1
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Nussberger S, Ghosh R, Wang S. New insights into the structure and dynamics of the TOM complex in mitochondria. Biochem Soc Trans 2024; 52:911-922. [PMID: 38629718 PMCID: PMC11088910 DOI: 10.1042/bst20231236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/21/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
To date, there is no general physical model of the mechanism by which unfolded polypeptide chains with different properties are imported into the mitochondria. At the molecular level, it is still unclear how transit polypeptides approach, are captured by the protein translocation machinery in the outer mitochondrial membrane, and how they subsequently cross the entropic barrier of a protein translocation pore to enter the intermembrane space. This deficiency has been due to the lack of detailed structural and dynamic information about the membrane pores. In this review, we focus on the recently determined sub-nanometer cryo-EM structures and our current knowledge of the dynamics of the mitochondrial two-pore outer membrane protein translocation machinery (TOM core complex), which provide a starting point for addressing the above questions. Of particular interest are recent discoveries showing that the TOM core complex can act as a mechanosensor, where the pores close as a result of interaction with membrane-proximal structures. We highlight unusual and new correlations between the structural elements of the TOM complexes and their dynamic behavior in the membrane environment.
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Affiliation(s)
- Stephan Nussberger
- Department of Biophysics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Robin Ghosh
- Department of Bioenergetics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Shuo Wang
- Department of Biophysics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
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2
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Sergeev AA, Naberezhnykh GA, Khomenko VA, Amosov AV, Nepomnyaschiy AV, Solov'eva TF, Chistyulin DK, Tutov MV, Kulchin YN, Novikova OD. In situ-Synthesized cadmium sulfide quantum dots in pore-forming protein and polysaccharide matrices for optical biosensing applications. Colloids Surf B Biointerfaces 2022; 217:112607. [PMID: 35671573 DOI: 10.1016/j.colsurfb.2022.112607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 05/12/2022] [Accepted: 05/27/2022] [Indexed: 10/18/2022]
Abstract
The main limitation for practical implementation of quantum dots-based sensors and biosensors is the possible contamination of sensing media with quantum dots (QDs) moved out from the sensor structure, being critical for living systems measurements. Numerous efforts have addressed the challenge of pre-synthesized QDs incorporation into porous matrix provide, on the one hand, proper fixation of quantum dots in its volume and preserving a free analyte transfer from the sensing media to them - on the other hand. Here, we propose an alternative insight into this problem. Instead of using preliminary synthesized particles for doping a matrix, we have in situ synthesized cadmium sulfide QDs in porous biopolymeric matrices, both in an aqueous solution and on a mica substrate. The proposed technique allows obtaining QDs in a matrix acting simultaneously as a ligand passivating surface defects and preventing QDs aggregation. The conjugates were used as a photoluminescence sensor for the metal ions and glutathione detection in an aqueous media. Different kinds of sensor responses have been found depending on the analyte nature. Zinc ions' presence initiates the intraband QDs emission increases due to the reduction of non-radiative processes. The presence of copper ions, in contrast, leads to a gradual photoluminescence decrease due to the formation of the non-luminescent copper-based alloy in the QDs structure. Finally, the presence of glutathione initiates a ligand exchange process followed by some QDs surface treatment enhancing defect-related photoluminescence. As a result, three different kinds of sensor responses for three analytes allow claiming development of a new selective QD-based sensor suitable for biomedical applications.
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Affiliation(s)
- A A Sergeev
- Institute of Automation and Control Processes, Far Eastern Branch of the Russian Academy of Sciences, 5, Radio street, Vladivostok 690041, Russia
| | - G A Naberezhnykh
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 159, prospect 100 Let Vladivostoku, Vladivostok 690022, Russia
| | - V A Khomenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 159, prospect 100 Let Vladivostoku, Vladivostok 690022, Russia
| | - A V Amosov
- Institute of Automation and Control Processes, Far Eastern Branch of the Russian Academy of Sciences, 5, Radio street, Vladivostok 690041, Russia
| | - A V Nepomnyaschiy
- Institute of Automation and Control Processes, Far Eastern Branch of the Russian Academy of Sciences, 5, Radio street, Vladivostok 690041, Russia
| | - T F Solov'eva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 159, prospect 100 Let Vladivostoku, Vladivostok 690022, Russia
| | - D K Chistyulin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 159, prospect 100 Let Vladivostoku, Vladivostok 690022, Russia
| | - M V Tutov
- Far Eastern Federal University, 10, Ajax Bay, Russky Island, Vladivostok 690922, Russia
| | - Yu N Kulchin
- Institute of Automation and Control Processes, Far Eastern Branch of the Russian Academy of Sciences, 5, Radio street, Vladivostok 690041, Russia
| | - O D Novikova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 159, prospect 100 Let Vladivostoku, Vladivostok 690022, Russia
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3
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Molecular Insights into Mitochondrial Protein Translocation and Human Disease. Genes (Basel) 2021; 12:genes12071031. [PMID: 34356047 PMCID: PMC8305315 DOI: 10.3390/genes12071031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/27/2021] [Accepted: 06/30/2021] [Indexed: 12/11/2022] Open
Abstract
In human mitochondria, mtDNA encodes for only 13 proteins, all components of the OXPHOS system. The rest of the mitochondrial components, which make up approximately 99% of its proteome, are encoded in the nuclear genome, synthesized in cytosolic ribosomes and imported into mitochondria. Different import machineries translocate mitochondrial precursors, depending on their nature and the final destination inside the organelle. The proper and coordinated function of these molecular pathways is critical for mitochondrial homeostasis. Here, we will review molecular details about these pathways, which components have been linked to human disease and future perspectives on the field to expand the genetic landscape of mitochondrial diseases.
