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Neginskaya MA, Strubbe JO, Amodeo GF, West BA, Yakar S, Bazil JN, Pavlov EV. The very low number of calcium-induced permeability transition pores in the single mitochondrion. J Gen Physiol 2020; 152:e202012631. [PMID: 32810269 PMCID: PMC7537349 DOI: 10.1085/jgp.202012631] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/22/2020] [Accepted: 07/24/2020] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial permeability transition (PT) is a phenomenon of stress-induced increase in nonspecific permeability of the mitochondrial inner membrane that leads to disruption of oxidative phosphorylation and cell death. Quantitative measurement of the membrane permeability increase during PT is critically important for understanding the PT's impact on mitochondrial function. The elementary unit of PT is a PT pore (PTP), a single channel presumably formed by either ATP synthase or adenine nucleotide translocator (ANT). It is not known how many channels are open in a single mitochondrion during PT, which makes it difficult to quantitatively estimate the overall degree of membrane permeability. Here, we used wide-field microscopy to record mitochondrial swelling and quantitatively measure rates of single-mitochondrion volume increase during PT-induced high-amplitude swelling. PT was quantified by calculating the rates of water flux responsible for measured volume changes. The total water flux through the mitochondrial membrane of a single mitochondrion during PT was in the range of (2.5 ± 0.4) × 10-17 kg/s for swelling in 2 mM Ca2+ and (1.1 ± 0.2) × 10-17 kg/s for swelling in 200 µM Ca2+. Under these experimental conditions, a single PTP channel with ionic conductance of 1.5 nS could allow passage of water at the rate of 0.65 × 10-17 kg/s. Thus, we estimate the integral ionic conductance of the whole mitochondrion during PT to be 5.9 ± 0.9 nS for 2 mM concentration of Ca2+ and 2.6 ± 0.4 nS for 200 µM of Ca2+. The number of PTPs per mitochondrion ranged from one to nine. Due to the uncertainties in PTP structure and model parameters, PTP count results may be slightly underestimated. However, taking into account that each mitochondrion has ∼15,000 copies of ATP synthases and ANTs, our data imply that PTP activation is a rare event that occurs only in a small subpopulation of these proteins.
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Affiliation(s)
- Maria A. Neginskaya
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY
| | - Jasiel O. Strubbe
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI
- Department of Physiology, Michigan State University, East Lansing, MI
| | - Giuseppe F. Amodeo
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY
| | - Benjamin A. West
- Department of Physiology, Michigan State University, East Lansing, MI
| | - Shoshana Yakar
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY
| | - Jason N. Bazil
- Department of Physiology, Michigan State University, East Lansing, MI
| | - Evgeny V. Pavlov
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY
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Bernabei M, Pérez-Soto R, Gómez García I, Haranczyk M. Towards stable porous crystalline phases of molecular belts. CrystEngComm 2017. [DOI: 10.1039/c7ce01679d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A chemical modification of a molecular belt (M1) renders the molecule (M2) into a stable supramolecular nanotube porous crystal.
