151
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Balasubramanian R, Pal S, Joshi H, Rao A, Naik A, Varma M, Chakraborty B, Maiti PK. DNA Translocation through Hybrid Bilayer Nanopores. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2019; 123:11908-11916. [PMID: 31316684 PMCID: PMC6636640 DOI: 10.1021/acs.jpcc.9b00399] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Pore functionalization has been explored by several groups as a strategy to control DNA translocation through solid-state nanopores. Here we present a hybrid nanopore system consisting of single-layer graphene and a DNA origami layer to achieve base-selective control of DNA translocation rate through aligned nanopores of the two layers. This is achieved by incorporating unpaired dangling bases called overhangs to the origami near the pore region. Molecular dynamics simulations were used to optimize the design of the origami nanopore and the overhangs. Specifically, we considered the influence of the number and spatial distribution of overhangs on translocation times. The simulations revealed that specific interactions between the overhangs and the translocating single-stranded DNA resulted in base-specific residence times.
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Affiliation(s)
| | - Sohini Pal
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Himanshu Joshi
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, United States
| | - Akshay Naik
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Manoj Varma
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India
- Corresponding Authors: Dr. Banani Chakraborty: ., Prof. Manoj Varma: ., Prof. Prabal K. Maiti:
| | - Banani Chakraborty
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
- Corresponding Authors: Dr. Banani Chakraborty: ., Prof. Manoj Varma: ., Prof. Prabal K. Maiti:
| | - Prabal K. Maiti
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
- Corresponding Authors: Dr. Banani Chakraborty: ., Prof. Manoj Varma: ., Prof. Prabal K. Maiti:
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152
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Borsley S, Haugland MM, Oldknow S, Cooper JA, Burke MJ, Scott A, Grantham W, Vallejo J, Brechin EK, Lusby PJ, Cockroft SL. Electrostatic Forces in Field-Perturbed Equilibria: Nanopore Analysis of Cage Complexes. Chem 2019. [DOI: 10.1016/j.chempr.2019.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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153
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Visualizing Biological Membrane Organization and Dynamics. J Mol Biol 2019; 431:1889-1919. [DOI: 10.1016/j.jmb.2019.02.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/02/2019] [Accepted: 02/13/2019] [Indexed: 11/22/2022]
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154
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Yu Y, Fan J, Xia J, Zhu Y, Wu H, Wang F. Dehydration impeding ionic conductance through two-dimensional angstrom-scale slits. NANOSCALE 2019; 11:8449-8457. [PMID: 30985841 DOI: 10.1039/c9nr00317g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
There has been long-standing academic interest in the study of ion transport in nanochannel systems, owing to its vast implications in understanding the nature of numerous environmental, biological and chemical processes. Here, we investigate ion transport through two-dimensional slits using molecular dynamics simulations. These slits with angstrom-scale height dimensions can be realistically replicated in the simulation, which leads to direct comparisons between simulations and experiments. In particular, this new confining geometry allows the size exclusion effect to be unambiguously decoupled from other mechanisms. As the slit size approaches the ultimate scale, dehydration at the entry impedes the ionic conductance significantly, and even induces a complete ion rejection. We demonstrate that energy barriers required to accomplish the ion permeation can be theoretically connected to the partial dehydration process. The proposed model is further validated by simulations. Our results offer insights into the atomistic details of ion permeation, which may also shed light on developing effective ways for water filtration and desalination.
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Affiliation(s)
- YanZi Yu
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics, University of Science and Technology of China, Hefei, Anhui 230027, China.
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155
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Insights into protein sequencing with an α-Hemolysin nanopore by atomistic simulations. Sci Rep 2019; 9:6440. [PMID: 31015503 PMCID: PMC6478933 DOI: 10.1038/s41598-019-42867-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/25/2019] [Indexed: 12/12/2022] Open
Abstract
Single molecule protein sequencing would represent a disruptive burst in proteomic research with important biomedical impacts. Due to their success in DNA sequencing, nanopore based devices have been recently proposed as possible tools for the sequencing of peptide chains. One of the open questions in nanopore protein sequencing concerns the ability of such devices to provide different signals for all the 20 standard amino acids. Here, using equilibrium all-atom molecular dynamics simulations, we estimated the pore clogging in α-Hemolysin nanopore associated to 20 different homopeptides, one for each standard amino acid. Our results show that pore clogging is affected by amino acid volume, hydrophobicity and net charge. The equilibrium estimations are also supported by non-equilibrium runs for calculating the current blockades for selected homopeptides. Finally, we discuss the possibility to modify the α-Hemolysin nanopore, cutting a portion of the barrel region close to the trans side, to reduce spurious signals and, hence, to enhance the sensitivity of the nanopore.
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156
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Ghosh B, Chaudhury S. Translocation Dynamics of an Asymmetrically Charged Polymer through a Pore under the Influence of Different pH Conditions. J Phys Chem B 2019; 123:4318-4323. [DOI: 10.1021/acs.jpcb.8b12301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Bappa Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Srabanti Chaudhury
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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157
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Atomistic modeling and molecular dynamics analysis of human Ca V1.2 channel using external electric field and ion pulling simulations. Biochim Biophys Acta Gen Subj 2019; 1863:1116-1126. [PMID: 30978379 DOI: 10.1016/j.bbagen.2019.04.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 03/19/2019] [Accepted: 04/08/2019] [Indexed: 11/24/2022]
Abstract
BACKGROUND Human CaV1.2 (hCav1.2), a calcium selective voltage-gated channel, plays important roles in normal cardiac and neuronal functions. Calcium influx and gating mechanisms leading to the activation of hCaV1.2 are critical for its functionalities. Lack of an experimentally resolved structure of hCaV1.2 remains a significant impediment in molecular-level understanding of this channel. This work focuses on building atomistic hCaV1.2 model and studying calcium influx using computational approaches. METHODS We employed homology modeling and molecular dynamics (MD) to build the structure of hCaV1.2. Subsequently, we employed steered molecular dynamics (SMD) to understand calcium ion permeation in hCaV1.2. RESULTS We report a comprehensive three-dimensional model of a closed state hCaV1.2 refined under physiological membrane-bound conditions using MD simulations. Our SMD simulations on the model revealed four important barriers for ion permeation: this includes three calcium binding sites formed by the EEEE- and TTTT- rings within the selectivity filter region and a large barrier rendered by the hydrophobic internal gate. Our results also revealed that the first hydration shell of calcium remained intact throughout the simulations, thus playing an important role in ion permeation in hCaV1.2. CONCLUSIONS Our results have provided some important mechanistic insights into the structure, dynamics and ion permeation in hCaV1.2. The significant barriers for ion permeation formed by the four phenylalanine residues at the internal gate region suggest that this site is important for channel activation.
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158
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Wilson J, Sarthak K, Si W, Gao L, Aksimentiev A. Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model. ACS Sens 2019; 4:634-644. [PMID: 30821441 DOI: 10.1021/acssensors.8b01375] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nanopore sensing has emerged as a versatile approach to detection and identification of biomolecules. Presently, researchers rely on experience and intuition for choosing or modifying the nanopores to detect a target analyte. The field would greatly benefit from a computational method that could relate the atomic-scale geometry of the nanopores and analytes to the blockade nanopore currents they produce. Existing computational methods are either computationally too expensive to be used routinely in experimental laboratories or not sensitive enough to account for the atomic structure of the pore and the analytes. Here, we demonstrate a robust and inexpensive computational approach-the steric exclusion model (SEM) of nanopore conductance-that is orders of magnitude more efficient than all-atom MD and yet is sensitive enough to account for the atomic structure of the nanopore and the analyte. The method combines the computational efficiency of a finite element solver with the atomic precision of a nanopore conductance map to yield unprecedented speed and accuracy of ionic current prediction. We validate our SEM approach through comparison with the current blockades computed using the all-atom molecular dynamics method for a range of proteins confined to a solid-state nanopore, biological channels embedded in a lipid bilayer membranes, and blockade currents produced by DNA homopolymers in MspA. We illustrate potential applications of SEM by computing blockade currents produced by nucleosome proteins in a solid-state nanopore, individual amino acids in MspA, and by testing the effect of point mutations on amino acid distinguishability. We expect our SEM approach to become an integral part of future development of the nanopore sensing field.
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Affiliation(s)
| | | | - Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments and School of Mechanical Engineering, Southeast University, Nanjing, 210096, China
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159
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Zhao S, Restrepo-Pérez L, Soskine M, Maglia G, Joo C, Dekker C, Aksimentiev A. Electro-Mechanical Conductance Modulation of a Nanopore Using a Removable Gate. ACS NANO 2019; 13:2398-2409. [PMID: 30715850 PMCID: PMC6494462 DOI: 10.1021/acsnano.8b09266] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Ion channels form the basis of information processing in living cells by facilitating the exchange of electrical signals across and along cellular membranes. Applying the same principles to man-made systems requires the development of synthetic ion channels that can alter their conductance in response to a variety of external manipulations. By combining single-molecule electrical recordings with all-atom molecular dynamics simulations, we here demonstrate a hybrid nanopore system that allows for both a stepwise change of its conductance and a nonlinear current-voltage dependence. The conductance modulation is realized by using a short flexible peptide gate that carries opposite electric charge at its ends. We show that a constant transmembrane bias can position (and, in a later stage, remove) the peptide gate right at the most-sensitive sensing region of a biological nanopore FraC, thus partially blocking its channel and producing a stepwise change in the conductance. Increasing or decreasing the bias while having the peptide gate trapped in the pore stretches or compresses the peptide within the nanopore, thus modulating its conductance in a nonlinear but reproducible manner. We envision a range of applications of this removable-gate nanopore system, e.g. from an element of biological computing circuits to a test bed for probing the elasticity of intrinsically disordered proteins.
