1
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Müller WA, Sarkis JR, Marczak LDF, Muniz AR. Computational analysis of the simultaneous application of ultrasound and electric fields in a lipid bilayer. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184364. [PMID: 38901662 DOI: 10.1016/j.bbamem.2024.184364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 06/07/2024] [Accepted: 06/13/2024] [Indexed: 06/22/2024]
Abstract
The combined application of electric fields and ultrasonic waves has shown promise in controlling cell membrane permeability, potentially resulting in synergistic effects that can be explored in the biotechnology industry. However, further clarification on how these processes interact is still needed. The objective of the present study was to investigate the atomic-scale effects of these processes on a DPPC lipid bilayer using molecular dynamics simulations. For higher electric fields, capable of independently forming pores, the application of an ultrasonic wave in the absence of cavitation yielded no additional effects on pore formation. However, for lower electric fields, the reduction in bilayer thickness induced by the shock wave catalyzed the electroporation process, effectively shortening the mean path that water molecules must traverse to form pores. When cavitation was considered, synergistic effects were evident only if the wave alone was able to generate pores through the formation of a water nanojet. In these cases, sonoporation acted as a mean to focus the electroporation effects on the initial pore formed by the nanojet. This study contributes to a better understanding of the synergy between electric fields and ultrasonic waves and to an optimal selection of processing parameters in practical applications of these processes.
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Affiliation(s)
- Wagner Augusto Müller
- Universidade Federal do Rio Grande do Sul (UFRGS), Department of Chemical Engineering, Porto Alegre, RS, Brazil
| | - Júlia Ribeiro Sarkis
- Universidade Federal do Rio Grande do Sul (UFRGS), Department of Chemical Engineering, Porto Alegre, RS, Brazil
| | | | - André Rodrigues Muniz
- Universidade Federal do Rio Grande do Sul (UFRGS), Department of Chemical Engineering, Porto Alegre, RS, Brazil.
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2
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Electroporation, electrochemotherapy and electro-assisted drug delivery in cancer. A state-of-the-art review. Biophys Chem 2022; 286:106819. [DOI: 10.1016/j.bpc.2022.106819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/06/2022] [Accepted: 04/12/2022] [Indexed: 01/08/2023]
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3
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Rems L, Tang X, Zhao F, Pérez-Conesa S, Testa I, Delemotte L. Identification of electroporation sites in the complex lipid organization of the plasma membrane. eLife 2022; 11:e74773. [PMID: 35195069 PMCID: PMC8912918 DOI: 10.7554/elife.74773] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
The plasma membrane of a biological cell is a complex assembly of lipids and membrane proteins, which tightly regulate transmembrane transport. When a cell is exposed to strong electric field, the membrane integrity becomes transiently disrupted by formation of transmembrane pores. This phenomenon termed electroporation is already utilized in many rapidly developing applications in medicine including gene therapy, cancer treatment, and treatment of cardiac arrhythmias. However, the molecular mechanisms of electroporation are not yet sufficiently well understood; in particular, it is unclear where exactly pores form in the complex organization of the plasma membrane. In this study, we combine coarse-grained molecular dynamics simulations, machine learning methods, and Bayesian survival analysis to identify how formation of pores depends on the local lipid organization. We show that pores do not form homogeneously across the membrane, but colocalize with domains that have specific features, the most important being high density of polyunsaturated lipids. We further show that knowing the lipid organization is sufficient to reliably predict poration sites with machine learning. Additionally, by analysing poration kinetics with Bayesian survival analysis we show that poration does not depend solely on local lipid arrangement, but also on membrane mechanical properties and the polarity of the electric field. Finally, we discuss how the combination of atomistic and coarse-grained molecular dynamics simulations, machine learning methods, and Bayesian survival analysis can guide the design of future experiments and help us to develop an accurate description of plasma membrane electroporation on the whole-cell level. Achieving this will allow us to shift the optimization of electroporation applications from blind trial-and-error approaches to mechanistic-driven design.
