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PreprintCited by 3Protein Structure and DynamicsBiochemical and Structural CharacterizationEnzyme Structure and Function

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Two different and robustly modeled DNA binding modes of Competence Protein ComP - systematic modeling with AlphaFold 3, RoseTTAFold2NA, Chai-1 and re-docking in HADDOCK

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Helsem, Stian Aleksander, Alfsnes, Kristian, Frye, Stephan A., Hesselberg Løvestad, Alexander, Ambur, Ole Herman·2024·PLoS ONE
DOI 10.1101/2024.11.23.625027PMC PMC12061091

Preprint — published as 10.1371/journal.pone.0315160 · Paper page

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Abstract

The competence protein ComP is a Type IV minor pilin and the extracellular DNA binding protein involved in natural transformation in the human pathogens Neisseria gonorrhoeae , Neisseria meningitidis, Eikenella corrodens and related Neisseriaceae bacteria. Details of the DNA binding mode of ComP is enigmatic, and the 3D structure of the DNA :: protein complex remains unresolved. Here we characterize the ComP orthologs in a set of Neisseriaceae family members, model their common structural domains and their interaction with different preferred 12 base pair long DNA binding motifs, DNA Uptake Sequences (DUS) and scrambled versions of these. Through systematic in silico modeling using AlphaFold 3, RoseTTAFold2NA, and Chai-1 and model comparisons, we bring a new understanding of the interactions between DNA and ComP. We report six distinct binding modes of which two, here named Epsilon and Gamma, were robustly modeled across platforms and different ComPs. The characteristics and robustness of the predicted models and DNA binding modes from each tool are assessed and discussed. This work expands the knowledge on the ComP :: DUS interaction and guides further wet- and dry-lab systematic and experimental characterization of these complexes through which molecular and clinical interventions may be developed.

