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Fertig D, Sarkadi Z, Valiskó M, Boda D. Scaling for rectification of bipolar nanopores as a function of a modified Dukhin number: the case of 1:1 electrolytes. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1939330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Dávid Fertig
- Center for Natural Sciences, University of Pannonia, Veszprém, Hungary
| | - Zsófia Sarkadi
- Center for Natural Sciences, University of Pannonia, Veszprém, Hungary
| | - Mónika Valiskó
- Center for Natural Sciences, University of Pannonia, Veszprém, Hungary
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Sarkadi Z, Fertig D, Ható Z, Valiskó M, Boda D. From nanotubes to nanoholes: Scaling of selectivity in uniformly charged nanopores through the Dukhin number for 1:1 electrolytes. J Chem Phys 2021; 154:154704. [PMID: 33887923 DOI: 10.1063/5.0040593] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Scaling of the behavior of a nanodevice means that the device function (selectivity) is a unique smooth and monotonic function of a scaling parameter that is an appropriate combination of the system's parameters. For the uniformly charged cylindrical nanopore studied here, these parameters are the electrolyte concentration, c, voltage, U, the radius and the length of the nanopore, R and H, and the surface charge density on the nanopore's surface, σ. Due to the non-linear dependence of selectivities on these parameters, scaling can only be applied in certain limits. We show that the Dukhin number, Du=|σ|/eRc∼|σ|λD 2/eR (λD is the Debye length), is an appropriate scaling parameter in the nanotube limit (H → ∞). Decreasing the length of the nanopore, namely, approaching the nanohole limit (H → 0), an alternative scaling parameter has been obtained, which contains the pore length and is called the modified Dukhin number: mDu ∼ Du H/λD ∼ |σ|λDH/eR. We found that the reason for non-linearity is that the double layers accumulating at the pore wall in the radial dimension correlate with the double layers accumulating at the entrances of the pore near the membrane on the two sides. Our modeling study using the Local Equilibrium Monte Carlo method and the Poisson-Nernst-Planck theory provides concentration, flux, and selectivity profiles that show whether the surface or the volume conduction dominates in a given region of the nanopore for a given combination of the variables. We propose that the inflection point of the scaling curve may be used to characterize the transition point between the surface and volume conductions.
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Affiliation(s)
- Zsófia Sarkadi
- Center for Natural Sciences, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
| | - Dávid Fertig
- Center for Natural Sciences, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
| | - Zoltán Ható
- Center for Natural Sciences, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
| | - Mónika Valiskó
- Center for Natural Sciences, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
| | - Dezső Boda
- Center for Natural Sciences, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
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Eisenberg RS. Maxwell Equations without a Polarization Field, Using a Paradigm from Biophysics. ENTROPY (BASEL, SWITZERLAND) 2021; 23:172. [PMID: 33573137 PMCID: PMC7912333 DOI: 10.3390/e23020172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/26/2021] [Accepted: 01/26/2021] [Indexed: 01/17/2023]
Abstract
When forces are applied to matter, the distribution of mass changes. Similarly, when an electric field is applied to matter with charge, the distribution of charge changes. The change in the distribution of charge (when a local electric field is applied) might in general be called the induced charge. When the change in charge is simply related to the applied local electric field, the polarization field P is widely used to describe the induced charge. This approach does not allow electrical measurements (in themselves) to determine the structure of the polarization fields. Many polarization fields will produce the same electrical forces because only the divergence of polarization enters Maxwell's first equation, relating charge and electric forces and field. The curl of any function can be added to a polarization field P without changing the electric field at all. The divergence of the curl is always zero. Additional information is needed to specify the curl and thus the structure of the P field. When the structure of charge changes substantially with the local electric field, the induced charge is a nonlinear and time dependent function of the field and P is not a useful framework to describe either the electrical or structural basis-induced charge. In the nonlinear, time dependent case, models must describe the charge distribution and how it varies as the field changes. One class of models has been used widely in biophysics to describe field dependent charge, i.e., the phenomenon of nonlinear time dependent induced charge, called 'gating current' in the biophysical literature. The operational definition of gating current has worked well in biophysics for fifty years, where it has been found to makes neurons respond sensitively to voltage. Theoretical estimates of polarization computed with this definition fit experimental data. I propose that the operational definition of gating current be used to define voltage and time dependent induced charge, although other definitions may be needed as well, for example if the induced charge is fundamentally current dependent. Gating currents involve substantial changes in structure and so need to be computed from a combination of electrodynamics and mechanics because everything charged interacts with everything charged as well as most things mechanical. It may be useful to separate the classical polarization field as a component of the total induced charge, as it is in biophysics. When nothing is known about polarization, it is necessary to use an approximate representation of polarization with a dielectric constant that is a single real positive number. This approximation allows important results in some cases, e.g., design of integrated circuits in silicon semiconductors, but can be seriously misleading in other cases, e.g., ionic solutions.
