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Solov'yov AV, Verkhovtsev AV, Mason NJ, Amos RA, Bald I, Baldacchino G, Dromey B, Falk M, Fedor J, Gerhards L, Hausmann M, Hildenbrand G, Hrabovský M, Kadlec S, Kočišek J, Lépine F, Ming S, Nisbet A, Ricketts K, Sala L, Schlathölter T, Wheatley AEH, Solov'yov IA. Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment. Chem Rev 2024. [PMID: 38842266 DOI: 10.1021/acs.chemrev.3c00902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.
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Affiliation(s)
- Andrey V Solov'yov
- MBN Research Center, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | | | - Nigel J Mason
- School of Physics and Astronomy, University of Kent, Canterbury CT2 7NH, United Kingdom
| | - Richard A Amos
- Department of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K
| | - Ilko Bald
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Gérard Baldacchino
- Université Paris-Saclay, CEA, LIDYL, 91191 Gif-sur-Yvette, France
- CY Cergy Paris Université, CEA, LIDYL, 91191 Gif-sur-Yvette, France
| | - Brendan Dromey
- Centre for Light Matter Interactions, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
| | - Martin Falk
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Juraj Fedor
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Luca Gerhards
- Institute of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
- Faculty of Engineering, University of Applied Sciences Aschaffenburg, Würzburger Str. 45, 63743 Aschaffenburg, Germany
| | | | - Stanislav Kadlec
- Eaton European Innovation Center, Bořivojova 2380, 25263 Roztoky, Czech Republic
| | - Jaroslav Kočišek
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Franck Lépine
- Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France
| | - Siyi Ming
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Andrew Nisbet
- Department of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K
| | - Kate Ricketts
- Department of Targeted Intervention, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Leo Sala
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Thomas Schlathölter
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- University College Groningen, University of Groningen, Hoendiepskade 23/24, 9718 BG Groningen, The Netherlands
| | - Andrew E H Wheatley
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Ilia A Solov'yov
- Institute of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
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Acharya A, Jana K, Kleinekathöfer U. Antibiotic Charge Profile Determines the Extent of L3 Dynamics in OmpF: An Expedited Passage for Molecules with a Positive Charge. J Phys Chem B 2023; 127:10766-10777. [PMID: 38064341 DOI: 10.1021/acs.jpcb.3c04557] [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: 12/22/2023]
Abstract
Efficient permeation into Gram-negative bacterial cells is a much-desired property in the design of antibacterial agents. The goal is to arrive at one or more chemical modifications of molecules that improve their uptake into the cell while maintaining a good binding affinity to the intracellular target. Previously, we proposed a mechanistic rationale for the fast permeation of bulky antibiotics that involves induced conformational dynamics in the constriction loop L3 of the OmpF channel. This flexibility is caused by the perturbation of a hydrogen bond network stabilizing the L3 loop due to the strong interactions of the positively charged moiety on the antibiotic with the residues of the L3 loop. In the present work, we examine how differences in the charge profile of antibiotic molecules can affect the permeation process, in particular, the L3 dynamics. To this end, we have performed all-atom molecular dynamics simulations to study the permeation process of molecules with differences in the net charge through the Escherichia coli OmpF channel. The results from these simulations suggest that a positively charged moiety on the antibiotic is responsible for strong interactions with the negatively charged residues of the L3 loop, promoting conformational dynamics in the L3 loop. In contrast, antibiotics without a positively charged moiety are unable to initiate such a dynamic response in the L3 loop. This distinct behavior of the L3 loop in the presence of molecules with different charge characteristics provides a plausible mechanism whereby large molecules with an appropriate charge distribution can leverage an L3 dynamic-dependent pathway to permeate efficiently. The results are relevant to the structure-based design of molecules with improved uptake properties achieved through systematic chemical modifications that effectively engage the L3 loop.
