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Punia B, Chaudhury S. Macromolecular Crowding Facilitates ssDNA Capture within Biological Nanopores: Role of Size Variation and Solution Heterogeneity. J Phys Chem B 2024; 128:1876-1883. [PMID: 38355410 DOI: 10.1021/acs.jpcb.3c08350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Genetic sequencing is a vital process that requires the transport of charged nucleic acids through transmembrane nanopores. Single-molecule studies show that macromolecular bulk crowding facilitates the capture of these polymers, leading to a high throughput of nanopore sensors. Motivated by these observations, a minimal discrete-state stochastic framework was developed to describe the role of poly(ethylene glycol) (PEG) crowders in varying concentrations in the transport of ssDNA through α-hemolysin nanopores. This theory suggested that the cooperative partitioning of polycationic PEGs controls the capture of ssDNA due to underlying electrostatic interactions. Herein, we investigate the impact of the size variation of PEGs on the capture event. Even though larger crowders attract ssDNA strongly to enhance its capture, our results show that considerable cooperative partitioning of PEGs is also required to achieve high interevent frequency. The exact analytical results are supported by existing single-molecule studies. Since real cellular conditions are heterogeneous, its influence on the ssDNA capture rate is studied by introducing a binary mixture of crowders. Our results indicate that the "polymer-pushing-polymer" concept possibly affects the capture rate depending on the mixture composition. These new findings provide valuable insights into the microscopic mechanism of the capture process, which eventually allows for accurate genome sequencing in crowded solutions.
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Affiliation(s)
- Bhawakshi Punia
- 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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Meirow M, Luijten E. Coarse-Grained Modeling of Polymer Cleavage within a Porous Catalytic Support. ACS Macro Lett 2023; 12:189-194. [PMID: 36693211 DOI: 10.1021/acsmacrolett.2c00682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The chemical upcycling of plastic waste to valuable liquid products requires catalytic cleavage architectures that afford control over the resulting product distributions. Recently, a catalyst was synthesized in which polymer chains are cleaved at the bottoms of pores to yield a narrow distribution of alkane products. An attractive feature of this architecture is the ability to modulate the product distribution by tuning physical parameters like the diameter of the pore. Understanding how such parameters affect product distributions is an important requirement of further synthetic improvements. We demonstrate that the pore diameter controls the products of the cleavage reaction via two distinct mechanisms. Our coarse-grained, particle-based simulations yield insight into the interplay of chain cleavage and pore residence times and show that the pore size can bias which bonds along a chain are cleaved.
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Affiliation(s)
- Max Meirow
- Department of Chemistry, Northwestern University, Evanston, Illinois60208, United States
| | - Erik Luijten
- Department of Chemistry, Northwestern University, Evanston, Illinois60208, United States.,Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois60208, United States.,Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois60208, United States.,Department of Physics and Astronomy, Northwestern University, Evanston, Illinois60208, United States
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Liu W, Nestorovich EM. Probing Protein Nanopores with Poly(ethylene glycol)s. Proteomics 2022; 22:e2100055. [PMID: 35030301 DOI: 10.1002/pmic.202100055] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/16/2021] [Accepted: 01/10/2022] [Indexed: 11/08/2022]
Abstract
Neutral water-soluble poly(ethylene glycol)s (PEGs) have been extensively explored in protein nanopore research for the past several decades. The principal use of PEGs is to investigate the membrane protein ion channel physical characteristics and transport properties. In addition, protein nanopores are used to study polymer-protein interactions and polymer physicochemical properties. In this review, we focus on the biophysical studies on probing protein ion channels with PEGs, specifically on nanopore sizing by PEG partitioning. We discuss the fluctuation analysis of ion channel currents in response to the PEGs moving within their confined geometries. The advantages, limitations, and recent developments of the approach are also addressed. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Wenxing Liu
- Department of Biology, The Catholic University of America, 620 Michigan Ave, Washington, DC, 20064, USA
| | - Ekaterina M Nestorovich
- Department of Biology, The Catholic University of America, 620 Michigan Ave, Washington, DC, 20064, USA
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Larimi MG, Mayse LA, Movileanu L. Interactions of a Polypeptide with a Protein Nanopore Under Crowding Conditions. ACS NANO 2019; 13:4469-4477. [PMID: 30925041 PMCID: PMC6482057 DOI: 10.1021/acsnano.9b00008] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Molecular crowding, a ubiquitous feature of the cellular environment, has significant implications in the kinetics and equilibrium of biopolymer interactions. In this study, a single charged polypeptide is exposed to competing forces that drive it into a transmembrane protein pore versus forces that pull it outside. Using single-molecule electrophysiology, we provide compelling experimental evidence that the kinetic details of the polypeptide-pore interactions are substantially affected by high concentrations of less-penetrating polyethylene glycols (PEGs). At a polymer concentration above a critical value, the presence of these neutral macromolecular crowders increases the rate constant of association but decreases the rate constant of dissociation, resulting in a stronger polypeptide-pore interaction. Moreover, a larger-molecular weight PEG exhibits a lower rate constant of association but a higher rate constant of dissociation than those values corresponding to a smaller-molecular weight PEG. These outcomes are in accord with a lower diffusion constant of the polypeptide and higher depletion-attraction forces between the polypeptide and transmembrane protein pore under crowding and confinement conditions.