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Affiliation(s)
- Shidi Zhao
- Center for Biophysics and Quantitative Biology, Department of Physics and Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Laura Restrepo-Pérez
- Department of Bionanoscience, Kavli Institute of Nanoscience , Delft University of Technology , van der Maasweg 9 , 2629 HZ Delft , The Netherlands
| | - Misha Soskine
- Groningen Biomolecular Sciences & Biotechnology Institute , University of Groningen , 9747 AG Groningen , The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute , University of Groningen , 9747 AG Groningen , The Netherlands
| | - Chirlmin Joo
- Department of Bionanoscience, Kavli Institute of Nanoscience , Delft University of Technology , van der Maasweg 9 , 2629 HZ Delft , The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience , Delft University of Technology , van der Maasweg 9 , 2629 HZ Delft , The Netherlands
| | - Aleksei Aksimentiev
- Center for Biophysics and Quantitative Biology, Department of Physics and Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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160
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Ma J, Li K, Li Z, Qiu Y, Si W, Ge Y, Sha J, Liu L, Xie X, Yi H, Ni Z, Li D, Chen Y. Drastically Reduced Ion Mobility in a Nanopore Due to Enhanced Pairing and Collisions between Dehydrated Ions. J Am Chem Soc 2019; 141:4264-4272. [PMID: 30773010 DOI: 10.1021/jacs.8b08488] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Ion transport through nanopores is a process of fundamental significance in nature and in engineering practice. Over the past decade, it has been found that the ion conductivity in nanopores could be drastically enhanced, and different mechanisms have been proposed to explain this observation. To date, most reported studies have been carried out with relatively dilute electrolytes, while ion transport in nanopores under high electrolyte concentrations (>1 M) has been rarely explored. Through systematic experimental and atomistic simulation studies with NaCl solutions, here we show that at high electrolyte concentrations, ion mobility in small nanopores could be significantly reduced from the corresponding bulk value. Subsequent molecular dynamics studies indicate that in addition to the low mobility of surface-bound ions in the Stern layer, enhanced pairing and collisions between partially dehydrated ions of opposite charges also make important contributions to the reduced ion mobility. Furthermore, we show that the extent of mobility reduction depends on the association constant between cations and anions in different electrolytes with a more drastic reduction for a larger association constant.
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Affiliation(s)
- Jian Ma
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Kun Li
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Zhongwu Li
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Yinghua Qiu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Yanyan Ge
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Lei Liu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Xiao Xie
- China Education Council Key Laboratory of MEMS , Southeast University , Nanjing 210096 , China
| | - Hong Yi
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Zhonghua Ni
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Deyu Li
- Department of Mechanical Engineering , Vanderbilt University , Nashville , Tennessee 37235-1592 , United States
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
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161
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Abstract
PDZ domains contain 80-100 amino acids and bind short C-terminal sequences of target proteins. Their specificity is essential for cellular signaling pathways. We studied the binding of the Tiam1 PDZ domain to peptides derived from the C-termini of its Syndecan-1 and Caspr4 targets. We used free energy perturbation (FEP) to characterize the binding energetics of one wild-type and 17 mutant complexes by simulating 21 alchemical transformations between pairs of complexes. Thirteen complexes had known experimental affinities. FEP is a powerful tool to understand protein/ligand binding. It depends, however, on the accuracy of molecular dynamics force fields and conformational sampling. Both aspects require continued testing, especially for ionic mutations. For six mutations that did not modify the net charge, we obtained excellent agreement with experiment using the additive, AMBER ff99SB force field, with a root mean square deviation (RMSD) of 0.37 kcal/mol. For six ionic mutations that modified the net charge, agreement was also good, with one large error (3 kcal/mol) and an RMSD of 0.9 kcal/mol for the other five. The large error arose from the overstabilization of a protein/peptide salt bridge by the additive force field. Four of the ionic mutations were also simulated with the polarizable Drude force field, which represents the first test of this force field for protein/ligand binding free energy changes. The large error was eliminated and the RMS error for the four mutations was reduced from 1.8 to 1.2 kcal/mol. The overall accuracy of FEP indicates it can be used to understand PDZ/peptide binding. Importantly, our results show that for ionic mutations in buried regions, electronic polarization plays a significant role.
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162
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Bartsch A, Llabrés S, Pein F, Kattner C, Schön M, Diehn M, Tanabe M, Munk A, Zachariae U, Steinem C. High-resolution experimental and computational electrophysiology reveals weak β-lactam binding events in the porin PorB. Sci Rep 2019; 9:1264. [PMID: 30718567 PMCID: PMC6362148 DOI: 10.1038/s41598-018-37066-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 12/03/2018] [Indexed: 12/18/2022] Open
Abstract
The permeation of most antibiotics through the outer membrane of Gram-negative bacteria occurs through porin channels. To design drugs with increased activity against Gram-negative bacteria in the face of the antibiotic resistance crisis, the strict constraints on the physicochemical properties of the permeants imposed by these channels must be better understood. Here we show that a combination of high-resolution electrophysiology, new noise-filtering analysis protocols and atomistic biomolecular simulations reveals weak binding events between the β-lactam antibiotic ampicillin and the porin PorB from the pathogenic bacterium Neisseria meningitidis. In particular, an asymmetry often seen in the electrophysiological characteristics of ligand-bound channels is utilised to characterise the binding site and molecular interactions in detail, based on the principles of electro-osmotic flow through the channel. Our results provide a rationale for the determinants that govern the binding and permeation of zwitterionic antibiotics in porin channels.
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Affiliation(s)
- Annika Bartsch
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstraße 2, 37077, Göttingen, Germany
| | - Salomé Llabrés
- Computational Biology, School of Life Sciences, University of Dundee, Nethergate, Dundee, DD1 5EH, UK
| | - Florian Pein
- Institute for Mathematical Stochastics, University of Göttingen, Goldschmidtstraße 7, 37077, Göttingen, Germany
| | - Christof Kattner
- ZIK HALOmem, Membrane Protein Biochemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes Straße 3, 06120, Halle (Saale), Germany
- Juno Therapeutics GmbH, Göttingen, Germany
| | - Markus Schön
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstraße 2, 37077, Göttingen, Germany
| | - Manuel Diehn
- Institute for Mathematical Stochastics, University of Göttingen, Goldschmidtstraße 7, 37077, Göttingen, Germany
| | - Mikio Tanabe
- Institute of Materials Structure Science, Structural Biology Research Center, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Axel Munk
- Institute for Mathematical Stochastics, University of Göttingen, Goldschmidtstraße 7, 37077, Göttingen, Germany
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Nethergate, Dundee, DD1 5EH, UK.
- Physics, School of Science and Engineering, University of Dundee, Nethergate, Dundee, DD1 4NH, UK.
| | - Claudia Steinem
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstraße 2, 37077, Göttingen, Germany.
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163
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Bhamidimarri SP, Zahn M, Prajapati JD, Schleberger C, Söderholm S, Hoover J, West J, Kleinekathöfer U, Bumann D, Winterhalter M, van den Berg B. A Multidisciplinary Approach toward Identification of Antibiotic Scaffolds for Acinetobacter baumannii. Structure 2019; 27:268-280.e6. [DOI: 10.1016/j.str.2018.10.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 08/19/2018] [Accepted: 10/23/2018] [Indexed: 11/16/2022]
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164
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Golla VK, Sans-Serramitjana E, Pothula KR, Benier L, Bafna JA, Winterhalter M, Kleinekathöfer U. Fosfomycin Permeation through the Outer Membrane Porin OmpF. Biophys J 2019; 116:258-269. [PMID: 30616836 PMCID: PMC6350074 DOI: 10.1016/j.bpj.2018.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/21/2018] [Accepted: 12/03/2018] [Indexed: 01/14/2023] Open
Abstract
Fosfomycin is a frequently prescribed drug in the treatment of acute urinary tract infections. It enters the bacterial cytoplasm and inhibits the biosynthesis of peptidoglycans by targeting the MurA enzyme. Despite extensive pharmacological studies and clinical use, the permeability of fosfomycin across the bacterial outer membrane is largely unexplored. Here, we investigate the fosfomycin permeability across the outer membrane of Gram-negative bacteria by electrophysiology experiments as well as by all-atom molecular dynamics simulations including free-energy and applied-field techniques. Notably, in an electrophysiological zero-current assay as well as in the molecular simulations, we found that fosfomycin can rapidly permeate the abundant Escherichia coli porin OmpF. Furthermore, two triple mutants in the constriction region of the porin have been investigated. The permeation rates through these mutants are slightly lower than that of the wild type but fosfomycin can still permeate. Altogether, this work unravels molecular details of fosfomycin permeation through the outer membrane porin OmpF of E. coli and moreover provides hints for understanding the translocation of phosphonic acid antibiotics through other outer membrane pores.