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4
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Novikova OD, Naberezhnykh GA, Sergeev AA. Nanostructured Biosensors Based on Components of Bacterial Membranes. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921040187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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5
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Bausewein T, Naveed H, Liang J, Nussberger S. The structure of the TOM core complex in the mitochondrial outer membrane. Biol Chem 2021; 401:687-697. [PMID: 32142473 DOI: 10.1515/hsz-2020-0104] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 03/03/2020] [Indexed: 02/05/2023]
Abstract
In the past three decades, significant advances have been made in providing the biochemical background of TOM (translocase of the outer mitochondrial membrane)-mediated protein translocation into mitochondria. In the light of recent cryoelectron microscopy-derived structures of TOM isolated from Neurospora crassa and Saccharomyces cerevisiae, the interpretation of biochemical and biophysical studies of TOM-mediated protein transport into mitochondria now rests on a solid basis. In this review, we compare the subnanometer structure of N. crassa TOM core complex with that of yeast. Both structures reveal remarkably well-conserved symmetrical dimers of 10 membrane protein subunits. The structural data also validate predictions of weakly stable regions in the transmembrane β-barrel domains of the protein-conducting subunit Tom40, which signal the existence of β-strands located in interfaces of protein-protein interactions.
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Affiliation(s)
- Thomas Bausewein
- Max-Planck-Institute of Biophysics, Department of Structural Biology, Max-von-Laue-Str. 3, D-60438Frankfurt am Main, Germany
| | - Hammad Naveed
- National University of Computer and Emerging Sciences, Department of Computer Science, A. K. Brohi Road H-11/4, Islamabad 44000, Pakistan
| | - Jie Liang
- Richard and Loan Hill Department of Bioengineering, MC-063, University of Illinois, Chicago, IL 60607-7052, USA
| | - Stephan Nussberger
- University of Stuttgart, Institute of Biomaterials and Biomolecular Systems, Department of Biophysics, Pfaffenwaldring 57, D-70569Stuttgart, Germany
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6
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Restrepo-Pérez L, Wong CH, Maglia G, Dekker C, Joo C. Label-Free Detection of Post-translational Modifications with a Nanopore. NANO LETTERS 2019; 19:7957-7964. [PMID: 31602979 PMCID: PMC6856961 DOI: 10.1021/acs.nanolett.9b03134] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/10/2019] [Indexed: 05/21/2023]
Abstract
Post-translational modifications (PTMs) of proteins play key roles in cellular processes. Hence, PTM identification is crucial for elucidating the mechanism of complex cellular processes and disease. Here we present a method for PTM detection at the single-molecule level using FraC biological nanopores. We focus on two major PTMs, phosphorylation and glycosylation, that mutually compete for protein modification sites, an important regulatory process that has been implicated in the pathogenic pathways of many diseases. We show that phosphorylated and glycosylated peptides can be clearly differentiated from nonmodified peptides by differences in the relative current blockade and dwell time in nanopore translocations. Furthermore, we show that these PTM modifications can be mutually differentiated, demonstrating the identification of phosphorylation and glycosylation in a label-free manner. The results represent an important step for the single-molecule, label-free identification of proteoforms, which have tremendous potential for disease diagnosis and cell biology.
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Affiliation(s)
- Laura Restrepo-Pérez
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Chun Heung Wong
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Giovanni Maglia
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Cees Dekker
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
- E-mail:
| | - Chirlmin Joo
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
- E-mail:
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7
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Restrepo-Pérez L, Joo C, Dekker C. Paving the way to single-molecule protein sequencing. NATURE NANOTECHNOLOGY 2018; 13:786-796. [PMID: 30190617 DOI: 10.1038/s41565-018-0236-6] [Citation(s) in RCA: 219] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/16/2018] [Indexed: 05/22/2023]
Abstract
Proteins are major building blocks of life. The protein content of a cell and an organism provides key information for the understanding of biological processes and disease. Despite the importance of protein analysis, only a handful of techniques are available to determine protein sequences, and these methods face limitations, for example, requiring a sizable amount of sample. Single-molecule techniques would revolutionize proteomics research, providing ultimate sensitivity for the detection of low-abundance proteins and the realization of single-cell proteomics. In recent years, novel single-molecule protein sequencing schemes that use fluorescence, tunnelling currents and nanopores have been proposed. Here, we present a review of these approaches, together with the first experimental efforts towards their realization. We discuss their advantages and drawbacks, and present our perspective on the development of single-molecule protein sequencing techniques.