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Affiliation(s)
| | | | - Ismael Gómez García
- IMDEA Materials Institute
- 28096 Getafe
- Spain
- Departamento de Materiales
- Universidad Carlos III de Madrid
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Glukhova OE, Prytkova TR, Savostyanov GV. Simulation of High Density Lipoprotein Behavior on a Few Layer Graphene Undergoing Non-Uniform Mechanical Load. J Phys Chem B 2016; 120:3593-600. [DOI: 10.1021/acs.jpcb.5b12648] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Olga E. Glukhova
- Saratov State University, Astrakhanskaya 83, 410012, Saratov, Russia
| | - Tatiana R. Prytkova
- Schmid College of Science & Technology, Chapman University, Orange, California 92866, United States
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Thomas M, Enciso M, Hilder TA. Insertion Mechanism and Stability of Boron Nitride Nanotubes in Lipid Bilayers. J Phys Chem B 2015; 119:4929-36. [DOI: 10.1021/acs.jpcb.5b00102] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Michael Thomas
- Computational
Biophysics Group, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
- Molecular Modelling Group, Faculty of Science,
Technology and Engineering, School of Molecular Sciences, Department
of Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
- Life Science Computation Centre, Victorian Life Sciences Computation Initiative, Carlton, VIC 3010, Australia
| | - Marta Enciso
- Molecular Modelling Group, Faculty of Science,
Technology and Engineering, School of Molecular Sciences, Department
of Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Tamsyn A. Hilder
- Computational
Biophysics Group, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
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Thomas M, Corry B, Hilder TA. What have we learnt about the mechanisms of rapid water transport, ion rejection and selectivity in nanopores from molecular simulation? SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:1453-1465. [PMID: 24851242 DOI: 10.1002/smll.201302968] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Nanopores have demonstrated an extraordinary ability to allow water molecules to pass through their interiors at rates far exceeding expectations based on continuum theory. Moreover, simulation studies suggest that particular nanoscale pores have the potential to discriminate between water and salts as well as to distinguish between a range of different ion types. Some of the unusual features of transport in these nanopores have been elucidated with molecular dynamics simulation, specifically the spontaneous filling and rapid transport of water, the rejection of ions and the selection between ions. The main focus of this review, however, is the physical mechanisms which act to produce such remarkable behaviour at this scale, drawing on the many studies that have been conducted in the last decade. Since molecular dynamics simulations allow the motion of individual atoms to be followed over time, they have the potential to provide fundamental insight into the reasons why transport in nanoscale pores differs from expectations based on macroscopic theory. Gaining an understanding of the mechanisms of transport in these tiny pores should guide future experiments in this area aimed at developing novel technologies and improving existing membrane separation techniques.
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He Z, Zhou J, Lu X, Corry B. Bioinspired graphene nanopores with voltage-tunable ion selectivity for Na(+) and K(+). ACS NANO 2013; 7:10148-10157. [PMID: 24151957 DOI: 10.1021/nn4043628] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Biological protein channels have many remarkable properties such as gating, high permeability, and selectivity, which have motivated researchers to mimic their functions for practical applications. Herein, using molecular dynamics simulations, we design bioinspired nanopores in graphene sheets that can discriminate between Na(+) and K(+), two ions with very similar properties. The simulation results show that, under transmembrane voltage bias, a nanopore containing four carbonyl groups to mimic the selectivity filter of the KcsA K(+) channel preferentially conducts K(+) over Na(+). A nanopore functionalized by four negatively charged carboxylate groups to mimic the selectivity filter of the NavAb Na(+) channel selectively binds Na(+) but transports K(+) over Na(+). Surprisingly, the ion selectivity of the smaller diameter pore containing three carboxylate groups can be tuned by changing the magnitude of the applied voltage bias. Under lower voltage bias, it transports ions in a single-file manner and exhibits Na(+) selectivity, dictated by the knock-on ion conduction and selective blockage by Na(+). Under higher voltage bias, the nanopore is K(+)-selective, as the blockage by Na(+) is destabilized and the stronger affinity for carboxylate groups slows the passage of Na(+) compared with K(+). The computational design of biomimetic ion-selective nanopores helps to understand the mechanisms of selectivity in biological ion channels and may also lead to a wide range of potential applications such as sensitive ion sensors, nanofiltration membranes for Na(+)/K(+) separation, and voltage-tunable nanofluidic devices.
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Affiliation(s)
- Zhongjin He
- School of Chemistry and Chemical Engineering, South China University of Technology , Guangzhou, Guangdong 510640, China
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A prospective overview of the essential requirements in molecular modeling for nanomedicine design. Future Med Chem 2013; 5:929-46. [PMID: 23682569 DOI: 10.4155/fmc.13.67] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Nanotechnology has presented many new challenges and opportunities in the area of nanomedicine design. The issues related to nanoconjugation, nanosystem-mediated targeted drug delivery, transitional stability of nanovehicles, the integrity of drug transport, drug-delivery mechanisms and chemical structural design require a pre-estimated and determined course of assumptive actions with property and characteristic estimations for optimal nanomedicine design. Molecular modeling in nanomedicine encompasses these pre-estimations and predictions of pertinent design data via interactive computographic software. Recently, an increasing amount of research has been reported where specialized software is being developed and employed in an attempt to bridge the gap between drug discovery, materials science and biology. This review provides an assimilative and concise incursion into the current and future strategies of molecular-modeling applications in nanomedicine design and aims to describe the utilization of molecular models and theoretical-chemistry computographic techniques for expansive nanomedicine design and development.
