301
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Gamble T, Decker K, Plett T, Pevarnik M, Pietschmann JF, Vlassiouk I, Aksimentiev A, Siwy ZS. Rectification of Ion Current in Nanopores Depends on the Type of Monovalent Cations: Experiments and Modeling. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2014; 118:9809-9819. [PMID: 25678940 PMCID: PMC4317049 DOI: 10.1021/jp501492g] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 03/24/2014] [Indexed: 05/04/2023]
Abstract
Rectifying nanopores feature ion currents that are higher for voltages of one polarity compared to the currents recorded for corresponding voltages of the opposite polarity. Rectification of nanopores has been found to depend on the pore opening diameter and distribution of surface charges on the pore walls as well as pore geometry. Very little is known, however, on the dependence of ionic rectification on the type of transported ions of the same charge. We performed experiments with single conically shaped nanopores in a polymer film and recorded current-voltage curves in three electrolytes: LiCl, NaCl, and KCl. Rectification degrees of the pores, quantified as the ratio of currents recorded for voltages of opposite polarities, were the highest for KCl and the lowest for LiCl. The experimental observations could not be explained by a continuum modeling based on the Poisson-Nernst-Planck equations. All-atom molecular dynamics simulations revealed differential binding between Li+, Na+, and K+ ions and carboxyl groups on the pore walls, resulting in changes to both the effective surface charge of the nanopore and cation mobility within the pore.
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Affiliation(s)
- Trevor Gamble
- Department
of Physics and Astronomy, University of
California, Irvine, Irvine, California 92697, United States
| | - Karl Decker
- Department
of Physics, Beckman Institute, University
of Illinois, Urbana, Illinois 61820, United
States
| | - Timothy
S. Plett
- Department
of Physics and Astronomy, University of
California, Irvine, Irvine, California 92697, United States
| | - Matthew Pevarnik
- Department
of Physics and Astronomy, University of
California, Irvine, Irvine, California 92697, United States
| | | | - Ivan Vlassiouk
- Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Aleksei Aksimentiev
- Department
of Physics, Beckman Institute, University
of Illinois, Urbana, Illinois 61820, United
States
- E-mail (A.A.)
| | - Zuzanna S. Siwy
- Department
of Physics and Astronomy, University of
California, Irvine, Irvine, California 92697, United States
- Department of Chemistry and Department of Biomedical Engineering, University of California, Irvine, California 92697, United States
- E-mail (Z.S.S.)
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302
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Martin HSC, Jha S, Coveney PV. Comparative analysis of nucleotide translocation through protein nanopores using steered molecular dynamics and an adaptive biasing force. J Comput Chem 2014; 35:692-702. [PMID: 24403093 PMCID: PMC4274958 DOI: 10.1002/jcc.23525] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 11/13/2013] [Accepted: 12/07/2013] [Indexed: 12/17/2022]
Abstract
The translocation of nucleotide molecules across biological and synthetic nanopores has attracted attention as a next generation technique for sequencing DNA. Computer simulations have the ability to provide atomistic-level insight into important states and processes, delivering a means to develop a fundamental understanding of the translocation event, for example, by extracting the free energy of the process. Even with current supercomputing facilities, the simulation of many-atom systems in fine detail is limited to shorter timescales than the real events they attempt to recreate. This imposes the need for enhanced simulation techniques that expand the scope of investigation in a given timeframe. There are numerous free energy calculation and translocation methodologies available, and it is by no means clear which method is best applied to a particular problem. This article explores the use of two popular free energy calculation methodologies in a nucleotide-nanopore translocation system, using the α-hemolysin nanopore. The first uses constant velocity-steered molecular dynamics (cv-SMD) in conjunction with Jarzynski's equality. The second applies an adaptive biasing force (ABF), which has not previously been applied to the nucleotide-nanpore system. The purpose of this study is to provide a comprehensive comparison of these methodologies, allowing for a detailed comparative assessment of the scientific merits, the computational cost, and the statistical quality of the data obtained from each technique. We find that the ABF method produces results that are closer to experimental measurements than those from cv-SMD, whereas the net errors are smaller for the same computational cost.
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Affiliation(s)
- Hugh S C Martin
- Department of Chemistry, Centre for Computational ScienceUCL, 20 Gordon Street, London, United Kingdom
| | - Shantenu Jha
- Department of Electrical Engineering BuildingRutgers, 94 Brett Road, Piscataway, New Jersey
| | - Peter V Coveney
- Department of Chemistry, Centre for Computational ScienceUCL, 20 Gordon Street, London, United Kingdom
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303
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Adelman JL, Sheng Y, Choe S, Abramson J, Wright EM, Rosenberg JM, Grabe M. Structural determinants of water permeation through the sodium-galactose transporter vSGLT. Biophys J 2014; 106:1280-9. [PMID: 24655503 PMCID: PMC3984995 DOI: 10.1016/j.bpj.2014.01.006] [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: 10/31/2013] [Revised: 12/19/2013] [Accepted: 01/02/2014] [Indexed: 01/26/2023] Open
Abstract
Sodium-glucose transporters (SGLTs) facilitate the movement of water across the cell membrane, playing a central role in cellular homeostasis. Here, we present a detailed analysis of the mechanism of water permeation through the inward-facing state of vSGLT based on nearly 10 μs of molecular dynamics simulations. These simulations reveal the transient formation of a continuous water channel through the transporter that permits water to permeate the protein. Trajectories in which spontaneous release of galactose is observed, as well as those in which galactose remains in the binding site, show that the permeation rate, although modulated by substrate occupancy, is not tightly coupled to substrate release. Using a, to our knowledge, novel channel-detection algorithm, we identify the key residues that control water flow through the transporter and show that solvent gating is regulated by side-chain motions in a small number of residues on the extracellular face. A sequence alignment reveals the presence of two insertion sites in mammalian SGLTs that flank these outer-gate residues. We hypothesize that the absence of these sites in vSGLT may account for the high water permeability values for vSGLT determined via simulation compared to the lower experimental estimates for mammalian SGLT1.
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Affiliation(s)
- Joshua L Adelman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ying Sheng
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Seungho Choe
- School of Basic Science, College of Convergence, Daegu Gyeongbuk Institute of Science & Technology, Daegu, Korea
| | - Jeff Abramson
- Department of Physiology, University of California, Los Angeles, California
| | - Ernest M Wright
- Department of Physiology, University of California, Los Angeles, California
| | - John M Rosenberg
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania.
| | - Michael Grabe
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania; Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, California.
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304
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Laghaei R, Kowallis W, Evans DG, Coalson RD. Calculation of Iron Transport through Human H-chain Ferritin. J Phys Chem A 2014; 118:7442-53. [DOI: 10.1021/jp500198u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Rozita Laghaei
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - William Kowallis
- Department
of Chemistry, Carlow University, Pittsburgh, Pennsylvania 15213, United States
| | - Deborah G. Evans
- The
Nanoscience and Microsystems Program and the Department of Chemistry
and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
| | - Rob D. Coalson
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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305
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Chaudhry JH, Comer J, Aksimentiev A, Olson LN. A Stabilized Finite Element Method for Modified Poisson-Nernst-Planck Equations to Determine Ion Flow Through a Nanopore. COMMUNICATIONS IN COMPUTATIONAL PHYSICS 2014; 15:10.4208/cicp.101112.100413a. [PMID: 24363784 PMCID: PMC3867981 DOI: 10.4208/cicp.101112.100413a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The conventional Poisson-Nernst-Planck equations do not account for the finite size of ions explicitly. This leads to solutions featuring unrealistically high ionic concentrations in the regions subject to external potentials, in particular, near highly charged surfaces. A modified form of the Poisson-Nernst-Planck equations accounts for steric effects and results in solutions with finite ion concentrations. Here, we evaluate numerical methods for solving the modified Poisson-Nernst-Planck equations by modeling electric field-driven transport of ions through a nanopore. We describe a novel, robust finite element solver that combines the applications of the Newton's method to the nonlinear Galerkin form of the equations, augmented with stabilization terms to appropriately handle the drift-diffusion processes. To make direct comparison with particle-based simulations possible, our method is specifically designed to produce solutions under periodic boundary conditions and to conserve the number of ions in the solution domain. We test our finite element solver on a set of challenging numerical experiments that include calculations of the ion distribution in a volume confined between two charged plates, calculations of the ionic current though a nanopore subject to an external electric field, and modeling the effect of a DNA molecule on the ion concentration and nanopore current.
