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Jiang W, Lin YC, Botello-Smith W, Contreras JE, Harris AL, Maragliano L, Luo YL. Free energy and kinetics of cAMP permeation through connexin26 via applied voltage and milestoning. Biophys J 2021; 120:2969-2983. [PMID: 34214529 DOI: 10.1016/j.bpj.2021.06.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/08/2021] [Accepted: 06/17/2021] [Indexed: 11/18/2022] Open
Abstract
The connexin family is a diverse group of highly regulated wide-pore channels permeable to biological signaling molecules. Despite the critical roles of connexins in mediating selective molecular signaling in health and disease, the basis of molecular permeation through these pores remains unclear. Here, we report the thermodynamics and kinetics of binding and transport of a second messenger, adenosine-3',5'-cyclophosphate (cAMP), through a connexin26 hemichannel (Cx26). First, inward and outward fluxes of cAMP molecules solvated in KCl solution were obtained from 4 μs of ± 200 mV simulations. These fluxes data yielded a single-channel permeability of cAMP and cAMP/K+ permeability ratio consistent with experimentally measured values. The results from voltage simulations were then compared with the potential of mean force (PMF) and the mean first passage times (MFPTs) of a single cAMP without voltage, obtained from a total of 16.5 μs of Voronoi-tessellated Markovian milestoning simulations. Both the voltage simulations and the milestoning simulations revealed two cAMP-binding sites, for which the binding constants KD and dissociation rates koff were computed from PMF and MFPTs. The protein dipole inside the pore produces an asymmetric PMF, reflected in unequal cAMP MFPTs in each direction once within the pore. The free energy profiles under opposite voltages were derived from the milestoning PMF and revealed the interplay between voltage and channel polarity on the total free energy. In addition, we show how these factors influence the cAMP dipole vector during permeation, and how cAMP affects the local and nonlocal pore diameter in a position-dependent manner.
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Affiliation(s)
- Wenjuan Jiang
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, California
| | - Yi-Chun Lin
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, California
| | - Wesley Botello-Smith
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, California
| | - Jorge E Contreras
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, California.
| | - Andrew L Harris
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey.
| | - Luca Maragliano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy; Center for Synaptic Neuroscience and Technology, Italian Institute of Technology, Genoa, Italy.
| | - Yun Lyna Luo
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, California.
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Koutsoukos S, Philippi F, Malaret F, Welton T. A review on machine learning algorithms for the ionic liquid chemical space. Chem Sci 2021; 12:6820-6843. [PMID: 34123314 PMCID: PMC8153233 DOI: 10.1039/d1sc01000j] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/28/2021] [Indexed: 01/05/2023] Open
Abstract
There are thousands of papers published every year investigating the properties and possible applications of ionic liquids. Industrial use of these exceptional fluids requires adequate understanding of their physical properties, in order to create the ionic liquid that will optimally suit the application. Computational property prediction arose from the urgent need to minimise the time and cost that would be required to experimentally test different combinations of ions. This review discusses the use of machine learning algorithms as property prediction tools for ionic liquids (either as standalone methods or in conjunction with molecular dynamics simulations), presents common problems of training datasets and proposes ways that could lead to more accurate and efficient models.
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Affiliation(s)
- Spyridon Koutsoukos
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London White City Campus London W12 0BZ UK
| | - Frederik Philippi
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London White City Campus London W12 0BZ UK
| | - Francisco Malaret
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK
| | - Tom Welton
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London White City Campus London W12 0BZ UK
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3
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Alberini G, Benfenati F, Maragliano L. Structural Mechanism of ω-Currents in a Mutated Kv7.2 Voltage Sensor Domain from Molecular Dynamics Simulations. J Chem Inf Model 2021; 61:1354-1367. [PMID: 33570938 PMCID: PMC8023575 DOI: 10.1021/acs.jcim.0c01407] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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Activation of voltage-gated
ion channels is regulated by conformational
changes of the voltage sensor domains (VSDs), four water- and ion-impermeable
modules peripheral to the central, permeable pore domain. Anomalous
currents, defined as ω-currents, have been recorded in response
to mutations of residues on the VSD S4 helix and associated with ion
fluxes through the VSDs. In humans, gene defects in the potassium
channel Kv7.2 result in a broad range of epileptic disorders, from
benign neonatal seizures to severe epileptic encephalopathies. Experimental
evidence suggests that the R207Q mutation in S4, associated with peripheral
nerve hyperexcitability, induces ω-currents at depolarized potentials,
but the fine structural details are still elusive. In this work, we
use atom-detailed molecular dynamics simulations and a refined model
structure of the Kv7.2 VSD in the active conformation in a membrane/water
environment to study the effect of R207Q and four additional mutations
of proven clinical importance. Our results demonstrate that the R207Q
mutant shows the most pronounced increase of hydration in the internal
VSD cavity, a feature favoring the occurrence of ω-currents.
