Skip to main content
Dryad logo

Molecular models of the FtsQ-FtsL-FtsB-FtsW-FtsI complex (FtsQLBWI) in mono- and diprotomeric configurations

Citation

Condon, Samson G. F.; Craven, Samuel J.; Senes, Alessandro (2022), Molecular models of the FtsQ-FtsL-FtsB-FtsW-FtsI complex (FtsQLBWI) in mono- and diprotomeric configurations, Dryad, Dataset, https://doi.org/10.5061/dryad.69p8cz957

Abstract

The data consists of five Protein Data Bank (PDB) structure files of the complex formed by FtsQ, FtsL, FtsB, FtsW, and FtsI of the divisome of Escherichia coli (FtsQLBWI).  The five PDB files consist of an original AlphaFold2 model, partially validated through mutagenesis in vivo, and a series of derivatives remodeled seeking insight into the potential structural transitions that lead to activation of the FtsWI complex, which produced peptidoglycan during cell division. In the original model (file FtsQLBWI_protomer_original.pdb), FtsLB serves as a support for FtsI, placing its periplasmic domain in an extended and possibly active conformation.  We remodeled the periplasmic domain of FtsI to assess it the model is compatible with a compact and possibly inactive conformation (file FtsQLBWI_protomer_compact.pdb). Additionally, the complex was remodeled to assume an Fts[QLBWI]2 diprotomeric configuration, using FtsLB as a central hub (file FtsQLBWI_diprotomer_clashing.pdb).  This was performed by applying the C2 symmetry operation (180° rotation) to the Fts[QLBWI]1 complex that reconstructs the Fts[LB]2 complex in the Y-model configuration from the Fts[LB]1 AlphaFold2 prediction.  In this model, a severe steric overlap occurs between FtsQ and FtsI, which occupy the same region of space adjacent to FtsLB. To address whether this clash could be solved by providing flexibility to a hinge in the CCD region of FtsLB, we used a procedure, based on docking of FtsQ with HADDOCK followed by loop reconstruction with Rosetta (file FtsQLBWI_diprotomer_extended.pdb). Finally, we reconfigured the initial diprotomeric model in a compact state (file FtsQLBWI_diprotomer_compact.pdb).

Methods

The original data was obtained by submitting the sequences of FtsQ, FtsL, FtsB, FtsW, and FtsI to AlphaFold2 (ColaFold) (1). The monoprotomeric FtsQLBWI complex was reconfigured using homology modeling using the SWISS-MODEL webserver (2). The reconfiguration in a diprotomeric configuration was performed using a program written with MSL (3). Remodeling of FtsQ in the diprotomeric extended state was performed with HADDOCK (4) and Rosetta (5).

References:

1. Mirdita M, Ovchinnikov S, Steinegger M. ColabFold - Making protein folding accessible to all [Internet]. Bioinformatics; 2021 Aug [cited 2021 Sep 14].

2. Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 2018 Jul 2;46(W1):W296–303.

3. Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G, et al. Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL). J Comput Chem. 2012 Jul 30;33(20):1645–61.

4. Dominguez C, Boelens R, Bonvin AMJJ. HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information. J Am Chem Soc. 2003 Feb 19;125(7):1731–7.

5. Huang PS, Ban YEA, Richter F, Andre I, Vernon R, Schief WR, et al. RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design. Uversky VN, editor. PLoS ONE. 2011 Aug 31;6(8):e24109.

Usage Notes

A PDB viewer such as PyMOL or Swiss PDB viewer.

Funding

National Institutes of Health, Award: R35-GM130339