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Affiliation(s)
| | - Jeffrey Comer
- Department for Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Aleksei Aksimentiev
- Department for Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Luke N. Olson
- Department for Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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306
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A Microscopic View of the Mechanisms of Active Transport Across the Cellular Membrane. ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1016/b978-0-444-63378-1.00004-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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307
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Noskov SY, Rostovtseva TK, Bezrukov SM. ATP transport through VDAC and the VDAC-tubulin complex probed by equilibrium and nonequilibrium MD simulations. Biochemistry 2013; 52:9246-56. [PMID: 24245503 PMCID: PMC7259721 DOI: 10.1021/bi4011495] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Voltage-dependent anion channel (VDAC), the major channel of the mitochondrial outer membrane, serves as a principal pathway for ATP, ADP, and other respiratory substrates across this membrane. Using umbrella-sampling simulations, we established the thermodynamic and kinetic components governing ATP transport across the VDAC1 channel. We found that there are several low-affinity binding sites for ATP along the translocation pathway and that the main barrier for ATP transport is located around the center of the channel and is formed predominantly by residues in the N-terminus. The binding affinity of ATP to an open channel was found to be in the millimolar to micromolar range. However, we show that this weak binding increases the ATP translocation probability by about 10-fold compared with the VDAC pore in which attractive interactions were artificially removed. Recently, it was found that free dimeric tubulin induces a highly efficient, reversible blockage of VDAC reconstituted into planar lipid membranes. It was proposed that by blocking VDAC permeability for ATP/ADP and other mitochondrial respiratory substrates tubulin controls mitochondrial respiration. Using the Rosetta protein-protein docking algorithm, we established a tentative structure of the VDAC-tubulin complex. An extensive set of equilibrium and nonequilibrium (under applied electric field) molecular dynamics (MD) simulations was used to establish the conductance of the open and blocked channel. It was found that the presence of the unstructured C-terminal tail of tubulin in the VDAC pore decreases its conductance by more than 40% and switches its selectivity from anionic to cationic. The subsequent 1D potential of mean force (PMF) computations for the VDAC-tubulin complex show that the state renders ATP transport virtually impossible. A number of residues pivotal for tubulin binding to the channel were identified that help to clarify the molecular details of VDAC-tubulin interaction and to provide new insight into the mechanism of the control of mitochondria respiration by VDAC.
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Affiliation(s)
- Sergei Yu. Noskov
- Center for Molecular Simulations, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Tatiana K. Rostovtseva
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Sergey M. Bezrukov
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
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308
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Larkin J, Henley R, Bell DC, Cohen-Karni T, Rosenstein JK, Wanunu M. Slow DNA transport through nanopores in hafnium oxide membranes. ACS NANO 2013; 7:10121-10128. [PMID: 24083444 PMCID: PMC4729694 DOI: 10.1021/nn404326f] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We present a study of double- and single-stranded DNA transport through nanopores fabricated in ultrathin (2-7 nm thick) freestanding hafnium oxide (HfO2) membranes. The high chemical stability of ultrathin HfO2 enables long-lived experiments with <2 nm diameter pores that last several hours, in which we observe >50 000 DNA translocations with no detectable pore expansion. Mean DNA velocities are slower than velocities through comparable silicon nitride pores, providing evidence that HfO2 nanopores have favorable physicochemical interactions with nucleic acids that can be leveraged to slow down DNA in a nanopore.
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Affiliation(s)
- Joseph Larkin
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Robert Henley
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - David C. Bell
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Tzahi Cohen-Karni
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jacob K. Rosenstein
- School of Engineering, Brown University, Providence, Rhode Island 02912, United States
| | - Meni Wanunu
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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309
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He Z, Zhou J, Lu X, Corry B. Bioinspired graphene nanopores with voltage-tunable ion selectivity for Na(+) and K(+). ACS NANO 2013; 7:10148-10157. [PMID: 24151957 DOI: 10.1021/nn4043628] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Biological protein channels have many remarkable properties such as gating, high permeability, and selectivity, which have motivated researchers to mimic their functions for practical applications. Herein, using molecular dynamics simulations, we design bioinspired nanopores in graphene sheets that can discriminate between Na(+) and K(+), two ions with very similar properties. The simulation results show that, under transmembrane voltage bias, a nanopore containing four carbonyl groups to mimic the selectivity filter of the KcsA K(+) channel preferentially conducts K(+) over Na(+). A nanopore functionalized by four negatively charged carboxylate groups to mimic the selectivity filter of the NavAb Na(+) channel selectively binds Na(+) but transports K(+) over Na(+). Surprisingly, the ion selectivity of the smaller diameter pore containing three carboxylate groups can be tuned by changing the magnitude of the applied voltage bias. Under lower voltage bias, it transports ions in a single-file manner and exhibits Na(+) selectivity, dictated by the knock-on ion conduction and selective blockage by Na(+). Under higher voltage bias, the nanopore is K(+)-selective, as the blockage by Na(+) is destabilized and the stronger affinity for carboxylate groups slows the passage of Na(+) compared with K(+). The computational design of biomimetic ion-selective nanopores helps to understand the mechanisms of selectivity in biological ion channels and may also lead to a wide range of potential applications such as sensitive ion sensors, nanofiltration membranes for Na(+)/K(+) separation, and voltage-tunable nanofluidic devices.
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Affiliation(s)
- Zhongjin He
- School of Chemistry and Chemical Engineering, South China University of Technology , Guangzhou, Guangdong 510640, China
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310
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Lu J, Modi N, Kleinekathöfer U. Simulation of Ion Transport through an N-Acetylneuraminic Acid-Inducible Membrane Channel: From Understanding to Engineering. J Phys Chem B 2013; 117:15966-75. [DOI: 10.1021/jp408495v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Jing Lu
- School of Engineering and
Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Niraj Modi
- School of Engineering and
Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- School of Engineering and
Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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311
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Harb F, Tinland B. Electric migration of α-hemolysin in supported n-bilayers: a model for transmembrane protein microelectrophoresis. Electrophoresis 2013; 34:3054-63. [PMID: 23925931 DOI: 10.1002/elps.201300202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 06/26/2013] [Accepted: 07/12/2013] [Indexed: 11/06/2022]
Abstract
Proteome analysis involves separating proteins as a preliminary step toward their characterization. This paper reports on the translational migration of a model transmembrane protein (α-hemolysin) in supported n-bilayers (n, the number of bilayers, varies from 1 to around 500 bilayers) when an electric field parallel to the membrane plane is applied. The migration changes in direction as the charge on the protein changes its sign. Its electrophoretic mobility is shown to depend on size and charge. The electrophoretic mobility varies as 1/R(2), with R the equivalent geometric radius of the embedded part of the protein. Measuring mobilities at differing pH in our system enables us to determine the pI and the charge of the protein. Establishing all these variations points to the feasibility of electrophoretic transport of a charged object in this medium and is a first step toward electrophoretic separation of membrane proteins in n-bilayer systems.
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Affiliation(s)
- Frédéric Harb
- Aix-Marseille Université, CINaM, CNRS, Marseille, France
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312
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Zoonens M, Comer J, Masscheleyn S, Pebay-Peyroula E, Chipot C, Miroux B, Dehez F. Dangerous liaisons between detergents and membrane proteins. The case of mitochondrial uncoupling protein 2. J Am Chem Soc 2013; 135:15174-82. [PMID: 24021091 DOI: 10.1021/ja407424v] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The extraction of membrane proteins from their native environment by detergents is central to their biophysical characterization. Recent studies have emphasized that detergents may perturb the structure locally and modify the dynamics of membrane proteins. However, it remains challenging to determine whether these perturbations are negligible or could be responsible for misfolded conformations, altering the protein's function. In this work, we propose an original strategy combining functional studies and molecular simulations to address the physiological relevance of membrane protein structures obtained in the presence of detergents. We apply our strategy to a structure of isoform 2 of an uncoupling protein (UCP2) binding an inhibitor recently obtained in dodecylphosphocholine detergent micelles. Although this structure shares common traits with the ADP/ATP carrier, a member of the same protein family, its functional and biological significance remains to be addressed. In the present investigation, we demonstrate how dodecylphosphocholine severely alters the structure as well as the function of UCPs. The proposed original strategy opens new vistas for probing the physiological relevance of three-dimensional structures of membrane proteins obtained in non-native environments.