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Affiliation(s)
- Robert S. Eisenberg
- Department of Applied Mathematics, Illinois Institute of Technology, Chicago, IL 60616, USA; ; Tel.: +1-708-932-2597
- Department of Physiology and Biophysics, Rush University Medical Center, Chicago, IL 60612, USA
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Boda D, Valiskó M, Gillespie D. Modeling the Device Behavior of Biological and Synthetic Nanopores with Reduced Models. ENTROPY 2020; 22:e22111259. [PMID: 33287027 PMCID: PMC7711659 DOI: 10.3390/e22111259] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 01/08/2023]
Abstract
Biological ion channels and synthetic nanopores are responsible for passive transport of ions through a membrane between two compartments. Modeling these ionic currents is especially amenable to reduced models because the device functions of these pores, the relation of input parameters (e.g., applied voltage, bath concentrations) and output parameters (e.g., current, rectification, selectivity), are well defined. Reduced models focus on the physics that produces the device functions (i.e., the physics of how inputs become outputs) rather than the atomic/molecular-scale physics inside the pore. Here, we propose four rules of thumb for constructing good reduced models of ion channels and nanopores. They are about (1) the importance of the axial concentration profiles, (2) the importance of the pore charges, (3) choosing the right explicit degrees of freedom, and (4) creating the proper response functions. We provide examples for how each rule of thumb helps in creating a reduced model of device behavior.
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Affiliation(s)
- Dezső Boda
- Department of Physical Chemistry, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary;
- Correspondence: ; Tel.: +36-88-624-000 (ext. 6041)
| | - Mónika Valiskó
- Department of Physical Chemistry, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary;
| | - Dirk Gillespie
- Department of Physiology and Biophysics, Rush University Medical Center, Chicago, IL 60612, USA;
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Fertig D, Valiskó M, Boda D. Rectification of bipolar nanopores in multivalent electrolytes: effect of charge inversion and strong ionic correlations. Phys Chem Chem Phys 2020; 22:19033-19045. [PMID: 32812580 DOI: 10.1039/d0cp03237a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bipolar nanopores have powerful rectification properties due to the asymmetry in the charge pattern on the wall of the nanopore. In particular, bipolar nanopores have positive and negative surface charges along the pore axis. Rectification is strong if the radius of the nanopore is small compared to the screening length of the electrolyte so that both cations and anions have depletion zones in the respective regions. The depths of these depletion zones is sensitive to sign of the external voltage. In this work, we are interested in the effect of the presence of strong ionic correlations (both between ions and between ions and surface charge) due to the presence of multivalent ions and large surface charges. We show that strong ionic correlations cause leakage of the coions, a phenomenon that is absent in mean field theories. In this modeling study, we use both the mean-field Poisson-Nernst-Planck (PNP) theory and a particle simulation method, Local Equilibrium Monte Carlo (LEMC), to show that phenomena such as overcharging and charge inversion cannot be reproduced with PNP, while LEMC is able to produce nonmonotonic dependence of currents and rectification as a function of surface charge strength.
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Affiliation(s)
- Dávid Fertig
- Department of Physical Chemistry, University of Pannonia, P. O. Box 158, H-8201 Veszprém, Hungary.