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Affiliation(s)
- Laura Restrepo-Pérez
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Chirlmin Joo
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
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8
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Robertson JWF, Reiner JE. The Utility of Nanopore Technology for Protein and Peptide Sensing. Proteomics 2018; 18:e1800026. [PMID: 29952121 PMCID: PMC10935609 DOI: 10.1002/pmic.201800026] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/13/2018] [Indexed: 04/29/2024]
Abstract
Resistive pulse nanopore sensing enables label-free single-molecule analysis of a wide range of analytes. An increasing number of studies have demonstrated the feasibility and usefulness of nanopore sensing for protein and peptide characterization. Nanopores offer the potential to study a variety of protein-related phenomena that includes unfolding kinetics, differences in unfolding pathways, protein structure stability, and free-energy profiles of DNA-protein and RNA-protein binding. In addition to providing a tool for fundamental protein characterization, nanopores have also been used as highly selective protein detectors in various solution mixtures and conditions. This review highlights these and other developments in the area of nanopore-based protein and peptide detection.
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Affiliation(s)
- Joseph W F Robertson
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA, 23284, USA
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9
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Identification of single amino acid differences in uniformly charged homopolymeric peptides with aerolysin nanopore. Nat Commun 2018; 9:966. [PMID: 29511176 PMCID: PMC5840376 DOI: 10.1038/s41467-018-03418-2] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/09/2018] [Indexed: 12/31/2022] Open
Abstract
There are still unmet needs in finding new technologies for biomedical diagnostic and industrial applications. A technology allowing the analysis of size and sequence of short peptide molecules of only few molecular copies is still challenging. The fast, low-cost and label-free single-molecule nanopore technology could be an alternative for addressing these critical issues. Here, we demonstrate that the wild-type aerolysin nanopore enables the size-discrimination of several short uniformly charged homopeptides, mixed in solution, with a single amino acid resolution. Our system is very sensitive, allowing detecting and characterizing a few dozens of peptide impurities in a high purity commercial peptide sample, while conventional analysis techniques fail to do so.
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10
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The vascular disrupting agent combretastatin A-4 phosphate causes prolonged elevation of proteins involved in heme flux and function in resistant tumor cells. Oncotarget 2017; 9:4090-4101. [PMID: 29423106 PMCID: PMC5790523 DOI: 10.18632/oncotarget.23734] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 12/15/2017] [Indexed: 01/24/2023] Open
Abstract
Vascular disrupting agents (VDAs) represent a promising class of anti-cancer drugs for solid tumor treatment. Here, we aim to better understand the mechanisms underlying tumor reccurrence and treatment resistance following the administration of a VDA, combretastatin A-4 phosphate (CA4P). Firstly, we used photoacoustic tomography to noninvasively map the effect of CA4P on blood oxygen levels throughout subcutaneous non-small cell lung cancer (NSCLC) tumors in mice. We found that the oxygenation of peripheral tumor vessels was significantly decreased at 1 and 3 hours post-CA4P treatment. The oxygenation of the tumor core reduced significantly at 1 and 3 hours, and reached anoxia after 24 hours. Secondly, we examined the effect of CA4P on the levels of proteins involved in heme flux and function, which are elevated in lung tumors. Using immunohistochemistry, we found that CA4P substantially enhanced the levels of enzymes involved in heme biosynthesis, uptake, and degradation, as well as oxygen-utilizing hemoproteins. Furthermore, measurements of markers of mitochondrial function suggest that CA4P did not diminish mitochondrial function in resistant tumor cells. These results suggest that elevated levels of heme flux and function contribute to tumor regrowth and treatment resistance post-VDA administration.
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11
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Denkert N, Schendzielorz AB, Barbot M, Versemann L, Richter F, Rehling P, Meinecke M. Cation selectivity of the presequence translocase channel Tim23 is crucial for efficient protein import. eLife 2017; 6. [PMID: 28857742 PMCID: PMC5578737 DOI: 10.7554/elife.28324] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/31/2017] [Indexed: 01/09/2023] Open
Abstract
Virtually all mitochondrial matrix proteins and a considerable number of inner membrane proteins carry a positively charged, N-terminal presequence and are imported by the TIM23 complex (presequence translocase) located in the inner mitochondrial membrane. The voltage-regulated Tim23 channel constitutes the actual protein-import pore wide enough to allow the passage of polypeptides with a secondary structure. In this study, we identify amino acids important for the cation selectivity of Tim23. Structure based mutants show that selectivity is provided by highly conserved, pore-lining amino acids. Mutations of these amino acid residues lead to reduced selectivity properties, reduced protein import capacity and they render the Tim23 channel insensitive to substrates. We thus show that the cation selectivity of the Tim23 channel is a key feature for substrate recognition and efficient protein import. The cells of animals, plants and other eukaryotic organisms contain compartments known as organelles that play many different roles. For example, compartments called mitochondria are responsible for supplying the chemical energy cells need to survive and grow. Two membranes surround each mitochondrion and energy is converted on the surface of the inner one. Mitochondria contain over 1,000 different proteins, most of which are produced in the main part of the cell and have to be transported into the mitochondria. A transport protein called Tim23 is part of a larger group or ‘complex’ of proteins that helps to import many other proteins into the mitochondria. This complex sits in the inner membrane, with the Tim23 protein forming a large, water-filled pore through its core that provides a route for proteins to pass through the membrane. Proteins are made of building blocks called amino acids. The proteins transported by the complex containing Tim23 all have a short chain of amino acids at one end known as an N-terminal presequence. However, it is not clear how the inside of the Tim23 channel identifies and transports this presequence to allow the right proteins to pass through the inner membrane. Denkert, Schendzielorz et al. studied the normal and mutant versions of a Tim23 channel from yeast to find out which parts of the protein are involved in detecting the N-terminal presequence after it enters the pore. The experiments show that there are several amino acids in Tim23 that play important roles in this process. Furthermore, mitochondria containing mutant Tim23 channels, that are less able to identify the N-terminal presequence, are impaired in their ability to import proteins. Tim23 proteins in humans and other organisms also contain most or all of the specific amino acids identified in this study, suggesting that the findings of Denkert, Schendzielorz et al. will also apply to other species. Furthermore, the experimental strategy used in this study could be adapted to investigate transport proteins in other cell compartments.