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Affiliation(s)
- Manuela Zoonens
- CNRS UMR 7099, Institut de Biologie Physico Chimique (IBPC), 75005 Paris, France
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313
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Dyrka W, Bartuzel MM, Kotulska M. Optimization of 3D Poisson-Nernst-Planck model for fast evaluation of diverse protein channels. Proteins 2013; 81:1802-22. [PMID: 23720356 DOI: 10.1002/prot.24326] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 05/02/2013] [Accepted: 05/09/2013] [Indexed: 12/12/2022]
Abstract
We show the accuracy and applicability of our fast algorithmic implementation of a three-dimensional Poisson-Nernst-Planck (3D-PNP) flow model for characterizing different protein channels. Due to its high computational efficiency, our model can predict the full current-voltage characteristics of a channel within minutes, based on the experimental 3D structure of the channel or its computational model structure. Compared with other methods, such as Brownian dynamics, which currently needs a few weeks of the computational time, or even much more demanding molecular dynamics modeling, 3D-PNP is the only available method for a function-based evaluation of very numerous tentative structural channel models. Flow model tests of our algorithm and its optimal parametrization are provided for five native channels whose experimental structures are available in the protein data bank (PDB) in an open conductive state, and whose experimental current-voltage characteristics have been published. The channels represent very different geometric and structural properties, which makes it the widest test to date of the accuracy of 3D-PNP on real channels. We test whether the channel conductance, rectification, and charge selectivity obtained from the flow model, could be sufficiently sensitive to single-point mutations, related to unsignificant changes in the channel structure. Our results show that the classical 3D-PNP model, under proper parametrization, is able to achieve a qualitative agreement with experimental data for a majority of the tested characteristics and channels, including channels with narrow and irregular conductivity pores. We propose that although the standard PNP model cannot provide insight into complex physical phenomena due to its intrinsic limitations, its semiquantitative agreement is achievable for rectification and selectivity at a level sufficient for the bioinformatical purpose of selecting the best structural models with a great advantage of a very short computational time.
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Affiliation(s)
- Witold Dyrka
- Group of Bioinformatics and Biophysics of Nanopores, Institute of Biomedical Engineering and Instrumentation, Wroclaw University of Technology, Wroclaw, Poland
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314
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Buchsbaum SF, Mitchell N, Martin H, Wiggin M, Marziali A, Coveney PV, Siwy Z, Howorka S. Disentangling steric and electrostatic factors in nanoscale transport through confined space. NANO LETTERS 2013; 13:3890-3896. [PMID: 23819625 DOI: 10.1021/nl401968r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The voltage-driven passage of biological polymers through nanoscale pores is an analytically, technologically, and biologically relevant process. Despite various studies on homopolymer translocation there are still several open questions on the fundamental aspects of pore transport. One of the most important unresolved issues revolves around the passage of biopolymers which vary in charge and volume along their sequence. Here we exploit an experimentally tunable system to disentangle and quantify electrostatic and steric factors. This new, fundamental framework facilitates the understanding of how complex biopolymers are transported through confined space and indicates how their translocation can be slowed down to enable future sensing methods.
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Affiliation(s)
- Steven F Buchsbaum
- School of Physical Sciences, University of California, Irvine, California 92697, United States
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315
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Modi N, Bárcena-Uribarri I, Bains M, Benz R, Hancock REW, Kleinekathöfer U. Role of the central arginine R133 toward the ion selectivity of the phosphate specific channel OprP: effects of charge and solvation. Biochemistry 2013; 52:5522-32. [PMID: 23875754 DOI: 10.1021/bi400522b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The outer membrane porin OprP of Pseudomonas aeruginosa forms a highly specific phosphate selective channel. This channel is responsible for the high-affinity uptake of phosphate ions into the periplasmic space of the bacteria. A detailed investigation of the structure-function relationship of OprP is inevitable to decipher the anion and phosphate selectivity of this porin in particular and to broaden the present understanding of the ion selectivity of different channels. To this end we investigated the role of the central arginine of OprP, R133, in terms of its effects in selectivity and ion transport properties of the pore. Electrophysiological bilayer measurements and free-energy molecular dynamics simulations were carried out to probe the transport of different ions through various R133 mutants. For these mutants, the change in phosphate binding specificity, ion conduction, and anion selectivity was determined and compared to previous molecular dynamic calculations and electrophysiological measurements with wild-type OprP. Molecular analysis revealed a rather particular role of arginine 133 and its charge, while at the same time this residue together with the network of other residues, namely, D94 and Y114, has the ability to dehydrate the permeating ion. These very specific features govern the ion selectivity of OprP.
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Affiliation(s)
- Niraj Modi
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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316
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Liu Y, Zhu F. Collective diffusion model for ion conduction through microscopic channels. Biophys J 2013; 104:368-76. [PMID: 23442858 DOI: 10.1016/j.bpj.2012.11.3826] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 11/21/2012] [Accepted: 11/29/2012] [Indexed: 10/27/2022] Open
Abstract
Ion conduction through microscopic channels is of central importance in both biology and nanotechnology. To better understand the current-voltage (I-V) dependence of ion channels, here we describe and prove a collective diffusion model that quantitatively relates the spontaneous ion permeation at equilibrium to the stationary ionic fluxes driven by small voltages. The model makes it possible to determine the channel conductance in the linear I-V range from equilibrium simulations without the application of a voltage. To validate the theory, we perform molecular-dynamics simulations on two channels-a conical-shaped nanopore and the transmembrane pore of an α-hemolysin-under both equilibrium and nonequilibrium conditions. The simulations reveal substantial couplings between the motions of cations and anions, which are effectively captured by the collective coordinate in the model. Although the two channels exhibit very different linear ranges in the I-V curves, in both cases the channel conductance at small voltages is in reasonable agreement with the prediction from the equilibrium simulation. The simulations also suggest that channel charges, rather than geometric asymmetry, play a more prominent role in current rectification.
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Affiliation(s)
- Yingting Liu
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana, USA
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317
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Pöyry S, Cramariuc O, Postila PA, Kaszuba K, Sarewicz M, Osyczka A, Vattulainen I, Róg T. Atomistic simulations indicate cardiolipin to have an integral role in the structure of the cytochrome bc1 complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:769-78. [DOI: 10.1016/j.bbabio.2013.03.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 03/05/2013] [Accepted: 03/13/2013] [Indexed: 10/27/2022]
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318
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Reiner JE, Balijepalli A, Robertson JWF, Drown BS, Burden DL, Kasianowicz JJ. The effects of diffusion on an exonuclease/nanopore-based DNA sequencing engine. J Chem Phys 2013; 137:214903. [PMID: 23231259 DOI: 10.1063/1.4766363] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Over 15 years ago, the ability to electrically detect and characterize individual polynucleotides as they are driven through a single protein ion channel was suggested as a potential method for rapidly sequencing DNA, base-by-base, in a ticker tape-like fashion. More recently, a variation of this method was proposed in which a nanopore would instead detect single nucleotides cleaved sequentially by an exonuclease enzyme in close proximity to one pore entrance. We analyze the exonuclease/nanopore-based DNA sequencing engine using analytical theory and computer simulations that describe nucleotide transport. The available data and analytical results suggest that the proposed method will be limited to reading <80 bases, imposed, in part, by the short lifetime each nucleotide spends in the vicinity of the detection element within the pore and the ability to accurately discriminate between the four mononucleotides.
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Affiliation(s)
- Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, USA
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319
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Tian K, He Z, Wang Y, Chen SJ, Gu LQ. Designing a polycationic probe for simultaneous enrichment and detection of microRNAs in a nanopore. ACS NANO 2013; 7:3962-9. [PMID: 23550815 PMCID: PMC3675772 DOI: 10.1021/nn305789z] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The nanopore sensor can detect cancer-derived nucleic acid biomarkers such as microRNAs (miRNAs), providing a noninvasive tool potentially useful in medical diagnostics. However, the nanopore-based detection of these biomarkers remains confounded by the presence of numerous other nucleic acid species found in biofluid extracts. Their nonspecific interactions with the nanopore inevitably contaminate the target signals, reducing the detection accuracy. Here we report a novel method that utilizes a polycationic peptide-PNA probe as the carrier for selective miRNA detection in the nucleic acid mixture. The cationic probe hybridized with microRNA forms a dipole complex, which can be captured by the pore using a voltage polarity that is opposite the polarity used to capture negatively charged nucleic acids. As a result, nontarget species are driven away from the pore opening, and the target miRNA can be detected accurately without interference. In addition, we demonstrate that the PNA probe enables accurate discrimination of miRNAs with single-nucleotide difference. This highly sensitive and selective nanodielectrophoresis approach can be applied to the detection of clinically relevant nucleic acid fragments in complex samples.