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Affiliation(s)
- Lea Rems
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
- University of Ljubljana, Faculty of Electrical EngineeringLjubljanaSlovenia
| | - Xinru Tang
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
- University of Chinese Academy of SciencesBeijingChina
| | - Fangwei Zhao
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
- University of Chinese Academy of SciencesBeijingChina
| | - Sergio Pérez-Conesa
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
| | - Ilaria Testa
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
| | - Lucie Delemotte
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
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4
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Jara-Quijada E, Pérez-Won M, Tabilo-Munizaga G, González-Cavieres L, Lemus-Mondaca R. An Overview Focusing on Food Liposomes and Their Stability to Electric Fields. FOOD ENGINEERING REVIEWS 2022. [DOI: 10.1007/s12393-022-09306-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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5
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Guo F, Wang J, Zhou J, Qian K, Qu H, Liu P, Zhai S. All-atom molecular dynamics simulations of the combined effects of different phospholipids and cholesterol content on electroporation. RSC Adv 2022; 12:24491-24500. [PMID: 36128384 PMCID: PMC9425445 DOI: 10.1039/d2ra03895a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 07/27/2022] [Indexed: 11/21/2022] Open
Abstract
In this paper, we applied all-atom molecular dynamics (MD) simulations to study the effects of phospholipids and cholesterol content on bilayer membrane electroporation.
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Affiliation(s)
- Fei Guo
- Institute of Ecological Safety, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Ji Wang
- Institute of Ecological Safety, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Jiong Zhou
- Institute of Ecological Safety, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Kun Qian
- Institute of Ecological Safety, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Hongchun Qu
- Institute of Ecological Safety, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Ping Liu
- Institute of Ecological Safety, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Shidong Zhai
- Institute of Ecological Safety, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
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6
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Rasouli A, Jamali Y, Tajkhorshid E, Bavi O, Pishkenari HN. Mechanical properties of ester- and ether-DPhPC bilayers: A molecular dynamics study. J Mech Behav Biomed Mater 2021; 117:104386. [PMID: 33588213 PMCID: PMC8009841 DOI: 10.1016/j.jmbbm.2021.104386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 01/03/2021] [Accepted: 02/04/2021] [Indexed: 10/22/2022]
Abstract
In addition to its biological importance, DPhPC lipid bilayers are widely used in droplet bilayers, study of integral membrane proteins, drug delivery systems as well as patch-clamp electrophysiology of ion channels, yet their mechanical properties are not fully measured. Herein, we examined the effect of the ether linkage on the mechanical properties of ester- and ether-DPhPC lipid bilayers using all-atom molecular dynamics simulation. The values of area per lipid, thickness, intrinsic lateral pressure profile, order parameter, and elasticity moduli were estimated using various computational frameworks and were compared with available experimental values. Overall, a good agreement was observed between the two. The global properties of the two lipid bilayers are vastly different, with ether bilayer being stiffer, less ordered, and thicker than ester bilayer. Moreover, ether linkage decreased the area per lipid in the ether lipid bilayer. Our computational framework and output demonstrate how ether modification changes the mechano-chemical properties of DPhPC bilayers.
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Affiliation(s)
- Ali Rasouli
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, And Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yousef Jamali
- School of Mathematical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, And Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Omid Bavi
- Department of Mechanical and Aerospace Engineering, Shiraz University of Technology, Shiraz, Iran.
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7
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Perera-Bel E, Yagüe C, Mercadal B, Ceresa M, Beitel-White N, Davalos RV, Ballester MAG, Ivorra A. EView: An electric field visualization web platform for electroporation-based therapies. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 197:105682. [PMID: 32795723 PMCID: PMC7998513 DOI: 10.1016/j.cmpb.2020.105682] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/27/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND OBJECTIVES Electroporation is the phenomenon by which cell membrane permeability to ions and macromolecules is increased when the cell is briefly exposed to high electric fields. In electroporation-based treatments, such exposure is typically performed by delivering high voltage pulses across needle electrodes in tissue. For a given tissue and pulsing protocol, an electric field magnitude threshold exists that must be overreached for treatment efficacy. However, it is hard to preoperatively infer the treatment volume because the electric field distribution intricately depends on the electrodes' positioning and length, the applied voltage, and the electric conductivity of the treated tissues. For illustrating such dependencies, we have created EView (https://eview.upf.edu), a web platform that estimates the electric field distribution for arbitrary needle electrode locations and orientations and overlays it on 3D medical images. METHODS A client-server approach has been implemented to let the user set the electrode configuration easily on the web browser, whereas the simulation is computed on a dedicated server. By means of the finite element method, the electric field is solved in a 3D volume. For the sake of simplicity, only a homogeneous tissue is modeled, assuming the same properties for healthy and pathologic tissues. The non-linear dependence of tissue conductivity on the electric field due to the electroporation effect is modeled. The implemented model has been validated against a state of the art finite element solver, and the server has undergone a heavy load test to ensure reliability and to report execution times. RESULTS The electric field is rapidly computed for any electrode and tissue configuration, and alternative setups can be easily compared. The platform provides the same results as the state of the art finite element solver (Dice = 98.3 ± 0.4%). During the high load test, the server remained responsive. Simulations are computed in less than 2 min for simple cases consisting of two electrodes and take up to 40 min for complex scenarios consisting of 6 electrodes. CONCLUSIONS With this free platform we provide expert and non-expert electroporation users a way to rapidly model the electric field distribution for arbitrary electrode configurations.