Free energy and kinetics calculations of sodium permeation through
the native and mutated VSD indicate as more favorable the formation
of a cationic current in the latter. Overall, our simulations establish
a mechanistic linkage between genetic variations and their physiological
outcome, by providing a computational description that includes both
thermodynamic and kinetic features of ion permeation associated with
ω-currents.
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Affiliation(s)
- Giulio Alberini
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, 16132 Genova, Italy.,Department of Experimental Medicine, Università degli Studi di Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, 16132 Genova, Italy.,IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi, 10, 16132 Genova, Italy
| | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, 16132 Genova, Italy.,Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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4
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Wang X, Kerr R, Chen F, Goujon N, Pringle JM, Mecerreyes D, Forsyth M, Howlett PC. Toward High-Energy-Density Lithium Metal Batteries: Opportunities and Challenges for Solid Organic Electrolytes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1905219. [PMID: 31961989 DOI: 10.1002/adma.201905219] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/29/2019] [Indexed: 06/10/2023]
Abstract
With increasing demands for safe, high capacity energy storage to support personal electronics, newer devices such as unmanned aerial vehicles, as well as the commercialization of electric vehicles, current energy storage technologies are facing increased challenges. Although alternative batteries have been intensively investigated, lithium (Li) batteries are still recognized as the preferred energy storage solution for the consumer electronics markets and next generation automobiles. However, the commercialized Li batteries still have disadvantages, such as low capacities, potential safety issues, and unfavorable cycling life. Therefore, the design and development of electromaterials toward high-energy-density, long-life-span Li batteries with improved safety is a focus for researchers in the field of energy materials. Herein, recent advances in the development of novel organic electrolytes are summarized toward solid-state Li batteries with higher energy density and improved safety. On the basis of new insights into ionic conduction and design principles of organic-based solid-state electrolytes, specific strategies toward developing these electrolytes for Li metal anodes, high-energy-density cathode materials (e.g., high voltage materials), as well as the optimization of cathode formulations are outlined. Finally, prospects for next generation solid-state electrolytes are also proposed.
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Affiliation(s)
- Xiaoen Wang
- Institute for Frontier Materials (IFM), Deakin University, Geelong, VIC, 3217, Australia
| | - Robert Kerr
- Institute for Frontier Materials (IFM), Deakin University, Geelong, VIC, 3217, Australia
| | - Fangfang Chen
- Institute for Frontier Materials (IFM), Deakin University, Geelong, VIC, 3217, Australia
- ARC Centre of Excellence for Electromaterials Science (ACES), Deakin University, Burwood, VIC, 3125, Australia
| | - Nicolas Goujon
- Institute for Frontier Materials (IFM), Deakin University, Geelong, VIC, 3217, Australia
- POLYMAT University of the Basque Country UPV/EHU, Joxe Mari Korta Center, Avda. Tolosa 72, 20018, Donostia-San Sebastian, Spain
| | - Jennifer M Pringle
- Institute for Frontier Materials (IFM), Deakin University, Geelong, VIC, 3217, Australia
- ARC Centre of Excellence for Electromaterials Science (ACES), Deakin University, Burwood, VIC, 3125, Australia
| | - David Mecerreyes
- POLYMAT University of the Basque Country UPV/EHU, Joxe Mari Korta Center, Avda. Tolosa 72, 20018, Donostia-San Sebastian, Spain
| | - Maria Forsyth
- Institute for Frontier Materials (IFM), Deakin University, Geelong, VIC, 3217, Australia
- ARC Centre of Excellence for Electromaterials Science (ACES), Deakin University, Burwood, VIC, 3125, Australia
- POLYMAT University of the Basque Country UPV/EHU, Joxe Mari Korta Center, Avda. Tolosa 72, 20018, Donostia-San Sebastian, Spain
| | - Patrick C Howlett
- Institute for Frontier Materials (IFM), Deakin University, Geelong, VIC, 3217, Australia
- ARC Centre of Excellence for Electromaterials Science (ACES), Deakin University, Burwood, VIC, 3125, Australia
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Liu C, Wood GPF, Santiso EE. Modelling nucleation from solution with the string method in the osmotic ensemble. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1482016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Chengxiang Liu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | | | - Erik E. Santiso
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
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