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Mádai E, Valiskó M, Boda D. Application of a bipolar nanopore as a sensor: rectification as an additional device function. Phys Chem Chem Phys 2019; 21:19772-19784. [PMID: 31475284 DOI: 10.1039/c9cp03821c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We model and simulate a nanopore sensor that selectively binds analyte ions. This binding leads to the modulation of the local concentrations of the ions of the background electrolyte (KCl), and, thus, to the modulation of the ionic current flowing through the pore. The nanopore's wall has a bipolar charge pattern with a larger positive buffer region determining the anions as the main charge carriers and a smaller negative binding region containing binding sites. This charge pattern proved to be an appropriate one as shown by a previous comparative study of varying charge patterns (Mádai et al. J. Mol. Liq., 2019, 283, 391-398.). Binding of the positive analyte ions attracts more anions in the pore thus increasing the current. The asymmetric nature of the pore results in an additional device function, rectification. Our model, therefore, is a dual response device. Using a reduced model of the nanopore studied by a hybrid computer simulation method (Local Equilibrium Monte Carlo coupled with the Nernst-Planck equation) we show that we can create a sensor whose underlying mechanisms are based on the changes in the local electric field as a response to changing thermodynamic conditions. The change in the electric field results in changes in the local ionic concentrations (depletion zones), and, thus, changes in ionic currents.
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Affiliation(s)
- Eszter Mádai
- Department of Material- and Geo-Sciences, Technische Universität Darmstadt, Petersenstr. 23, D-64287 Darmstadt, Germany
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Valiskó M, Matejczyk B, Ható Z, Kristóf T, Mádai E, Fertig D, Gillespie D, Boda D. Multiscale analysis of the effect of surface charge pattern on a nanopore's rectification and selectivity properties: From all-atom model to Poisson-Nernst-Planck. J Chem Phys 2019; 150:144703. [PMID: 30981242 DOI: 10.1063/1.5091789] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
We report a multiscale modeling study for charged cylindrical nanopores using three modeling levels that include (1) an all-atom explicit-water model studied with molecular dynamics, and reduced models with implicit water containing (2) hard-sphere ions studied with the Local Equilibrium Monte Carlo simulation method (computing ionic correlations accurately), and (3) point ions studied with Poisson-Nernst-Planck theory (mean-field approximation). We show that reduced models are able to reproduce device functions (rectification and selectivity) for a wide variety of charge patterns, that is, reduced models are useful in understanding the mesoscale physics of the device (i.e., how the current is produced). We also analyze the relationship of the reduced implicit-water models with the explicit-water model and show that diffusion coefficients in the reduced models can be used as adjustable parameters with which the results of the explicit- and implicit-water models can be related. We find that the values of the diffusion coefficients are sensitive to the net charge of the pore but are relatively transferable to different voltages and charge patterns with the same total charge.
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Affiliation(s)
- Mónika Valiskó
- Department of Physical Chemistry, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
| | - Bartłomiej Matejczyk
- Department of Mathematics, University of Warwick, CV4 7AL Coventry, United Kingdom
| | - Zoltán Ható
- Department of Physical Chemistry, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
| | - Tamás Kristóf
- Department of Physical Chemistry, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
| | - Eszter Mádai
- Department of Physical Chemistry, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
| | - Dávid Fertig
- Department of Physical Chemistry, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
| | - Dirk Gillespie
- Department of Physiology and Biophysics, Rush University Medical Center, Chicago, Illinois 60612, USA
| | - Dezső Boda
- Department of Physical Chemistry, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
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Fertig D, Valiskó M, Boda D. Controlling ionic current through a nanopore by tuning pH: a local equilibrium Monte Carlo study. Mol Phys 2019. [DOI: 10.1080/00268976.2018.1554194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Dávid Fertig
- Department of Physical Chemistry, University of Pannonia, P. O. Box 158, H-8201 Veszprém, Hungary
| | - Mónika Valiskó
- Department of Physical Chemistry, University of Pannonia, P. O. Box 158, H-8201 Veszprém, Hungary
| | - Dezső Boda
- Department of Physical Chemistry, University of Pannonia, P. O. Box 158, H-8201 Veszprém, Hungary
- Institute of Advanced Studies Kőszeg (iASK), Chernel u. 14, H-9730 Kőszeg, Hungary
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Mádai E, Matejczyk B, Dallos A, Valiskó M, Boda D. Controlling ion transport through nanopores: modeling transistor behavior. Phys Chem Chem Phys 2018; 20:24156-24167. [DOI: 10.1039/c8cp03918f] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We present a modeling study of a nanopore-based transistor computed by a mean-field continuum theory (Poisson–Nernst–Planck, PNP) and a hybrid method including particle simulation (Local Equilibrium Monte Carlo, LEMC) that is able to take ionic correlations into account including the finite size of ions.
