Computational Observation of an Ion Permeation Through a Channel Protein

Suenaga, Atsushi; Komeiji, Yuto; Uebayasi, Masami; Meguro, T.; Saito, Minoru; Yamato, Ichiro

doi:10.1023/a:1022292801256

Cited by 56 publications

(66 citation statements)

References 13 publications

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“…Accordingly, its structure displays a large number of basic residues inside the pore and an unusually narrow constriction zone located approximately halfway along the pore axis (25). Recent MD studies showed that even the small chloride ions experience intimate interactions with charged amino acids arranged as a "basic ladder" and located in the channel constriction (26), a situation that is less obvious but also present in porins exhibiting a larger pore cross-section such as OmpF from Escherichia coli (27,28). The affinity of D. acidovorans toward organic acids as carbon source, together with the strong anion selectivity and the small channel diameter of Omp32, suggests that a certain level of substrate specificity may also be present in a porin that would be attributed as unspecific by its structure according to the current classification (3).…”

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confidence: 99%

High Resolution Crystal Structures and Molecular Dynamics Studies Reveal Substrate Binding in the Porin Omp32

Zachariae

Klühspies

et al. 2006

Journal of Biological Chemistry

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The porin Omp32 is the major outer membrane protein of the bacterium Delftia acidovorans. The crystal structures of the strongly anion-selective porin alone and in complex with the substrate malate were solved at 1.5 and 1.45 Å resolution, respectively, and revealed a malate-binding motif adjacent to the channel constriction zone. Binding is mediated by interaction with a cluster of two arginine residues and two threonines. This binding site is specific for Omp32 and reflects the physiological adaptation of the organism to organic acids. Structural studies are combined with a 7-ns unbiased molecular dynamics simulation of the trimeric channel in a model membrane. Molecular dynamics trajectories show how malate ions are efficiently captured from the surrounding bulk solution by the electrostatic potential of the channel, translocated to the binding site region, and immobilized in the constriction zone. In accordance with these results, conductance measurements with Omp32 inserted in planar lipid membranes revealed binding of malate. The anion-selective channel Omp32 is the first reported example of a porin with a 16-stranded ␤-barrel and proven substrate specificity. This finding suggests a new view on the correlation of porin structure with substrate binding in specific channels.Porins are channel proteins that facilitate the exchange of ions and small hydrophilic substrate molecules across the outer membrane present in Gram-negative bacteria, mitochondria, and chloroplasts (1, 2). A number of bacterial porins have been studied structurally. They all possess ␤-barrels as the common structural principle (3). The trimeric bacterial porins are usually classified according to their number of barrelforming ␤-strands (3, 4); 18-stranded porins function as substratespecific channels and provide periplasmic binding proteins and uptake systems of the inner membrane with their specific substrates (5, 6), and 16-stranded porins are reported to merely act as unspecific ("general") diffusion pores, however, typically with a distinct ion selectivity (7-11).The current classification is mainly based on the crystal structures of 3 different 18-stranded and seven 16-stranded porins from Proteobacteria. Structural studies of substrate binding to trimeric porins were, thus, restricted to the sugar-specific maltoporins and to ScrY (5, 6). The nucleoside-specific pore protein Tsx and the fatty acid-binding transporter FadL are monomeric 12-and 14-stranded ␤-barrel proteins, respectively (17, 18). They are not regarded as porins proper; however, they also belong to the class of passive outer membrane channel proteins. Thus, in a more general view, substrate binding is not a special feature of 18-stranded outer membrane proteins. Several theories were developed to describe channel-substrate interactions which apply to diffusion pores in general (19). A decisive step of substrate translocation was modeled for maltoporin by conjugate peak refinement (20). Nonequilibrium molecular dynamics (MD) 2 and docking methods were applied to inves...

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confidence: 99%

High Resolution Crystal Structures and Molecular Dynamics Studies Reveal Substrate Binding in the Porin Omp32

Zachariae

Klühspies

et al. 2006

Journal of Biological Chemistry

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“…Second, the variation in the concentration of mobile ions inside the channel due to adsorption processes as suggested by a number of different approaches. Thus, fluorescence experiments [21], MD simulations [22], free-energy calculations [13], and site-directed mutagenesis experiments [23] pointed to the existence of a binding site for monovalent cations located around the central constriction of the OmpF channel [13,14,22]. X-ray structures in MgCl 2 showed a binding site in the selectivity filter [24] as confirmed by selectivity experiments involving selected mutants in salts of multivalent cations [25].…”

Section: Resultsmentioning

confidence: 86%

Excess white noise to probe transport mechanisms in a membrane channel

2015

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Current fluctuation analysis has been successfully used over the years to investigate the physical properties of different systems. Here, we perform single-channel time-resolved current experiments in a protein channel to evaluate the different transport mechanisms governing the channel function. Using different salts of monovalent and divalent cations in a wide range of concentrations and applied potentials, we analyze current fluctuations focusing on the voltage dependence of the additional white noise that appears in the low-frequency range of the spectra. We demonstrate that the channel displays two characteristic transport regimes: at low salt concentrations (10 mM to 1 M) ion permeation is controlled by the protein fixed charges that induce accumulation or exclusion of ions to preserve local electroneutrality. At high salt concentrations (>1 M) adsorption processes associated to the binding of cations to the channel charges regulate the transport properties.

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“…Realistic simulations of porins have been performed with explicit ions, solvent molecules 105 and also phospholipid bilayer membrane. 106 To explore the mechanism of ion conduction, Suenaga et al simulated OmpF in the presence of an applied transmembrane potential.…”

Section: Porinsmentioning

confidence: 99%

“…106 To explore the mechanism of ion conduction, Suenaga et al simulated OmpF in the presence of an applied transmembrane potential. 105 The translocation of a single Na + through the channel was observed in 1.3 ns under the influence of a potential of 500 mV. Tieleman and Berendsen 106 generated a 1 ns MD simulation of an atomic model of OmpF trimer embedded into an explicit phospholipid bilayer membrane with a few explicite counterions (those needed to balance the total charge of OmpF).…”

Section: Porinsmentioning

confidence: 99%

Concepts in Bionanomachines: Translocators

Baumgaertner¹

2008

Jnl of Comp & Theo Nano

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This review summarizes, without pretension on completeness, a perspective on some biological relevant biomolecular machines. The attempt to give a kind of general overview would be necessarily incomplete, since this scientific field is one of the most rapidly expanding and changing in computational sciences. Any attempt to be as complete as possible would be obsolete anyway very soon. However, the kind of synopsis may still be valid in the future. The review is restricted to membrane proteins which translocate ions, small molecules and macromolecules across a cellular membrane ("translocators"). The report is focused on computational studies and theories, but references are made to experimental work as well.

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Computational Observation of an Ion Permeation Through a Channel Protein

Cited by 56 publications

References 13 publications

High Resolution Crystal Structures and Molecular Dynamics Studies Reveal Substrate Binding in the Porin Omp32

High Resolution Crystal Structures and Molecular Dynamics Studies Reveal Substrate Binding in the Porin Omp32

Excess white noise to probe transport mechanisms in a membrane channel

Concepts in Bionanomachines: Translocators

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