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Affiliation(s)
- Vinaya Kumar Golla
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen, Germany
| | | | | | - Lorraine Benier
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Jayesh Arun Bafna
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen, Germany.
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165
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Calero C, Franzese G. Membranes with different hydration levels: The interface between bound and unbound hydration water. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.10.074] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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166
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Si W, Liu C, Sha J, Zhang Y, Chen Y. Computational modeling of ionic currents through difform graphene nanopores with consistent cross-sectional areas. Phys Chem Chem Phys 2019; 21:26166-26174. [DOI: 10.1039/c9cp05459f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Unveiling the mystery of ion transport behavior in nanopores with consistent cross-sectional areas shows that this behavior is highly related to the geometry and hydrophobicity of the nanopores.
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Affiliation(s)
- Wei Si
- School of Mechanical Engineering
- Southeast University
- Nanjing 211189
- China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments
| | - Chenhan Liu
- School of Mechanical Engineering
- Southeast University
- Nanjing 211189
- China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments
| | - Jingjie Sha
- School of Mechanical Engineering
- Southeast University
- Nanjing 211189
- China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments
| | - Yin Zhang
- School of Mechanical Engineering
- Southeast University
- Nanjing 211189
- China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments
| | - Yunfei Chen
- School of Mechanical Engineering
- Southeast University
- Nanjing 211189
- China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments
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167
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Lopes-Rodrigues M, Zanuy D, Alemán C, Michaux C, Perpète EA. 3D structure of a Brucella melitensis porin: molecular modelling in lipid membranes. J Biomol Struct Dyn 2018; 37:3923-3935. [DOI: 10.1080/07391102.2018.1529627] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Maximilien Lopes-Rodrigues
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium
- Namur Institute of Structured Matter, University of Namur, Namur, Belgium
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, Barcelona, Spain
- Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - David Zanuy
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Carlos Alemán
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, Barcelona, Spain
- Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Catherine Michaux
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium
- Namur Institute of Structured Matter, University of Namur, Namur, Belgium
- Namur Research Institute for Life Sciences, University of Namur, Namur, Belgium
| | - Eric A. Perpète
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium
- Namur Institute of Structured Matter, University of Namur, Namur, Belgium
- Institute of Life-Earth-Environment, University of Namur, Namur, Belgium
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168
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Van Liefferinge F, Krammer EM, Sengupta D, Prévost M. Lipid composition and salt concentration as regulatory factors of the anion selectivity of VDAC studied by coarse-grained molecular dynamics simulations. Chem Phys Lipids 2018; 220:66-76. [PMID: 30448398 DOI: 10.1016/j.chemphyslip.2018.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/08/2018] [Accepted: 11/12/2018] [Indexed: 12/27/2022]
Abstract
The voltage-dependent anion channel (VDAC) is a mitochondrial outer membrane protein whose fundamental function is to facilitate and regulate the flow of metabolites between the cytosol and the mitochondrial intermembrane space. Using coarse-grained molecular dynamics simulations, we investigated the dependence of VDAC selectivity towards small inorganic anions on two factors: the ionic strength and the lipid composition. In agreement with experimental data we found that VDAC becomes less anion selective with increasing salt concentration due to the screening of a few basic residues that point into the pore lumen. The molecular dynamics simulations provide insight into the regulation mechanism of VDAC selectivity by the composition in the lipid membrane and suggest that the ion distribution is differently modulated by POPE compared to the POPC bilayer. This occurs through the more persistent interactions of acidic residues located at both rims of the β-barrel with head groups of POPE which in turn impact the electrostatic potential and thereby the selectivity of the pore. This mechanism occurs not only in POPE single component membranes but also in a mixed POPE/POPC bilayer by an enrichment of POPE over POPC lipids on the surface of VDAC. Thus we show here that computationally-inexpensive coarse-grained simulations are able to capture, in a semi-quantitative way, essential features of VDAC anion selectivity and could pave the way toward a molecular level understanding of metabolite transport in natural membranes.
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Affiliation(s)
- F Van Liefferinge
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - E-M Krammer
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - D Sengupta
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411 008, India
| | - M Prévost
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles (ULB), Brussels, Belgium.
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169
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Ma P, Cardenas AE, Chaudhari MI, Elber R, Rempe SB. Probing Translocation in Mutants of the Anthrax Channel: Atomically Detailed Simulations with Milestoning. J Phys Chem B 2018; 122:10296-10305. [PMID: 30338689 DOI: 10.1021/acs.jpcb.8b08304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Anthrax toxin consists of a cation channel and two protein factors. Translocation of the anthrax protein factors from endosomal to the cytosolic compartment is a complex process which utilizes the cation channel. An atomically detailed understanding of the function of the anthrax translocation machinery is incomplete. We report atomically detailed simulations of the lethal factor and channel mutants. Kinetic and thermodynamic properties of early events in the translocation process are computed within the Milestoning theory and algorithm. Several mutants of the channel illustrate that long-range electrostatic interactions provide the dominant driving force for translocation. No external energy input is required because the lower pH in the endosome relative to the cytosol drives the initial translocation process forward. Channel mutants with variable sizes cause smaller effects on translocation events relative to charge manipulations. Comparison with available experimental data is provided.
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Affiliation(s)
| | | | - Mangesh I Chaudhari
- Biological and Engineering Sciences , Sandia National Laboratories , Albuquerque , New Mexico 87185 , United States
| | | | - Susan B Rempe
- Biological and Engineering Sciences , Sandia National Laboratories , Albuquerque , New Mexico 87185 , United States
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170
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Mahinthichaichan P, Morris DM, Wang Y, Jensen GJ, Tajkhorshid E. Selective Permeability of Carboxysome Shell Pores to Anionic Molecules. J Phys Chem B 2018; 122:9110-9118. [PMID: 30193460 PMCID: PMC6311388 DOI: 10.1021/acs.jpcb.8b06822] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Carboxysomes are closed polyhedral cellular microcompartments that increase the efficiency of carbon fixation in autotrophic bacteria. Carboxysome shells consist of small proteins that form hexameric units with semipermeable central pores containing binding sites for anions. This feature is thought to selectively allow access to RuBisCO enzymes inside the carboxysome by HCO3- (the dominant form of CO2 in the aqueous solution at pH 7.4) but not O2, which leads to a nonproductive reaction. To test this hypothesis, here we use molecular dynamics simulations to characterize the energetics and permeability of CO2, O2, and HCO3- through the central pores of two different shell proteins, namely, CsoS1A of α-carboxysome and CcmK4 of β-carboxysome shells. We find that the central pores are in fact selectively permeable to anions such as HCO3-, as predicted by the model.
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Affiliation(s)
- Paween Mahinthichaichan
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801-3028 , United States
| | - Dylan M Morris
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
| | - Yi Wang
- Department of Physics , The Chinese University of Hong Kong , Shatin , New Territories, Hong Kong SAR , The People's Republic of China
| | - Grant J Jensen
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
- Howard Hughes Medical Institute , California Insitute of Technology , Pasadena , California 91125 , United States
| | - Emad Tajkhorshid
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801-3028 , United States
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171
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The Role of Lipid Interactions in Simulations of the α-Hemolysin Ion-Channel-Forming Toxin. Biophys J 2018; 115:1720-1730. [PMID: 30287110 DOI: 10.1016/j.bpj.2018.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 09/04/2018] [Accepted: 09/07/2018] [Indexed: 01/25/2023] Open
Abstract
Molecular dynamics simulations were performed to describe the function of the ion-channel-forming toxin α-hemolysin (αHL) in lipid membranes that were composed of either 1,2-diphytanoyl-sn-glycero-3-phospho-choline or 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-choline. The simulations highlight the importance of lipid type in maintaining αHL structure and function, enabling direct comparison to experiments for biosensing applications. We determined that although the two lipids studied are similar in structure, 1,2-diphytanoyl-sn-glycero-3-phospho-choline membranes better match the hydrophobic thickness of αHL compared to 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-choline membranes. This hydrophobic match is essential to maintaining proper alignment of β-sheet loops at the trans entrance of αHL, which, when disrupted, creates an additional constriction to ion flow that decreases the channel current below experimental values and creates greater variability in channel conductance. Agreement with experiments was further improved with sufficient lipid membrane equilibration and allowed the discrimination of subtle αHL conduction states with lipid type. Finally, we explore the effects of truncating the extramembrane cap of αHL and its role in maintaining proper alignment of αHL in the membrane and channel conductance. Our results demonstrate the essential role of lipid type and lipid-protein interactions in simulations of αHL and will considerably improve the interpretation of experimental data.
