2. The pores that appear in this work
2. The pores that appear in this work¶
| Pore | Class | Oligomer | Mass | Overall shape | Interior | Charge / selectivity | PDB |
|---|---|---|---|---|---|---|---|
| αHL (α-hemolysin, S. aureus) | β-PFT | 7 (>90% heptamer) | 232 kDa | mushroom, 11 nm tall × 10 nm wide; 4 nm β-barrel stem | cis vestibule 3.5 nm entry × 5 nm; 6 nm long × 2 nm channel; 1.6 nm constriction (Glu111/Lys147) | balanced; slightly anion-selective | 7AHL (pore), 4YHD (monomer, 33 kDa) |
| ClyA (cytolysin A, E. coli / S. typhi) | α-PFT | 12 (also 13, 14) | 408 kDa | cylinder, 14 nm tall × 11 nm outer | cis lumen ⌀5.5 nm × 10 nm; trans constriction ⌀3.6 nm × 4 nm | −60 e at pH 7.5, mostly on interior walls; cation-selective | 2WCD (E. coli 12-mer), 6MRT (Peng 2019), 1QOY (monomer, 34 kDa) |
| FraC (fragaceatoxin C, A. fragacea) | α-PFT | 8 (also 7, 6) | 176 kDa | funnel, 7 nm tall; outer ⌀11 nm (cis) / 3.5 nm (trans) | ⌀6 nm cis → 1.6 nm trans constriction | negative interior, esp. constriction; cation-selective | 4TSY (with 3 sphingomyelins/protomer), 3VWI (monomer, 20 kDa) |
| PlyAB (pleurotolysin AB, P. ostreatus) | β-PFT, MACPF | 13 subunits, each (PlyA)₂·PlyB → 39 chains | 1067 kDa | mushroom, 13 nm tall; head ⌀22 nm, stem ⌀9 nm | cis entry ⌀10.5 nm → 5.5 nm constriction at 3 nm depth → lumen ⌀7.2 nm × 10 nm | predominantly negative | 4V2T (Cα only), 4OEB/4OEJ (monomers) |
| MspA (M. smegmatis porin A) | β-barrel porin | octameric [std] | — | — | narrow constriction [std] | — | — |
| Aerolysin (AeL, A. hydrophila) | β-PFT | heptameric [std] | — | — | — | — | — |
| CsgG (E. coli) | β-barrel | — | — | — | — | — | — |
The thesis gives no dimensions for MspA, aerolysin or CsgG; it cites MspA and CsgG as the pores behind commercial DNA sequencing. Sub-stoichiometries matter: FraC 8/7/6-mers have constrictions of 1.6 / 1.1 / 0.84 nm; ClyA Type I/II/III (12/13/14-mer) have 3.3–4.0 / 3.7–4.4 / 4.2–5.2 nm; PlyAB is 75% 13-mer. Any simulation must state which oligomer it models.