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Affiliation(s)
- Kai Tian
- Department of Biological Engineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA
| | - Zhaojian He
- Department of Physics, University of Missouri, Columbia, MO 65211, USA
| | - Yong Wang
- Department of Biological Engineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA
| | - Shi-Jie Chen
- Department of Physics, University of Missouri, Columbia, MO 65211, USA
| | - Li-Qun Gu
- Department of Biological Engineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA
- Correspondence author: Li-Qun Gu, PhD Associate Professor of Biological Engineering and Dalton Cardiovascular Research Center University of Missouri, Columbia, MO 65211 Tel: 573-882-2057, Fax: 573-884-4232
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320
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Balijepalli A, Robertson JWF, Reiner JE, Kasianowicz JJ, Pastor RW. Theory of polymer-nanopore interactions refined using molecular dynamics simulations. J Am Chem Soc 2013; 135:7064-72. [PMID: 23590258 DOI: 10.1021/ja4026193] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Molecular dynamics simulations were used to refine a theoretical model that describes the interaction of single polyethylene glycol (PEG) molecules with α-hemolysin (αHL) nanopores. The simulations support the underlying assumptions of the model, that PEG decreases the pore conductance by binding cations (which reduces the number of mobile ions in the pore) and by volume exclusion, and provide bounds for fits to new experimental data. Estimation of cation binding indicates that four monomers coordinate a single K(+) in a crown-ether-like structure, with, on average, 1.5 cations bound to a PEG 29-mer at a bulk electrolyte concentration of 4 M KCl. Additionally, PEG is more cylindrical and has a larger cross-section area in the pore than in solution, although its volume is similar. Two key experimental quantities of PEG are described by the model: the ratio of single channel current in the presence of PEG to that in the polymer's absence (blockade depth) and the mean residence time of PEG in the pore. The refined theoretical model is simultaneously fit to the experimentally determined current blockade depth and the mean residence times for PEGs with 15 to 45 monomers, at applied transmembrane potentials of -40 to -80 mV and for three electrolyte concentrations. The model estimates the free energy of the PEG-cation complexes to be -5.3 kBT. Finally the entropic penalty of confining PEG to the pore is found to be inversely proportional to the electrolyte concentration.
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Affiliation(s)
- Arvind Balijepalli
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
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321
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Piguet F, Foster DP. Translocation of short and long polymers through an interacting pore. J Chem Phys 2013; 138:084902. [DOI: 10.1063/1.4792716] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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322
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Stock L, Souza C, Treptow W. Structural Basis for Activation of Voltage-Gated Cation Channels. Biochemistry 2013; 52:1501-13. [DOI: 10.1021/bi3013017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Letícia Stock
- Laboratório
de Biofísica Teórica
e Computacional, Departamento de Biologia Celular, Universidade de Brasília, DF, Brasília, Brazil
| | - Caio Souza
- Laboratório
de Biofísica Teórica
e Computacional, Departamento de Biologia Celular, Universidade de Brasília, DF, Brasília, Brazil
| | - Werner Treptow
- Laboratório
de Biofísica Teórica
e Computacional, Departamento de Biologia Celular, Universidade de Brasília, DF, Brasília, Brazil
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323
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Caballero J, Poblete H, Navarro C, Alzate-Morales JH. Association of nicotinic acid with a poly(amidoamine) dendrimer studied by molecular dynamics simulations. J Mol Graph Model 2013; 39:71-8. [DOI: 10.1016/j.jmgm.2012.11.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 11/08/2012] [Accepted: 11/08/2012] [Indexed: 11/16/2022]
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324
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Dong J, Qiu J, Zhang Y, Lu C, Dai X, Wang J, Li H, Wang X, Tan W, Luo M, Niu X, Deng X. Oroxylin A inhibits hemolysis via hindering the self-assembly of α-hemolysin heptameric transmembrane pore. PLoS Comput Biol 2013; 9:e1002869. [PMID: 23349625 PMCID: PMC3547825 DOI: 10.1371/journal.pcbi.1002869] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 11/16/2012] [Indexed: 02/06/2023] Open
Abstract
Alpha-hemolysin (α-HL) is a self-assembling, channel-forming toxin produced by most Staphylococcus aureus strains as a 33.2-kDa soluble monomer. Upon binding to a susceptible cell membrane, the monomer self-assembles to form a 232.4-kDa heptamer that ultimately causes host cell lysis and death. Consequently, α-HL plays a significant role in the pathogenesis of S. aureus infections, such as pneumonia, mastitis, keratitis and arthritis. In this paper, experimental studies show that oroxylin A (ORO), a natural compound without anti-S. aureus activity, can inhibit the hemolytic activity of α-HL. Molecular dynamics simulations, free energy calculations, and mutagenesis assays were performed to understand the formation of the α-HL-ORO complex. This combined approach revealed that the catalytic mechanism of inhibition involves the direct binding of ORO to α-HL, which blocks the conformational transition of the critical “Loop” region of the α-HL protein thereby inhibiting its hemolytic activity. This mechanism was confirmed by experimental data obtained from a deoxycholate-induced oligomerization assay. It was also found that, in a co-culture system with S. aureus and human alveolar epithelial (A549) cells, ORO could protect against α-HL-mediated injury. These findings indicate that ORO hinders the lytic activity of α-HL through a novel mechanism, which should facilitate the design of new and more effective antibacterial agents against S. aureus. The mechanism controlling protein-ligand interactions is one of the most important processes in rational drug design. X-ray crystallography is a traditional tool used to investigate the interaction of ligands and proteins in a complex. However, protein crystallography is inefficient, and the development of crystal technology and research remains unequally distributed. Thus, it seems impractical to explore the structure of the α-hemolysin-ORO monomer complex by crystallography. Therefore, we used molecular dynamics simulations to investigate the receptor-ligand interaction in the α-HL-ORO monomer complex. In this study, we found that oroxylin A (ORO), a natural compound with little anti-S. aureus activity, can inhibit the hemolytic activity of α-HL at low concentrations. Through molecular docking and molecular dynamics simulations, we determined the potential binding mode of the protein-ligand interaction. The data revealed that ORO directly binds to α-HL, an interaction that blacks the conformational transition of the critical “Loop” region in α-HL and thus prevents the formation of the α-HL heptameric transmembrane pore, which ultimately inhibits the hemolytic activity of α-HL. This mechanism was confirmed by experimental data. Furthermore, we demonstrated that ORO could protect against α-HL-mediated injury in human alveolar epithelial (A549) cells.
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Affiliation(s)
- Jing Dong
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
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325
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Niu X, Qiu J, Wang X, Gao X, Dong J, Wang J, Li H, Zhang Y, Dai X, Lu C, Deng X. Molecular insight into the inhibition mechanism of cyrtominetin to α-hemolysin by molecular dynamics simulation. Eur J Med Chem 2013; 62:320-8. [PMID: 23376250 DOI: 10.1016/j.ejmech.2013.01.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 01/04/2013] [Accepted: 01/08/2013] [Indexed: 11/16/2022]
Abstract
The protein α-hemolysin (α-HL) is a self-assembling exotoxin that binds to the membrane of a susceptible host cell. In this paper, experimental studies show that cyrtominetin (CTM) can inhibit the hemolytic activity of α-HL. To understand how CTM can affect hemolytic activity, molecular dynamics simulations were carried out for α-HL-CTM complex and these results were compared with the crystal structure of monomeric α-HL. With this approach, the analysis revealed that the inhibition of CTM involves CTM directly binding to α-HL. Due to the binding of CTM, the conformation of the critical "Loop" region was restrained. This mechanism was confirmed by the experimental data. These findings indicate that CTM hinders the lysis activity of α-HL through a novel mechanism.
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Affiliation(s)
- Xiaodi Niu
- Department of Food Quality and Safety, Jilin University, Changchun 130062, China
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326
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Göpfrich K, Kulkarni CV, Pambos OJ, Keyser UF. Lipid nanobilayers to host biological nanopores for DNA translocations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:355-364. [PMID: 23214950 DOI: 10.1021/la3041506] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We characterize a recently introduced novel nanobilayer technique [Gornall, J. L., Mahendran, K. R., Pambos, O. J., Steinbock, L. J., Otto, O., Chimerel, C., Winterhalter, M., and Keyser, U. F. Simple reconstitution of protein pores in nano lipid bilayers. Nano Lett. 2011, 11 (8), 3334-3340] and its practical aspects for incorporating the biological nanopore α-hemolysin from Staphylococcus aureus and subsequent studies on the translocation of biomolecules under various conditions. This technique provides advantages over classical bilayer methods, especially the quick formation and extended stability of a bilayer. We have also developed a methodology to prepare a uniform quality of giant unilamellar vesicles (GUVs) in a reproducible way for producing nanobilayers. The process and the characteristics of the reconstitution of α-hemolysin in nanobilayers were examined by exploiting various important parameters, including pH, applied voltage, salt concentration, and number of nanopores. Protonation of α-hemolysin residues in the low pH region affects the translocation durations, which, in turn, changes the statistics of event types as a result of electrostatics and potentially the structural changes in DNA. When the pH and applied voltage were varied, it was possible to investigate and partly control the capture rates and type of translocation events through α-hemolysin nanopores. This study could be helpful to use the nanobilayer technique for further explorations, particularly owing to its advantages and technical ease compared to existing bilayer methods.
