Activation of polycystin-1 signaling by binding of stalk-derived peptide agonists
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, United States
- Clinical Laboratory Sciences, University of Kansas Medical Center, United States
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, United States
- Department of Pharmacology and Computational Medicine Program, University of North Carolina, United States
- Department of Physics, and Center for Biophysics and Computational Biology, Temple University, United States
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, United States
Figures
Figure 1 with 2 supplements
Synthetic peptides derived from the stalk sequence of polycystin-1 (PC1) can stimulate the signaling of stalkless PC1 C-terminal fragment (CTF).
(A) Alignment of CTF stalk sequences from human (h) and mouse (m) PC1. CTF∆st has a 21-residue deletion from the N-terminal end of the stalk region. Arrow, GPCR proteolysis site (GPS) cleavage site. …
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Figure 1—source data 1
Uncropped and labeled Western blot data for Figure 1C.
- https://cdn.elifesciences.org/articles/95992/elife-95992-fig1-data1-v1.zip
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Figure 1—source data 2
Raw unedited Western blot data for Figure 1C.
- https://cdn.elifesciences.org/articles/95992/elife-95992-fig1-data2-v1.zip
Figure 1—figure supplement 1
Cell surface expression of mouse polycystin-1 (PC1) C-terminal fragment (CTF), and mCTF∆stk.
Representative Western blot of a surface biotinylation experiment with mCTF and mCTF∆stk. (A) ‘- biotin’ control was included using CTF-transfected cells for which the NHS-biotin reagent was omitted …
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Figure 1—figure supplement 1—source data 1
Uncropped and labeled Western blot data for Figure 1—figure supplements 1 and 2.
- https://cdn.elifesciences.org/articles/95992/elife-95992-fig1-figsupp1-data1-v1.zip
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Figure 1—figure supplement 1—source data 2
Raw unedited Western blot data for Figure 1—figure supplements 1 and 2.
- https://cdn.elifesciences.org/articles/95992/elife-95992-fig1-figsupp1-data2-v1.zip
Figure 1—figure supplement 2
Solubility tag peptide treatment of ev- or CTF∆st-transfected cells.
(A) Sequences of the p17 stalk peptide derived from human polycystin-1 (PC1) and the solubility tag peptide (sol tag). Residues differing from the mouse PC1 stalk sequence are shown in blue. (B–D) …
Figure 2 with 3 supplements
Free energy profile and low-energy conformations of the p9-bound ΔStalk CTF obtained from Pep-GaMD simulations.
(A) Free energy profile of the p9-bound ΔStalk CTF regarding the number of atom contacts between p9 and extracellular domains of CTF and the distance between the CZ atom of R3848 and the CD atom of …
Figure 2—figure supplement 1
Peptide docking conformations and computational model for Peptide GaMD (Pep-GaMD) simulations.
(A–B) Docking conformations of p9, p17, and p21 to ΔStalk CTF. (C) Pep-GaMD simulation system of ΔStalk polycystin-1 (PC1) C-terminal fragment (CTF) (blue cartoon) embedded in a …
Figure 2—figure supplement 2
Contact maps showing residue-pairs in contact (black squares) between the peptide (y-axis) and the extracellular domains of C-terminal fragment (CTF) (x-axis), in the representative ‘Bound’ state for p21 (top), p17 (middle), and p9 (bottom).
Contacts were defined by a distance less than 4 Å between any atom in each residue pair. The secondary structure annotation is colored as in Figure 5, and the sequence is annotated with amino acids …
Figure 2—figure supplement 3
2D free energy profiles of the p9 system regarding the number of atom contacts between the p9 and protein extracellular domains and the R3848-E4078 distance (the CZ atom in R3848 and the CD atom in E4078) calculated from (A) Sim1, (B) Sim2, (C) Sim3, (D) Sim4, and (E) Sim5 of the Peptide GaMD (Pep-GaMD) simulations.
Important low-energy conformational states are identified, including the ‘Unbound’ and ‘Bound’.
Figure 3 with 1 supplement
Free energy profile and low-energy conformations of the p17-bound ΔStalk CTF obtained from Pep-GaMD simulations.
(A) Free energy profile of the p17-bound ΔStalk CTF regarding the number of atom contacts between p17 and extracellular domains of CTF and the distance between the CZ atom of R3848 and the CD atom …
Figure 3—figure supplement 1
2D free energy profiles of the p17 system regarding the number of atom contacts between the p17 and protein extracellular domains and the R3848-E4078 distance (the CZ atom in R3848 and the CD atom in E4078) calculated from (A) Sim1, (B) Sim2, (C) Sim3, (D) Sim4, and (E) Sim5 of the Peptide GaMD (Pep-GaMD) simulations.
Important low-energy conformational states are identified, including the ‘Unbound’ ‘Intermediate,’ and ‘Bound’.
Figure 4 with 2 supplements
Free energy profile and low-energy conformations of the p21-bound ΔStalk CTF obtained from Pep-GaMD simulations.
(A) Free energy profile of the p21-bound ΔStalk CTF regarding the number of atom contacts between p21 and extracellular domains of CTF and the distance between the CZ atom of R3848 and the CD atom …
Figure 4—figure supplement 1
Time courses of the p21 system obtained from the five Peptide GaMD (Pep-GaMD) simulations.
(A) Time courses of the p21 system regarding the TOP-pore loop (PL) interaction distance between the CZ atom in R3848 and the CD atom in E4078. (B) Time courses of the root-mean-square deviation …
Figure 4—figure supplement 2
2D free energy profiles of the p21 system regarding the number of atom contacts between the p21 and protein extracellular domains and the R3848-E4078 distance (the CZ atom in R3848 and the CD atom in E4078) calculated from (A) Sim1, (B) Sim2, (C) Sim3, (D) Sim4, and (E) Sim5 of the Peptide GaMD (Pep-GaMD) simulations.
