Literature DB >> 28630164

Single-molecule nanopore enzymology.

Kherim Willems1,2, Veerle Van Meervelt1,3, Carsten Wloka3, Giovanni Maglia4.   

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'.
© 2017 The Author(s).

Entities:  

Keywords:  nanopore enzymology; protein trapping; review; single-molecule

Mesh:

Substances:

Year:  2017        PMID: 28630164      PMCID: PMC5483527          DOI: 10.1098/rstb.2016.0230

Source DB:  PubMed          Journal:  Philos Trans R Soc Lond B Biol Sci        ISSN: 0962-8436            Impact factor:   6.237


  109 in total

1.  Ion-beam sculpting at nanometre length scales.

Authors:  J Li; D Stein; C McMullan; D Branton; M J Aziz; J A Golovchenko
Journal:  Nature       Date:  2001-07-12       Impact factor: 49.962

2.  Can non-mechanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation.

Authors:  R B Best; B Li; A Steward; V Daggett; J Clarke
Journal:  Biophys J       Date:  2001-10       Impact factor: 4.033

3.  Single-molecule covalent chemistry with spatially separated reactants.

Authors:  Tudor Luchian; Seong-Ho Shin; Hagan Bayley
Journal:  Angew Chem Int Ed Engl       Date:  2003-08-18       Impact factor: 15.336

4.  Identification of single nucleotides in MoS2 nanopores.

Authors:  Jiandong Feng; Ke Liu; Roman D Bulushev; Sergey Khlybov; Dumitru Dumcenco; Andras Kis; Aleksandra Radenovic
Journal:  Nat Nanotechnol       Date:  2015-09-21       Impact factor: 39.213

5.  Imaging alpha-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map.

Authors:  Aleksij Aksimentiev; Klaus Schulten
Journal:  Biophys J       Date:  2005-03-11       Impact factor: 4.033

6.  Single-molecule analysis of DNA-protein complexes using nanopores.

Authors:  Breton Hornblower; Amy Coombs; Richard D Whitaker; Anatoly Kolomeisky; Stephen J Picone; Amit Meller; Mark Akeson
Journal:  Nat Methods       Date:  2007-03-04       Impact factor: 28.547

7.  Polymer capture by electro-osmotic flow of oppositely charged nanopores.

Authors:  C T A Wong; M Muthukumar
Journal:  J Chem Phys       Date:  2007-04-28       Impact factor: 3.488

8.  Unfoldase-mediated protein translocation through an α-hemolysin nanopore.

Authors:  Jeff Nivala; Douglas B Marks; Mark Akeson
Journal:  Nat Biotechnol       Date:  2013-02-03       Impact factor: 54.908

9.  Modulation of DNA Polymerase Noncovalent Kinetic Transitions by Divalent Cations.

Authors:  Joseph M Dahl; Kate R Lieberman; Hongyun Wang
Journal:  J Biol Chem       Date:  2016-01-21       Impact factor: 5.157

10.  Mapping the position of DNA polymerase-bound DNA templates in a nanopore at 5 A resolution.

Authors:  Brett Gyarfas; Felix Olasagasti; Seico Benner; Daniel Garalde; Kate R Lieberman; Mark Akeson
Journal:  ACS Nano       Date:  2009-06-23       Impact factor: 15.881

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  12 in total

1.  Membrane pores: from structure and assembly, to medicine and technology.

Authors:  Robert J C Gilbert; Hagan Bayley; Gregor Anderluh
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2017-08-05       Impact factor: 6.237

2.  Note: Diffusion-limited annihilation in cavities.

Authors:  Leonardo Dagdug; Alexander M Berezhkovskii; Vladimir Yu Zitserman
Journal:  J Chem Phys       Date:  2018-06-28       Impact factor: 3.488

3.  Exploring lipid-dependent conformations of membrane-bound α-synuclein with the VDAC nanopore.

Authors:  David P Hoogerheide; Tatiana K Rostovtseva; Sergey M Bezrukov
Journal:  Biochim Biophys Acta Biomembr       Date:  2021-05-07       Impact factor: 4.019

4.  Electro-Osmotic Vortices Promote the Capture of Folded Proteins by PlyAB Nanopores.

Authors:  Gang Huang; Kherim Willems; Mart Bartelds; Pol van Dorpe; Misha Soskine; Giovanni Maglia
Journal:  Nano Lett       Date:  2020-04-13       Impact factor: 11.189

5.  Thermostable virus portal proteins as reprogrammable adapters for solid-state nanopore sensors.

Authors:  Benjamin Cressiot; Sandra J Greive; Mehrnaz Mojtabavi; Alfred A Antson; Meni Wanunu
Journal:  Nat Commun       Date:  2018-11-07       Impact factor: 14.919

6.  Engineering and Modeling the Electrophoretic Trapping of a Single Protein Inside a Nanopore.

Authors:  Kherim Willems; Dino Ruić; Annemie Biesemans; Nicole Stéphanie Galenkamp; Pol Van Dorpe; Giovanni Maglia
Journal:  ACS Nano       Date:  2019-08-20       Impact factor: 15.881

7.  A Nanopore Phosphorylation Sensor for Single Oligonucleotides and Peptides.

Authors:  Yi-Lun Ying; Jie Yang; Fu-Na Meng; Shuang Li; Meng-Ying Li; Yi-Tao Long
Journal:  Research (Wash D C)       Date:  2019-11-04

8.  Autonomous and Active Transport Operated by an Entropic DNA Piston.

Authors:  Mariam Bayoumi; Stefanos K Nomidis; Kherim Willems; Enrico Carlon; Giovanni Maglia
Journal:  Nano Lett       Date:  2020-12-19       Impact factor: 11.189

9.  Laser-based temperature control to study the roles of entropy and enthalpy in polymer-nanopore interactions.

Authors:  Christopher E Angevine; Joseph W F Robertson; Amala Dass; Joseph E Reiner
Journal:  Sci Adv       Date:  2021-04-21       Impact factor: 14.136

10.  Real-Time Conformational Changes and Controlled Orientation of Native Proteins Inside a Protein Nanoreactor.

Authors:  Veerle Van Meervelt; Misha Soskine; Shubham Singh; Gea K Schuurman-Wolters; Hein J Wijma; Bert Poolman; Giovanni Maglia
Journal:  J Am Chem Soc       Date:  2017-12-13       Impact factor: 15.419

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