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Affiliation(s)
- Motahareh Ghahari Larimi
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Lauren Ashley Mayse
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, USA
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Bouhid de Aguiar I, Schroën K, Meireles M, Bouchoux A. Compressive resistance of granular-scale microgels: From loose to dense packing. Colloids Surf A Physicochem Eng Asp 2018. [DOI: 10.1016/j.colsurfa.2018.05.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Gurnev PA, Stanley CB, Aksoyoglu MA, Hong K, Parsegian VA, Bezrukov SM. Poly(ethylene glycol)s in Semidilute Regime: Radius of Gyration in the Bulk and Partitioning into a Nanopore. Macromolecules 2017; 50:2477-2483. [PMID: 29033467 DOI: 10.1021/acs.macromol.6b02571] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Using two approaches, small-angle neutron scattering (SANS) from bulk solutions and nanopore conductance-fluctuation analysis, we studied structural and dynamic features of poly(ethylene glycol) (PEG) water/salt solutions in the dilute and semidilute regimes. SANS measurements on PEG 3400 at the zero-average contrast yielded the single chain radius of gyration (Rg) over 1-30 wt %. We observed a small but statistically reliable decrease in Rg with increasing PEG concentration: at 30 wt % the chain contracts by a factor of 0.94. Analyzing conductance fluctuations of the α-hemolysin nanopore in the mixtures of PEG 200 with PEG 3400, we demonstrated that polymer partitioning into the nanopore is mostly due to PEG 200. Specifically, for a 1:1 wt/wt mixture the smaller polymer dominates to the extent that only about 1/25 of the nanopore volume is taken by the larger polymer. These findings advance our conceptual and quantitative understanding of nanopore polymer partitioning; they also support the main assumptions of the recent "polymers-pushing-polymers" model.
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Affiliation(s)
- Philip A Gurnev
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Christopher B Stanley
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - M Alphan Aksoyoglu
- Department of Physics, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Kunlun Hong
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - V Adrian Parsegian
- Department of Physics, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Sergey M Bezrukov
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
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Size-dependent forced PEG partitioning into channels: VDAC, OmpC, and α-hemolysin. Proc Natl Acad Sci U S A 2016; 113:9003-8. [PMID: 27466408 DOI: 10.1073/pnas.1602716113] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nonideal polymer mixtures of PEGs of different molecular weights partition differently into nanosize protein channels. Here, we assess the validity of the recently proposed theoretical approach of forced partitioning for three structurally different β-barrel channels: voltage-dependent anion channel from outer mitochondrial membrane VDAC, bacterial porin OmpC (outer membrane protein C), and bacterial channel-forming toxin α-hemolysin. Our interpretation is based on the idea that relatively less-penetrating polymers push the more easily penetrating ones into nanosize channels in excess of their bath concentration. Comparison of the theory with experiments is excellent for VDAC. Polymer partitioning data for the other two channels are consistent with theory if additional assumptions regarding the energy penalty of pore penetration are included. The obtained results demonstrate that the general concept of "polymers pushing polymers" is helpful in understanding and quantification of concrete examples of size-dependent forced partitioning of polymers into protein nanopores.
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Maggs AC, Podgornik R. General theory of asymmetric steric interactions in electrostatic double layers. SOFT MATTER 2016; 12:1219-1229. [PMID: 26584630 DOI: 10.1039/c5sm01757b] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We study the mean-field Poisson-Boltzmann equation in the context of dense ionic liquids where steric effects become important. We generalise lattice gas theory by introducing a Flory-Huggins entropy for ions of differing volumes and then compare the effective free energy density to other existing lattice gas approximations, not based on the Flory-Huggins Ansatz. Within the methodology presented we also invoke more realistic equations of state, such as the Carnahan-Starling approximation, that are not based on the lattice gas approximation and lead to thermodynamic functions and properties that differ strongly from the lattice gas case. We solve the Carnahan-Starling model in the high density limit, and demonstrate a slow, power-law convergence at high potentials. We elucidate how equivalent convex free energy functions can be constructed that describe steric effects in a manner which is more convenient for numerical minimisation.
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Affiliation(s)
- A C Maggs
- Laboratoire PCT, Gulliver CNRS-ESPCI UMR 7083, 10 rue Vauquelin, 75231 Paris Cedex 05, France
| | - R Podgornik
- Department of Theoretical Physics, J. Stefan Institute and Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
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