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Spontaneous formation of structurally diverse membrane channel architectures from a single antimicrobial peptide

View Article: PubMed Central - PubMed

ABSTRACT

Many antimicrobial peptides (AMPs) selectively target and form pores in microbial membranes. However, the mechanisms of membrane targeting, pore formation and function remain elusive. Here we report an experimentally guided unbiased simulation methodology that yields the mechanism of spontaneous pore assembly for the AMP maculatin at atomic resolution. Rather than a single pore, maculatin forms an ensemble of structurally diverse temporarily functional low-oligomeric pores, which mimic integral membrane protein channels in structure. These pores continuously form and dissociate in the membrane. Membrane permeabilization is dominated by hexa-, hepta- and octamers, which conduct water, ions and small dyes. Pores form by consecutive addition of individual helices to a transmembrane helix or helix bundle, in contrast to current poration models. The diversity of the pore architectures—formed by a single sequence—may be a key feature in preventing bacterial resistance and could explain why sequence–function relationships in AMPs remain elusive.

No MeSH data available.


Pore ensemble structure variation.Oligomeric channel-like structures observed in the assembly simulations, together with a corresponding top-view assembly scheme show the versatility of the structural arrangement of the peptides (N: N terminus up, C: C terminus up). The symmetric antiparallel arrangements, assembled from antiparallel peptide pairs (dimer 2a is the basic building block) are always the most populated cluster for each oligomer (cluster ‘a'). Membrane thickness can markedly influence the architecture of the TM oligomers formed by maculatin. In thin membranes (for example, 1,2-dimyristoyl-sn-glycero-3-phosphocholine; DMPC) only oligomers with a small number of peptides are formed. Oligomers with more than five peptides are found only in thicker membranes (1,2-dipalmitoyl-sn-glycero-3-phosphocholine; DPPC), where peptides tilt less, with the octamer forming the largest pore.
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f5: Pore ensemble structure variation.Oligomeric channel-like structures observed in the assembly simulations, together with a corresponding top-view assembly scheme show the versatility of the structural arrangement of the peptides (N: N terminus up, C: C terminus up). The symmetric antiparallel arrangements, assembled from antiparallel peptide pairs (dimer 2a is the basic building block) are always the most populated cluster for each oligomer (cluster ‘a'). Membrane thickness can markedly influence the architecture of the TM oligomers formed by maculatin. In thin membranes (for example, 1,2-dimyristoyl-sn-glycero-3-phosphocholine; DMPC) only oligomers with a small number of peptides are formed. Oligomers with more than five peptides are found only in thicker membranes (1,2-dipalmitoyl-sn-glycero-3-phosphocholine; DPPC), where peptides tilt less, with the octamer forming the largest pore.

Mentions: To assess the architectural diversity of the channel-like pores formed, we developed software to identify and cluster structurally similar oligomeric TM assemblies (see Methods). This revealed hundreds of different channel architectures for maculatin, of which usually <10 are significantly populated. Only small pores with 3–8 peptides were observed. Larger aggregates were found only rarely and consisted of smaller channels in lateral contact. The most populated cluster for each oligomer are shown in Figs 4 and 5. Interestingly, very similar oligomers were found for all simulations, with a strong preference for antiparallel peptide arrangements (90%). The recurring structural motif is an antiparallel dimer offset by 8–10 residues, with tight inter-helical packing of the C-terminal moieties of the peptides (Supplementary Fig. 1). Larger oligomers are symmetric combinations of this basic dimer motif.


Spontaneous formation of structurally diverse membrane channel architectures from a single antimicrobial peptide
Pore ensemble structure variation.Oligomeric channel-like structures observed in the assembly simulations, together with a corresponding top-view assembly scheme show the versatility of the structural arrangement of the peptides (N: N terminus up, C: C terminus up). The symmetric antiparallel arrangements, assembled from antiparallel peptide pairs (dimer 2a is the basic building block) are always the most populated cluster for each oligomer (cluster ‘a'). Membrane thickness can markedly influence the architecture of the TM oligomers formed by maculatin. In thin membranes (for example, 1,2-dimyristoyl-sn-glycero-3-phosphocholine; DMPC) only oligomers with a small number of peptides are formed. Oligomers with more than five peptides are found only in thicker membranes (1,2-dipalmitoyl-sn-glycero-3-phosphocholine; DPPC), where peptides tilt less, with the octamer forming the largest pore.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5121426&req=5

f5: Pore ensemble structure variation.Oligomeric channel-like structures observed in the assembly simulations, together with a corresponding top-view assembly scheme show the versatility of the structural arrangement of the peptides (N: N terminus up, C: C terminus up). The symmetric antiparallel arrangements, assembled from antiparallel peptide pairs (dimer 2a is the basic building block) are always the most populated cluster for each oligomer (cluster ‘a'). Membrane thickness can markedly influence the architecture of the TM oligomers formed by maculatin. In thin membranes (for example, 1,2-dimyristoyl-sn-glycero-3-phosphocholine; DMPC) only oligomers with a small number of peptides are formed. Oligomers with more than five peptides are found only in thicker membranes (1,2-dipalmitoyl-sn-glycero-3-phosphocholine; DPPC), where peptides tilt less, with the octamer forming the largest pore.
Mentions: To assess the architectural diversity of the channel-like pores formed, we developed software to identify and cluster structurally similar oligomeric TM assemblies (see Methods). This revealed hundreds of different channel architectures for maculatin, of which usually <10 are significantly populated. Only small pores with 3–8 peptides were observed. Larger aggregates were found only rarely and consisted of smaller channels in lateral contact. The most populated cluster for each oligomer are shown in Figs 4 and 5. Interestingly, very similar oligomers were found for all simulations, with a strong preference for antiparallel peptide arrangements (90%). The recurring structural motif is an antiparallel dimer offset by 8–10 residues, with tight inter-helical packing of the C-terminal moieties of the peptides (Supplementary Fig. 1). Larger oligomers are symmetric combinations of this basic dimer motif.

View Article: PubMed Central - PubMed

ABSTRACT

Many antimicrobial peptides (AMPs) selectively target and form pores in microbial membranes. However, the mechanisms of membrane targeting, pore formation and function remain elusive. Here we report an experimentally guided unbiased simulation methodology that yields the mechanism of spontaneous pore assembly for the AMP maculatin at atomic resolution. Rather than a single pore, maculatin forms an ensemble of structurally diverse temporarily functional low-oligomeric pores, which mimic integral membrane protein channels in structure. These pores continuously form and dissociate in the membrane. Membrane permeabilization is dominated by hexa-, hepta- and octamers, which conduct water, ions and small dyes. Pores form by consecutive addition of individual helices to a transmembrane helix or helix bundle, in contrast to current poration models. The diversity of the pore architectures&mdash;formed by a single sequence&mdash;may be a key feature in preventing bacterial resistance and could explain why sequence&ndash;function relationships in AMPs remain elusive.

No MeSH data available.