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Affiliation(s)
- Enric Perera-Bel
- BCN MedTech, Department of Information and Communication Technologies, Universitat Pompeu Fabra, c/ Roc Boronat 138 Edifici Tanger 55.119, 08018 Barcelona, Spain.
| | - Carlos Yagüe
- BCN MedTech, Department of Information and Communication Technologies, Universitat Pompeu Fabra, c/ Roc Boronat 138 Edifici Tanger 55.119, 08018 Barcelona, Spain
| | - Borja Mercadal
- BCN MedTech, Department of Information and Communication Technologies, Universitat Pompeu Fabra, c/ Roc Boronat 138 Edifici Tanger 55.119, 08018 Barcelona, Spain
| | - Mario Ceresa
- BCN MedTech, Department of Information and Communication Technologies, Universitat Pompeu Fabra, c/ Roc Boronat 138 Edifici Tanger 55.119, 08018 Barcelona, Spain
| | - Natalie Beitel-White
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, USA; Bradley Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Rafael V Davalos
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, USA
| | - Miguel A González Ballester
- BCN MedTech, Department of Information and Communication Technologies, Universitat Pompeu Fabra, c/ Roc Boronat 138 Edifici Tanger 55.119, 08018 Barcelona, Spain; ICREA, Barcelona, Spain
| | - Antoni Ivorra
- BCN MedTech, Department of Information and Communication Technologies, Universitat Pompeu Fabra, c/ Roc Boronat 138 Edifici Tanger 55.119, 08018 Barcelona, Spain; Serra Húnter Fellow Programme, Universitat Pompeu Fabra, Barcelona, Spain
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8
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Bignucolo O, Bernèche S. The Voltage-Dependent Deactivation of the KvAP Channel Involves the Breakage of Its S4 Helix. Front Mol Biosci 2020; 7:162. [PMID: 32850956 PMCID: PMC7403406 DOI: 10.3389/fmolb.2020.00162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 06/24/2020] [Indexed: 11/13/2022] Open
Abstract
Voltage-gated potassium channels (Kv) allow ion permeation upon changes of the membrane electrostatic potential (Vm). Each subunit of these tetrameric channels is composed of six transmembrane helices, of which the anti-parallel helix bundle S1-S4 constitutes the voltage-sensor domain (VSD) and S5-S6 forms the pore domain. Here, using 82 molecular dynamics (MD) simulations involving 266 replicated VSDs, we report novel responses of the archaebacterial potassium channel KvAP to membrane polarization. We show that the S4 α-helix, which is straight in the experimental crystal structure solved under depolarized conditions (Vm ∼ 0), breaks into two segments when the cell membrane is hyperpolarized (Vm << 0), and reversibly forms a single straight helix following depolarization (Vm = 0). The outermost segment of S4 translates along the normal to the membrane, bringing new perspective to previously paradoxical accessibility experiments that were initially thought to imply the displacement of the whole VSD across the membrane. The novel model is applied through steered and unbiased MD simulations to the recently solved whole structure of KvAP. The simulations show that the resting state involves a re-orientation of the S5 α-helix by ∼ 5-6 degrees in respect to the normal of the bilayer, which could result in the constriction and closure of the selectivity filter. Our findings support the idea that the breakage of S4 under (hyper)polarization is a general feature of Kv channels with a non-swapped topology.
