The inhibitory mechanism of a small protein reveals its role in antimicrobial peptide sensing

Jiang, Shan; Steup, Lydia C.; Kippnich, Charlotte; Lazaridi, Symela; Malengo, Gabriele; Lemmin, Thomas; Yuan, Jing

doi:10.1073/pnas.2309607120

Cited by 7 publications

(3 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Furthermore, the validity of our generated models opens exciting avenues for further studies on PhoQ itself. These models can be instrumental in exploring PhoQ's modulation by small peptides [63] and antimicrobial agents, potentially leading to the development of novel therapeutic strategies.…”

Section: 𝐻 𝑇𝑀𝐷mentioning

confidence: 99%

Atomic insights into the signaling landscape ofE. coliPhoQ Histidine Kinase from Molecular Dynamics simulations

Lazaridi,

Yuan,

Lemmin

2024

Preprint

Self Cite

View full text Add to dashboard Cite

Bacteria rely on two-component systems to sense environmental cues and regulate gene expression for adaptation. The PhoQ/PhoP system exemplifies this crucial role, playing a key part in sensing magnesium (Mg2+) levels, antimicrobial peptides, mild acidic pH, osmotic upshift, and long-chain unsaturated fatty acids, promoting virulence in certain bacterial species. However, the precise details of PhoQ activation remain elusive. To elucidate PhoQ's signaling mechanism at atomic resolution, we combined AlphaFold2 predictions with molecular modeling and carried out extensive Molecular Dynamics (MD) simulations. Our MD simulations revealed three distinct PhoQ conformations that were validated by experimental data. Notably, one conformation was characterized by Mg2+ bridging the acidic patch in the sensor domain to the membrane, potentially representing a repressed state. Furthermore, the high hydration observed in a putative intermediate state lends support to the hypothesis of water-mediated conformational changes during PhoQ signaling. Our findings not only revealed specific conformations within the PhoQ signaling pathway, but also hold significant promise for understanding the broader histidine kinase family due to their shared structural features. Our approach paves the way for a more comprehensive understanding of histidine kinase signaling mechanisms across various bacterial species and opens the door for developing novel therapeutics that target PhoQ modulation.

show abstract

Section: 𝐻 𝑇𝑀𝐷mentioning

confidence: 99%

Atomic insights into the signaling landscape ofE. coliPhoQ Histidine Kinase from Molecular Dynamics simulations

Lazaridi,

Yuan,

Lemmin

2024

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Small proteins (SPs), typically consisting of 100 amino acids (AA) or fewer, are indispensable components in cells, serving critical functions such as cell defense, adaptive immunity, and intercellular communication ( Sberro et al, 2019 ). For instance, the SP MgrB regulates the activity of the sensor kinase PhoQ in response to antimicrobial peptides during bacterial infection ( Jiang et al, 2023 ). Toddler, another SP, facilitates cell migration during embryonic gastrulation ( Pauli et al, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

PSPI: A deep learning approach for prokaryotic small protein identification

Weston,

Hu,

2024

Front. Genet.

View full text Add to dashboard Cite

Small Proteins (SPs) are pivotal in various cellular functions such as immunity, defense, and communication. Despite their significance, identifying them is still in its infancy. Existing computational tools are tailored to specific eukaryotic species, leaving only a few options for SP identification in prokaryotes. In addition, these existing tools still have suboptimal performance in SP identification. To fill this gap, we introduce PSPI, a deep learning-based approach designed specifically for predicting prokaryotic SPs. We showed that PSPI had a high accuracy in predicting generalized sets of prokaryotic SPs and sets specific to the human metagenome. Compared with three existing tools, PSPI was faster and showed greater precision, sensitivity, and specificity not only for prokaryotic SPs but also for eukaryotic ones. We also observed that the incorporation of (n, k)-mers greatly enhances the performance of PSPI, suggesting that many SPs may contain short linear motifs. The PSPI tool, which is freely available at https://www.cs.ucf.edu/∼xiaoman/tools/PSPI/, will be useful for studying SPs as a tool for identifying prokaryotic SPs and it can be trained to identify other types of SPs as well.

show abstract

“…Small membrane proteins also target individual larger membrane proteins, regulating their stability and function. For example, MgrB and SafA participate in cell signaling by regulating the activity of the sensor kinase PhoQ [14][15][16][17]. MgtS and MntS regulate magnesium and manganese transport by targeting the respective transporter proteins [18,19].…”

Section: Introductionmentioning

confidence: 99%

A cell-free system for functional studies of small membrane proteins

Jiang,

Çelen,

Glatter

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

Numerous small proteins have been discovered across all domains of life, among which many are hydrophobic and predicted to localize to the cell membrane. Based on a few that are well-studied, small membrane proteins are regulators involved in various biological processes, such as cell signaling, nutrient transport, drug resistance, and stress response. However, the function of most recently identified small membrane proteins remains elusive. Their small size and hydrophobicity make protein production challenging, hindering function discovery. Here, we combined a cell-free system with lipid sponge droplets and synthesized small membrane proteins in vitro. Lipid sponge droplets contain a dense network of lipid bilayers, which accommodates and extracts newly synthesized small membrane proteins from the aqueous surroundings. Using small bacterial membrane proteins MgrB and SafA as proof of principle, we showed that the in vitro produced membrane proteins reached sufficient concentrations for downstream analysis, and more importantly, they are functionally active. The cell-free system was also suitable for synthesizing other small membrane proteins, including one from human, indicating its high level of versatility. Furthermore, we showed that small proteins produced in this system can be used for in vitro pull-down assays to identify interaction partners. This work presents a robust alternative approach for producing small membrane proteins, which may aid their function discovery in all domains of life.

show abstract

The inhibitory mechanism of a small protein reveals its role in antimicrobial peptide sensing

Cited by 7 publications

References 50 publications

Atomic insights into the signaling landscape ofE. coliPhoQ Histidine Kinase from Molecular Dynamics simulations

Atomic insights into the signaling landscape ofE. coliPhoQ Histidine Kinase from Molecular Dynamics simulations

PSPI: A deep learning approach for prokaryotic small protein identification

A cell-free system for functional studies of small membrane proteins

Contact Info

Product

Resources

About