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Krott LB, Bordin JR. Distinct dynamical and structural properties of a core-softened fluid when confined between fluctuating and fixed walls. J Chem Phys 2013; 139:154502. [DOI: 10.1063/1.4824860] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Bordin JR, Diehl A, Barbosa MC. Relation Between Flow Enhancement Factor and Structure for Core-Softened Fluids Inside Nanotubes. J Phys Chem B 2013; 117:7047-56. [DOI: 10.1021/jp402141f] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- José Rafael Bordin
- Programa de Pós-Graduação em Física,
Instituto de Física, Universidade Federal do Rio Grande do Sul, Caixa Postal 15051, CEP 91501-970, Porto
Alegre, RS, Brazil
- Institut für Computerphysik, Universität Stuttgart, Almandring 3, 70569 Stuttgart, Germany
| | - Alexandre Diehl
- Departamento de Física, Instituto de Física
e Matemática, Universidade Federal de Pelotas, Caixa Postal 354, CEP 96010-900, Pelotas, RS, Brazil
| | - Marcia C. Barbosa
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Caixa Postal 15051, CEP
91501-970, Porto Alegre, RS, Brazil
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Müller EA. Purification of water through nanoporous carbon membranes: a molecular simulation viewpoint. Curr Opin Chem Eng 2013. [DOI: 10.1016/j.coche.2013.02.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Hayashida Y, Kinoshita T, Motomura T. Interfacing neurons through the patch membrane pierced with single-walled carbon nanotubes. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2013; 2013:4502-4505. [PMID: 24110734 DOI: 10.1109/embc.2013.6610547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The usability of single-walled carbon nanotubes (CNTs) as electrically conductive channels across the cell membrane was examined at the submicroscopic level. By using the patch-clamp technique, we found the surface-modified single-walled CNTs dispersed in the micropipette solution can provide an electrical access to the intracellular space across the patch of cell membrane in dissociated mammalian neurons, thereby enabling us to measure the membrane excitabilities in the 'pierced-patch' whole-cell mode.
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Zhao K, Wu H. Size Effects of Pore Density and Solute Size on Water Osmosis through Nanoporous Membrane. J Phys Chem B 2012; 116:13459-66. [DOI: 10.1021/jp3076595] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kuiwen Zhao
- School of Mechanical Engineering, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai,
200240, China
| | - Huiying Wu
- School of Mechanical Engineering, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai,
200240, China
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Bordin JR, de Oliveira AB, Diehl A, Barbosa MC. Diffusion enhancement in core-softened fluid confined in nanotubes. J Chem Phys 2012; 137:084504. [DOI: 10.1063/1.4746748] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Bordin JR, Diehl A, Barbosa MC, Levin Y. Ion fluxes through nanopores and transmembrane channels. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:031914. [PMID: 22587130 DOI: 10.1103/physreve.85.031914] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 02/08/2012] [Indexed: 05/31/2023]
Abstract
We introduce an implicit solvent Molecular Dynamics approach for calculating ionic fluxes through narrow nanopores and transmembrane channels. The method relies on a dual-control-volume grand-canonical molecular dynamics (DCV-GCMD) simulation and the analytical solution for the electrostatic potential inside a cylindrical nanopore recently obtained by Levin [Europhys. Lett. 76, 163 (2006)]. The theory is used to calculate the ionic fluxes through an artificial transmembrane channel which mimics the antibacterial gramicidin A channel. Both current-voltage and current-concentration relations are calculated under various experimental conditions. We show that our results are comparable to the characteristics associated to the gramicidin A pore, especially the existence of two binding sites inside the pore and the observed saturation in the current-concentration profiles.
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Affiliation(s)
- J R Bordin
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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