Ion Selectivity of α-Hemolysin with β-Cyclodextrin Adapter. II. Multi-Ion Effects Studied with Grand Canonical Monte Carlo/Brownian Dynamics Simulations

Egwolf, Bernhard; Luo, Yun; Walters, D. Eric; Roux, Benoı̂t

doi:10.1021/jp906791b

Cited by 40 publications

(48 citation statements)

References 44 publications

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“…The BD simulations using the GCMC/BD web interface successfully reproduced the previous BD simulation results 15,16 and the results from both diffusion models are in line with the experimentally measured properties. In addition, the 1D multi-ion PMF profile reveals that the anion selectivity arises from the ring of positively charged residues (Lys147) in the constriction region.…”

Section: Resultssupporting

confidence: 82%

“…Wildtype α-HL, as well as a modified structure with a molecular adaptor (covalently or non-covalently attached β-cyclodextrin) placed at the constriction region have been extensively studied using experiments 5,34 and simulations. 15,16,35,36 α-HL is mildly anion-selective and its conduction properties are known to be asymmetric around V mp = 0, i.e., showing rectification effect. The protein structure (PDB:7AHL) 33 used in the current simulations was also obtained from OPM.…”

Section: Resultsmentioning

confidence: 99%

“…The applicability of GCMC/BD has been validated from previous simulation studies for the outer membrane porin F (OmpF), 14 α-Hemolysin (α-HL), 15,16 and the voltage dependent anion channel (VDAC). 17 The simulation results agree well with experimental data and other simulations, and have been analyzed to investigate the channel conductance, ion selectivity, and the underlying physical mechanisms of permeation.…”

Section: Introductionmentioning

confidence: 99%

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Web interface for brownian dynamics simulation of ion transport and its applications to beta‐barrel pores

Lee

Rui

et al. 2011

J Comput Chem

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Brownian dynamics (BD) in a suitably constructed potential of mean force is an efficient and accurate method for simulating ion transport through wide ion channels. Here, a web-based graphical user interface (GUI) is presented for grand canonical Monte Carlo (GCMC) BD simulations of channel proteins: http://www.charmm-gui.org/input/gcmcbd. The webserver is designed to help users avoid most of the technical difficulties and issues encountered in setting up and simulating complex pore systems. GCMC/BD simulation results for three proteins, the voltage dependent anion channel (VDAC), α-Hemolysin, and the protective antigen pore of the anthrax toxin (PA), are presented to illustrate system setup, input preparation, and typical output (conductance, ion density profile, ion selectivity, and ion asymmetry). Two models for the input diffusion constants for potassium and chloride ions in the pore are compared: scaling of the bulk diffusion constants by 0.5, as deduced from previous all-atom molecular dynamics simulations of VDAC; and a hydrodynamics based model (HD) of diffusion through a tube. The HD model yields excellent agreement with experimental conductances for VDAC and α-Hemolysin, while scaling bulk diffusion constants by 0.5 leads to underestimates of 10–20%. For PA, simulated ion conduction values overestimate experimental values by a factor of 1.5 to 7 (depending on His protonation state and the transmembrane potential), implying that the currently available computational model of this protein requires further structural refinement.

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Section: Resultssupporting

confidence: 82%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Web interface for brownian dynamics simulation of ion transport and its applications to beta‐barrel pores

Lee

Rui

et al. 2011

J Comput Chem

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“…The work also provides information valuable for the design of new binding sites within the lumen of the αHL pore or within other β-barrel proteins. Our results will be of interest to others exploring the interactions of CDs with the αHL pore (16, 17), including groups involved in computational studies (18,19). In addition CDs bind to a variety of other pores, including porins (20, 21) and connexins (22), and are being tested in vivo as blockers of the anthrax protective antigen pore (23,24).…”

mentioning

confidence: 89%

Molecular bases of cyclodextrin adapter interactions with engineered protein nanopores