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172
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Chowdhury R, Ren T, Shankla M, Decker K, Grisewood M, Prabhakar J, Baker C, Golbeck JH, Aksimentiev A, Kumar M, Maranas CD. PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore. Nat Commun 2018; 9:3661. [PMID: 30202038 PMCID: PMC6131167 DOI: 10.1038/s41467-018-06097-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/17/2018] [Indexed: 11/30/2022] Open
Abstract
Monodispersed angstrom-size pores embedded in a suitable matrix are promising for highly selective membrane-based separations. They can provide substantial energy savings in water treatment and small molecule bioseparations. Such pores present as membrane proteins (chiefly aquaporin-based) are commonplace in biological membranes but difficult to implement in synthetic industrial membranes and have modest selectivity without tunable selectivity. Here we present PoreDesigner, a design workflow to redesign the robust beta-barrel Outer Membrane Protein F as a scaffold to access three specific pore designs that exclude solutes larger than sucrose (>360 Da), glucose (>180 Da), and salt (>58 Da) respectively. PoreDesigner also enables us to design any specified pore size (spanning 3-10 Å), engineer its pore profile, and chemistry. These redesigned pores may be ideal for conducting sub-nm aqueous separations with permeabilities exceeding those of classical biological water channels, aquaporins, by more than an order of magnitude at over 10 billion water molecules per channel per second.
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Affiliation(s)
- Ratul Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Tingwei Ren
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Manish Shankla
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Karl Decker
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Matthew Grisewood
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jeevan Prabhakar
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Carol Baker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - John H Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Manish Kumar
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.
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173
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Kasimova MA, Lindahl E, Delemotte L. Determining the molecular basis of voltage sensitivity in membrane proteins. J Gen Physiol 2018; 150:1444-1458. [PMID: 30150239 PMCID: PMC6168238 DOI: 10.1085/jgp.201812086] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 08/07/2018] [Indexed: 12/31/2022] Open
Abstract
The identification of voltage-sensing elements in membrane proteins is challenging due to the diversity of voltage-sensing mechanisms. Kasimova et al. present a computational approach to predict the elements involved in voltage sensing, which they validate using voltage-gated ion channels. Voltage-sensitive membrane proteins are united by their ability to transform changes in membrane potential into mechanical work. They are responsible for a spectrum of physiological processes in living organisms, including electrical signaling and cell-cycle progression. Although the mechanism of voltage-sensing has been well characterized for some membrane proteins, including voltage-gated ion channels, even the location of the voltage-sensing elements remains unknown for others. Moreover, the detection of these elements by using experimental techniques is challenging because of the diversity of membrane proteins. Here, we provide a computational approach to predict voltage-sensing elements in any membrane protein, independent of its structure or function. It relies on an estimation of the propensity of a protein to respond to changes in membrane potential. We first show that this property correlates well with voltage sensitivity by applying our approach to a set of voltage-sensitive and voltage-insensitive membrane proteins. We further show that it correctly identifies authentic voltage-sensitive residues in the voltage-sensor domain of voltage-gated ion channels. Finally, we investigate six membrane proteins for which the voltage-sensing elements have not yet been characterized and identify residues and ions that might be involved in the response to voltage. The suggested approach is fast and simple and enables a characterization of voltage sensitivity that goes beyond mere identification of charges. We anticipate that its application before mutagenesis experiments will significantly reduce the number of potential voltage-sensitive elements to be tested.
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Affiliation(s)
- Marina A Kasimova
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Erik Lindahl
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Lucie Delemotte
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
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174
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Single-Molecule Dynamics and Discrimination between Hydrophilic and Hydrophobic Amino Acids in Peptides, through Controllable, Stepwise Translocation across Nanopores. Polymers (Basel) 2018; 10:polym10080885. [PMID: 30960810 PMCID: PMC6403800 DOI: 10.3390/polym10080885] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/04/2018] [Accepted: 08/06/2018] [Indexed: 02/07/2023] Open
Abstract
In this work, we demonstrate the proof-of-concept of real-time discrimination between patches of hydrophilic and hydrophobic monomers in the primary structure of custom-engineered, macro-dipole-like peptides, at uni-molecular level. We employed single-molecule recordings to examine the ionic current through the α-hemolysin (α-HL) nanopore, when serine or isoleucine residues, flanked by segments of oppositely charged arginine and glutamic amino acids functioning as a voltage-dependent “molecular brake” on the peptide, were driven at controllable rates across the nanopore. The observed differences in the ionic currents blockades through the nanopore, visible at time resolutions corresponding to peptide threading through the α-HL’s constriction region, was explained by a simple model of the volumes of electrolyte excluded by either amino acid species, as groups of serine or isoleucine monomers transiently occupy the α-HL. To provide insights into the conditions ensuring optimal throughput of peptide readout through the nanopore, we probed the sidedness-dependence of peptide association to and dissociation from the electrically and geometrically asymmetric α-HL.
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175
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Wang Y, Gu LQ, Tian K. The aerolysin nanopore: from peptidomic to genomic applications. NANOSCALE 2018; 10:13857-13866. [PMID: 29998253 PMCID: PMC6157726 DOI: 10.1039/c8nr04255a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The aerolysin pore (ARP) is a newly emerging nanopore that has been extensively used for peptide and protein sensing. Recently, several groups have explored the application of ARP in detecting genetic and epigenetic markers. This brief review summarizes the current applications of ARP, progressing from peptidomic to genomic detection; the recently reported site-directed mutagenesis of ARP; and new genomic DNA sensing approaches, and their advantages and disadvantages. This review will also discuss the perspectives and future applications of ARP for nucleic acid sequencing and biomolecule sensing.
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Affiliation(s)
- Yong Wang
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Li-Qun Gu
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA.
| | - Kai Tian
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA.
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176
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Triandafilidi V, Hatzikiriakos SG, Rottler J. Molecular simulations of the piezoionic effect. SOFT MATTER 2018; 14:6222-6229. [PMID: 30022190 DOI: 10.1039/c8sm00939b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We present a molecular dynamics study of two polyelectrolyte gels with different degrees of ionization coupled in a slab geometry. Our simulations show that a pressure gradient emerges between the two gels that results in the buildup of a Nernst-Donnan potential. This methodology is reverse to experiments of the piezoionic or mechanoelectric effect, in which an electric potential gradient appears upon application of a pressure gradient to a hydrogel. The Nernst-Donnan potential at the interface is found to scale linearly with temperature with the coefficient of proportionality given by the fraction of concentrations of the uncondensed counterions. We show that the potential difference can also be expressed as a linear function of the lateral pressure, thus providing a molecular interpretation of the piezoionic effect.
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Affiliation(s)
- Vasilii Triandafilidi
- Department of Chemical Engineering, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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177
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Mapping the sensing spots of aerolysin for single oligonucleotides analysis. Nat Commun 2018; 9:2823. [PMID: 30026547 PMCID: PMC6053387 DOI: 10.1038/s41467-018-05108-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 06/05/2018] [Indexed: 12/05/2022] Open
Abstract
Nanopore sensing is a powerful single-molecule method for DNA and protein sequencing. Recent studies have demonstrated that aerolysin exhibits a high sensitivity for single-molecule detection. However, the lack of the atomic resolution structure of aerolysin pore has hindered the understanding of its sensing capabilities. Herein, we integrate nanopore experimental results and molecular simulations based on a recent pore structural model to precisely map the sensing spots of this toxin for ssDNA translocation. Rationally probing ssDNA length and composition upon pore translocation provides new important insights for molecular determinants of the aerolysin nanopore. Computational and experimental results reveal two critical sensing spots (R220, K238) generating two constriction points along the pore lumen. Taking advantage of the sensing spots, all four nucleobases, cytosine methylation and oxidation of guanine can be clearly identified in a mixture sample. The results provide evidence for the potential of aerolysin as a nanosensor for DNA sequencing. Nanopores are an emerging powerful single-molecule method of DNA sequencing. Here the authors map the structure of aerolysin for use as a nanopore and show detection of modified and unmodified nucleobases.
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178
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Abstract
Access resistance indicates how well current carriers from a bulk medium can converge to a pore or opening and is an important concept in nanofluidic devices and in cell physiology. In simplified scenarios, when the bulk dimensions are infinite in all directions, it depends only on the resistivity and pore radius. These conditions are not valid in all-atom molecular dynamics simulations of transport, due to the computational cost of large simulation cells, and can even break down in micro- and nanoscale systems due to strong confinement. Here, we examine a scaling theory for the access resistance that predicts a special simulation cell aspect ratio-the golden aspect ratio-where finite-size effects are eliminated. Using both continuum and all-atom simulations, we demonstrate that this golden aspect ratio exists and that it takes on a universal value in linear response and moderate concentrations. Outside of linear response, it gains an apparent dependence on characteristics of the transport scenario (concentration, voltages, etc.) for small simulation cells, but this dependence vanishes at larger length scales. These results will enable the use of all-atom molecular dynamics simulations to study contextual properties of access resistance-its dependence on protein and molecular-scale fluctuations, the presence of charges, and other functional groups-and yield the opportunity to quantitatively compare computed and measured resistances.