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Affiliation(s)
- Niels Denkert
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | | | - Mariam Barbot
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Lennart Versemann
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Frank Richter
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany.,Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Göttinger Zentrum für Molekulare Biowissenschaften, Göttingen, Germany
| | - Michael Meinecke
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany.,Göttinger Zentrum für Molekulare Biowissenschaften, Göttingen, Germany.,European Neuroscience Institute Göttingen, Göttingen, Germany
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12
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Dhanasekar NN, Aliouane S, Winterhalter M, Pagès JM, Bolla JM. Peptide translocation across MOMP, the major outer membrane channel from Campylobacter jejuni. Biochem Biophys Rep 2017; 11:79-83. [PMID: 28955771 PMCID: PMC5614690 DOI: 10.1016/j.bbrep.2017.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 04/12/2017] [Accepted: 06/22/2017] [Indexed: 11/17/2022] Open
Abstract
Here we report on translocation of short poly-arginines across the MOMP porin, the major outer membrane protein in the cell wall of Campylobacter jejuni. MOMP was purified to homogeneity from a pathogenic strain of C. jejuni. Its reconstitution in lipid membranes and measuring the ion-current revealed two main distinct populations of protein channels which we interpreted as mono and trimers. Addition of poly-arginines causes concentration and voltage dependent ion-current fluctuations. Increasing the transmembrane potential decreases the residence time of the peptide inside the channel indicating successful translocation. We conclude that poly-arginines can cross the outer membrane of Campylobacter through the MOMP channel. Translocation of short poly-arginines across the MOMP channel has been determined. Penta-arginine and Hepta-arginine translocate across the MOMP channel. Voltage dependent kinetics to distinguish binding from translocation.
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Affiliation(s)
| | | | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28719 Bremen, Germany
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13
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Bhamidimarri SP, Prajapati JD, van den Berg B, Winterhalter M, Kleinekathöfer U. Role of Electroosmosis in the Permeation of Neutral Molecules: CymA and Cyclodextrin as an Example. Biophys J 2017; 110:600-611. [PMID: 26840725 DOI: 10.1016/j.bpj.2015.12.027] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/23/2015] [Accepted: 12/28/2015] [Indexed: 11/25/2022] Open
Abstract
To quantify the flow of small uncharged molecules into and across nanopores, one often uses ion currents. The respective ion-current fluctuations caused by the presence of the analyte make it possible to draw some conclusions about the direction and magnitude of the analyte flow. However, often this flow appears to be asymmetric with respect to the applied voltage. As a possible reason for this asymmetry, we identified the electroosmotic flow (EOF), which is the water transport associated with ions driven by the external transmembrane voltage. As an example, we quantify the contribution of the EOF through a nanopore by investigating the permeation of α-cyclodextrin through CymA, a cyclodextrin-specific channel from Klebsiella oxytoca. To understand the results from electrophysiology on a molecular level, all-atom molecular dynamics simulations are used to detail the effect of the EOF on substrate entry to and exit from a CymA channel in which the N-terminus has been deleted. The combined experimental and computational results strongly suggest that one needs to account for the significant contribution of the EOF when analyzing the penetration of cyclodextrins through the CymA pore. This example study at the same time points to the more general finding that the EOF needs to be considered in translocation studies of neutral molecules and, at least in many cases, should be able to help in discriminating between translocation and binding events.
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Affiliation(s)
| | | | - Bert van den Berg
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - 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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14
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Bieligmeyer M, Artukovic F, Nussberger S, Hirth T, Schiestel T, Müller M. Reconstitution of the membrane protein OmpF into biomimetic block copolymer-phospholipid hybrid membranes. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:881-92. [PMID: 27547605 PMCID: PMC4979867 DOI: 10.3762/bjnano.7.80] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 05/18/2016] [Indexed: 06/06/2023]
Abstract
Structure and function of many transmembrane proteins are affected by their environment. In this respect, reconstitution of a membrane protein into a biomimetic polymer membrane can alter its function. To overcome this problem we used membranes formed by poly(1,4-isoprene-block-ethylene oxide) block copolymers blended with 1,2-diphytanoyl-sn-glycero-3-phosphocholine. By reconstituting the outer membrane protein OmpF from Escherichia coli into these membranes, we demonstrate functionality of this protein in biomimetic lipopolymer membranes, independent of the molecular weight of the block copolymers. At low voltages, the channel conductance of OmpF in 1 M KCl was around 2.3 nS. In line with these experiments, integration of OmpF was also revealed by impedance spectroscopy. Our results indicate that blending synthetic polymer membranes with phospholipids allows for the reconstitution of transmembrane proteins under preservation of protein function, independent of the membrane thickness.