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Figures

Fig 1 Flowchart of the study showing the steps taken to model native ComPnat with Chai-1, RF2NA and AF3 and re-docking of top-ranking RF2NA models in HADDOCK. AF3 modeling of ComPscr follow dashed lines on the right side. Boxes with inputs are white, processes light gray and outputs dark grey. All data sources and parameters used are described in the text.
Fig 1 Flowchart of the study showing the steps taken to model native ComPnat with Chai-1, RF2NA and AF3 and re-docking of top-ranking RF2NA models in HADDOCK. AF3 modeling of ComPscr follow dashed lines on the right side. Boxes with inputs are white, processes light gray and outputs dark grey. All data sources and parameters used are described in the text.CC BY · PubMed Central
Fig 2 Structural overlay of ComPs from seven Neisseriaceae species. These are AF3 models aligned on the α-carbons of the model with the best ipTM score, Purple: ComPK.den; Green: ComPN.sub. Turquoise: ComPB.den. Yellow: ComPN.muc. Pink: ComPE.cor. Grey: ComPN.men. Blue: ComPN.cin. The β-strands are numbered, and domains labelled. The three representations are 90° right turns around the N-terminal α-helix aligned on the y-axis.
Fig 2 Structural overlay of ComPs from seven Neisseriaceae species. These are AF3 models aligned on the α-carbons of the model with the best ipTM score, Purple: ComPK.den; Green: ComPN.sub. Turquoise: ComPB.den. Yellow: ComPN.muc. Pink: ComPE.cor. Grey: ComPN.men. Blue: ComPN.cin. The β-strands are numbered, and domains labelled. The three representations are 90° right turns around the N-terminal α-helix aligned on the y-axis.CC BY · PubMed Central
Fig 3 Robust ComPnat models from RF2NA, Chai-1 and AF3 for all seven ComPnat complexes(A-G). A: N.subnat; B: B.dennat; C: K. dennat; D: N. mucnat; E: E.cornat; F: N. cinnat; and G: N. mennat. PAE and pLDDT score ranges of models included in the overlay are listed next to each ComPnat overlay and in addition ipTM score ranges for AF3 and Chai-1 models. Each overlay is aligned on the α-carbon of the models with the best ipTM score or lowest PAE for RF2NA models. For each ComPnat modeled in AF3 and Chai-1, only the subset of models with ipTM ≥ 0.6 are represented and when no models were predicted above the ipTM threshold (D, F, and G and Fig 6 A), all predicted models are represented and labeled with *. For RF2NA, only models having PAE ≤ 10 are represented.
Fig 3 Robust ComPnat models from RF2NA, Chai-1 and AF3 for all seven ComPnat complexes(A-G). A: N.subnat; B: B.dennat; C: K. dennat; D: N. mucnat; E: E.cornat; F: N. cinnat; and G: N. mennat. PAE and pLDDT score ranges of models included in the overlay are listed next to each ComPnat overlay and in addition ipTM score ranges for AF3 and Chai-1 models. Each overlay is aligned on the α-carbon of the models with the best ipTM score or lowest PAE for RF2NA models. For each ComPnat modeled in AF3 and Chai-1, only the subset of models with ipTM ≥ 0.6 are represented and when no models were predicted above the ipTM threshold (D, F, and G and Fig 6 A), all predicted models are represented and labeled with *. For RF2NA, only models having PAE ≤ 10 are represented.CC BY · PubMed Central
Fig 4 A. PAE/pLDDT scatter plots or all binding modes of all ComPnats from AF3 (red), Chai-1 (blue) and RF2NA (green). B. Venn diagram of the resolved Epsilon scatters in A per color coded ComPnat species. Modeling platforms are represented with symbols as assigned in the right panel. C. Venn diagram of the resolved Gamma models in A per color coded ComPnat species. Modeling platforms are represented with symbols as assigned in right panel.
Fig 4 A. PAE/pLDDT scatter plots or all binding modes of all ComPnats from AF3 (red), Chai-1 (blue) and RF2NA (green). B. Venn diagram of the resolved Epsilon scatters in A per color coded ComPnat species. Modeling platforms are represented with symbols as assigned in the right panel. C. Venn diagram of the resolved Gamma models in A per color coded ComPnat species. Modeling platforms are represented with symbols as assigned in right panel.CC BY · PubMed Central
Fig 5 Violin plots of DockQ scores for paired all against all model comparisons of each ComPnat across platforms. The median and interquartile ranges are shown as horizontal bars, and paired model comparisons are depicted as swarms inside the violins. Paired inter-platform models which were assigned to two different binding modes are shown as “Different”. Horizontal red, yellow and green dashed lines represent DockQ of 0.23 (low), 0.49 (intermediate) and 0.8 (high), respectively. Red violins represent inter-platform model pairs in Epsilon, blue Gamma, light grey Other, dark grey Delta and green Different.
Fig 5 Violin plots of DockQ scores for paired all against all model comparisons of each ComPnat across platforms. The median and interquartile ranges are shown as horizontal bars, and paired model comparisons are depicted as swarms inside the violins. Paired inter-platform models which were assigned to two different binding modes are shown as “Different”. Horizontal red, yellow and green dashed lines represent DockQ of 0.23 (low), 0.49 (intermediate) and 0.8 (high), respectively. Red violins represent inter-platform model pairs in Epsilon, blue Gamma, light grey Other, dark grey Delta and green Different.CC BY · PubMed Central
Fig 6 A. Violin plots showing distributions of ipTM for native (“Native”) and scrambled DUS (“Scrambled”) runs in AF3 for the docking set consisting of five DUS dialects encompassing seven ComPnat/scr models. Box plots encompassing the median and interquartile ranges are seen inside the violins. AA-king3DUS (K.den). AG-DUS (B.den + N.sub). AG-eikDUS (E.cor). AG-mucDUS (N.muc). AT-DUS (N.men + N.cin). B: Same as in A for CPPM. Refer to S2 Code Output for statistical significance tests for Native vs. Scrambled for all DUS dialects.
Fig 6 A. Violin plots showing distributions of ipTM for native (“Native”) and scrambled DUS (“Scrambled”) runs in AF3 for the docking set consisting of five DUS dialects encompassing seven ComPnat/scr models. Box plots encompassing the median and interquartile ranges are seen inside the violins. AA-king3DUS (K.den). AG-DUS (B.den + N.sub). AG-eikDUS (E.cor). AG-mucDUS (N.muc). AT-DUS (N.men + N.cin). B: Same as in A for CPPM. Refer to S2 Code Output for statistical significance tests for Native vs. Scrambled for all DUS dialects.CC BY · PubMed Central

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Citations

Cites

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Metadata

Authors
Helsem, S. A., Alfsnes, K., Frye, S. A., Hesselberg Løvestad, A., & Ambur, O. H.
Affiliations
  • OsloMet – Oslo Metropolitan University (NO)
  • Norwegian Institute of Public Health (NO)
  • Oslo University Hospital (NO)
Corresponding author
Ambur, Ole Herman
ORCID
Venue
PLoS ONE
Publisher
openRxiv
Published
2024-11-24
Volume
20
Issue
5
Pages
e0315160-e0315160
ISSN
1932-6203 (ISSN-L)
DOI
10.1101/2024.11.23.625027
PMC
PMC12061091
OpenAlex
W4410204749
Cited by
3
References
2
Citations by year
2026: 1 · 2025: 2
FWCI
0.90
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS ONE (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Keywords
DNA binding modes, natural transformation, Neisseriaceae, protein-DNA complex, protein structure prediction, AlphaFold3, Chai-1, model robustness, Neisseria gonorrhoeae, Neisseria meningitidis, Eikenella corrodens
MeSH terms
Bacterial Proteins, Binding Sites, DNA, DNA-Binding Proteins, Humans, Models, Molecular, Protein Binding, Fimbriae Proteins, Molecular Docking Simulation

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