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Affiliation(s)
- Olivier Bignucolo
- Biozentrum, University of Basel, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel/Lausanne, Switzerland
| | - Simon Bernèche
- Biozentrum, University of Basel, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel/Lausanne, Switzerland
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9
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Molecular characterization of the outer membrane of Pseudomonas aeruginosa. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183151. [DOI: 10.1016/j.bbamem.2019.183151] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/28/2019] [Accepted: 12/06/2019] [Indexed: 01/07/2023]
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10
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Zhou C, Liu K. Molecular dynamics simulation of reversible electroporation with Martini force field. Biomed Eng Online 2019; 18:123. [PMID: 31878975 PMCID: PMC6933919 DOI: 10.1186/s12938-019-0743-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 12/12/2019] [Indexed: 11/12/2022] Open
Abstract
Background After the discovery of membrane-reversible electroporation decades ago, the procedure has been used extensively in biology, biotechnology and medicine. The research on the basic mechanism has increasingly attracted attention. Although most research has focused on models that consider all atomic and molecular interactions and much atomic-level information can be obtained, the huge computational demand limits the models to simulations of only a few nanometers on the spatial scale and a few nanoseconds on the time scale. In order to more comprehensively study the reversible electroporation mechanism of phospholipid membrane on the nanoscale and at longer time intervals of up to 100 ns, we developed a dipalmitoylphosphatidylcholine (DPPC) phospholipid membrane model with the coarse-grained Martini force field. The model was tested by separately examining the morphology of the phospholipid membrane, the hydrophilic channel size, the distribution of the voltage potential on both sides of the membrane, and the movement of water molecules and ions during electroporation. Results The results showed that the process went through several stages: (1) the formation of the pore with defects originating on the surface. (2) The maintenance of the pore. The defects expanded to large pores and the size remains unchanged for several nanoseconds. (3) Pore healing stage due to self-assembly. Phospholipid membrane shrunk and the pore size decreased until completely closed. The pores were not circular in cross-section for most of the time and the potential difference across the membrane decreased dramatically after the pores formed, with almost no restoration of membrane integrity even when the pores started to close. Conclusions The mechanism of the reversible electroporation process on the nanoscale level, including defects, expansion, stability, and pore closing stages on a longer time scale of up to 100 ns was demonstrated more comprehensively with the coarse-grained Martini force field, which took both the necessary molecular information and the calculation efficiency into account.
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Affiliation(s)
- Cheng Zhou
- Department of Light Sources & Illuminating Engineering, Fudan University, 220 Handan Road, Yangpu District, Shanghai, 200433, China
| | - Kefu Liu
- Department of Light Sources & Illuminating Engineering, Fudan University, 220 Handan Road, Yangpu District, Shanghai, 200433, China.
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11
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Miyazaki Y, Okazaki S, Shinoda W. pSPICA: A Coarse-Grained Force Field for Lipid Membranes Based on a Polar Water Model. J Chem Theory Comput 2019; 16:782-793. [DOI: 10.1021/acs.jctc.9b00946] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yusuke Miyazaki
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Susumu Okazaki
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Wataru Shinoda
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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12
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Pulsed electric field inactivation of microorganisms: from fundamental biophysics to synergistic treatments. Appl Microbiol Biotechnol 2019; 103:7917-7929. [DOI: 10.1007/s00253-019-10067-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 12/15/2022]
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13
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Hoejholt KL, Mužić T, Jensen SD, Dalgaard LT, Bilgin M, Nylandsted J, Heimburg T, Frandsen SK, Gehl J. Calcium electroporation and electrochemotherapy for cancer treatment: Importance of cell membrane composition investigated by lipidomics, calorimetry and in vitro efficacy. Sci Rep 2019; 9:4758. [PMID: 30894594 PMCID: PMC6427041 DOI: 10.1038/s41598-019-41188-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/20/2019] [Indexed: 12/21/2022] Open
Abstract
Calcium electroporation is a novel anti-cancer treatment investigated in clinical trials. We explored cell sensitivity to calcium electroporation and electroporation with bleomycin, using viability assays at different time and temperature points, as well as heat calorimetry, lipidomics, and flow cytometry. Three cell lines: HT29 (colon cancer), MDA-MB231 (breast cancer), and HDF-n (normal fibroblasts) were investigated for; (a) cell survival dependent on time of addition of drug relative to electroporation (1.2 kV/cm, 8 pulses, 99 µs, 1 Hz), at different temperatures (37 °C, 27 °C, 17 °C); (b) heat capacity profiles obtained by differential scanning calorimetry without added calcium; (c) lipid composition by mass spectrometry; (d) phosphatidylserine in the plasma membrane outer leaflet using flow cytometry. Temperature as well as time of drug administration affected treatment efficacy in HT29 and HDF-n cells, but not MDA-MB231 cells. Interestingly the HT29 cell line displayed a higher phase transition temperature (approximately 20 °C) versus 14 °C (HDF-n) and 15 °C (MDA-MB231). Furthermore the HT29 cell membranes had a higher ratio of ethers to esters, and a higher expression of phosphatidylserine in the outer leaflet. In conclusion, lipid composition and heat capacity of the membrane might influence permeabilisation of cells and thereby the effect of calcium electroporation and electrochemotherapy.
