ULP-1 Protease in NeSL-1

Molecular Modeling UCSF Chimera.

General Structure of the NeSL-1 ORF in Caenorhabitis sp.

General Structure of the NeSL-1 ORF

General Structure of the NeSL-1 ORF in Caenorhabitis

General Structure of the NeSL-1 ORF

General Structure of the NeSL-1 ORF

General Structure of the NeSL-1 ORF

Experimental Models of the ULP-1 Protease-SUMO-1 Interaction in NeSL-1

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Figure 3. Caenorhabitis elegans ULP-1 protease model after identification of template, 1EUV Chain A, (Saccharomyces cervisae ULP-1) within Swiss Model workspace. Hydrogen bonds generated and final reconstruction performed using UCSF Chimera, v.15.5.1.

 

Experimental Models of the ULP-1 Protease-SUMO-1 Interaction in NeSL-1

Figure 4. The Ulp-1 protease is shaded in green with SUMO-1 docked to the Caenorhabitis Ulp-1 without showing the surface zone. This was modeled using the template 1EUV (X-RAY STRUCTURE OF THE C-TERMINAL ULP1 PROTEASE DOMAIN IN COMPLEX WITH SMT3, THE YEAST ORTHEOLOG OF SUMO) in the Swiss-Model Workspace and rendered in UCSF Chimera.

Experimental Models of the ULP-1 Protease-SUMO-1 Interaction in NeSL-1

Figure 5. Both the Ulp-1 and SUMO protein models are shown. The Ulp-1 protein is shaded cyan, and the conserved catalytic residues are labeled. SUMO-1 is shaded pink for contrast.

Experimental Models of the ULP-1 Protease-SUMO-1 Interaction in NeSL-1

Figure 6. The surface region of the residues in the catalytic core is shaded red, representing the shallow cleft where the c-terminal residues of SUMO interact with the catalytic region in Ulp-1.

ULP-1 Residue Conservation• Table 2. The amino acid sequence of the ULP-1 protease in the Saccharomyces

cervisae C-terminal catalytic domain (1euv, Chain A) is aligned with the four sequences of the NeSL-1 Caenorhabitis Ulp-1 protease (T-Coffee).

ULP-1 Residue Conservation• Figure 7. The aligned residues of the Ulp-1 protease in all four

Caenorhabitis species with the ULP-1 protease of Saccharomyces cervisae are shown (Table 2). In the models above, the regions of poor conservation are in yellow and the conserved residues are in slate blue only with respect to the residues between the Ulp-1 of S. cervisae and Caenorhabitis NeSL-1 protease. The regions of conservation are in slate blue.

ULP-1 Secondary structure Residue Conservation• Table 2. The amino acid sequences of the NeSL-1 Ulp-1 protease are aligned to

identify the conserved residues only with respect to the Caenorhabitis species. The secondary structure is shown below the graph of conservation (JNET server @ Predict Protein).

ULP-1 Residue Conservation• Figure 8. The aligned residues of the Ulp-1 protease in all four

Caenorhabitis species are shown. In the models, the regions of poor conservation are in yellow and the conserved residues are in slate blue. The SUMO protein is presented without surface depiction to show the potential interactive sites between the Ulp-1 and SUMO-1.

ULP-1 Residue Conservation• Figure 9. The surface

zone interactions between the Ulp-1 protease and SUMO-1 models of Caenorhabitis NeSL-1 are shown above using a black background for contrast. The surfaces were colored by Coulombic ESP and rendered in UCSF Chimera. The interactive zones were identified and selected prior to computing the interface surface in InterSurf.