Deep learning-driven insights into super protein complexes for outer membrane protein biogenesis in bacteria
- Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, United States
- School of Computer Science, Georgia Institute of Technology, United States
Figures
Figure 1 with 1 supplement
E. coli super-translocon SecYEG/PpiD/YfgM.
(a) Computational screening for protein-protein interaction partners of PpiD and YfgM within the E. coli envelopome, respectively. A histogram displays the distribution of the top interface scores …
Figure 1—figure supplement 1
Comparison of a computed structure of SecY (silver) and two experimental structures (magenta).
(a) Superposition of an X-ray crystal structure of SecY from G. thermodenitrificans (PDB code: 5EUL) onto SecY from the predicted structure of the E. coli SecYEG/PpiD/YfgM supercomplex. In the …
Figure 2
Structural model of the SecYEG/PpiD/YfgM/DsbA supercomplex.
(a) Two views of the predicted structure. DsbA is shown in red, while the other proteins are colored the same as in Figure 1. Two cysteines, Cys49 and Cys52, essential to the enzymatic function of …
Figure 3
Predicted structure of the PpiD/YfgM/LepB/OmpA supercomplex.
(a) Two views in the cartoon representation are shown. Colors: PpiD (blue), YfgM (green), LepB (magenta), and OmpA (residue 1–87, yellow). For clarity, representations of PpiD and LepB are …
Figure 4 with 1 supplement
Structural models of SurA in the absence and presence of an OmpA substrate.
(a) Open and closed conformations of monomeric SurA, consisting of the core domain (N-terminal region in gray and C-terminal in tan), P1 (purple), P2 (red). (b and c) Two structures of SurA in the …
Figure 4—figure supplement 1
Structural models of the OmpA polypeptide in the absence of SurA.
(a) Predicted model of OmpA obtained with a shallow multiple sequence alignments (MSAs) and no structural templates. The N-terminal β-barrel domain is collapsed but not in its native fold; the …
Figure 5
Structural model of SurA docked to β-barrel assembly machine (BAM).
(a and b) Two views of the top ranked supercomplex model in the cartoon representation. The BAM constituents are BamA (green), BamB (pink), BamC (yellow), BamD (blue), and BamE (black). The …
Figure 6 with 1 supplement
Structural models of β-barrel assembly machine (BAM) and BepA.
(a) Computational protein-protein interaction screening identifies BepA as a top hit to BamA. (b) Top structural model of the heterodimeric complex of BamA (green) and BepA (purple) in cartoon …
Figure 6—figure supplement 1
Predicted structures of BepA compared to two experimental structures.
(a and b) Superposition of structural models of the lid (red/magenta) in closed and open states, respectively, onto a crystal structure (PDB code: 6AIT, cyan). (c) Superposition onto another crystal …
Figure 7
Proposed mechanisms involved in the outer membrane protein (OMP) biogenesis pathway in E. coli.
Complex structures resulting from this study accompany relevant cartoon diagrams. Powered by SecA, a precursor OmpA polypeptide (orange line) first passes through the SecYEG translocon in complex …
Additional files
-
Supplementary file 1
Top hits from the protein-protein interaction (PPI) screening over the E. coli envelopome with AF2Complex for query proteins: PpiD, YfgM, SurA, and BamA.
- https://cdn.elifesciences.org/articles/82885/elife-82885-supp1-v1.xlsx
-
MDAR checklist
- https://cdn.elifesciences.org/articles/82885/elife-82885-mdarchecklist1-v1.pdf
