Sensing of protein molecules through nanopores: a molecular dynamics study

Kannam, Sridhar Kumar; Kim, Sung‐Cheol; Rogers, Priscilla; Gunn, Natalie; Wagner, John; Harrer, Stefan; Downton, Matthew T.

doi:10.1088/0957-4484/25/15/155502

Cited by 27 publications

(22 citation statements)

References 30 publications

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“…This was predicted through molecular dynamics simulations recently wherein one, two, and three proteins were placed inside the pore and the current drop was shown to be nonadditive. 53 Since no changes in structure were modeled in the above study, the decreasing ΔI could be due to varying protein positions within the pore or a manipulation of ion flow due to the introduction of charges on the surface of the pore.…”

Section: Resultsmentioning

confidence: 99%

Nonequilibrium Capture Rates Induce Protein Accumulation and Enhanced Adsorption to Solid-State Nanopores

Freedman

Haq

Fletcher³

et al. 2014

ACS Nano

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Single molecule capturing of analytes using an electrically biased nanopore is the fundamental mechanism in which nearly all nanopore experiments are conducted. With pore dimensions being on the order of a single molecule, the spatial zone of sensing only contains approximately a zeptoliter of volume. As a result, nanopores offer high precision sensing within the pore but provide little to no information about the analytes outside the pore. In this study, we use capture frequency and rate balance theory to predict and study the accumulation of proteins at the entrance to the pore. Protein accumulation is found to have positive attributes such as capture rate enhancement over time but can additionally lead to negative effects such as long-term blockages typically attributed to protein adsorption on the surface of the pore. Working with the folded and unfolded states of the protein domain PDZ2 from SAP97, we show that applying short (e.g., 3-25 s in duration) positive voltage pulses, rather than a constant voltage, can prevent long-term current blockades (i.e., adsorption events). By showing that the concentration of proteins around the pore can be controlled in real time using modified voltage protocols, new experiments can be explored which study the role of concentration on single molecular kinetics including protein aggregation, folding, and protein binding.

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Section: Resultsmentioning

confidence: 99%

Nonequilibrium Capture Rates Induce Protein Accumulation and Enhanced Adsorption to Solid-State Nanopores

Freedman

Haq

Fletcher³

et al. 2014

ACS Nano

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“…(63) Similarly, a recent theoretical study modeled the effects of a nanopore's electric field on streptavidin and found potential changes in streptavidin's secondary structure under certain pulling conditions at 2 V through a 10-nm diameter hour-glass-shaped nanopore in 1 M KCl. (64) The sequence of residues composing monovalent streptavidin contribute a total charge of -12.2e at neutral pH, but the net charge does not give the full picture. The non-uniform nature of the charge distribution in proteins renders them highly susceptible to electrophoretic effects: negatively charged portions of the protein are pulled in the opposite direction from positive portions, resulting in stretching (60) or rupture in the case of sufficiently high voltages.…”

Section: Monovalent Streptavidinmentioning

confidence: 99%

Mapping shifts in nanopore signal to changes in protein and protein-DNA conformation

Carlsen

Tabard‐Cossa

2020

Preprint

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Solid-state nanopores have been used extensively in biomolecular studies involving DNA and proteins. However, the interpretation of signals generated by the translocation of proteins or protein-DNA complexes remains challenging. Here, we investigate the behavior of monovalent streptavidin and the complex it forms with short biotinylated DNA over a range of nanopore sizes, salts and voltages. We describe a simple geometric model that is broadly applicable and employ it to explain observed variations in conductance blockage and dwell time with experimental conditions. The general approach developed here underscores the value of nanopore-based protein analysis and represents progress toward the interpretation of complex translocation signals. STATEMENT OF SIGNIFICANCENanopore sensing allows investigation of biomolecular structure in aqueous solution, including electricfield-induced changes in protein conformation. This nanopore-based study probes the tetramer-dimer transition of streptavidin, observing the effects of increasing voltage with varying salt type and concentration. Binding of biotinylated DNA to streptavidin boosts the complex's structural integrity, while complicating signal analysis. We describe a broadly applicable geometric approach that maps stepwise changes in the nanopore signal to real-time conformational transitions. These results represent important progress toward accurate interpretation of nanopore signals generated by macromolecular complexes.

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“…Resistive pulse sensing can be used to investigate a broad variety of molecular biological systems with single-particle, single nucleotide and even single-binding site resolution. It is explicitly powerful to perform next-generation nanopore-based DNA-sequencing [10][11][12][13][14][15][16] and to investigate target-ligand interactions in the pre-clinical compound-to-hit, hit-to-lead, and lead optimization stages of the pharma pipeline [17][18][19][20][21][22] . Figure 1.…”

Section: Novel Sensors For Precision Medicine Applicationsmentioning

confidence: 99%

Front Matter: Volume 9517

Sánchez‐Rojas¹,

Brama²

2015

SPIE Proceedings

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The papers included in this volume were part of the technical conference cited on the cover and title page. Papers were selected and subject to review by the editors and conference program committee. Some conference presentations may not be available for publication. The papers published in these proceedings reflect the work and thoughts of the authors and are published herein as submitted. The publisher is not responsible for the validity of the information or for any outcomes resulting from reliance thereon.Please use the following format to cite material from this book:Publication of record for individual papers is online in the SPIE Digital Library. SPIEDigitalLibrary.orgPaper Numbering: Proceedings of SPIE follow an e-First publication model, with papers published first online and then in print. Papers are published as they are submitted and meet publication criteria. A unique citation identifier (CID) number is assigned to each article at the time of the first publication. Utilization of CIDs allows articles to be fully citable as soon as they are published online, and connects the same identifier to all online, print, and electronic versions of the publication. SPIE uses a six-digit CID article numbering system in which:The first four digits correspond to the SPIE volume number. The last two digits indicate publication order within the volume using a Base 36 numbering system employing both numerals and letters. These two-number sets start with 00, 01, 02, 03, 04, 05, 06, 07, 08, 09, 0A, 0B … 0Z, followed by 10-1Z, 20-2Z, etc.The CID Number appears on each page of the manuscript. The complete citation is used on the first page, and an abbreviated version on subsequent pages. Proc. of SPIE Vol. 9517 951701-2 Downloaded From: http://proceedings.spiedigitallibrary.org/ on 07/14/2015 Terms of Use: http://spiedl.org/terms

show abstract

Sensing of protein molecules through nanopores: a molecular dynamics study

Cited by 27 publications

References 30 publications

Nonequilibrium Capture Rates Induce Protein Accumulation and Enhanced Adsorption to Solid-State Nanopores

Nonequilibrium Capture Rates Induce Protein Accumulation and Enhanced Adsorption to Solid-State Nanopores

Mapping shifts in nanopore signal to changes in protein and protein-DNA conformation

Front Matter: Volume 9517

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