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Affiliation(s)
- Eszter Mádai
- Department of Physical Chemistry
- University of Pannonia
- H-8201 Veszprém
- Hungary
| | | | - András Dallos
- Department of Physical Chemistry
- University of Pannonia
- H-8201 Veszprém
- Hungary
| | - Mónika Valiskó
- Department of Physical Chemistry
- University of Pannonia
- H-8201 Veszprém
- Hungary
| | - Dezső Boda
- Department of Physical Chemistry
- University of Pannonia
- H-8201 Veszprém
- Hungary
- Institute of Advanced Studies Köszeg (iASK)
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Mádai E, Valiskó M, Dallos A, Boda D. Simulation of a model nanopore sensor: Ion competition underlies device behavior. J Chem Phys 2017; 147:244702. [PMID: 29289138 DOI: 10.1063/1.5007654] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We study a model nanopore sensor with which a very low concentration of analyte molecules can be detected on the basis of the selective binding of the analyte molecules to the binding sites on the pore wall. The bound analyte ions partially replace the current-carrier cations in a thermodynamic competition. This competition depends both on the properties of the nanopore and the concentrations of the competing ions (through their chemical potentials). The output signal given by the device is the current reduction caused by the presence of the analyte ions. The concentration of the analyte ions can be determined through calibration curves. We model the binding site with the square-well potential and the electrolyte as charged hard spheres in an implicit background solvent. We study the system with a hybrid method in which we compute the ion flux with the Nernst-Planck (NP) equation coupled with the Local Equilibrium Monte Carlo (LEMC) simulation technique. The resulting NP+LEMC method is able to handle both strong ionic correlations inside the pore (including finite size of ions) and bulk concentrations as low as micromolar. We analyze the effect of bulk ion concentrations, pore parameters, binding site parameters, electrolyte properties, and voltage on the behavior of the device.
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Affiliation(s)
- Eszter Mádai
- Department of Physical Chemistry, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
| | - Mónika Valiskó
- Department of Physical Chemistry, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
| | - András Dallos
- Department of Physical Chemistry, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
| | - Dezső Boda
- Department of Physical Chemistry, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
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Ható Z, Valiskó M, Kristóf T, Gillespie D, Boda D. Multiscale modeling of a rectifying bipolar nanopore: explicit-water versus implicit-water simulations. Phys Chem Chem Phys 2017; 19:17816-17826. [PMID: 28657634 DOI: 10.1039/c7cp01819c] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In a multiscale modeling approach, we present computer simulation results for a rectifying bipolar nanopore at two modeling levels. In an all-atom model, we use explicit water to simulate ion transport directly with the molecular dynamics technique. In a reduced model, we use implicit water and apply the Local Equilibrium Monte Carlo method together with the Nernst-Planck transport equation. This hybrid method makes the fast calculation of ion transport possible at the price of lost details. We show that the implicit-water model is an appropriate representation of the explicit-water model when we look at the system at the device (i.e., input vs. output) level. The two models produce qualitatively similar behavior of the electrical current for different voltages and model parameters. Looking at the details of concentration and potential profiles, we find profound differences between the two models. These differences, however, do not influence the basic behavior of the model as a device because they do not influence the z-dependence of the concentration profiles which are the main determinants of current. These results then address an old paradox: how do reduced models, whose assumptions should break down in a nanoscale device, predict experimental data? Our simulations show that reduced models can still capture the overall device physics correctly, even though they get some important aspects of the molecular-scale physics quite wrong; reduced models work because they include the physics that is necessary from the point of view of device function. Therefore, reduced models can suffice for general device understanding and device design, but more detailed models might be needed for molecular level understanding.
