α‐Helical Cytolysins: Molecular Tunnel‐Boring Machines in Action

Reitz, Simon; Essen, Lars‐Oliver

doi:10.1002/cbic.200900447

Cited by 2 publications

(4 citation statements)

References 18 publications

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“…As a consequence, many more β-PFT pore crystal structures [41][42][43][44][45] have been solved compared to α-PFTs, 8,46 whose membrane-inserted domains consist of amphipathic α helices leading to weaker inter-protomer contacts. 9,47,48 The stiffer RMSD landscapes for AHL are observed in both the all-atom as well as MARTINI simulations. The relative broadness of the MARTINI stiffness landscape is an indicator of softer potentials used in a coarse-grained representation.…”

Section: Stiffness Landscapes Of Clya and Ahlmentioning

confidence: 94%

“…In the case of β-PFTs such as α-hemolysin (AHL) from Staphylococcus aureaus, the dominant motifs are β sheets which form the membraneinserted β-barrel stabilized by inter-strand hydrogen bonding, and hence, β-PFTs have greater structural stability when compared with α toxins. 9,10 Membrane proteins have been extensively simulated using both atomistic as well as coarse-grained molecular dynamics (MD) simulations. [11][12][13][14][15][16][17] However, while many anti-microbial peptides have been extensively simulated, there are comparatively fewer MD simulations of pore forming toxins, either as water soluble monomers or transmembrane oligomeric pores.…”

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confidence: 99%

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Comparison of coarse-grained (MARTINI) and atomistic molecular dynamics simulations of $$\alpha $$ α and $$\beta $$ β toxin nanopores in lipid membranes

et al. 2017

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Pore forming toxins (PFTs) are virulent proteins whose primary goal is to lyse target cells by unregulated pore formation. Molecular dynamics simulations can potentially provide molecular insights on the properties of the pore complex as well as the underlying pathways for pore formation. In this manuscript we compare both coarse-grained (MARTINI force-field) and all-atom simulations, and comment on the accuracy of the MARTINI coarse-grained method for simulating these large membrane protein pore complexes. We report 20 μs long coarse-grained MARTINI simulations of prototypical pores from two different classes of pore forming toxins (PFTs) in lipid membranes-Cytolysin A (ClyA), which is an example of an α toxin, and α-hemolysin (AHL) which is an example of a β toxin. We compare and contrast structural attributes such as the root mean square deviation (RMSD) histograms and the inner pore radius profiles from the MARTINI simulations with all-atom simulations. RMSD histograms sampled by the MARTINI simulations are about a factor of 2 larger, and the radius profiles show that the transmembrane domains of both ClyA and AHL pores undergo significant distortions, when compared with the all-atom simulations. In addition to the fully inserted transmembrane pores, membrane-inserted proteo-lipid ClyA arcs show large shape distortions with a tendency to close in the MARTINI simulations. While this phenomenon could be biologically plausible given the fact that α-toxins can form pores of varying sizes, the additional flexibility is probably due to weaker inter-protomer interactions which are modulated by the elastic dynamic network in the MARTINI force-field. We conclude that there is further scope for refining inter-protomer contacts and perhaps membrane-protein interactions in the MARTINI coarse-grained framework. A robust coarse-grained force-field will enable one to reliably carry out mesoscopic simulations which are required to understand protomer oligomerization, pore formation and leakage.

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Section: Stiffness Landscapes Of Clya and Ahlmentioning

confidence: 94%

mentioning

confidence: 99%

Comparison of coarse-grained (MARTINI) and atomistic molecular dynamics simulations of $$\alpha $$ α and $$\beta $$ β toxin nanopores in lipid membranes