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Affiliation(s)
- Subin Sahu
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899
- Maryland NanoCenter, University of Maryland, College Park, MD 20742
| | - Michael Zwolak
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899
- Corresponding Author:
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179
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Wilson J, Aksimentiev A. Water-Compression Gating of Nanopore Transport. PHYSICAL REVIEW LETTERS 2018; 120:268101. [PMID: 30004740 PMCID: PMC6262874 DOI: 10.1103/physrevlett.120.268101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 04/18/2018] [Indexed: 05/22/2023]
Abstract
Electric field-driven motion of biomolecules is a process essential to many analytics methods, in particular, to nanopore sensing, where a transient reduction of nanopore ionic current indicates the passage of a biomolecule through the nanopore. However, before any molecule can be examined by a nanopore, the molecule must first enter the nanopore from the solution. Previously, the rate of capture by a nanopore was found to increase with the strength of the applied electric field. Here, we theoretically show that, in the case of narrow pores in graphene membranes, increasing the strength of the electric field can not only decrease the rate of capture, but also repel biomolecules from the nanopore. As the strong electric field polarizes water near and within the nanopore, the high gradient of the field also produces a strong dielectrophoretic force that compresses the water. The pressure difference caused by the sharp water density gradient produces a hydrostatic force that repels DNA or proteins from the nanopore, preventing, in certain conditions, their capture. We show that such local compression of fluid can regulate the transport of biomolecules through nanoscale passages in the absence of physical gates and sort proteins according to their phosphorylated states.
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Affiliation(s)
- James Wilson
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801 and Beckman Institute for Advanced Science and Technology
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180
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Xu K, Lin Z, Merlet C, Taberna PL, Miao L, Jiang J, Simon P. Tracking Ionic Rearrangements and Interpreting Dynamic Volumetric Changes in Two-Dimensional Metal Carbide Supercapacitors: A Molecular Dynamics Simulation Study. CHEMSUSCHEM 2018; 11:1892-1899. [PMID: 29211947 DOI: 10.1002/cssc.201702068] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Indexed: 06/07/2023]
Abstract
We present a molecular dynamics simulation study achieved on two-dimensional (2D) Ti3 C2 Tx MXenes in the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([EMIM]+ [TFSI]- ) electrolyte. Our simulations reproduce the different patterns of volumetric change observed experimentally for both the negative and positive electrodes. The analysis of ionic fluxes and structure rearrangements in the 2D material provide an atomic scale insight into the charge and discharge processes in the layer pore and confirm the existence of two different charge-storage mechanisms at the negative and positive electrodes. The ionic number variation and the structure rearrangement contribute to the dynamic volumetric changes of both electrodes: negative electrode expansion and positive electrode contraction.
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Affiliation(s)
- Kui Xu
- CIRIMAT UMR CNRS 5085, Université Paul Sabatier Toulouse III, 118 route de Narbonne, 31062, Toulouse, France
- School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P.R. China
- FR CNRS 3459, Réseau sur le Stockage Electrochimique de l'Energie (RS2E), 33 rue Saint Leu, 80039, Amiens, France
| | - Zifeng Lin
- CIRIMAT UMR CNRS 5085, Université Paul Sabatier Toulouse III, 118 route de Narbonne, 31062, Toulouse, France
- FR CNRS 3459, Réseau sur le Stockage Electrochimique de l'Energie (RS2E), 33 rue Saint Leu, 80039, Amiens, France
| | - Céline Merlet
- CIRIMAT UMR CNRS 5085, Université Paul Sabatier Toulouse III, 118 route de Narbonne, 31062, Toulouse, France
- FR CNRS 3459, Réseau sur le Stockage Electrochimique de l'Energie (RS2E), 33 rue Saint Leu, 80039, Amiens, France
| | - Pierre-Louis Taberna
- CIRIMAT UMR CNRS 5085, Université Paul Sabatier Toulouse III, 118 route de Narbonne, 31062, Toulouse, France
- FR CNRS 3459, Réseau sur le Stockage Electrochimique de l'Energie (RS2E), 33 rue Saint Leu, 80039, Amiens, France
| | - Ling Miao
- School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P.R. China
| | - Jianjun Jiang
- School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P.R. China
| | - Patrice Simon
- CIRIMAT UMR CNRS 5085, Université Paul Sabatier Toulouse III, 118 route de Narbonne, 31062, Toulouse, France
- FR CNRS 3459, Réseau sur le Stockage Electrochimique de l'Energie (RS2E), 33 rue Saint Leu, 80039, Amiens, France
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181
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Miranda WE, Ngo VA, Wang R, Zhang L, Chen SRW, Noskov SY. Molecular Mechanism of Conductance Enhancement in Narrow Cation-Selective Membrane Channels. J Phys Chem Lett 2018; 9:3497-3502. [PMID: 29886737 DOI: 10.1021/acs.jpclett.8b01005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Membrane proteins known as ryanodine receptors (RyRs) display large conductance of ∼1 nS and nearly ideal charge selectivity. Both properties are inversely correlated in other large-conductance but nonselective biological nanopores (i.e., α-hemolysin) used as industrial biosensors. Although recent cryo-electron microscopy structures of RyR2 show similarities to K+- and Na+-selective channels, it remains unclear whether similar ion conduction mechanisms occur in RyR2. Here, we combine microseconds of all-atom molecular dynamics (MD) simulations with mutagenesis and electrophysiology experiments to investigate large K+ conductance and charge selectivity (cation vs anion) in an open-state structure of RyR2. Our results show that a water-mediated knock-on mechanism enhances the cation permeation. The polar Q4863 ring may function as a confinement zone amplifying charge selectivity, while the cytoplasmic vestibule can contribute to the efficiency of the cation attraction. We also provide direct evidence that the rings of acidic residues at the channel vestibules are critical for both conductance and charge discrimination in RyRs.
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Affiliation(s)
- Williams E Miranda
- Centre for Molecular Simulations and Department of Biological Sciences , University of Calgary , Alberta T2N 1N4 , Canada
| | - Van A Ngo
- Centre for Molecular Simulations and Department of Biological Sciences , University of Calgary , Alberta T2N 1N4 , Canada
| | - Ruiwu Wang
- Department of Physiology and Pharmacology, Libin Cardiovascular Institute of Alberta , University of Calgary , Alberta T2N 1N4 , Canada
| | - Lin Zhang
- Department of Physiology and Pharmacology, Libin Cardiovascular Institute of Alberta , University of Calgary , Alberta T2N 1N4 , Canada
| | - S R Wayne Chen
- Department of Physiology and Pharmacology, Libin Cardiovascular Institute of Alberta , University of Calgary , Alberta T2N 1N4 , Canada
| | - Sergei Yu Noskov
- Centre for Molecular Simulations and Department of Biological Sciences , University of Calgary , Alberta T2N 1N4 , Canada
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182
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Talarimoghari M, Baaken G, Hanselmann R, Behrends JC. Size-dependent interaction of a 3-arm star poly(ethylene glycol) with two biological nanopores. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:77. [PMID: 29926213 DOI: 10.1140/epje/i2018-11687-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/31/2018] [Indexed: 06/08/2023]
Abstract
We use two pore-forming proteins, alpha-hemolysin and aerolysin, to compare the polymer size-dependence of ionic current block by two types of ethyleneglycol polymers: 1) linear and 2) 3-arm star poly(ethylene glycol), both applied as a polydisperse mixture of average mass 1kDa under high salt conditions. The results demonstrate that monomer size sensitivity, as known for linear PEGs, is conserved for the star polymers with only subtle differences in the dependence of the residual conductance on monomer number. To explain this absence of a dominant effect of polymer architecture, we propose that PEG adsorbs to the inner pore wall in a collapsed, salted-out state, likely due to the effect of hydrophobic residues in the pore wall on the availability of water for hydration.
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Affiliation(s)
- Monasadat Talarimoghari
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Hermann-Herder-Str. 7, 79104, Freiburg, Germany
| | - Gerhard Baaken
- Ionera Technologies GmbH, Hermann-Herder-Str. 7, 79104, Freiburg, Germany
| | - Ralf Hanselmann
- Institute for Macromolecular Chemistry, Stefan-Meier-Str. 31, 79104, Freiburg, Germany
- Freiburg Materials Research Centre, University of Freiburg, Stefan-Meier-Str. 19, 79104, Freiburg, Germany
| | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Hermann-Herder-Str. 7, 79104, Freiburg, Germany.
- Freiburg Materials Research Centre, University of Freiburg, Stefan-Meier-Str. 19, 79104, Freiburg, Germany.
- Freiburg Centre for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany.
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183
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Tu B, Bai S, Lu B, Fang Q. Conic shapes have higher sensitivity than cylindrical ones in nanopore DNA sequencing. Sci Rep 2018; 8:9097. [PMID: 29904117 PMCID: PMC6002541 DOI: 10.1038/s41598-018-27517-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 05/31/2018] [Indexed: 11/09/2022] Open
Abstract
Nanopores have emerged as helpful research tools for single molecule detection. Through continuum modeling, we investigated the effects of membrane thickness, nanopore size, and pore shape on current signal characteristics of DNA. The simulation results showed that, when reducing the pore diameter, the amplitudes of current signals of DNA increase. Moreover, we found that, compared to cylindrically shaped nanopores, conical-shaped nanopores produce greater signal amplitudes from biomolecules translocation. Finally, we demonstrated that continuum model simulations for the discrimination of DNA and RNA yield current characteristics approximately consistent with experimental measurements and that A-T and G-C base pairs can be distinguished using thin conical solid-state nanopores. Our study not only suggests that computational approaches in this work can be used to guide the designs of nanopore for single molecule detection, but it also provides several possible ways to improve the current amplitudes of nanopores for better resolution.
