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TitleStructural insights into pre-pore intermediates of alpha-hemolysin in the lipidic environment.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 6348, Year 2025
Publish dateJul 10, 2025
AuthorsArnab Chatterjee / Anupam Roy / Thejas Satheesh / Partho Pratim Das / Bapan Mondal / Prithiv Kishore / Mahipal Ganji / Somnath Dutta /
PubMed AbstractThe infectious microbe Staphylococcus aureus releases an array of cytotoxic pore-forming toxins (PFTs) that severely damage the cell membrane during bacterial infection. However, the interaction ...The infectious microbe Staphylococcus aureus releases an array of cytotoxic pore-forming toxins (PFTs) that severely damage the cell membrane during bacterial infection. However, the interaction interfaces between the host cell membrane and toxin were hardly explored. So far, there are no pore, and intermediate structures of these toxins available in the presence of bio-membrane, which could elucidate the pore-forming mechanism. Here, we investigate the structure of different conformational states of this alpha-hemolysin (α-HL/Hla), a β-PFT in lipidic environment using single-particle cryo-EM. Additionally, we explore lipid destabilization by the toxin, using single-molecule imaging, confocal imaging, and validation of lipid-protein interactions using mutational studies. We elucidate eight cryo-EM structures of wildtype α-HL with various liposomes, which are composed of either 10:0 PC or Egg-PC/Cholesterol or Egg-PC/Sphingomyelin or 10:0 PC/Sphingomyelin. Our structural and biophysical studies confirm that different chain lengths and various membrane compositions facilitate the formation of intermediate pre-pores and complete pore species. We also demonstrate that the percentage of pre-pore population increases due to sphingomyelin-induced membrane rigidity. Altogether, this study unveils the structure-function analysis of the pre-pore to pore transition of wildtype α-HL during its crosstalk with the lipid membrane.
External linksNat Commun / PubMed:40640160 / PubMed Central
MethodsEM (single particle)
Resolution2.6 - 3.2 Å
Structure data

EMDB-62302: Cryo-EM Density map of Staphylococcus aureus alpha-hemolysin pore structure derived from 12:0 Phosphatidylcholine (12:0 PC) liposome
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-62303: Structure of Alpha-hemolysin heptameric pore state derived from Egg-PC/SM liposomes.
Method: EM (single particle) / Resolution: 2.8 Å

62304

9kg0

9kto

EMDB-62304, PDB-9kg0:
Alpha-hemolysin heptameric late pre-pore state derived from 10:0 PC/Sphingomyelin liposomes
PDB-9kto: Alpha-hemolysin heptameric late pre-pore state with bound lipids derived from 10:0 PC/Sphingomyelin liposomes
Method: EM (single particle) / Resolution: 2.6 Å

62305

9kg1

9ktm

EMDB-62305, PDB-9kg1:
Alpha-hemolysin heptameric pre-pore state derived from 10:0 PC liposomes.
PDB-9ktm: Alpha-hemolysin heptameric pre-pore state bound to 10:PC lipid chains derived from 10:0 PC liposomes.
Method: EM (single particle) / Resolution: 2.9 Å

62307

9kg3

9kre

EMDB-62307, PDB-9kg3:
Alpha-hemolysin heptameric pore state derived from egg PC/Cholesterol (3:1 molar ratio) liposomes
PDB-9kre: Alpha-hemolysin heptameric POPC bound pore state derived from egg PC/Cholesterol (3:1 molar ratio) liposomes
Method: EM (single particle) / Resolution: 3.07 Å

EMDB-62308: Map of EggPC/SM derived prepore structure of alpha-hemolysin
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-62309: 12:0 PC liposome derived pre-pore structure of alpha hemolysin
Method: EM (single particle) / Resolution: 3.2 Å

62310

9kg6

9krf

EMDB-62310, PDB-9kg6:
Alpha-hemolysin heptameric pore state derived from 10:0 PC liposomes
PDB-9krf: Alpha-hemolysin heptameric pore state bound to 10:0 PC lipid chains derived from 10:0 PC liposomes
Method: EM (single particle) / Resolution: 2.8 Å

Chemicals

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

ChemComp-P1O:
1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DDPC, phospholipid*YM

Source
  • staphylococcus aureus (bacteria)
KeywordsLIPID BINDING PROTEIN / PFT / Liposomes

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