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Affiliation(s)
- Abhishek Acharya
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
| | - Kalyanashis Jana
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
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Vaneev AN, Timoshenko RV, Gorelkin PV, Klyachko NL, Erofeev AS. Recent Advances in Nanopore Technology for Copper Detection and Their Potential Applications. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:nano13091573. [PMID: 37177118 PMCID: PMC10181076 DOI: 10.3390/nano13091573] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/04/2023] [Accepted: 05/06/2023] [Indexed: 05/15/2023]
Abstract
Recently, nanopore technology has emerged as a promising technique for the rapid, sensitive, and selective detection of various analytes. In particular, the use of nanopores for the detection of copper ions has attracted considerable attention due to their high sensitivity and selectivity. This review discusses the principles of nanopore technology and its advantages over conventional techniques for copper detection. It covers the different types of nanopores used for copper detection, including biological and synthetic nanopores, and the various mechanisms used to detect copper ions. Furthermore, this review provides an overview of the recent advancements in nanopore technology for copper detection, including the development of new nanopore materials, improvements in signal amplification, and the integration of nanopore technology with other analytical methods for enhanced detection sensitivity and accuracy. Finally, we summarize the extensive applications, current challenges, and future perspectives of using nanopore technology for copper detection, highlighting the need for further research in the field to optimize the performance and applicability of the technique.
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Affiliation(s)
- Alexander N Vaneev
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia
- Research Laboratory of Biophysics, National University of Science and Technology "MISIS", 119049 Moscow, Russia
| | - Roman V Timoshenko
- Research Laboratory of Biophysics, National University of Science and Technology "MISIS", 119049 Moscow, Russia
| | - Petr V Gorelkin
- Research Laboratory of Biophysics, National University of Science and Technology "MISIS", 119049 Moscow, Russia
| | - Natalia L Klyachko
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Alexander S Erofeev
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia
- Research Laboratory of Biophysics, National University of Science and Technology "MISIS", 119049 Moscow, Russia
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Acharya A, Ghai I, Piselli C, Prajapati JD, Benz R, Winterhalter M, Kleinekathöfer U. Conformational Dynamics of Loop L3 in OmpF: Implications toward Antibiotic Translocation and Voltage Gating. J Chem Inf Model 2023; 63:910-927. [PMID: 36525563 DOI: 10.1021/acs.jcim.2c01108] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In the present work, we delineate the molecular mechanism of a bulky antibiotic permeating through a bacterial channel and uncover the role of conformational dynamics of the constriction loop in this process. Using the temperature accelerated sliced sampling approach, we shed light onto the dynamics of the L3 loop, in particular the F118 to S125 segment, at the constriction regions of the OmpF porin. We complement the findings with single channel electrophysiology experiments and applied-field simulations, and we demonstrate the role of hydrogen-bond stabilization in the conformational dynamics of the L3 loop. A molecular mechanism of permeation is put forward wherein charged antibiotics perturb the network of stabilizing hydrogen-bond interactions and induce conformational changes in the L3 segment, thereby aiding the accommodation and permeation of bulky antibiotic molecules across the constriction region. We complement the findings with single channel electrophysiology experiments and demonstrate the importance of the hydrogen-bond stabilization in the conformational dynamics of the L3 loop. The generality of the present observations and experimental results regarding the L3 dynamics enables us to identify this L3 segment as the source of gating. We propose a mechanism of OmpF gating that is in agreement with previous experimental data that showed the noninfluence of cysteine double mutants that tethered the L3 tip to the barrel wall on the OmpF gating behavior. The presence of similar loop stabilization networks in porins of other clinically relevant pathogens suggests that the conformational dynamics of the constriction loop is possibly of general importance in the context of antibiotic permeation through porins.
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Affiliation(s)
- Abhishek Acharya
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen 28759, Germany
| | - Ishan Ghai
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
| | - Claudio Piselli
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
| | | | - Roland Benz
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen 28759, Germany
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