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Affiliation(s)
- Bin Tu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, beijing, 100190, China
| | - Shiyang Bai
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, beijing, 100190, China
| | - Benzhuo Lu
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, beijing, 100190, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Qiaojun Fang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, beijing, 100190, China. .,Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, beijing, 100190, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Sino-Danish Center for Education and Research, Beijing, 101408, China.
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184
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Tse CH, Comer J, Wang Y, Chipot C. Link between Membrane Composition and Permeability to Drugs. J Chem Theory Comput 2018; 14:2895-2909. [PMID: 29771515 DOI: 10.1021/acs.jctc.8b00272] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Prediction of membrane permeability to small molecules represents an important aspect of drug discovery. First-principles calculations of this quantity require an accurate description of both the thermodynamics and kinetics that underlie translocation of the permeant across the lipid bilayer. In this contribution, the membrane permeability to three drugs, or drug-like molecules, namely, 9-anthroic acid (ANA), 2',3'-dideoxyadenosine (DDA), and hydrocortisone (HYL), are estimated in a pure 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) and in a POPC:cholesterol (2:1) mixture. On the basis of independent 2-5-μs free-energy calculations combined with a time-fractional Smoluchowski determination of the diffusivity, the estimated membrane permeabilities to these chemically diverse permeants fall within an order of magnitude from the experimental values obtained in egg-lecithin bilayers, with the exception of HYL in pure POPC. This exception is particularly interesting because the calculated permeability of the sterol-rich bilayer to HYL, in close agreement with the experimental value, is about 600 times lower than that of the pure POPC bilayer to HYL. In contrast, the permeabilities to ANA and DDA differ by less than a factor of 10 between the pure POPC and POPC:cholesterol bilayers. The unusual behavior of HYL, a large, amphiphilic compound, may be linked with the longer range perturbation of the lipid bilayer it induces, compared to ANA and DDA, suggestive of a possibly different translocation mechanism. We find that the tendency of lower permeabilities of the POPC:cholesterol bilayer relative to those of the pure POPC one is a consequence of increased free-energy barriers. Beyond reporting accurate estimates of the membrane permeability, the present contribution also demonstrates that rigorous free-energy calculations and a fractional-diffusion model are key in revealing the molecular phenomena linking the composition of a membrane to its permeability to drugs.
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Affiliation(s)
- Chi Hang Tse
- Shenzhen Research Institute , The Chinese University of Hong Kong , Shatin , Hong Kong SAR , China.,Department of Physics , The Chinese University of Hong Kong , Shatin , Hong Kong SAR , China
| | - Jeffrey Comer
- Institute of Computational Comparative Medicine and Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology , Kansas State University , Manhattan , Kansas 66506 , United States
| | - Yi Wang
- Shenzhen Research Institute , The Chinese University of Hong Kong , Shatin , Hong Kong SAR , China.,Department of Physics , The Chinese University of Hong Kong , Shatin , Hong Kong SAR , China
| | - Christophe Chipot
- Laboratoire International Associé Centre, National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche No. 7019 , Université de Lorraine , B.P. 70239, 54506 Vandœuvre-lès-Nancy cedex , France.,Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , 405 North Mathews Avenue , Urbana , Illinois 61801 , United States.,Department of Physics , University of Illinois at Urbana-Champaign , 1110 West Green Street , Urbana , Illinois 61801 , United States
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185
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Chinappi M, Cecconi F. Protein sequencing via nanopore based devices: a nanofluidics perspective. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:204002. [PMID: 29595524 DOI: 10.1088/1361-648x/aababe] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Proteins perform a huge number of central functions in living organisms, thus all the new techniques allowing their precise, fast and accurate characterization at single-molecule level certainly represent a burst in proteomics with important biomedical impact. In this review, we describe the recent progresses in the developing of nanopore based devices for protein sequencing. We start with a critical analysis of the main technical requirements for nanopore protein sequencing, summarizing some ideas and methodologies that have recently appeared in the literature. In the last sections, we focus on the physical modelling of the transport phenomena occurring in nanopore based devices. The multiscale nature of the problem is discussed and, in this respect, some of the main possible computational approaches are illustrated.
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Affiliation(s)
- Mauro Chinappi
- Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, via del Politecnico 1, 00133 Roma, Italy
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186
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Möller D, Gellert M, Langel W, Lillig CH. Molecular dynamics simulations and in vitro analysis of the CRMP2 thiol switch. MOLECULAR BIOSYSTEMS 2018; 13:1744-1753. [PMID: 28726921 DOI: 10.1039/c7mb00160f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The collapsin response mediator protein CRMP2 (gene: DPYSL2) is crucial for neuronal development. The homotetrameric CRMP2 complex is regulated via two mechanisms: first by phosphorylation and second by the reduction and oxidation of the Cys504 residues of two adjacent subunits. Here, we have analysed the effects of this redox switch on the protein in vitro combined with force field molecular dynamics (MD). Earlier X-ray data reveal the structure of the rigid body of the molecule but lack the flexible C-terminus with the important sites for phosphorylation and redox regulation. An in silico model for this part was established by replica exchange simulations and homology modelling, which is consistent with the CD spectroscopy results of the recombinant protein. Thermofluor data indicated that the protein aggregates at bivalent ion concentrations below 200 mM. In simulations the protein surface was covered under these conditions by a large number of ions, which most likely prevent aggregation. A tryptophan residue (Trp295) in close proximity to the forming disulphide allowed the measurement of the structural relaxation of the rigid body upon reduction by fluorescence quenching. We were also able to determine the second-order rate constant of CRMP2 oxidation by H2O2. The simulated solvent accessible surface of the hydroxyl group of Ser518 significantly increased upon reduction of the disulphide bond. Our results give the first detailed insight into the profound structural changes of the tetrameric CRMP2 due to oxidation and indicate a tightly connected regulation by phosphorylation and redox modification.
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Affiliation(s)
- Daniel Möller
- Biophysical Chemistry, Institute of Biochemistry, University Greifswald, 17489 Greifswald, Germany
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187
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Chipot C, Dehez F, Schnell JR, Zitzmann N, Pebay-Peyroula E, Catoire LJ, Miroux B, Kunji ERS, Veglia G, Cross TA, Schanda P. Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies. Chem Rev 2018; 118:3559-3607. [PMID: 29488756 PMCID: PMC5896743 DOI: 10.1021/acs.chemrev.7b00570] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Indexed: 12/25/2022]
Abstract
Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents.
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Affiliation(s)
- Christophe Chipot
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
- Department
of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - François Dehez
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
| | - Jason R. Schnell
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Nicole Zitzmann
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | | | - Laurent J. Catoire
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Bruno Miroux
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Edmund R. S. Kunji
- Medical
Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Gianluigi Veglia
- Department
of Biochemistry, Molecular Biology, and Biophysics, and Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Timothy A. Cross
- National
High Magnetic Field Laboratory, Florida
State University, Tallahassee, Florida 32310, United States
| | - Paul Schanda
- Université
Grenoble Alpes, CEA, CNRS, IBS, Grenoble F-38000, France
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188
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Ren H, Cheyne CG, Fleming AM, Burrows CJ, White HS. Single-Molecule Titration in a Protein Nanoreactor Reveals the Protonation/Deprotonation Mechanism of a C:C Mismatch in DNA. J Am Chem Soc 2018; 140:5153-5160. [PMID: 29562130 DOI: 10.1021/jacs.8b00593] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Measurement of single-molecule reactions can elucidate microscopic mechanisms that are often hidden from ensemble analysis. Herein, we report the acid-base titration of a single DNA duplex confined within the wild-type α-hemolysin (α-HL) nanopore for up to 3 h, while monitoring the ionic current through the nanopore. Modulation between two states in the current-time trace for duplexes containing the C:C mismatch in proximity to the latch constriction of α-HL is attributed to the base flipping of the C:C mismatch. As the pH is lowered, the rate for the C:C mismatch to flip from the intra-helical state to the extra-helical state ( kintra-extra) decreases, while the rate for base flipping from the extra-helical state to the intra-helical state ( kextra-intra) remains unchanged. Both kintra-extra and kextra-intra are on the order of 1 × 10-2 s-1 to 1 × 10-1 s-1 and remain stable over the time scale of the measurement (several hours). Analysis of the pH-dependent kinetics of base flipping using a hidden Markov kinetic model demonstrates that protonation/deprotonation occurs while the base pair is in the intra-helical state. We also demonstrate that the rate of protonation is limited by transport of H+ into the α-HL nanopore. Single-molecule kinetic isotope experiments exhibit a large kinetic isotope effect (KIE) for kintra-extra ( kH/ kD ≈ 5) but a limited KIE for kextra-intra ( kH/ kD ≈ 1.3), supporting our model. Our experiments correspond to the longest single-molecule measurements performed using a nanopore, and demonstrate its application in interrogating mechanisms of single-molecule reactions in confined geometries.
