Structural investigation of syringomycin-E using molecular dynamics simulation and NMR

Mátyus, Edit; Monticelli, Luca; Kövér, Katalin E.; Xu, Zibo; Blaskó, Katalin; Fidy, Judit; Tieleman, D. Peter

doi:10.1007/s00249-006-0053-y

Cited by 4 publications

(1 citation statement)

References 33 publications

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“…A simple non-polar solvent was constructed using standard single point charge (SPC) water molecules with modified Leonard–Jones parameters and dipole moment. The well-depth Leonard–Jones parameter from the aliphatic carbon atoms within a reduced model for a dimyristoyl phosphatidylcholine (DMPC) lipid molecule ( Matyus et al, 2006 ) were used in place of the standard water parameters. This substitution changes the depth of the pair-potential well for the solvent molecule.…”

Section: Methodsmentioning

confidence: 99%

The Hydrophobic Effect Contributes to the Closed State of a Simplified Ion Channel through a Conserved Hydrophobic Patch at the Pore-Helix Crossing

Yonkunas

Kurnikova

2015

Front. Pharmacol.

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Ion selectivity-filter structures are strikingly similar throughout the large family of K++ channels and other p-loop-like receptors (i.e., glutamate receptors). At the same time, the triggers for opening these channels, or gating, are diverse. Two questions that remain unanswered regarding these channels are: (1) what force(s) stabilize the closed non-conducting channel-pore conformation? And (2) what is the free energy associated with transitioning from a closed (non-conducting) to an open (conducting) channel-pore conformation? The effects of charge and hydrophobicity on the conformational states of a model tetrameric biological ion channel are shown utilizing the amino acid sequence from the K+ channel KcsA as the model “channel”. Its widely conserved hydrophobic bundle crossing located adjacent to the lipid head-groups at the intracellular side of the membrane was calculated to have a 5 kcal/mol free energy difference between modeled open and closed conformations. Simulated mutants of amino acids within the hydrophobic region significantly contribute to the size of this difference. Specifically for KcsA, these residues are part of the pH sensor important for channel gating and our results are in agreement with published electrophysiology data. Our simulations support the idea that the hydrophobic effect contributes significantly to the stability of the closed conformation in tetrameric ion channels with a hydrophobic bundle crossing positioned in proximity to the lipid head groups of the biological membrane.

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Section: Methodsmentioning

confidence: 99%

The Hydrophobic Effect Contributes to the Closed State of a Simplified Ion Channel through a Conserved Hydrophobic Patch at the Pore-Helix Crossing

Yonkunas

Kurnikova

2015

Front. Pharmacol.

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Structure and dynamics of the antifungal molecules Syringotoxin-B and Syringopeptin-25A from molecular dynamics simulation

et al. 2007

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The phytopathogen Pseudomonas syringae pv. syringae produces toxic cyclic lipodepsipeptides (CLPs): nona-peptides and syringopeptins. All CLPs inhibit the growth of many fungal species, including human pathogens, although different fungi display different degrees of sensitivity. The best studied CLPs are Syringomycin-E (SR-E), Syringotoxin-B (ST-B) and Syringopeptin-25A (SP-25A). Their biological activity is affected by membrane composition and their structural differences. We previously (Matyus et al. in Eur Biophys J 35:459-467, 2006) reported the molecular features and structural preferences of SR-E in water and octane environments. Here we investigate in atomic detail the molecular features of the two other main CLP components, ST-B and SP-25A, in water and octane by 200 ns molecular dynamics simulations (MD), using distance restraints derived from NMR NOE data (Ballio et al. in Eur J Biochem 234:747-758, 1995). We have obtained three-dimensional models of ST-B and SP-25A CLPs in different environments. These models can now be used as a basis to investigate the interactions of ST-B and SP-25A with lipid membranes an important further step towards a better understanding of the antifungal and antibacterial activity of these peptides.

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The effects of light-induced reduction of the photosystem II reaction center

et al. 2009

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Accumulation of reduced pheophytin a (Pheo-D1) in photosystem II reaction center (PSII RC) under illumination at low redox potential is accompanied by changes in absorbance and circular dichroism spectra. The temperature dependences of these spectral changes have the potential to distinguish between changes caused by the excitonic interaction and temperature-dependent processes. We observed a conformational change in the PSII RC protein part and changes in the spatial positions of the PSII RC pigments of the active D1 branch upon reduction of Pheo-D1 only in the case of high temperature (298 K) dynamics. The resulting absorption difference spectra of PSII RC models equilibrated at temperatures of 77 K and 298 K were highly consistent with our previous experiments in which light-induced bleaching of the PSII RC absorbance spectrum was observable only at 298 K. These results support our previous hypothesis that Pheo-D1 does not interact excitonically with the other chlorins of the PSII RC, since the reduced form of Pheo-D1 causes absorption spectra bleaching only due to temperature-dependent processes.

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Structural investigation of syringomycin-E using molecular dynamics simulation and NMR

Cited by 4 publications

References 33 publications

The Hydrophobic Effect Contributes to the Closed State of a Simplified Ion Channel through a Conserved Hydrophobic Patch at the Pore-Helix Crossing

The Hydrophobic Effect Contributes to the Closed State of a Simplified Ion Channel through a Conserved Hydrophobic Patch at the Pore-Helix Crossing

Structure and dynamics of the antifungal molecules Syringotoxin-B and Syringopeptin-25A from molecular dynamics simulation

The effects of light-induced reduction of the photosystem II reaction center

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