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Affiliation(s)
- Matthias Bieligmeyer
- Institute of Interfacial Process Engineering and Plasma Technology, Department of Chemical Interfacial Process Engineering, University of Stuttgart, Nobelstraße 12, 70569 Stuttgart, Germany
| | - Franjo Artukovic
- Institute of Biomaterials and Biomolecular Systems, Department of Biophysics, University of Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart, Germany
| | - Stephan Nussberger
- Institute of Biomaterials and Biomolecular Systems, Department of Biophysics, University of Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart, Germany
| | - Thomas Hirth
- Institute of Interfacial Process Engineering and Plasma Technology, Department of Chemical Interfacial Process Engineering, University of Stuttgart, Nobelstraße 12, 70569 Stuttgart, Germany
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Department of Interfacial Engineering and Materials Science, Nobelstraße 12, 70569 Stuttgart, Germany
| | - Thomas Schiestel
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Department of Interfacial Engineering and Materials Science, Nobelstraße 12, 70569 Stuttgart, Germany
| | - Michaela Müller
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Department of Interfacial Engineering and Materials Science, Nobelstraße 12, 70569 Stuttgart, Germany
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15
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Cressiot B, Braselmann E, Oukhaled A, Elcock AH, Pelta J, Clark PL. Dynamics and Energy Contributions for Transport of Unfolded Pertactin through a Protein Nanopore. ACS NANO 2015; 9:9050-61. [PMID: 26302243 PMCID: PMC4835817 DOI: 10.1021/acsnano.5b03053] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To evaluate the physical parameters governing translocation of an unfolded protein across a lipid bilayer, we studied protein transport through aerolysin, a passive protein channel, at the single-molecule level. The protein model used was the passenger domain of pertactin, an autotransporter virulence protein. Transport of pertactin through the aerolysin nanopore was detected as transient partial current blockades as the unfolded protein partially occluded the aerolysin channel. We compared the dynamics of entry and transport for unfolded pertactin and a covalent end-to-end dimer of the same protein. For both the monomer and the dimer, the event frequency of current blockades increased exponentially with the applied voltage, while the duration of each event decreased exponentially as a function of the electrical potential. The blockade time was twice as long for the dimer as for the monomer. The calculated activation free energy includes a main enthalpic component that we attribute to electrostatic interactions between pertactin and the aerolysin nanopore (despite the low Debye length), plus an entropic component due to confinement of the unfolded chain within the narrow pore. Comparing our experimental results to previous studies and theory suggests that unfolded proteins cross the membrane by passing through the nanopore in a somewhat compact conformation according to the "blob" model of Daoud and de Gennes.
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Affiliation(s)
- Benjamin Cressiot
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Esther Braselmann
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | | | - Adrian H. Elcock
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
| | - Juan Pelta
- LAMBE UMR 8587 CNRS, University of Évry-Val-d'Essonne, Évry, France
| | - Patricia L. Clark
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556 USA
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16
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Kuszak AJ, Jacobs D, Gurnev PA, Shiota T, Louis JM, Lithgow T, Bezrukov SM, Rostovtseva TK, Buchanan SK. Evidence of Distinct Channel Conformations and Substrate Binding Affinities for the Mitochondrial Outer Membrane Protein Translocase Pore Tom40. J Biol Chem 2015; 290:26204-17. [PMID: 26336107 DOI: 10.1074/jbc.m115.642173] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Indexed: 12/14/2022] Open
Abstract
Nearly all mitochondrial proteins are coded by the nuclear genome and must be transported into mitochondria by the translocase of the outer membrane complex. Tom40 is the central subunit of the translocase complex and forms a pore in the mitochondrial outer membrane. To date, the mechanism it utilizes for protein transport remains unclear. Tom40 is predicted to comprise a membrane-spanning β-barrel domain with conserved α-helical domains at both the N and C termini. To investigate Tom40 function, including the role of the N- and C-terminal domains, recombinant forms of the Tom40 protein from the yeast Candida glabrata, and truncated constructs lacking the N- and/or C-terminal domains, were functionally characterized in planar lipid membranes. Our results demonstrate that each of these Tom40 constructs exhibits at least four distinct conductive levels and that full-length and truncated Tom40 constructs specifically interact with a presequence peptide in a concentration- and voltage-dependent manner. Therefore, neither the first 51 amino acids of the N terminus nor the last 13 amino acids of the C terminus are required for Tom40 channel formation or for the interaction with a presequence peptide. Unexpectedly, substrate binding affinity was dependent upon the Tom40 state corresponding to a particular conductive level. A model where two Tom40 pores act in concert as a dimeric protein complex best accounts for the observed biochemical and electrophysiological data. These results provide the first evidence for structurally distinct Tom40 conformations playing a role in substrate recognition and therefore in transport function.