Banerjee

Mikhailova

Cheley

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

108

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Engineered protein pores have several potential applications in biotechnology: as sensor elements in stochastic detection and ultrarapid DNA sequencing, as nanoreactors to observe singlemolecule chemistry, and in the construction of nano-and microdevices. One important class of pores contains molecular adapters, which provide internal binding sites for small molecules. Mutants of the α-hemolysin (αHL) pore that bind the adapter β-cyclodextrin (βCD) ∼10 4 times more tightly than the wild type have been obtained. We now use single-channel electrical recording, protein engineering including unnatural amino acid mutagenesis, and highresolution x-ray crystallography to provide definitive structural information on these engineered protein nanopores in unparalleled detail.alpha-hemolysin | single molecule | stochastic sensing | structure | unnatural amino acid M any research groups have used protein engineering to obtain enzymes and antibodies with new properties suited for specific tasks (1-6). Fewer groups have taken on the difficult problem of engineering membrane proteins (7). We have engineered the α-hemolysin protein pore, mindful of several potential applications in biotechnology, including its ability to act as a detector in stochastic sensing (8) and ultrarapid DNA sequencing (9), to serve as a nanoreactor for the observation of singlemolecule chemistry (10) and to act as a component for the construction of nano-and microdevices (11).An important breakthrough in this area, which enabled the stochastic sensing of organic molecules including the detection of DNA bases in the form of nucleoside monophosphates (12, 13), was the discovery of internal molecular adapters, a form of noncovalent protein modification (14). Most useful have been cyclodextrin (CD) adapters, which have until now been used in the absence of detailed structural information about how they work. The present paper is a definitive investigation, which provides such information through the application of a wide variety of technical approaches: single-channel electrical recording, protein engineering including unnatural amino acid mutagenesis, and x-ray crystallography. The studies employing mutagenesis show that the striking interactions seen in the crystal structures also occur in individual pores in lipid bilayers.We reveal that the tight-binding αHL mutants (15) M113N 7 and M113F 7 bind βCD in different orientations within the heptameric pore. In the case of M113N 7 , the top (primary hydroxyls) of the CD ring faces the trans entrance of the pore. In the case of M113F 7 , the bottom (secondary hydroxyls) of the CD ring faces the trans entrance, while the top of the ring is bonded to the pore through remarkable CH-π interactions. Another tight-binding mutant, M113V 7 , can bind the CD in both orientations. These results illustrate the exquisite level of engineering that can be achieved with protein nanopores, which is, for example, far beyond what is possible with solid-state pores. The work also provides information valuable for the design of ...

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“…Simulations of these effects would be interesting (using one of the electrostatic algorithms of Refs. [13][14][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][44][45][46][47] and can be the topic of future studies. However, the main conclusions of this study would not change.…”

Section: Discussionmentioning

confidence: 99%

Dynamic Monte Carlo Simulation of Coupled Transport through a Narrow Multiply-Occupied Pore

et al. 2013

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Dynamic Monte Carlo simulations are used to study coupled transport (co-transport) through sub-nanometer-diameter pores. In this classic Hodgkin-Keynes mechanism, an ion species uses the large flux of an abundant ion species to move against its concentration gradient. The efficiency of co-transport is examined for various pore parameters so that synthetic nanopores can be engineered to maximize this effect. In general, the pore must be narrow enough that ions cannot pass each other and the charge of the pore large enough to attract many ions so that they exchange momentum. Co-transport efficiency increases as pore length increases, but even very short pores exhibit co-transport, in contradiction to the usual perception that long pores are necessary. The parameter ranges where co-transport occurs is consistent with current and near-future synthetic nanopore geometry parameters, suggesting that co-transport of ions may be a new application of nanopores.

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Ion Selectivity of α-Hemolysin with β-Cyclodextrin Adapter. II. Multi-Ion Effects Studied with Grand Canonical Monte Carlo/Brownian Dynamics Simulations

Cited by 40 publications

References 44 publications

Web interface for brownian dynamics simulation of ion transport and its applications to beta‐barrel pores

Web interface for brownian dynamics simulation of ion transport and its applications to beta‐barrel pores

Molecular bases of cyclodextrin adapter interactions with engineered protein nanopores

Dynamic Monte Carlo Simulation of Coupled Transport through a Narrow Multiply-Occupied Pore

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