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Affiliation(s)
- Zoltán Ható
- Department of Physical Chemistry, University of Pannonia, P. O. Box 158, H-8201 Veszprém, Hungary. and Institute of Advanced Studies Köszeg (iASK), Chernel st. 14, H-9730 Köszeg, Hungary
| | - Mónika Valiskó
- Department of Physical Chemistry, University of Pannonia, P. O. Box 158, H-8201 Veszprém, Hungary.
| | - Tamás Kristóf
- Department of Physical Chemistry, University of Pannonia, P. O. Box 158, H-8201 Veszprém, Hungary.
| | - Dirk Gillespie
- Department of Physiology and Biophysics, Rush University Medical Center, Chicago, IL, USA
| | - Dezsö Boda
- Department of Physical Chemistry, University of Pannonia, P. O. Box 158, H-8201 Veszprém, Hungary. and Institute of Advanced Studies Köszeg (iASK), Chernel st. 14, H-9730 Köszeg, Hungary
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Matejczyk B, Valiskó M, Wolfram MT, Pietschmann JF, Boda D. Multiscale modeling of a rectifying bipolar nanopore: Comparing Poisson-Nernst-Planck to Monte Carlo. J Chem Phys 2017; 146:124125. [PMID: 28388126 DOI: 10.1063/1.4978942] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In the framework of a multiscale modeling approach, we present a systematic study of a bipolar rectifying nanopore using a continuum and a particle simulation method. The common ground in the two methods is the application of the Nernst-Planck (NP) equation to compute ion transport in the framework of the implicit-water electrolytemodel. The difference is that the Poisson-Boltzmann theory is used in the Poisson-Nernst-Planck (PNP) approach, while the Local Equilibrium Monte Carlo (LEMC) method is used in the particle simulation approach (NP+LEMC) to relate the concentration profile to the electrochemical potential profile. Since we consider a bipolar pore which is short and narrow, we perform simulations using two-dimensional PNP. In addition, results of a non-linear version of PNP that takes crowding of ions into account are shown. We observe that the mean field approximation applied in PNP is appropriate to reproduce the basic behavior of the bipolar nanopore (e.g., rectification) for varying parameters of the system (voltage, surface charge,electrolyte concentration, and pore radius). We present current data that characterize the nanopore's behavior as a device, as well as concentration, electrical potential, and electrochemical potential profiles.
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Affiliation(s)
- Bartłomiej Matejczyk
- Department of Mathematics, University of Warwick, CV4 7AL Coventry, United Kingdom
| | - Mónika Valiskó
- Department of Physical Chemistry, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
| | | | | | - Dezső Boda
- Department of Physical Chemistry, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
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Kingsley LJ, Lill MA. Substrate tunnels in enzymes: structure-function relationships and computational methodology. Proteins 2015; 83:599-611. [PMID: 25663659 DOI: 10.1002/prot.24772] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 01/08/2015] [Accepted: 01/14/2015] [Indexed: 12/14/2022]
Abstract
In enzymes, the active site is the location where incoming substrates are chemically converted to products. In some enzymes, this site is deeply buried within the core of the protein, and, in order to access the active site, substrates must pass through the body of the protein via a tunnel. In many systems, these tunnels act as filters and have been found to influence both substrate specificity and catalytic mechanism. Identifying and understanding how these tunnels exert such control has been of growing interest over the past several years because of implications in fields such as protein engineering and drug design. This growing interest has spurred the development of several computational methods to identify and analyze tunnels and how ligands migrate through these tunnels. The goal of this review is to outline how tunnels influence substrate specificity and catalytic efficiency in enzymes with buried active sites and to provide a brief summary of the computational tools used to identify and evaluate these tunnels.
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Affiliation(s)
- Laura J Kingsley
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana
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Gillespie D, Xu L, Meissner G. Selecting ions by size in a calcium channel: the ryanodine receptor case study. Biophys J 2014; 107:2263-73. [PMID: 25418295 PMCID: PMC4241444 DOI: 10.1016/j.bpj.2014.09.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 09/25/2014] [Accepted: 09/30/2014] [Indexed: 10/24/2022] Open
Abstract
Many calcium channels can distinguish between ions of the same charge but different size. For example, when cations are in direct competition with each other, the ryanodine receptor (RyR) calcium channel preferentially conducts smaller cations such as Li(+) and Na(+) over larger ones such as K(+) and Cs(+). Here, we analyze the physical basis for this preference using a previously established model of RyR permeation and selectivity. Like other calcium channels, RyR has four aspartate residues in its GGGIGDE selectivity filter. These aspartates have their terminal carboxyl group in the pore lumen, which take up much of the available space for permeating ions. We find that small ions are preferred by RyR because they can fit into this crowded environment more easily.