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Affiliation(s)
| | - Daniel Jacobs
- From the Laboratories of Molecular Biology and Program in Physical Biology, NICHD, National Institutes of Health, Bethesda, Maryland 20892
| | - Philip A Gurnev
- Program in Physical Biology, NICHD, National Institutes of Health, Bethesda, Maryland 20892, the Physics Department, University of Massachusetts, Amherst, Massachusetts 01003, and
| | - Takuya Shiota
- the Department of Microbiology, Monash University, Melbourne 3800, Victoria, Australia
| | | | - Trevor Lithgow
- the Department of Microbiology, Monash University, Melbourne 3800, Victoria, Australia
| | - Sergey M Bezrukov
- Program in Physical Biology, NICHD, National Institutes of Health, Bethesda, Maryland 20892
| | - Tatiana K Rostovtseva
- Program in Physical Biology, NICHD, National Institutes of Health, Bethesda, Maryland 20892,
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17
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Mugler A, Tans SJ, Mashaghi A. Circuit topology of self-interacting chains: implications for folding and unfolding dynamics. Phys Chem Chem Phys 2015; 16:22537-44. [PMID: 25228051 DOI: 10.1039/c4cp03402c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the relationship between molecular structure and folding is a central problem in disciplines ranging from biology to polymer physics and DNA origami. Topology can be a powerful tool to address this question. For a folded linear chain, the arrangement of intra-chain contacts is a topological property because rearranging the contacts requires discontinuous deformations. Conversely, the topology is preserved when continuously stretching the chain while maintaining the contact arrangement. Here we investigate how the folding and unfolding of linear chains with binary contacts is guided by the topology of contact arrangements. We formalize the topology by describing the relations between any two contacts in the structure, which for a linear chain can either be in parallel, in series, or crossing each other. We show that even when other determinants of folding rate such as contact order and size are kept constant, this 'circuit' topology determines folding kinetics. In particular, we find that the folding rate increases with the fractions of parallel and crossed relations. Moreover, we show how circuit topology constrains the conformational phase space explored during folding and unfolding: the number of forbidden unfolding transitions is found to increase with the fraction of parallel relations and to decrease with the fraction of series relations. Finally, we find that circuit topology influences whether distinct intermediate states are present, with crossed contacts being the key factor. The approach presented here can be more generally applied to questions on molecular dynamics, evolutionary biology, molecular engineering, and single-molecule biophysics.
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Affiliation(s)
- Andrew Mugler
- Department of Physics, Purdue University, 525 Northwestern Avenue, West Lafayette, IN 47907, USA
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18
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19
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Singh PR, Bajaj H, Benz R, Winterhalter M, Mahendran KR. Transport across the outer membrane porin of mycolic acid containing actinomycetales: Nocardia farcinica. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:654-61. [PMID: 25462168 DOI: 10.1016/j.bbamem.2014.11.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 11/11/2014] [Accepted: 11/17/2014] [Indexed: 12/11/2022]
Abstract
The role of the outer-membrane channel from a mycolic acid containing Gram-positive bacteria Nocardia farcinica, which forms a hydrophilic pathway across the cell wall, was characterized. Single channel electrophysiology measurements and liposome swelling assays revealed the permeation of hydrophilic solutes including sugars, amino acids and antibiotics. The cation selective N. farcinica channel exhibited strong interaction with the positively charged antibiotics; amikacin and kanamycin, and surprisingly also with the negatively charged ertapenem. Voltage dependent kinetics of amikacin and kanamycin interactions were studied to distinguish binding from translocation. Moreover, the importance of charged residues inside the channel was investigated using mutational studies that revealed rate limiting interactions during the permeation.
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Affiliation(s)
- Pratik Raj Singh
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany.
| | - Harsha Bajaj
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Roland Benz
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Mathias Winterhalter
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Kozhinjampara R Mahendran
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany.
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20
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Muthukumar M. Macromolecular mechanisms of protein translocation. Protein Pept Lett 2014; 21:209-16. [PMID: 24370256 PMCID: PMC5956915 DOI: 10.2174/09298665113209990079] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 11/10/2013] [Accepted: 11/21/2013] [Indexed: 11/22/2022]
Abstract
When macromolecules such as proteins are forced to translocate through a narrow pore, their conformational entropy is reduced, resulting in a free energy barrier. This free energy barrier is additionally modulated by protein-pore interactions. Furthermore, the driving force of the translocation such as the electrochemical potential gradient and electroosmotic flow navigates the transport of the protein through the free energy landscape. Depending on the specifics of the protein-pore system and the driving force, the details of the translocation process and their statistical properties such as the average translocation time can vary significantly. Nevertheless, there are a few fundamental physical concepts that underly the ubiquitous phenomenon of polymer translocation, which are reviewed here.
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Affiliation(s)
- M Muthukumar
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA.
