Structural and Biochemical Studies on Procaspase-8: New Insights on Initiator Caspase Activation  Nadine Keller, Jiří Mareš, Oliver Zerbe, Markus G. Grütter  Structure  Volume 17, Issue 3, Pages 438-448 (March 2009) DOI: 10.1016/j.str.2008.12.019 Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 1 Dynamic Analysis and Solution Structure of Procaspase-8 (A) 700 MHz [15N,1H]-HSQC spectrum of procaspase-8 recorded at 305 K. (B) 15N{1H}-NOE of the backbone amide moieties of procaspase-8. Values between 0.7 and 1 indicate rigidity of the protein, whereas values below 0.5 imply increasing flexibility. Values below 0 indicate complete loss of structure. Blank regions are due to amides that have not been assigned. (C) Superposition of the backbone atoms of secondary structural elements of the 20 lowest-energy structures of procaspase-8 as determined by NMR. The central β sheet is colored blue; the surrounding α helices are shown in red. The linker is depicted in green. The graphic was produced using MolMol (Koradi et al., 1996). (D) Stereo model of best energy structure of the 20-structure bundle. The color coding is the same as described in (C). The nomenclature of the different loops as used in this publication is annotated on the structure. Loops 4 and 5 are not defined in the NMR structure and are modeled as smooth loops in the presented stereo view. The actual position of these loops is unknown. This graphic was prepared using PyMOL (DeLano Scientific LLC, http://www.pymol.org). Structure 2009 17, 438-448DOI: (10.1016/j.str.2008.12.019) Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 2 Comparison of Procaspase-8 (Blue) with Active Caspase-8 (Red), Respective Linker Rearrangements, and Substrate Binding (A) Superposition of the solution procaspase-8 structure with one caspase-8 monomer (1QTN). The missing loops 4 and 5 are omitted in the procaspase-8 structure. (B–D) Differences in the positions of the loops and the linker. The molecules are depicted in light colors with the regions of interest shown in bright colors. Arrows indicate the rearrangements of the loops and the linker fragments during caspase-8 activation. (B) The top panel shows the rearrangement of loop 1 from procaspase-8 to caspase-8. The lower panel shows the NOE restrains defining the position of the procaspase-8 loop 1 respective to loop 3. For simplicity protons are omitted and restrains applied to the corresponding carbons. The involved residues are presented as labeled sticks. (C) Rearrangement of loop 3 during caspase-8 activation. (D) Relocation of the linker after processing. The P1 Asp of the two cleavage sites are shown as labeled sticks. The arrows define the movement of the C-terminal part of the α subunit (L2 loop) and the N-terminal part of the β subunit (L2′ loop). The central ten amino acids of the linker are removed during processing. (E) Binding of a DEVD tetrapeptide (yellow sticks) to the active site pocket of caspase-8 and modeling of the inhibitor into the corresponding region of procaspase-8. The linker is shown in green. Structure 2009 17, 438-448DOI: (10.1016/j.str.2008.12.019) Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 3 Definition of the Position of the Linker by NOE-Derived Restrains Observed NOEs between linker residues (green) and the rest of the protein (blue) are indicted by dashed lines. For clarity the hydrogen positions are omitted and the constraints applied to the corresponding carbons. Structure 2009 17, 438-448DOI: (10.1016/j.str.2008.12.019) Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 4 Overview of Caspase-8 Constructs Shown is the catalytic domain of caspase-8. The two subunits are defined as squares. The positions of the single amino acid substitutions and truncations are indicated (full-length caspase-8 numbering; C285A in accordance with caspase-1 numbering). Structure 2009 17, 438-448DOI: (10.1016/j.str.2008.12.019) Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 5 Structural Features Important for Dimerization of Caspase-8 (A) Backbone trace of caspase-8. The caspase-8 dimer is shown in red and the linker in green. (B) Close-up highlighting L2 loop interactions. Caspase-8 has the same orientation as in A, with one caspase-8 protomer being shown as a cartoon and the other as a surface presentation. The L2 loop of one protomer occupies a pocket formed by the L2′ loop and the core of the other protomer. L2 loop residues that are deleted in the α-trunc mutant are shown as sticks. (C) Interaction of Pro and Phe residues at the dimerization interface. The molecule is rotated by 180° compared with (A), now viewing from the back side of the dimer. Side chains of Pro466 and Phe468 are shown as green sticks. Structure 2009 17, 438-448DOI: (10.1016/j.str.2008.12.019) Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 6 Structure and Sequence Comparison of Procaspase-8 with Other Caspases (A) Superposition of procaspase-8 (blue) and procaspase-7 (brown, Protein Data Bank code 1K88). The proteins are depicted in light colors with the linker residues indicated in bright blue and brown, respectively. The X-ray structure for procaspase-7 reveals only the termini of the linker. (B) Sequence alignment of the linker segment of different initiator procaspases and the executioner procaspase-7. The caspase cleavage recognition motifs are highlighted. Structure 2009 17, 438-448DOI: (10.1016/j.str.2008.12.019) Copyright © 2009 Elsevier Ltd Terms and Conditions