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Affiliation(s)
- K L Hoejholt
- Center for Experimental Drug and Gene Electrotransfer, Department of Oncology, Copenhagen University Hospital Herlev, Herlev, Denmark
| | - T Mužić
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - S D Jensen
- Center for Experimental Drug and Gene Electrotransfer, Department of Oncology, Copenhagen University Hospital Herlev, Herlev, Denmark
| | - L T Dalgaard
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - M Bilgin
- Danish Cancer Society Research Center (DCRC), Copenhagen, Denmark
| | - J Nylandsted
- Danish Cancer Society Research Center (DCRC), Copenhagen, Denmark
| | - T Heimburg
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - S K Frandsen
- Center for Experimental Drug and Gene Electrotransfer, Department of Oncology, Copenhagen University Hospital Herlev, Herlev, Denmark.
- Center for Experimental Drug and Gene Electrotransfer, Department of Clinical Oncology and Palliative Care, Zealand University Hospital, Roskilde, Denmark.
| | - J Gehl
- Center for Experimental Drug and Gene Electrotransfer, Department of Oncology, Copenhagen University Hospital Herlev, Herlev, Denmark.
- Center for Experimental Drug and Gene Electrotransfer, Department of Clinical Oncology and Palliative Care, Zealand University Hospital, Roskilde, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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14
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Abstract
Although the pan and the core genome of Acinetobacter baumannii and its essential genes are relatively well characterized, functional characterization of these genes has not paralleled the genome-level studies. However, recently developed genetic tools and optimized protocols are poised to accelerate genetic manipulation of A. baumannii. Transferring exogenous DNA into the cytosol of bacteria cells is a critical step in genetic characterizations. Conjugation is restricted to the transfer of DNA from one bacterial cell to another, and only a portion of A. baumannii clinical isolates are naturally competent. Electroporation, which is thought to transiently create aqueous pores in the membrane, is a preferred method in transferring exogenous DNA as it does not have such limitations. Several factors contribute to efficiency of electroporation and often need to be empirically optimized to maximize efficiency of this procedure. Here we provide an optimized electroporation protocol and guidance for electroporation of clinical MDR isolates of A. baumannii.
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Affiliation(s)
- Mitchell G Thompson
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Süleyman Yildirim
- Department of Medical Microbiology, International School of Medicine, Istanbul Medipol University, Istanbul, Turkey.
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15
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Kotnik T, Rems L, Tarek M, Miklavčič D. Membrane Electroporation and Electropermeabilization: Mechanisms and Models. Annu Rev Biophys 2019; 48:63-91. [PMID: 30786231 DOI: 10.1146/annurev-biophys-052118-115451] [Citation(s) in RCA: 332] [Impact Index Per Article: 66.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Exposure of biological cells to high-voltage, short-duration electric pulses causes a transient increase in their plasma membrane permeability, allowing transmembrane transport of otherwise impermeant molecules. In recent years, large steps were made in the understanding of underlying events. Formation of aqueous pores in the lipid bilayer is now a widely recognized mechanism, but evidence is growing that changes to individual membrane lipids and proteins also contribute, substantiating the need for terminological distinction between electroporation and electropermeabilization. We first revisit experimental evidence for electrically induced membrane permeability, its correlation with transmembrane voltage, and continuum models of electropermeabilization that disregard the molecular-level structure and events. We then present insights from molecular-level modeling, particularly atomistic simulations that enhance understanding of pore formation, and evidence of chemical modifications of membrane lipids and functional modulation of membrane proteins affecting membrane permeability. Finally, we discuss the remaining challenges to our full understanding of electroporation and electropermeabilization.