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Affiliation(s)
- Kerstin Göpfrich
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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327
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Singh PR, Bárcena-Uribarri I, Modi N, Kleinekathöfer U, Benz R, Winterhalter M, Mahendran KR. Pulling peptides across nanochannels: resolving peptide binding and translocation through the hetero-oligomeric channel from Nocardia farcinica. ACS NANO 2012; 6:10699-10707. [PMID: 23121560 DOI: 10.1021/nn303900y] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We investigated translocation of cationic peptides through nanochannels derived from the Gram-positive bacterium Nocardia farcinica at the single-molecule level. The two subunits NfpA and NfpB form a hetero-oligomeric cation selective channel. On the basis of amino acid comparison we performed homology modeling and obtained a channel structurally related to MspA of Mycobacterium smegmatis. The quantitative single-molecule measurements provide an insight into transport processes of solutes through nanochannels. High-resolution ion conductance measurements in the presence of peptides of different charge and length revealed the kinetics of peptide binding. The observed asymmetry in peptide binding kinetics indicated a unidirectional channel insertion in the lipid bilayer. In the case of cationic peptides, the external voltage acts as a driving force that promotes the interaction of the peptide with the channel surface. At low voltage, the peptide just binds to the channel, whereas at higher voltage, the force is strong enough to pull the peptide across the channel. This allows distinguishing quantitatively between peptide binding and translocation through the channel.
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Affiliation(s)
- Pratik Raj Singh
- Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
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328
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Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A. Modeling and simulation of ion channels. Chem Rev 2012; 112:6250-84. [PMID: 23035940 PMCID: PMC3633640 DOI: 10.1021/cr3002609] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Swati Bhattacharya
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Jejoong Yoo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - David Wells
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
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329
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Mereuta L, Schiopu I, Asandei A, Park Y, Hahm KS, Luchian T. Protein nanopore-based, single-molecule exploration of copper binding to an antimicrobial-derived, histidine-containing chimera peptide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:17079-17091. [PMID: 23140333 DOI: 10.1021/la303782d] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Metal ions binding exert a crucial influence upon the aggregation properties and stability of peptides, and the propensity of folding in various substates. Herein, we demonstrate the use of the α-HL protein as a powerful nanoscopic tool to probe Cu(2+)-triggered physicochemical changes of a 20 aminoacids long, antimicrobial-derived chimera peptide with a His residue as metal-binding site, and simultaneously dissect the kinetics of the free- and Cu(2+)-bound peptide interaction to the α-HL pore. Combining single-molecule electrophysiology on reconstituted lipid membranes and fluorescence spectroscopy, we show that the association rate constant between the α-HL pore and a Cu(2+)-free peptide is higher than that of a Cu(2+)-complexed peptide. We posit that mainly due to conformational changes induced by the bound Cu(2+) on the peptide, the resulting complex encounters a higher energy barrier toward its association with the protein pore, stemming most likely from an extra entropy cost needed to fit the Cu(2+)-complexed peptide within the α-HL lumen region. The lower dissociation rate constant of the Cu(2+)-complexed peptide from α-HL pore, as compared to that of Cu(2+)-free peptide, supports the existence of a deeper free energy well for the protein interaction with a Cu(2+)-complexed peptide, which may be indicative of specific Cu(2+)-mediated contributions to the binding of the Cu(2+)-complexed peptide within the pore lumen.
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Affiliation(s)
- Loredana Mereuta
- Department of Physics, Laboratory of Molecular Biophysics and Medical Physics, Alexandru I. Cuza University, Blvd. Carol I, No. 11, Iasi 700506, Romania
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330
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Modi N, Benz R, Hancock REW, Kleinekathöfer U. Modeling the Ion Selectivity of the Phosphate Specific Channel OprP. J Phys Chem Lett 2012; 3:3639-3645. [PMID: 26290999 DOI: 10.1021/jz301637d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Ion selectivity of transport systems is an essential property of membranes from living organisms. These entities are used to regulate multifarious biological processes by virtue of selective participation of specific ions in transport processes. To understand this process, we studied the phosphate selectivity of the OprP porin from Pseudomonas aeruginosa using all-atom free-energy molecular dynamics simulations. These calculations were performed to define the energetics of phosphate, sulfate, chloride, and potassium ion transport through OprP. Atomic-level analysis revealed that the overall electrostatic environment of the channel was responsible for the anion selectivity of the channel, whereas the particular balance of interactions between the permeating ions and water as well as channel residues drove the selectivity between different anions. The selectivity of OprP is discussed in light of well-studied ion channels that are highly selective for potassium or chloride.
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Affiliation(s)
- Niraj Modi
- †School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany and
| | - Roland Benz
- †School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany and
| | - Robert E W Hancock
- ‡Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Ulrich Kleinekathöfer
- †School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany and
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331
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Comer J, Ho A, Aksimentiev A. Toward detection of DNA-bound proteins using solid-state nanopores: insights from computer simulations. Electrophoresis 2012; 33:3466-79. [PMID: 23147918 PMCID: PMC3789251 DOI: 10.1002/elps.201200164] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 07/05/2012] [Accepted: 07/09/2012] [Indexed: 11/07/2022]
Abstract
Through all-atom molecular dynamics simulations, we explore the use of nanopores in thin synthetic membranes for detection and identification of DNA binding proteins. Reproducing the setup of a typical experiment, we simulate electric field driven transport of DNA-bound proteins through nanopores smaller in diameter than the proteins. As model systems, we use restriction enzymes EcoRI and BamHI specifically and nonspecifically bound to a fragment of dsDNA, and streptavidin and NeutrAvidin proteins bound to dsDNA and ssDNA via a biotin linker. Our simulations elucidate the molecular mechanics of nanopore-induced rupture of a protein-DNA complex, the effective force applied to the DNA-protein bond by the electrophoretic force in a nanopore, and the role of DNA-surface interactions in the rupture process. We evaluate the ability of the nanopore ionic current and the local electrostatic potential measured by an embedded electrode to report capture of DNA, capture of a DNA-bound protein, and rupture of the DNA-protein bond. We find that changes in the strain on dsDNA can reveal the rupture of a protein-DNA complex by altering both the nanopore ionic current and the potential of the embedded electrode. Based on the results of our simulations, we suggest a new method for detection of DNA binding proteins that utilizes peeling of a nicked double strand under the electrophoretic force in a nanopore.
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Affiliation(s)
- Jeffrey Comer
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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332
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Langecker M, Arnaut V, Martin TG, List J, Renner S, Mayer M, Dietz H, Simmel FC. Synthetic lipid membrane channels formed by designed DNA nanostructures. Science 2012; 338:932-6. [PMID: 23161995 DOI: 10.1126/science.1225624] [Citation(s) in RCA: 566] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We created nanometer-scale transmembrane channels in lipid bilayers by means of self-assembled DNA-based nanostructures. Scaffolded DNA origami was used to create a stem that penetrated and spanned a lipid membrane, as well as a barrel-shaped cap that adhered to the membrane, in part via 26 cholesterol moieties. In single-channel electrophysiological measurements, we found similarities to the response of natural ion channels, such as conductances on the order of 1 nanosiemens and channel gating. More pronounced gating was seen for mutations in which a single DNA strand of the stem protruded into the channel. Single-molecule translocation experiments show that the synthetic channels can be used to discriminate single DNA molecules.