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Affiliation(s)
- Hang Ren
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Cameron G Cheyne
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Aaron M Fleming
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Cynthia J Burrows
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Henry S White
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
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189
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Effect of 5-trans Isomer of Arachidonic Acid on Model Liposomal Membranes Studied by a Combined Simulation and Experimental Approach. J Membr Biol 2018; 251:475-489. [PMID: 29610947 DOI: 10.1007/s00232-018-0029-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 03/08/2018] [Indexed: 02/07/2023]
Abstract
Unsaturated fatty acids are found in humans predominantly in the cis configuration. Fatty acids in the trans configuration are primarily the result of human processing (trans fats), but can also be formed endogenously by radical stress. The cis-trans isomerization of fatty acids by free radicals could be connected to several pathologies. Trans fats have been linked to an increased risk of coronary artery disease; however, the reasons for the resulting pathogenesis remain unclear. Here, we investigate the effect of a mono-trans isomer of arachidonic acid (C20:4-5trans, 8cis, 11cis, 14cis) produced by free radicals in physiological concentration on a model erythrocyte membrane using a combined experimental and theoretical approach. Molecular Dynamics (MD) simulations of two model lipid bilayers containing arachidonic acid and its 5-trans isomer in 3 mol% were carried out for this purpose. The 5-trans isomer formation in the phospholipids was catalyzed by HOCH2CH2S· radicals, generated from the corresponding thiol by γ-irradiation, in multilamellar vesicles of SAPC. Large unilamellar vesicles were made by the extrusion method (LUVET) as a biomimetic model for cis-trans isomerization. Atomic Force Microscopy and Dynamic Light Scattering were used to measure the average size, morphology, and the z-potential of the liposomes. Both results from MD simulations and experiments are in agreement and indicate that the two model membranes display different physicochemical properties in that the bilayers containing the trans fatty acids were more ordered and more rigid than those containing solely the cis arachidonic acid. Correspondingly, the average size of the liposomes containing trans isomers was smaller than the ones without.
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190
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Willems K, Van Meervelt V, Wloka C, Maglia G. Single-molecule nanopore enzymology. Philos Trans R Soc Lond B Biol Sci 2018. [PMID: 28630164 DOI: 10.1098/rstb.2016.0230] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Biological nanopores are a class of membrane proteins that open nanoscale water conduits in biological membranes. When they are reconstituted in artificial membranes and a bias voltage is applied across the membrane, the ionic current passing through individual nanopores can be used to monitor chemical reactions, to recognize individual molecules and, of most interest, to sequence DNA. In addition, a more recent nanopore application is the analysis of single proteins and enzymes. Monitoring enzymatic reactions with nanopores, i.e. nanopore enzymology, has the unique advantage that it allows long-timescale observations of native proteins at the single-molecule level. Here, we describe the approaches and challenges in nanopore enzymology.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.
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Affiliation(s)
- Kherim Willems
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.,Department of Life Sciences and Imaging, IMEC, Kapeldreef 75, 3001 Leuven, Belgium
| | - Veerle Van Meervelt
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.,Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Carsten Wloka
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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191
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Andersson AEV, Kasimova MA, Delemotte L. Exploring the Viral Channel Kcv PBCV-1 Function via Computation. J Membr Biol 2018; 251:419-430. [PMID: 29476260 PMCID: PMC6028866 DOI: 10.1007/s00232-018-0022-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/15/2018] [Indexed: 11/30/2022]
Abstract
Viral potassium channels (Kcv) are homologous to the pore module of complex \documentclass[12pt]{minimal}
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\begin{document}$$\hbox {K}^+$$\end{document}K+-selective ion channels of cellular organisms. Due to their relative simplicity, they have attracted interest towards understanding the principles of \documentclass[12pt]{minimal}
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\begin{document}$$\hbox {K}^+$$\end{document}K+ conduction and channel gating. In this work, we construct a homology model of the \documentclass[12pt]{minimal}
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\begin{document}$${\hbox {Kcv}}_{\text{PBCV-1}}$$\end{document}KcvPBCV-1 open state, which we validate by studying the binding of known blockers and by monitoring ion conduction through the channel. Molecular dynamics simulations of this model reveal that the re-orientation of selectivity filter carbonyl groups coincides with the transport of potassium ions, suggesting a possible mechanism for fast gating. In addition, we show that the voltage sensitivity of this mechanism can originate from the relocation of potassium ions inside the selectivity filter. We also explore the interaction of \documentclass[12pt]{minimal}
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\begin{document}$${\hbox {Kcv}}_{\text{PBCV-1}}$$\end{document}KcvPBCV-1 with the surrounding bilayer and observe the binding of lipids in the area between two adjacent subunits. The model is available to the scientific community to further explore the structure/function relationship of Kcv channels.
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Affiliation(s)
- Alma E V Andersson
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, SE-171 21, Solna, Sweden
| | - Marina A Kasimova
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, SE-171 21, Solna, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, SE-171 21, Solna, Sweden.
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192
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Zhou Y, Chen C, Pan J, Deng X, Wang J. Epigallocatechin gallate can attenuate human alveolar epithelial cell injury induced by alpha-haemolysin. Microb Pathog 2018; 115:222-226. [DOI: 10.1016/j.micpath.2017.12.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/18/2017] [Accepted: 12/19/2017] [Indexed: 10/18/2022]
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193
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Stereospecific Interactions of Cholesterol in a Model Cell Membrane: Implications for the Membrane Dipole Potential. J Membr Biol 2018; 251:507-519. [DOI: 10.1007/s00232-018-0016-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/25/2018] [Indexed: 12/11/2022]
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194
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Simakov NA, Kurnikova MG. Membrane Position Dependency of the pK a and Conductivity of the Protein Ion Channel. J Membr Biol 2018; 251:393-404. [PMID: 29340712 DOI: 10.1007/s00232-018-0013-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/04/2018] [Indexed: 10/18/2022]
Abstract
The dependency of current-voltage characteristics of the α-hemolysin channel on the channel position within the membrane was studied using Poisson-Nernst-Planck theory of ion conductivity with soft repulsion between mobile ions and protein atoms (SP-PNP). The presence of the membrane environment also influences the protonation state of the residues at the boundary of the water-lipid interface. In this work, we predict that Asp and Lys residues at the protein rim change their protonation state upon penetration to the lipid environment. Free energies of protein insertion in the membrane for different penetration depths were estimated using the Poisson-Boltzmann/solvent-accessible surface area (PB/SASA) model. The results show that rectification and reversal potentials are very sensitive to the relative position of channel in the membrane, which in turn contributes to alternative protonation states of lipid-penetrating ionizable groups. The prediction of channel position based on the matching of calculated rectification with experimentally determined rectification is in good agreement with recent neutron reflection experiments. Based on the results, we conclude that α-hemolysin membrane position is determined by a combination of factors and not only by the pattern of the surface hydrophobicity as is typically assumed.
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Affiliation(s)
- Nikolay A Simakov
- Chemistry Department, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Maria G Kurnikova
- Chemistry Department, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA.
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195
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Cressiot B, Greive SJ, Si W, Pascoa TC, Mojtabavi M, Chechik M, Jenkins HT, Lu X, Zhang K, Aksimentiev A, Antson AA, Wanunu M. Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization. ACS NANO 2017; 11:11931-11945. [PMID: 29120602 PMCID: PMC5963890 DOI: 10.1021/acsnano.7b06980] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Nanopore-based sensors for nucleic acid sequencing and single-molecule detection typically employ pore-forming membrane proteins with hydrophobic external surfaces, suitable for insertion into a lipid bilayer. In contrast, hydrophilic pore-containing molecules, such as DNA origami, have been shown to require chemical modification to favor insertion into a lipid environment. In this work, we describe a strategy for inserting polar proteins with an inner pore into lipid membranes, focusing here on a circular 12-subunit assembly of the thermophage G20c portal protein. X-ray crystallography, electron microscopy, molecular dynamics, and thermal/chaotrope denaturation experiments all find the G20c portal protein to have a highly stable structure, favorable for nanopore sensing applications. Porphyrin conjugation to a cysteine mutant in the protein facilitates the protein's insertion into lipid bilayers, allowing us to probe ion transport through the pore. Finally, we probed the portal interior size and shape using a series of cyclodextrins of varying sizes, revealing asymmetric transport that possibly originates from the portal's DNA-ratchet function.
