Volume 13, Issue 8, Pages 1193-1202 (August 2005) NMR Structural Characterization and Computational Predictions of the Major Intermediate in Oxidative Folding of Leech Carboxypeptidase Inhibitor  Joan L. Arolas, Loyola D’Silva, Grzegorz M. Popowicz, Francesc X. Aviles, Tad A. Holak, Salvador Ventura  Structure  Volume 13, Issue 8, Pages 1193-1202 (August 2005) DOI: 10.1016/j.str.2005.05.008 Copyright © 2005 Elsevier Ltd Terms and Conditions

Figure 1 RP-HPLC Analysis of the Folding Intermediates of LCI Trapped by Acidification Oxidative folding was carried out at 22°C in Tris-HCl buffer (0.1 M [pH 8.4]) with (Control +) or without (Control −) the redox agent 2-mercaptoethanol (0.25 mM). The protein concentration was 0.5 mg/ml. Folding intermediates were trapped at the noted times by acidification and were analyzed by RP-HPLC by using the conditions described in Experimental Procedures. “N” and “R” indicate the elution positions of the native and fully reduced species of LCI, respectively. “III-A” and “III-B” are two major intermediates containing three native disulfides, and “scrambled forms” are isomers with four disulfides. Structure 2005 13, 1193-1202DOI: (10.1016/j.str.2005.05.008) Copyright © 2005 Elsevier Ltd Terms and Conditions

Figure 2 2D 1H-15N-HSQC Spectra of Uniformly 15N-Labeled Native LCI and the III-A Intermediate (A and B) Backbone crosspeak assignments are indicated for both (A) native LCI and (B) III-A. The experiments were carried out with 1 mM protein concentration in H2O/D2O (9:1) at pH 3.5 and 27°C. Structure 2005 13, 1193-1202DOI: (10.1016/j.str.2005.05.008) Copyright © 2005 Elsevier Ltd Terms and Conditions

Figure 3 Stereoview of the Structure of Native LCI and the III-A Intermediate Ribbon representation of the calculated structure for native LCI (upper panel) and III-A (lower panel). β strands are shown in blue, and the α helix is shown in red. “N” and “C” indicate the location of the N- and C-terminal tails of both proteins. The disulfide bonds are shown in yellow. Structure 2005 13, 1193-1202DOI: (10.1016/j.str.2005.05.008) Copyright © 2005 Elsevier Ltd Terms and Conditions

Figure 4 Stereoview with the Superposition of the Calculated Structures for Native LCI and the III-A Intermediate The pictures show the backbone atoms of the bundle of lowest-energy structures calculated for native LCI (upper panel) and III-A (lower panel). β strands are indicated in blue, and the α helix is shown in red. The N- and C-terminal tails are labeled. Structure 2005 13, 1193-1202DOI: (10.1016/j.str.2005.05.008) Copyright © 2005 Elsevier Ltd Terms and Conditions

Figure 5 Comparison of Local Rmsd Values for Backbone Atoms of Native LCI and III-A The rms deviations of the backbone atoms from the 20 calculated structures are plotted versus the residue number (residues 6–64). Secondary structure elements for native LCI are indicated inside the graphic. Structure 2005 13, 1193-1202DOI: (10.1016/j.str.2005.05.008) Copyright © 2005 Elsevier Ltd Terms and Conditions

Figure 6 Folding Pathway Prediction for LCI Hierarchy of structure formation for LCI computed with Fold-X software. The residue number is reported on the vertical axis. The horizontal axis corresponds to the percentage of ordered residues. The secondary structure elements of the native protein are shown on the left side. The color code reflects the probability for a residue to be ordered during the folding process (dark blue corresponds to 0%, and red corresponds to 100%). Structure 2005 13, 1193-1202DOI: (10.1016/j.str.2005.05.008) Copyright © 2005 Elsevier Ltd Terms and Conditions