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Affiliation(s)
- Martin Langecker
- Lehrstuhl für Bioelektronik, Physics Department and ZNN/WSI, Technische Universität München, 85748 Garching, Germany
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333
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Ando G, Hyun C, Li J, Mitsui T. Directly observing the motion of DNA molecules near solid-state nanopores. ACS NANO 2012; 6:10090-7. [PMID: 23046052 PMCID: PMC3508321 DOI: 10.1021/nn303816w] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We investigate the diffusion and the drift motion of λ DNA molecules near solid-state nanopores prior to their translocation through the nanopores using fluorescence microscopy. The radial dependence of the electric field near a nanopore generated by an applied voltage in ionic solution can be estimated quantitatively in 3D by analyzing the motion of negatively charged DNA molecules. We find that the electric field is approximately spherically symmetric around the nanopore under the conditions investigated. In addition, DNA clogging at the nanopore was directly observed. Surprisingly, the probability of the clogging event increases with increasing external bias voltage. We also find that DNA molecules clogging the nanopore reduce the electric field amplitude at the nanopore membrane surface. To better understand these experimental results, analytical method with Ohm's law and computer simulation with Poisson and Nernst-Planck (PNP) equations are used to calculate the electric field near the nanopore. These results are of great interest in both experimental and theoretical considerations of the motion of DNA molecules near voltage-biased nanopores. These findings will also contribute to the development of solid-state nanopore-based DNA sensing devices.
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Affiliation(s)
- Genki Ando
- Aoyama-Gakuin University. Sagamihara Campus L617, 5-10-1 Fuchinobe, Chuo, Sagamihara, Kanagawa, 252-5258, Japan
| | - Changbae Hyun
- Physics Department, University of Arkansas, Fayetteville, AR 72701, USA
| | - Jiali Li
- Physics Department, University of Arkansas, Fayetteville, AR 72701, USA
| | - Toshiyuki Mitsui
- Aoyama-Gakuin University. Sagamihara Campus L617, 5-10-1 Fuchinobe, Chuo, Sagamihara, Kanagawa, 252-5258, Japan
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334
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Niedzwiecki D, Mohammad M, Movileanu L. Inspection of the engineered FhuA ΔC/Δ4L protein nanopore by polymer exclusion. Biophys J 2012; 103:2115-24. [PMID: 23200045 PMCID: PMC3512039 DOI: 10.1016/j.bpj.2012.10.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 10/03/2012] [Accepted: 10/10/2012] [Indexed: 12/11/2022] Open
Abstract
Extensive engineering of protein nanopores for biotechnological applications using native scaffolds requires further inspection of their internal geometry and size. Recently, we redesigned ferric hydroxamate uptake component A (FhuA), a 22-β-stranded protein containing an N-terminal 160-residue cork domain (C). The cork domain and four large extracellular loops (4L) were deleted to obtain an unusually stiff engineered FhuA ΔC/Δ4L nanopore. We employed water-soluble poly(ethylene glycols) and dextran polymers to examine the interior of FhuA ΔC/Δ4L. When this nanopore was reconstituted into a synthetic planar lipid bilayer, addition of poly(ethylene glycols) produced modifications in the single-channel conductance, allowing for the evaluation of the nanopore diameter. Here, we report that FhuA ΔC/Δ4L features an approximate conical internal geometry with the cis entrance smaller than the trans entrance, in accord with the asymmetric nature of the crystal structure of the wild-type FhuA protein. Further experiments with impermeable dextran polymers indicated an average internal diameter of ~2.4 nm, a conclusion we arrived at based upon the polymer-induced alteration of the access resistance contribution to the nanopore's total resistance. Molecular insights inferred from this work represent a platform for future protein engineering of FhuA that will be employed for specific tasks in biotechnological applications.
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Affiliation(s)
| | | | - Liviu Movileanu
- Department of Physics, Syracuse University, Syracuse, New York
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, Syracuse, New York
- Syracuse Biomaterials Institute, Syracuse University, Syracuse, New York
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335
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Reiner JE, Balijepalli A, Robertson JWF, Campbell J, Suehle J, Kasianowicz JJ. Disease Detection and Management via Single Nanopore-Based Sensors. Chem Rev 2012; 112:6431-51. [DOI: 10.1021/cr300381m] [Citation(s) in RCA: 195] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Joseph E. Reiner
- Department of Physics, Virginia
Commonwealth University, 701 W. Grace Street, Richmond, Virginia 23284,
United States
| | - Arvind Balijepalli
- Physical
Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899-8120, United States
- Laboratory of Computational Biology,
National Heart Lung and Blood Institute, Rockville, Maryland 20852,
United States
| | - Joseph W. F. Robertson
- Physical
Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899-8120, United States
| | - Jason Campbell
- Physical
Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899-8120, United States
| | - John Suehle
- Physical
Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899-8120, United States
| | - John J. Kasianowicz
- Physical
Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899-8120, United States
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336
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Robertson JWF, Kasianowicz JJ, Banerjee S. Analytical Approaches for Studying Transporters, Channels and Porins. Chem Rev 2012; 112:6227-49. [DOI: 10.1021/cr300317z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Joseph W. F. Robertson
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - John J. Kasianowicz
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - Soojay Banerjee
- National
Institute of Neurological
Disorders and Stroke, Bethesda, Maryland 20824, United States
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337
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Campos E, Asandei A, McVey CE, Dias JC, Oliveira ASF, Soares CM, Luchian T, Astier Y. The role of Lys147 in the interaction between MPSA-gold nanoparticles and the α-hemolysin nanopore. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:15643-15650. [PMID: 23046444 DOI: 10.1021/la302613g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Single channel recordings were used to determine the effect of direct electrostatic interactions between sulfonate-coated gold nanoparticles and the constriction of the Staphylococcus aureus α-hemolysin protein channel on the ionic current amplitude. We provide evidence that Lys147 of α-hemolysin can interact with the sulfonate groups at the nanoparticle surface, and these interactions can reversibly block 100% of the residual ionic current. Lys147 is normally involved in a salt bridge with Glu111. The capture of a nanoparticle leads to a partial current block at neutral pH values, but protonation of Glu111 at pH 2.8 results in a full current block when the nanoparticle is captured. At pH 2.8, we suggest that Lys147 is free to engage in electrostatic interactions with sulfonates at the nanoparticle surface. To verify our results, we engineered a mutation in the α-hemolysin protein, where Glu111 is substituted by Ala (E111A), thus removing Glu111-Lys147 interactions and facilitating Lys147-sulfonate electrostatic interactions. This mutation leads to a 100% current block at pH 2.8 and a 92% block at pH 8.0, showing that electrostatic interactions are formed between the nanopore and the nanoparticle surface. Besides demonstrating the effect of electrostatic interactions on cross channel ionic current, this work offers a novel approach to controlling open and closed states of the α-hemolysin nanopore as a function of external gears.
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Affiliation(s)
- Elisa Campos
- Single Molecule Processes Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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338
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Harb F, Sarkis J, Ferte N, Tinland B. Beyond Saffman-Delbruck approximation: a new regime for 2D diffusion of α-hemolysin complexes in supported lipid bilayer. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2012; 35:118. [PMID: 23160766 DOI: 10.1140/epje/i2012-12118-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 09/10/2012] [Accepted: 10/11/2012] [Indexed: 06/01/2023]
Abstract
Cell mechanisms are actively modulated by membrane dynamics. We studied the dynamics of a first-stage biomimetic system by Fluorescence Recovery After Patterned Photobleaching. Using this simple biomimetic system, constituted by α -hemolysin from Staphylococcus aureus inserted as single heptameric pore or complexes of pores in a glass-supported DMPC bilayer, we observed true diffusion behavior, with no immobile fraction. We find two situations: i) when incubation is shorter than 15 hours, the protein inserts as a heptameric pore and diffuses roughly three times more slowly than its host lipid bilayer; ii) incubation longer than 15 hours leads to the formation of larger complexes which diffuse more slowly. Our results indicate that, while the Saffman-Delbruck model adequately describes the diffusion coefficient D for small radii, D of the objects decreases as 1/R(2) for the size range explored in this study. Additionally, in the presence of inserted proteins, the gel-to-fluid transition of the supported bilayer as well as a temperature shift in the gel-to-fluid transition are observed.
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Affiliation(s)
- Frédéric Harb
- CNRS, UMR, Aix-Marseille Université, CINaM, Marseille, France
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339
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Abstract
Molecular dynamics simulation is utilized to investigate the ionic transport of NaCl in solution through a graphene nanopore under an applied electric field. Results show the formation of concentration polarization layers in the vicinity of the graphene sheet. The nonuniformity of the ion distribution gives rise to an electric pressure which drives vortical motions in the fluid if the electric field is sufficiently strong to overcome the influence of viscosity and thermal fluctuations. The relative importance of hydrodynamic transport and thermal fluctuations in determining the pore conductivity is investigated. A second important effect that is observed is the mass transport of water through the nanopore, with an average velocity proportional to the applied voltage and independent of the pore diameter. The flux arises as a consequence of the asymmetry in the ion distribution which can be attributed to differing mobilities of the sodium and chlorine ions and to the polarity of water molecules. The accumulation of liquid molecules in the vicinity of the nanopore due to re-orientation of the water dipoles by the local electric field is seen to result in a local increase in the liquid density. Results confirm that the electric conductance is proportional to the nanopore diameter for the parameter regimes that we simulated. The occurrence of fluid vortices is found to result in an increase in the effective electrical conductance.