et al. 2017

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“…While pore structures and assembly mechanisms of β-PFTs such as Staphylococcus aureus α -hemolysin, Staphylococcus aureus γ -hemolysin, and Vibrio cholerae cytolysin have been extensively studied, molecular mechanisms of α-PFT oligomerization and lipid reorganization during pore formation are poorly understood. ,,,,− Intrinsic participation of the membrane lipids along with the inserted transmembrane helices to form the pore complex is a recurring theme for α-PFTs. , Escherichia coli cytolsin A (ClyA) is currently one of only two α-helical PFTs with available crystal structures of both the water-soluble monomer and the membrane-inserted pore complex . Thus, ClyA can be conveniently used to decipher the assembly mechanism for the class of α-helical PFTs. ,, The crystal structure of the pore reveals the formation of a dodecameric homo-oligomeric complex having a total length of 13 nm, with the inner channel diameter varying from 7 nm at the extracellular end to 4 nm at the transmembrane or cytosolic end . The current understanding and challenges regarding the pore-forming pathway of ClyA are detailed below.…”

Section: Introductionmentioning

confidence: 99%

“…16 Thus, ClyA can be conveniently used to decipher the assembly mechanism for the class of α-helical PFTs. 16,20,26 The crystal structure of the pore reveals the formation of a dodecameric homo-oligomeric complex having a total length of 13 nm, with the inner channel diameter varying from 7 nm at the extracellular end to 4 nm at the transmembrane or cytosolic end. 16 The current understanding and challenges regarding the pore-forming pathway of ClyA are detailed below.…”

Section: ■ Introductionmentioning

confidence: 99%

Assessing the Structure and Stability of Transmembrane Oligomeric Intermediates of an α-Helical Toxin

2017

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Protein membrane interactions play an important role in our understanding of diverse phenomena ranging from membrane-assisted protein aggregation to oligomerization and folding. Pore-forming toxins (PFTs) are the primary vehicle for infection by several strains of bacteria. These proteins which are expressed in a water-soluble form (monomers) bind to the target membrane and conformationally transform (protomers) and self-assemble to form a multimer transmembrane pore complex through a process of oligomerization. On the basis of the structure of the transmembrane domains, PFTs are broadly classified into β or α toxins. In contrast to β-PFTs, the paucity of available crystal structures coupled with the amphipathic nature of the transmembrane domains has hindered our understanding of α-PFT pore formation. In this article, we use molecular dynamics (MD) simulations to examine the process of pore formation of the bacterial α-PFT, cytolysin A from Escherichia coli (ClyA) in lipid bilayer membranes. Using atomistic MD simulations ranging from 50 to 500 ns, we show that transmembrane oligomeric intermediates or "arcs" form stable proteolipidic complexes consisting of protein arcs with toroidal lipids lining the free edges. By creating initial conditions where the lipids are contained within the arcs, we study the dynamics of spontaneous lipid evacuation and toroidal edge formation. This process occurs on the time scale of tens of nanoseconds, suggesting that once protomers oligomerize, transmembrane arcs are rapidly stabilized to form functional water channels capable of leakage. Using umbrella sampling with a coarse-grained molecular model, we obtain the free energy of insertion of a single protomer into the membrane. A single inserted protomer has a stabilization free energy of -52.9 ± 1.2 kJ/mol and forms a stable transmembrane water channel capable of leakage. Our simulations reveal that arcs are stable and viable intermediates that can occur during the pore-formation pathway for ClyA.

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α‐Helical Cytolysins: Molecular Tunnel‐Boring Machines in Action

Abstract: Lethal weapon: The X‐ray crystal structure of a cytotoxic pore‐forming complex revealed brilliant new insights into the mechanism and structure of an all‐α‐helical toxin.

Cited by 2 publications

References 18 publications

Comparison of coarse-grained (MARTINI) and atomistic molecular dynamics simulations of $$\alpha $$ α and $$\beta $$ β toxin nanopores in lipid membranes

Comparison of coarse-grained (MARTINI) and atomistic molecular dynamics simulations of $$\alpha $$ α and $$\beta $$ β toxin nanopores in lipid membranes

Assessing the Structure and Stability of Transmembrane Oligomeric Intermediates of an α-Helical Toxin

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