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21
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Movileanu L. Watching single proteins using engineered nanopores. Protein Pept Lett 2014; 21:235-46. [PMID: 24370252 PMCID: PMC3924890 DOI: 10.2174/09298665113209990078] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 11/03/2012] [Accepted: 11/10/2012] [Indexed: 12/22/2022]
Abstract
Recent studies in the area of single-molecule detection of proteins with nanopores show a great promise in fundamental science, bionanotechnology and proteomics. In this mini-review, I discuss a comprehensive array of examinations of protein detection and characterization using protein and solid-state nanopores. These investigations demonstrate the power of the single-molecule nanopore measurements to reveal a broad range of functional, structural, biochemical and biophysical features of proteins, such as their backbone flexibility, enzymatic activity, binding affinity as well as their concentration, size and folding state. Engineered nanopores in organic materials and in inorganic membranes coupled with surface modification and protein engineering might provide a new generation of sensing devices for molecular biomedical diagnostics.
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Affiliation(s)
- Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA.
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22
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23
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A theoretical study on entropy-driven polymer translocation through a finite-sized nanochannel. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.02.059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Mahendran KR, Lamichhane U, Romero-Ruiz M, Nussberger S, Winterhalter M. Polypeptide Translocation Through the Mitochondrial TOM Channel: Temperature-Dependent Rates at the Single-Molecule Level. J Phys Chem Lett 2013; 4:78-82. [PMID: 26291215 DOI: 10.1021/jz301790h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The TOM protein complex facilitates the transfer of nearly all mitochondrial preproteins across outer mitochondrial membranes. Here we characterized the effect of temperature on facilitated translocation of a mitochondrial presequence peptide pF1β. Ion current fluctuations analysis through single TOM channels revealed thermodynamic and kinetic parameters of substrate binding and allowed determining the energy profile of peptide translocation. The activation energy for the on-rate and off-rate of the presequence peptide into the TOM complex was symmetric with respect to the electric field and estimated to be about 15 and 22 kT per peptide. These values are above that expected for free diffusion of ions in water (6 kT) and reflect the stronger interaction in the channel. Both values are in the range for typical enzyme kinetics and suggest one process without involving large conformational changes within the channel protein.
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Affiliation(s)
- Kozhinjampara R Mahendran
- †School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Usha Lamichhane
- †School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Mercedes Romero-Ruiz
- ‡Biophysics Department, Institute of Biology, University of Stuttgart, D-70550 Stuttgart, Germany
| | - Stephan Nussberger
- ‡Biophysics Department, Institute of Biology, University of Stuttgart, D-70550 Stuttgart, Germany
| | - Mathias Winterhalter
- †School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
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25
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Lamichhane U, Islam T, Prasad S, Weingart H, Mahendran KR, Winterhalter M. Peptide translocation through the mesoscopic channel: binding kinetics at the single molecule level. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2012; 42:363-9. [DOI: 10.1007/s00249-012-0885-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 11/30/2012] [Accepted: 12/13/2012] [Indexed: 12/21/2022]
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26
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Oukhaled A, Bacri L, Pastoriza-Gallego M, Betton JM, Pelta J. Sensing proteins through nanopores: fundamental to applications. ACS Chem Biol 2012; 7:1935-49. [PMID: 23145870 DOI: 10.1021/cb300449t] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Proteins subjected to an electric field and forced to pass through a nanopore induce blockades of ionic current that depend on the protein and nanopore characteristics and interactions between them. Recent advances in the analysis of these blockades have highlighted a variety of phenomena that can be used to study protein translocation and protein folding, to probe single-molecule catalytic reactions in order to obtain kinetic and thermodynamic information, and to detect protein-antibody complexes, proteins with DNA and RNA aptamers, and protein-pore interactions. Nanopore design is now well controlled, allowing the development of future biotechnologies and medicine applications.
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Affiliation(s)
- Abdelghani Oukhaled
- CNRS-UMR 8587,
LAMBE, Université de Cergy-Pontoise et Université d’Evry, France
| | - Laurent Bacri
- CNRS-UMR 8587,
LAMBE, Université de Cergy-Pontoise et Université d’Evry, France
| | | | - Jean-Michel Betton
- Unité de Microbiologie
Structurale, CNRS-URA 3528, Institut Pasteur, France
| | - Juan Pelta
- CNRS-UMR 8587,
LAMBE, Université de Cergy-Pontoise et Université d’Evry, France
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27
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Gurnev PA, Queralt-Martin M, Aguilella VM, Rostovtseva TK, Bezrukov SM. Probing tubulin-blocked state of VDAC by varying membrane surface charge. Biophys J 2012; 102:2070-6. [PMID: 22824270 DOI: 10.1016/j.bpj.2012.03.058] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 03/12/2012] [Accepted: 03/20/2012] [Indexed: 11/25/2022] Open
Abstract
Reversible blockage of the voltage-dependent anion channel (VDAC) of the mitochondrial outer membrane by dimeric tubulin is being recognized as a potent regulator of mitochondrial respiration. The tubulin-blocked state of VDAC is impermeant for ATP but only partially closed for small ions. This residual conductance allows studying the nature of the tubulin-blocked state in single-channel reconstitution experiments. Here we probe this state by changing lipid bilayer charge from positive to neutral to negative. We find that voltage sensitivity of the tubulin-VDAC blockage practically does not depend on the lipid charge and salt concentration with the effective gating charge staying within the range of 10-14 elementary charges. At physiologically relevant low salt concentrations, the conductance of the tubulin-blocked state is decreased by positive and increased by negative charge of the lipids, whereas the conductance of the open channel is much less sensitive to this parameter. Such a behavior supports the model in which tubulin's negatively charged tail enters the VDAC pore, inverting its anionic selectivity to cationic and increasing proximity of ion pathways to the nearest lipid charges as compared with the open state of the channel.