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Affiliation(s)
- Benjamin Cressiot
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Sandra J. Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Wei Si
- Department of Physics, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments and School of Mechanical Engineering, Southeast University, Nanjing 210096, China
| | - Tomas C. Pascoa
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Mehrnaz Mojtabavi
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Xueguang Lu
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Ke Zhang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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196
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Asandei A, Rossini AE, Chinappi M, Park Y, Luchian T. Protein Nanopore-Based Discrimination between Selected Neutral Amino Acids from Polypeptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:14451-14459. [PMID: 29178796 DOI: 10.1021/acs.langmuir.7b03163] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Nanopore probing of biological polymers has the potential to achieve single-molecule sequencing at low cost, high throughput, portability, and minimal sample preparation and apparatus. In this article, we explore the possibility of discrimination between neutral amino acid residues from the primary structure of 30 amino acids long, engineered peptides, through the analysis of single-molecule ionic current fluctuations accompanying their slowed-down translocation across the wild type α-hemolysin (α-HL) nanopore, and molecular dynamics simulations. We found that the transient presence inside the α-HL of alanine or tryptophan residues from the primary sequence of engineered peptides results in distinct features of the ionic current fluctuation pattern associated with the peptide reversibly blocking the nanopore. We propose that α-HL sensitivity to the molecular exclusion at the most constricted region mediates ionic current blockade events correlated with the volumes that are occluded by at least three alanine or tryptophan residues, and provides the specificity needed to discriminate between groups of neutral amino acids. Further, we find that the pattern of current fluctuations depends on the orientation of the threaded amino acid residues, suggestive of a conformational anisotropy of the ensemble of conformations of the peptide on the restricted nanopore region, related to its relative axial orientation inside the nanopore.
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Affiliation(s)
| | - Aldo E Rossini
- Department of Basic and Applied Science for Engineering, Sapienza University of Rome , Via A. Scarpa14, 00161 Rome, Italy
| | - Mauro Chinappi
- Department of Industrial Engineering, University of Rome Tor Vergata , Via del Politecnico 1, 00133 Rome, Italy
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia , Via Regina Elena 291, 00161 Rome, Italy
| | - Yoonkyung Park
- Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University , Gwangju, Korea
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197
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Experton J, Wu X, Martin CR. From Ion Current to Electroosmotic Flow Rectification in Asymmetric Nanopore Membranes. NANOMATERIALS (BASEL, SWITZERLAND) 2017; 7:E445. [PMID: 29240676 PMCID: PMC5746935 DOI: 10.3390/nano7120445] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/06/2017] [Accepted: 12/11/2017] [Indexed: 12/12/2022]
Abstract
Asymmetrically shaped nanopores have been shown to rectify the ionic current flowing through pores in a fashion similar to a p-n junction in a solid-state diode. Such asymmetric nanopores include conical pores in polymeric membranes and pyramidal pores in mica membranes. We review here both theoretical and experimental aspects of this ion current rectification phenomenon. A simple intuitive model for rectification, stemming from previously published more quantitative models, is discussed. We also review experimental results on controlling the extent and sign of rectification. It was shown that ion current rectification produces a related rectification of electroosmotic flow (EOF) through asymmetric pore membranes. We review results that show how to measure and modulate this EOF rectification phenomenon. Finally, EOF rectification led to the development of an electroosmotic pump that works under alternating current (AC), as opposed to the currently available direct current EOF pumps. Experimental results on AC EOF rectification are reviewed, and advantages of using AC to drive EOF are discussed.
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Affiliation(s)
- Juliette Experton
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA.
| | - Xiaojian Wu
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA.
| | - Charles R Martin
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA.
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198
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Tamburrino G, Llabrés S, Vickery ON, Pitt SJ, Zachariae U. Modulation of the Neisseria gonorrhoeae drug efflux conduit MtrE. Sci Rep 2017; 7:17091. [PMID: 29213101 PMCID: PMC5719041 DOI: 10.1038/s41598-017-16995-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 11/21/2017] [Indexed: 11/09/2022] Open
Abstract
Widespread antibiotic resistance, especially of Gram-negative bacteria, has become a severe concern for human health. Tripartite efflux pumps are one of the major contributors to resistance in Gram-negative pathogens, by efficiently expelling a broad spectrum of antibiotics from the organism. In Neisseria gonorrhoeae, one of the first bacteria for which pan-resistance has been reported, the most expressed efflux complex is MtrCDE. Here we present the electrophysiological characterisation of the outer membrane component MtrE and the membrane fusion protein MtrC, obtained by a combination of planar lipid bilayer recordings and in silico techniques. Our in vitro results show that MtrE can be regulated by periplasmic binding events and that the interaction between MtrE and MtrC is sufficient to stabilize this complex in an open state. In contrast to other efflux conduits, the open complex only displays a slight preference for cations. The maximum conductance we obtain in the in vitro recordings is comparable to that seen in our computational electrophysiology simulations conducted on the MtrE crystal structure, indicating that this state may reflect a physiologically relevant open conformation of MtrE. Our results suggest that the MtrC/E binding interface is an important modulator of MtrE function, which could potentially be targeted by new efflux inhibitors.
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Affiliation(s)
- Giulia Tamburrino
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Physics, School of Science and Engineering, University of Dundee, Dundee, DD1 4NH, UK
| | - Salomé Llabrés
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Physics, School of Science and Engineering, University of Dundee, Dundee, DD1 4NH, UK
| | - Owen N Vickery
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Physics, School of Science and Engineering, University of Dundee, Dundee, DD1 4NH, UK
| | - Samantha J Pitt
- School of Medicine, University of St Andrews, St Andrews, KY16 9TF, UK.
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
- Physics, School of Science and Engineering, University of Dundee, Dundee, DD1 4NH, UK.
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199
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Ma P, Cardenas AE, Chaudhari MI, Elber R, Rempe SB. The Impact of Protonation on Early Translocation of Anthrax Lethal Factor: Kinetics from Molecular Dynamics Simulations and Milestoning Theory. J Am Chem Soc 2017; 139:14837-14840. [PMID: 29019235 PMCID: PMC5656527 DOI: 10.1021/jacs.7b07419] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We report atomically detailed molecular dynamics simulations of the permeation of the lethal factor (LF) N-terminal segment through the anthrax channel. The N-terminal chain is unstructured and leads the permeation process for the LF protein. The simulations were conducted in explicit solvent with milestoning theory, making it possible to extract kinetic information from nanosecond to millisecond time scales. We illustrate that the initial event is strongly influenced by the protonation states of the permeating amino acids. While the N-terminal segment passes easily at high protonation state through the anthrax channel (and the ϕ clamp), the initial permeation represents a critical step, which can be irreversible and establishes a hook in the channel mouth.
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Affiliation(s)
- Piao Ma
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712
| | - Alfredo E. Cardenas
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX, 78712
| | - Mangesh I. Chaudhari
- Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, NM 87185
| | - Ron Elber
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX, 78712
| | - Susan B. Rempe
- Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, NM 87185
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200
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Desikan R, Maiti PK, Ayappa KG. Assessing the Structure and Stability of Transmembrane Oligomeric Intermediates of an α-Helical Toxin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:11496-11510. [PMID: 28930630 DOI: 10.1021/acs.langmuir.7b02277] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Protein membrane interactions play an important role in our understanding of diverse phenomena ranging from membrane-assisted protein aggregation to oligomerization and folding. Pore-forming toxins (PFTs) are the primary vehicle for infection by several strains of bacteria. These proteins which are expressed in a water-soluble form (monomers) bind to the target membrane and conformationally transform (protomers) and self-assemble to form a multimer transmembrane pore complex through a process of oligomerization. On the basis of the structure of the transmembrane domains, PFTs are broadly classified into β or α toxins. In contrast to β-PFTs, the paucity of available crystal structures coupled with the amphipathic nature of the transmembrane domains has hindered our understanding of α-PFT pore formation. In this article, we use molecular dynamics (MD) simulations to examine the process of pore formation of the bacterial α-PFT, cytolysin A from Escherichia coli (ClyA) in lipid bilayer membranes. Using atomistic MD simulations ranging from 50 to 500 ns, we show that transmembrane oligomeric intermediates or "arcs" form stable proteolipidic complexes consisting of protein arcs with toroidal lipids lining the free edges. By creating initial conditions where the lipids are contained within the arcs, we study the dynamics of spontaneous lipid evacuation and toroidal edge formation. This process occurs on the time scale of tens of nanoseconds, suggesting that once protomers oligomerize, transmembrane arcs are rapidly stabilized to form functional water channels capable of leakage. Using umbrella sampling with a coarse-grained molecular model, we obtain the free energy of insertion of a single protomer into the membrane. A single inserted protomer has a stabilization free energy of -52.9 ± 1.2 kJ/mol and forms a stable transmembrane water channel capable of leakage. Our simulations reveal that arcs are stable and viable intermediates that can occur during the pore-formation pathway for ClyA.
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Affiliation(s)
- Rajat Desikan
- Department of Chemical Engineering, ‡Centre for Condensed Matter Theory, Department of Physics, and §Centre for Biosystems Science and Engineering, Indian Institute of Science , Bengaluru, India 560012
| | - Prabal K Maiti
- Department of Chemical Engineering, ‡Centre for Condensed Matter Theory, Department of Physics, and §Centre for Biosystems Science and Engineering, Indian Institute of Science , Bengaluru, India 560012
| | - K Ganapathy Ayappa
- Department of Chemical Engineering, ‡Centre for Condensed Matter Theory, Department of Physics, and §Centre for Biosystems Science and Engineering, Indian Institute of Science , Bengaluru, India 560012
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