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Affiliation(s)
- Guohui Hu
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Modern Mechanics Division, E-Institutes of Shanghai Universities, Shanghai University, 149 Yanchang Road, Shanghai 200072, People's Republic of China
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340
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Jensen MØ, Jogini V, Borhani DW, Leffler AE, Dror RO, Shaw DE. Mechanism of voltage gating in potassium channels. Science 2012; 336:229-33. [PMID: 22499946 DOI: 10.1126/science.1216533] [Citation(s) in RCA: 433] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The mechanism of ion channel voltage gating-how channels open and close in response to voltage changes-has been debated since Hodgkin and Huxley's seminal discovery that the crux of nerve conduction is ion flow across cellular membranes. Using all-atom molecular dynamics simulations, we show how a voltage-gated potassium channel (KV) switches between activated and deactivated states. On deactivation, pore hydrophobic collapse rapidly halts ion flow. Subsequent voltage-sensing domain (VSD) relaxation, including inward, 15-angstrom S4-helix motion, completes the transition. On activation, outward S4 motion tightens the VSD-pore linker, perturbing linker-S6-helix packing. Fluctuations allow water, then potassium ions, to reenter the pore; linker-S6 repacking stabilizes the open pore. We propose a mechanistic model for the sodium/potassium/calcium voltage-gated ion channel superfamily that reconciles apparently conflicting experimental data.
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341
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Bhattacharya S, Derrington IM, Pavlenok M, Niederweis M, Gundlach JH, Aksimentiev A. Molecular dynamics study of MspA arginine mutants predicts slow DNA translocations and ion current blockades indicative of DNA sequence. ACS NANO 2012; 6:6960-8. [PMID: 22747101 PMCID: PMC3448955 DOI: 10.1021/nn3019943] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The protein nanopore Mycobacteria smegmatis porin A (MspA), can be used to sense individual nucleotides within DNA, potentially enabling a technique known as nanopore sequencing. In this technique, single-stranded DNA electrophoretically moves through the nanopore and results in an ionic current that is nucleotide-specific. However, with a high transport velocity of the DNA within the nanopore, the ionic current cannot be used to distinguish signals within noise. Through extensive (~100 μs in total) all-atom molecular dynamics simulations, we examine the effect of positively charged residues on DNA translocation rate and the ionic current blockades in MspA. Simulation of several arginine mutations show a ~10-30 fold reduction of DNA translocation speed without eliminating the nucleotide induced current blockages. Comparison of our results with similar engineering efforts on a different nanopore (α-hemolysin) reveals a nontrivial effect of nanopore geometry on the ionic current blockades in mutant nanopores.
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Affiliation(s)
- Swati Bhattacharya
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W. Green Street, Urbana, IL 61801, USA
| | - Ian M. Derrington
- Department of Microbiology, University of Alabama at Birmingham, 609 Bevill Biomedical Research Building, 845 19th Street South, Birmingham, AL 35294, U.S.A
| | - Mikhail Pavlenok
- Department of Physics, University of Washington Seattle, 3910 15 Ave., Seattle, WA NE 98195 U.S.A
| | - Michael Niederweis
- Department of Physics, University of Washington Seattle, 3910 15 Ave., Seattle, WA NE 98195 U.S.A
| | - Jens H. Gundlach
- Department of Microbiology, University of Alabama at Birmingham, 609 Bevill Biomedical Research Building, 845 19th Street South, Birmingham, AL 35294, U.S.A
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W. Green Street, Urbana, IL 61801, USA
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342
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Luan B, Zhou R. Nanopore-Based Sensors for Detecting Toxicity of a Carbon Nanotube to Proteins. J Phys Chem Lett 2012; 2012:2337-2341. [PMID: 23002420 PMCID: PMC3445412 DOI: 10.1021/jz3007832] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
A carbon nanotube (CNT) can be toxic to a living cell by binding to proteins and then impairing their functionalities; however, an efficient screening method that examines binding capability of a CNT to protein molecules in vitro is still unavailable. Here, we show that a nanopore-based sensor can be used to investigate CNT-protein interactions. With proof-of-principle molecular dynamics simulations, we have measured ionic currents in a nanopore when threading a CNT-protein complex through the pore, and demonstrated that CNT's binding capability, and thus potential nanotoxicity, can be inferred from current signals. We have then further investigated mechanics and energetics of CNT-protein interactions with the nanopore sensor. These findings indicate that solid-state nanopores have the potential to be ultra-sensitive and high-throughput sensors for nanotoxicity.
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343
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Kasianowicz JJ, Reiner JE, Robertson JWF, Henrickson SE, Rodrigues C, Krasilnikov OV. Detecting and characterizing individual molecules with single nanopores. Methods Mol Biol 2012; 870:3-20. [PMID: 22528255 DOI: 10.1007/978-1-61779-773-6_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Single-nanometer-scale pores have demonstrated the capability for the detection, identification, and characterization of individual molecules. This measurement method could soon extend the existing commercial instrumentation or provide solutions to niche applications in many fields, including health care and the basic sciences. However, that paradigm shift requires a significantly better understanding of the physics and chemistry that govern the interactions between nanopores and analytes. We describe herein some of our methods and approaches to address this issue.
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Affiliation(s)
- John J Kasianowicz
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
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344
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Ravaud S, Bidon-Chanal A, Blesneac I, Machillot P, Juillan-Binard C, Dehez F, Chipot C, Pebay-Peyroula E. Impaired transport of nucleotides in a mitochondrial carrier explains severe human genetic diseases. ACS Chem Biol 2012; 7:1164-9. [PMID: 22497660 DOI: 10.1021/cb300012j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The mitochondrial ADP/ATP carrier (AAC) is a prominent actor in the energetic regulation of the cell, importing ADP into the mitochondria and exporting ATP toward the cytoplasm. Severe genetic diseases have been ascribed to specific mutations in this membrane protein. How minute, well-localized modifications of the transporter impact the function of the mitochondria remains, however, largely unclear. Here, for the first time, the relationship between all documented pathological mutations of the AAC and its transport properties is established. Activity measurements combined synergistically with molecular-dynamics simulations demonstrate how all documented pathological mutations alter the binding affinity and the translocation kinetics of the nucleotides. Throwing a bridge between the pathologies and their molecular origins, these results reveal two distinct mechanisms responsible for AAC-related genetic disorders, wherein the mutations either modulate the association of the nucleotides to the carrier by modifying its electrostatic signature or reduce its conformational plasticity.