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Affiliation(s)
- Philip A Gurnev
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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28
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Cressiot B, Oukhaled A, Patriarche G, Pastoriza-Gallego M, Betton JM, Auvray L, Muthukumar M, Bacri L, Pelta J. Protein transport through a narrow solid-state nanopore at high voltage: experiments and theory. ACS NANO 2012; 6:6236-6243. [PMID: 22670559 DOI: 10.1021/nn301672g] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We report experimentally the transport of an unfolded protein through a narrow solid-state nanopore of 3 nm diameter as a function of applied voltage. The random coil polypeptide chain is larger than the nanopore. The event frequency dependency of current blockades from 200 to 750 mV follows a van't Hoff-Arrhenius law due to the confinement of the unfolded chain. The protein is an extended conformation inside the pore at high voltage. We observe that the protein dwell time decreases exponentially at medium voltage and is inversely proportional to voltage for higher values. This is consistent with the translocation mechanism where the protein is confined in the pore, creating an entropic barrier, followed by electrophoretic transport. We compare these results to our previous work with a larger pore of 20 nm diameter. Our data suggest that electro-osmotic flow and protein adsorption on the narrowest nanopore wall are minimized. We discuss the experimental data obtained as compared with recent theory for the polyelectrolyte translocation process. This theory reproduces clearly the experimental crossover between the entropic barrier regime with medium voltage and the electrophoretic regime with higher voltage.
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29
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Harsman A, Niemann M, Pusnik M, Schmidt O, Burmann BM, Hiller S, Meisinger C, Schneider A, Wagner R. Bacterial origin of a mitochondrial outer membrane protein translocase: new perspectives from comparative single channel electrophysiology. J Biol Chem 2012; 287:31437-45. [PMID: 22778261 DOI: 10.1074/jbc.m112.392118] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mitochondria are of bacterial ancestry and have to import most of their proteins from the cytosol. This process is mediated by Tom40, an essential protein that forms the protein-translocating pore in the outer mitochondrial membrane. Tom40 is conserved in virtually all eukaryotes, but its evolutionary origin is unclear because bacterial orthologues have not been identified so far. Recently, it was shown that the parasitic protozoon Trypanosoma brucei lacks a conventional Tom40 and instead employs the archaic translocase of the outer mitochondrial membrane (ATOM), a protein that shows similarities to both eukaryotic Tom40 and bacterial protein translocases of the Omp85 family. Here we present electrophysiological single channel data showing that ATOM forms a hydrophilic pore of large conductance and high open probability. Moreover, ATOM channels exhibit a preference for the passage of cationic molecules consistent with the idea that it may translocate unfolded proteins targeted by positively charged N-terminal presequences. This is further supported by the fact that the addition of a presequence peptide induces transient pore closure. An in-depth comparison of these single channel properties with those of other protein translocases reveals that ATOM closely resembles bacterial-type protein export channels rather than eukaryotic Tom40. Our results support the idea that ATOM represents an evolutionary intermediate between a bacterial Omp85-like protein export machinery and the conventional Tom40 that is found in mitochondria of other eukaryotes.
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Affiliation(s)
- Anke Harsman
- Biophysik, Fachbereich Biologie/Chemie, Universität Osnabrück, 49076 Osnabrück, Germany
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30
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Feld GK, Brown MJ, Krantz BA. Ratcheting up protein translocation with anthrax toxin. Protein Sci 2012; 21:606-24. [PMID: 22374876 DOI: 10.1002/pro.2052] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 02/21/2012] [Accepted: 02/22/2012] [Indexed: 01/09/2023]
Abstract
Energy-consuming nanomachines catalyze the directed movement of biopolymers in the cell. They are found both dissolved in the aqueous cytosol as well as embedded in lipid bilayers. Inquiries into the molecular mechanism of nanomachine-catalyzed biopolymer transport have revealed that these machines are equipped with molecular parts, including adjustable clamps, levers, and adaptors, which interact favorably with substrate polypeptides. Biological nanomachines that catalyze protein transport, known as translocases, often require that their substrate proteins unfold before translocation. An unstructured protein chain is likely entropically challenging to bind, push, or pull in a directional manner, especially in a way that produces an unfolding force. A number of ingenious solutions to this problem are now evident in the anthrax toxin system, a model used to study protein translocation. Here we highlight molecular ratchets and current research on anthrax toxin translocation. A picture is emerging of proton-gradient-driven anthrax toxin translocation, and its associated ratchet mechanism likely applies broadly to other systems. We suggest a cyclical thermodynamic order-to-disorder mechanism (akin to a heat-engine cycle) is central to underlying protein translocation: peptide substrates nonspecifically bind to molecular clamps, which possess adjustable affinities; polypeptide substrates compress into helical structures; these clamps undergo proton-gated switching; and the substrate subsequently expands regaining its unfolded state conformational entropy upon translocation.
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Affiliation(s)
- Geoffrey K Feld
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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