Important low-energy conformational state is identified, including the ‘Bound’.
Figure 5 with 2 supplements
Potts covariation analysis of residue interactions in polycystin-1 (PC1).
(A) Potts interaction map based on the Polycystic Kidney Disease 1 (PKD1) multiple-sequence-alignment illustrated in Figure 5—figure supplement 2, showing interactions with the stalk. Gray dots are …
Figure 5—figure supplement 1
Sequence alignment of Polycystic Kidney Disease 1 (PKD1) homologs showing the 394-residue extracellular region included in the Potts model.
The full alignment includes 4383 sequences, and only six diverse homologs are shown for illustration. The polycystin-1 (PC1) sequence is shown including inserts relative to the alignment (lower case …
Figure 5—figure supplement 2
Comparison of residue-residue interactions within the end of the polycystin-1 (PC1) GPCR autoproteolysis inducing (GAIN) domain.
(A) Interactions predicted using the Potts model, shaded by interaction strength. Secondary structure elements predicted using an Alphafold structure is annotated along the axes. (B) Contacts …
Author response image 1
Tables
Table 1
Summary of MM/PBSA binding free energy analysis for the peptides p9, p17 and p21 and polycystin-1 (PC1) C-terminal fragment (CTF) in the bound state sampled during Peptide GaMD (Pep-GaMD) simulations.
| System | ΔG (kcal/mol) |
|---|---|
| p21 | –40.29±6.94 |
| p9 | –17.30±4.50 |
| p17 | –12.74±5.62 |
Table 2
Summary of residue-wise energy decomposition analysis between the peptide p9 and polycystin-1 (PC1) C-terminal fragment (CTF) in the bound state sampled during Peptide GaMD (Pep-GaMD) simulations.
| Residue | ΔG (kcal/mol) |
|---|---|
| T1 | –10.47±6.92 |
| A2 | –3.28±2.18 |
| F3 | –2.62±2.62 |
| G4 | –0.30±2.38 |
| A5 | –1.61±2.67 |
| S6 | –0.59±4.49 |
| L7 | –0.28±2.96 |
| F8 | –1.51±1.84 |
| V9 | –10.14±5.68 |
| R3891 | –0.14±7.26 |
| R3892 | –0.31±7.85 |
| F3888 | –3.24±2.95 |
| H3864 | –0.03±3.86 |
| R3970 | –0.94±2.62 |
| R3968 | –0.27±1.67 |
Table 3
Summary of residue-wise energy decomposition analysis between the peptide p17 and polycystin-1 (PC1) C-terminal fragment (CTF) in the bound state sampled during Peptide GaMD (Pep-GaMD) simulations.
| Residue | ΔG (kcal/mol) |
|---|---|
| T1 | –10.98±2.32 |
| A2 | –0.36±2.34 |
| F3 | –0.23±3.82 |
| G4 | –0.03±3.83 |
| A5 | –0.86±3.08 |
| S6 | –0.48±4.06 |
| L7 | –0.05±2.90 |
| F8 | –0.21±4.42 |
| V9 | –0.19±3.41 |
| P10 | –0.72±2.64 |
| P11 | –0.09±3.23 |
| S12 | –0.29±4.92 |
| H13 | –1.19±7.37 |
| V14 | –1.25±3.08 |
| R15 | –10.63±3.76 |
| F16 | –0.93±5.52 |
| V17 | –10.20±3.83 |
| Y3307 | –0.11±2.68 |
| H3311 | –0.04±3.25 |
| R3314 | –8.90±1.65 |
| R3700 | –14.63±7.8 |
| Q3707 | –0.27±4.96 |
| S3711 | –0.08±4.06 |
| E3708 | –10.14±4.15 |
Table 4
Summary of residue-wise energy decomposition analysis between the peptide p21 and polycystin-1 (PC1) C-terminal fragment (CTF) in the bound state sampled during Peptide GaMD (Pep-GaMD) simulations.
| Residue | ΔG (kcal/mol) |
|---|---|
| T1 | –0.25±1.66 |
| A2 | –1.02±2.90 |
| F3 | –0.08±0.10 |
| G4 | –2.42±2.65 |
| A5 | –0.11±2.15 |
| S6 | –0.09±1.31 |
| L7 | –0.83±1.43 |
| F8 | –0.68±1.10 |
| V9 | –8.17±2.10 |
| P10 | –6.16±1.79 |
| P11 | –1.22±2.83 |
| S12 | –0.05±2.56 |
| H13 | –1.13±3.74 |
| V14 | –1.16±1.78 |
| R15 | –0.59±1.02 |
| F16 | –0.59±1.02 |
| V17 | –1.59±1.13 |
| F18 | –0.20±1.37 |
| P19 | –7.09±1.51 |
| E20 | –3.76±2.24 |
| P21 | –8.43±2.01 |
| L3863 | –0.33±2.28 |
| L3701 | –0.04±2.39 |
| I3705 | –0.51±2.16 |
| E3708 | –1.68±3.11 |
| R3712 | –3.85±1.56 |
| F3714 | –0.01±2.28 |
| W3726 | –2.93±2.11 |
| H3729 | –0.56±2.00 |
| L3732 | –0.26±2.49 |
| P3733 | –0.61±2.33 |
| N3738 | –0.07±4.91 |
| S3741 | –0.03±4.27 |