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Affiliation(s)
- Tadej Kotnik
- Faculty of Electrical Engineering, University of Ljubljana, SI-1000 Ljubljana, Slovenia; ,
| | - Lea Rems
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 17165 Solna, Sweden;
| | - Mounir Tarek
- Université de Lorraine, CNRS, LPCT, F-54000 Nancy, France;
| | - Damijan Miklavčič
- Faculty of Electrical Engineering, University of Ljubljana, SI-1000 Ljubljana, Slovenia; ,
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16
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Chen G, Huang K, Miao M, Feng B, Campanella OH. Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art. Compr Rev Food Sci Food Saf 2018; 18:243-263. [PMID: 33337012 DOI: 10.1111/1541-4337.12406] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/07/2018] [Accepted: 10/10/2018] [Indexed: 12/14/2022]
Abstract
Molecular dynamics (MD) simulation is a useful technique to study the interaction between molecules and how they are affected by various processes and processing conditions. This review summarizes the application of MD simulations in food processing and safety, with an emphasis on the effects that emerging nonthermal technologies (for example, high hydrostatic pressure, pulsed electric field) have on the molecular and structural characteristics of foods and biomaterials. The advances and potential projection of MD simulations in the science and engineering aspects of food materials are discussed and focused on research work conducted to study the effects of emerging technologies on food components. It is expected by showing key case studies that it will stir novel developments as a valuable tool to study the effects of emerging food technologies on biomaterials. This review is useful to food researchers and the food industry, as well as researchers and practitioners working on flavor and nutraceutical encapsulations, dietary carbohydrate product developments, modified starches, protein engineering, and other novel food applications.
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Affiliation(s)
- Gang Chen
- School of Food Science and Technology, Henan Univ. of Technology, 100 Lianhua St., Zhengzhou 450001, Henan, P. R. China.,State Key Laboratory of Food Science and Technology, Jiangnan Univ., 1800 Lihu Ave., Wuxi, 214122, Jiangsu, P. R. China
| | - Kai Huang
- State Key Laboratory of Food Science and Technology, Jiangnan Univ., 1800 Lihu Ave., Wuxi, 214122, Jiangsu, P. R. China
| | - Ming Miao
- State Key Laboratory of Food Science and Technology, Jiangnan Univ., 1800 Lihu Ave., Wuxi, 214122, Jiangsu, P. R. China
| | - Biao Feng
- State Key Laboratory of Food Science and Technology, Jiangnan Univ., 1800 Lihu Ave., Wuxi, 214122, Jiangsu, P. R. China
| | - Osvaldo H Campanella
- State Key Laboratory of Food Science and Technology, Jiangnan Univ., 1800 Lihu Ave., Wuxi, 214122, Jiangsu, P. R. China.,Agricultural and Biological Engineering, and Dept. of Food Science, Whistler Center for Carbohydrate Research, Purdue Univ., 745 Agriculture Mall Dr., West Lafayette, IN, 47906, U.S.A
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Lin X, Nair V, Zhou Y, Gorfe AA. Membrane potential and dynamics in a ternary lipid mixture: insights from molecular dynamics simulations. Phys Chem Chem Phys 2018; 20:15841-15851. [PMID: 29845130 DOI: 10.1039/c8cp01629a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transmembrane potential (Vm) plays critical roles in cell signaling and other functions. However, the impact of Vm on the structure and dynamics of membrane lipids and proteins, which are critical for the regulation of signaling, is still an open question. All-atom molecular dynamics (MD) simulation is emerging as a useful technique to address this issue. Previous atomistic MD simulations of pure or binary model membranes indicated that both ion imbalance and electric field can be used to generate Vm, but both approaches failed to yield structural changes in lipids with statistical significance. We hypothesized that a possible reason for this could be oversimplified membrane composition or limited sampling. In this work, we tested if and how Vm modulates the structure and dynamics of lipids in a physiologically relevant model membrane. Using a detailed side-by-side comparison, we first show that while both ion imbalance and electric field generate Vm in our complex membranes, only the latter could produce physiologically relevant Vm. We further show that double bonds in lipid acyl chains have a relatively large sensitivity to Vm. A single-bilayer model with an electric field showed the highest sensitivity in simulations under the isothermal-isobaric (NPT) ensemble, reproducing expected responses of head-group dipoles to Vm and suggesting that this approach may be more suitable for studying the structural effects of Vm. Our findings also shed light on the relationship between the macroscopic Vm and its atomic-level underpinnings.