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Affiliation(s)
- Dirk Gillespie
- Department of Molecular Biophysics and Physiology, Rush University Medical Center, Chicago, Illinois.
| | - Le Xu
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina
| | - Gerhard Meissner
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina
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Berti C, Furini S, Gillespie D, Boda D, Eisenberg RS, Sangiorgi E, Fiegna C. Three-Dimensional Brownian Dynamics Simulator for the Study of Ion Permeation through Membrane Pores. J Chem Theory Comput 2014; 10:2911-26. [DOI: 10.1021/ct4011008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Claudio Berti
- Department
of Molecular Biophysics and Physiology, Rush University Medical Center, Chicago,Illinois, United States
- ARCES
and DEI, University of Bologna and IUNET, Cesena, Italy
| | - Simone Furini
- Department
of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Dirk Gillespie
- Department
of Molecular Biophysics and Physiology, Rush University Medical Center, Chicago,Illinois, United States
| | - Dezső Boda
- Department
of Physical Chemistry, University of Pannonia, Veszprém, Hungary
| | - Robert S. Eisenberg
- Department
of Molecular Biophysics and Physiology, Rush University Medical Center, Chicago,Illinois, United States
| | | | - Claudio Fiegna
- ARCES
and DEI, University of Bologna and IUNET, Cesena, Italy
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Boda D. Monte Carlo Simulation of Electrolyte Solutions in Biology. ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1016/b978-0-444-63378-1.00005-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Kaufman I, Luchinsky DG, Tindjong R, McClintock PVE, Eisenberg RS. Energetics of discrete selectivity bands and mutation-induced transitions in the calcium-sodium ion channels family. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:052712. [PMID: 24329301 DOI: 10.1103/physreve.88.052712] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Indexed: 06/03/2023]
Abstract
We use Brownian dynamics (BD) simulations to study the ionic conduction and valence selectivity of a generic electrostatic model of a biological ion channel as functions of the fixed charge Q(f) at its selectivity filter. We are thus able to reconcile the discrete calcium conduction bands recently revealed in our BD simulations, M0 (Q(f)=1e), M1 (3e), M2 (5e), with a set of sodium conduction bands L0 (0.5e), L1 (1.5e), thereby obtaining a completed pattern of conduction and selectivity bands vs Q(f) for the sodium-calcium channels family. An increase of Q(f) leads to an increase of calcium selectivity: L0 (sodium-selective, nonblocking channel) → M0 (nonselective channel) → L1 (sodium-selective channel with divalent block) → M1 (calcium-selective channel exhibiting the anomalous mole fraction effect). We create a consistent identification scheme where the L0 band is putatively identified with the eukaryotic sodium channel The scheme created is able to account for the experimentally observed mutation-induced transformations between nonselective channels, sodium-selective channels, and calcium-selective channels, which we interpret as transitions between different rows of the identification table. By considering the potential energy changes during permeation, we show explicitly that the multi-ion conduction bands of calcium and sodium channels arise as the result of resonant barrierless conduction. The pattern of periodic conduction bands is explained on the basis of sequential neutralization taking account of self-energy, as Q(f)(z,i)=ze(1/2+i), where i is the order of the band and z is the valence of the ion. Our results confirm the crucial influence of electrostatic interactions on conduction and on the Ca(2+)/Na(+) valence selectivity of calcium and sodium ion channels. The model and results could be also applicable to biomimetic nanopores with charged walls.
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Affiliation(s)
- I Kaufman
- Department of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - D G Luchinsky
- Department of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom and Mission Critical Technologies Inc., 2041 Rosecrans Ave. Suite 225 El Segundo, California 90245, USA
| | - R Tindjong
- Department of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - P V E McClintock
- Department of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - R S Eisenberg
- Department of Molecular Biophysics and Physiology, Rush Medical College, 1750 West Harrison, Chicago, Illinois 60612, USA
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