.2 Å. Rendered using the PyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC. To see this figure in color, go online. Biophysical Journal 2016 111, 2368-2376DOI: (10.1016/j.bpj.2016.08.027) Copyright © 2016 Biophysical Society Terms and Conditions

Figure 2 NMR detected high pressure unfolding of pp32 at 303 K and 1.4 M urea. (A–C) Examples of 1H-15N HSQC spectra at different pressures as indicated. (D) Examples of three residues exhibiting distinct unfolding profiles. To see this figure in color, go online. Biophysical Journal 2016 111, 2368-2376DOI: (10.1016/j.bpj.2016.08.027) Copyright © 2016 Biophysical Society Terms and Conditions

Figure 3 Distribution of the apparent ΔVf and ΔGf0 values (top and middle panels, respectively) obtained from fits of the residue-specific pressure unfolding profiles at each temperature as indicated. The lines in the top and middle panels represent a Gaussian fits to each parameter distribution. The bottom panels provide the means and SDs of the distributions at each temperature; the error bars represent the SD of the fitted Gaussian distributions. To see this figure in color, go online. Biophysical Journal 2016 111, 2368-2376DOI: (10.1016/j.bpj.2016.08.027) Copyright © 2016 Biophysical Society Terms and Conditions

Figure 4 Fractional contact maps for pp32 calculated from the NMR HSQC peak intensity as described in the text at 900 bar, 1.4 M urea, and at different temperatures as indicated. Fraction represents the probability that a contact is formed in the ensemble. The color scale is the same for all temperatures. Gray dots above the diagonal correspond to native contacts calculated from the crystal structure (PDB: 2JE0), colored dots below the diagonal correspond to contact probabilities calculated from the NMR data as described in the text. The full color scale corresponds to fractional contacts between 60 and 90%. To see this figure in color, go online. Biophysical Journal 2016 111, 2368-2376DOI: (10.1016/j.bpj.2016.08.027) Copyright © 2016 Biophysical Society Terms and Conditions

Figure 5 Histograms of the probability of native contact at 900 bar and 1.4 M urea at all four tested temperatures, as listed. The histogram is colored for each repeat and cap using the color code in Fig. 1. Each residue contributing to a contact is counted in the repeat it belongs to, such that interfacial contacts are counted once in each repeat, and those involved in a residue pair within a repeat are counted twice in the repeat. To see this figure in color, go online. Biophysical Journal 2016 111, 2368-2376DOI: (10.1016/j.bpj.2016.08.027) Copyright © 2016 Biophysical Society Terms and Conditions

Figure 6 Heat maps of RMSD versus Q (percentage of native contacts) for conformational ensembles of pp32 obtained from the coarse-grained simulations at 298, 293, 298, and 303 K in 1.4 M urea. Note the heat map scale is logarithmic. To see this figure in color, go online. Biophysical Journal 2016 111, 2368-2376DOI: (10.1016/j.bpj.2016.08.027) Copyright © 2016 Biophysical Society Terms and Conditions

Figure 7 (Inset) Pseudo-free energy landscape as extracted from the simulations using the data obtained at 293 K. The displayed structures are reconstructed from the free energy regions indicated by the corresponding letters (A–F). Representative structures were obtained as described in the Materials and Methods. Structures are colored as in Fig. 1. Similar figures for other temperatures can be found in the Supporting Material. To see this figure in color, go online. Biophysical Journal 2016 111, 2368-2376DOI: (10.1016/j.bpj.2016.08.027) Copyright © 2016 Biophysical Society Terms and Conditions