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Affiliation(s)
- Stéphanie Ravaud
- Université
Grenoble 1,
IBS, Institut de Biologie Structurale, 41, rue Jules Horowitz, 38027
Grenoble cedex 1, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Axel Bidon-Chanal
- Nancy Université, BP239,
54506 Vandoeuvre-lès-Nancy Cedex, France
- CNRS, SRSMC, Nancy, France
| | - Iulia Blesneac
- Université
Grenoble 1,
IBS, Institut de Biologie Structurale, 41, rue Jules Horowitz, 38027
Grenoble cedex 1, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Paul Machillot
- Université
Grenoble 1,
IBS, Institut de Biologie Structurale, 41, rue Jules Horowitz, 38027
Grenoble cedex 1, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Céline Juillan-Binard
- Université
Grenoble 1,
IBS, Institut de Biologie Structurale, 41, rue Jules Horowitz, 38027
Grenoble cedex 1, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - François Dehez
- Nancy Université, BP239,
54506 Vandoeuvre-lès-Nancy Cedex, France
- CNRS, SRSMC, Nancy, France
| | - Chris Chipot
- Nancy Université, BP239,
54506 Vandoeuvre-lès-Nancy Cedex, France
- CNRS, SRSMC, Nancy, France
| | - Eva Pebay-Peyroula
- Université
Grenoble 1,
IBS, Institut de Biologie Structurale, 41, rue Jules Horowitz, 38027
Grenoble cedex 1, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
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345
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Wong-Ekkabut J, Karttunen M. Assessment of Common Simulation Protocols for Simulations of Nanopores, Membrane Proteins, and Channels. J Chem Theory Comput 2012; 8:2905-11. [PMID: 26592129 DOI: 10.1021/ct3001359] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular dynamics (MD) simulation has become a common technique to study biological systems. Transport of small molecules through carbon nanotubes and membrane proteins has been an intensely studied topic, and MD simulations have been able to provide valuable predictions, many of which have later been experimentally proven. Simulations of such systems pose challenges, and unexpected problems in commonly used protocols and methods have been found in the past few years. The two main reasons why some were not found before are that most of these newly discovered errors do not lead to unstable simulations. Furthermore, some of them manifest themselves only after relatively long simulation times. We assessed the reliability of the most common simulations protocols by MD and stochastic dynamics (SD) or Langevin dynamics, simulations of an alpha hemolysin nanochannel embedded in a palmitoyloleoylphosphatidylcholine (POPC) lipid bilayer. Our findings are that (a) reaction field electrostatics should not be used in simulations of such systems, (b) local thermostats should be preferred over global ones since the latter may lead to an unphysical temperature distribution,
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Affiliation(s)
- Jirasak Wong-Ekkabut
- Department of Physics, Faculty of Science, Kasetsart University , 50 Phahon Yothin Road, Chatuchak, Bangkok 10900, Thailand
| | - Mikko Karttunen
- Department of Chemistry, University of Waterloo , 200 University Avenue West, Waterloo, Ontario, Canada N2L 3G1
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346
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De Biase P, Solano CJF, Markosyan S, Czapla L, Noskov SY. BROMOC-D: Brownian Dynamics/Monte-Carlo Program Suite to Study Ion and DNA Permeation in Nanopores. J Chem Theory Comput 2012; 8:2540-2551. [PMID: 22798730 PMCID: PMC3396124 DOI: 10.1021/ct3004244] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Indexed: 11/29/2022]
Abstract
A theoretical framework is presented to model ion and DNA translocation across a nanopore confinement under an applied electric field. A combined Grand Canonical Monte Carlo Brownian Dynamics (GCMC/BD) algorithm offers a general approach to study ion permeation through wide molecular pores with a direct account of ion-ion and ion-DNA correlations. This work extends previously developed theory by incorporating the recently developed coarse-grain polymer model of DNA by de Pablo and colleagues [Knotts, T. A.; Rathore, N.; Schwartz, D. C.; de Pablo, J. J. J. Chem. Phys. 2007, 126] with explicit ions for simulations of polymer dynamics. Atomistic MD simulations were used to guide model developments. The power of the developed scheme is illustrated with studies of single-stranded DNA (ss-DNA) oligomer translocation in two model cases: a cylindrical pore with a varying radius and a well-studied experimental system, the staphylococcal α-hemolysin channel. The developed model shows good agreement with experimental data for model studies of two homopolymers: ss-poly(dA)(n) and ss-poly(dC)(n). The developed protocol allows for direct evaluation of different factors (charge distribution and pore shape and size) controlling DNA translocation in a variety of nanopores.
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Affiliation(s)
| | | | | | - Luke Czapla
- Institute for Biocomplexity and Informatics, Department
of Biological Sciences, University of Calgary, Calgary, AB, Canada,
T2N 1N4
| | - Sergei Yu. Noskov
- Institute for Biocomplexity and Informatics, Department
of Biological Sciences, University of Calgary, Calgary, AB, Canada,
T2N 1N4
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347
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Musgaard M, Thøgersen L, Schiøtt B, Tajkhorshid E. Tracing cytoplasmic Ca(2+) ion and water access points in the Ca(2+)-ATPase. Biophys J 2012; 102:268-77. [PMID: 22339863 DOI: 10.1016/j.bpj.2011.12.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 11/17/2011] [Accepted: 12/05/2011] [Indexed: 11/28/2022] Open
Abstract
Sarco(endo)plasmic reticulum Ca(2+)-ATPase (SERCA) transports two Ca(2+) ions across the membrane of the sarco(endo)plasmic reticulum against the concentration gradient, harvesting the required energy by hydrolyzing one ATP molecule during each transport cycle. Although SERCA is one of the best structurally characterized membrane transporters, it is still largely unknown how the transported Ca(2+) ions reach their transmembrane binding sites in SERCA from the cytoplasmic side. Here, we performed extended all-atom molecular dynamics simulations of SERCA. The calculated electrostatic potential of the protein reveals a putative mechanism by which cations may be attracted to and bind to the Ca(2+)-free state of the transporter. Additional molecular dynamics simulations performed on a Ca(2+)-bound state of SERCA reveal a water-filled pathway that may be used by the Ca(2+) ions to reach their buried binding sites from the cytoplasm. Finally, several residues that are involved in attracting and guiding the cations toward the possible entry channel are identified. The results point to a single Ca(2+) entry site close to the kinked part of the first transmembrane helix, in a region loaded with negatively charged residues. From this point, a water pathway outlines a putative Ca(2+) translocation pathway toward the transmembrane ion-binding sites.
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Affiliation(s)
- Maria Musgaard
- Department of Chemistry, Aarhus University, Aarhus, Denmark
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348
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Molecular Dynamics Simulations of Lipid Membrane Electroporation. J Membr Biol 2012; 245:531-43. [DOI: 10.1007/s00232-012-9434-6] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 04/30/2012] [Indexed: 10/28/2022]
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349
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Dayani Y, Malmstadt N. Lipid bilayers covalently anchored to carbon nanotubes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:8174-8182. [PMID: 22568448 PMCID: PMC3378680 DOI: 10.1021/la301094h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The unique physical and electrical properties of carbon nanotubes make them an exciting material for applications in various fields such as bioelectronics and biosensing. Due to the poor water solubility of carbon nanotubes, functionalization for such applications has been a challenge. Of particular need are functionalization methods for integrating carbon nanotubes with biomolecules and constructing novel hybrid nanostructures for bionanoelectronic applications. We present a novel method for the fabrication of dispersible, biocompatible carbon nanotube-based materials. Multiwalled carbon nanotubes (MWCNTs) are covalently modified with primary amine-bearing phospholipids in a carbodiimide-activated reaction. These modified carbon nanotubes have good dispersibility in nonpolar solvents. Fourier transform infrared (FTIR) spectroscopy shows peaks attributable to the formation of amide bonds between lipids and the nanotube surface. Simple sonication of lipid-modified nanotubes with other lipid molecules leads to the formation of a uniform lipid bilayer coating the nanotubes. These bilayer-coated nanotubes are highly dispersible and stable in aqueous solution. Confocal fluorescence microscopy shows labeled lipids on the surface of bilayer-modified nanotubes. Transmission electron microscopy (TEM) shows the morphology of dispersed bilayer-coated MWCNTs. Fluorescence quenching of lipid-coated MWCNTs confirms the bilayer configuration of the lipids on the nanotube surface, and fluorescence anisotropy measurements show that the bilayer is fluid above the gel-to-liquid transition temperature. The membrane protein α-hemolysin spontaneously inserts into the MWCNT-supported bilayer, confirming the biomimetic membrane structure. These biomimetic nanostructures are a promising platform for the integration of carbon nanotube-based materials with biomolecules.
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Affiliation(s)
| | - Noah Malmstadt
- Corresponding Author: Phone: (213)821-2034. Fax: (213)740-1056. . Address: 925 Bloom Walk, HED 216, Los Angeles, CA 90089
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350
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Delemotte L, Klein ML, Tarek M. Molecular dynamics simulations of voltage-gated cation channels: insights on voltage-sensor domain function and modulation. Front Pharmacol 2012; 3:97. [PMID: 22654756 PMCID: PMC3361024 DOI: 10.3389/fphar.2012.00097] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 05/01/2012] [Indexed: 11/26/2022] Open
Abstract
Since their discovery in the 1950s, the structure and function of voltage-gated cation channels (VGCC) has been largely understood thanks to results stemming from electrophysiology, pharmacology, spectroscopy, and structural biology. Over the past decade, computational methods such as molecular dynamics (MD) simulations have also contributed, providing molecular level information that can be tested against experimental results, thereby allowing the validation of the models and protocols. Importantly, MD can shed light on elements of VGCC function that cannot be easily accessed through “classical” experiments. Here, we review the results of recent MD simulations addressing key questions that pertain to the function and modulation of the VGCC’s voltage-sensor domain (VSD) highlighting: (1) the movement of the S4-helix basic residues during channel activation, articulating how the electrical driving force acts upon them; (2) the nature of the VSD intermediate states on transitioning between open and closed states of the VGCC; and (3) the molecular level effects on the VSD arising from mutations of specific S4 positively charged residues involved in certain genetic diseases.
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Affiliation(s)
- Lucie Delemotte
- Equipe de Chimie et Biochimie Théoriques, UMR Synthèse et Réactivité de Systèmes Moléculaires Complexes, Centre National de la Recherche Scientifique Université de Lorraine Nancy, France
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