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Affiliation(s)
- Xubo Lin
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Texas 77030, USA
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18
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Gupta R, Rai B. Electroporation of Skin Stratum Corneum Lipid Bilayer and Molecular Mechanism of Drug Transport: A Molecular Dynamics Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:5860-5870. [PMID: 29708340 DOI: 10.1021/acs.langmuir.8b00423] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The electroporation technique has been used significantly to increase drug permeation through the skin. This technique relies on the application of short-timed (microseconds to millisecond) electric fields (generally, order of 50--300 V) on the skin to create microscopic pores. However, the molecular mechanism of pore formation, resulting in an enhanced flux of active molecules through the skin, remains poorly understood. In this study, extensive atomistic molecular dynamics simulation of skin lipids [made up of ceramide (CER), cholesterol (CHOL), and free fatty acid (FFA)] has been performed at various external electric fields. We show for the first time the pore formation in the skin lipid bilayer during electroporation. We show the effect of the applied external electrical field (0.6-1.0 V/nm) on the pore formation dynamics in the lipid bilayer of different sizes (154, 616, and 2464 lipids) and compositions (CER/CHOL/FFA, 1:0:0, 1:0:1, 1:1:0, 1:1:1). The pore formation and resealing kinetics were different and were found to be highly dependent on the composition of the skin lipid bilayer. The pore formation time decreased with increase in the bilayer size. The pore sustaining electric field was found to be in the range of 0.20-0.25 V/nm for equimolar CER, CHOL, and FFA lipid bilayers. The skin lipid bilayer (1:1:1) sealed itself within 20 ns after the removal of the external electric field. We also present the molecular mechanism of enhancement of drug permeation in the presence of external field as compared to the passive diffusion. The molecular-level understanding obtained here could help in optimizing/designing the electroporation experiments for effective drug delivery. For a given skin composition and size of the drug molecule, the combination of pore formation time and pore growth model can be used to know a priori the desired electric field and time for the application of the electric field.
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Affiliation(s)
- Rakesh Gupta
- Physical Science Research Area, Tata Research Development & Design Centre, TCS Innovation Labs , Pune 411013 , India
| | - Beena Rai
- Physical Science Research Area, Tata Research Development & Design Centre, TCS Innovation Labs , Pune 411013 , India
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Atomistic Simulations of Electroporation of Model Cell Membranes. ADVANCES IN ANATOMY EMBRYOLOGY AND CELL BIOLOGY 2018; 227:1-15. [PMID: 28980037 DOI: 10.1007/978-3-319-56895-9_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Electroporation is a phenomenon that modifies the fundamental function of the cell since it perturbs transiently or permanently the integrity of its membrane. Today, this technique is applied in fields ranging from biology and biotechnology to medicine, e.g., for drug and gene delivery into cells, tumor therapy, etc., in which it made it to preclinical and clinical treatments. Experimentally, due to the complexity and heterogeneity of cell membranes, it is difficult to provide a description of the electroporation phenomenon in terms of atomically resolved structural and dynamical processes, a prerequisite to optimize its use. Atomistic modeling in general and molecular dynamics (MD) simulations in particular have proven to be an effective approach for providing such a level of detail. This chapter provides the reader with a comprehensive account of recent advances in using such a technique to complement conventional experimental approaches in characterizing several aspects of cell membranes electroporation.
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20
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The role of gel-phase domains in electroporation of vesicles. Sci Rep 2018; 8:4758. [PMID: 29555940 PMCID: PMC5859178 DOI: 10.1038/s41598-018-23097-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 03/06/2018] [Indexed: 12/18/2022] Open
Abstract
Transient permeabilisation of the cell membrane is a critical step to introduce drugs or DNA into living cells, yet challenging for both biological research and therapeutic applications. To achieve this, electroporation (or electropermeabilisation) has become a widely used method due to its simplicity to deliver almost any biomolecule to any cell type. Although this method demonstrates promise in the field of drug/gene delivery, the underlying physical mechanisms of the response of the heterogeneous cell membrane to strong electric pulses is still unknown. In this study, we have investigated the role of gel-phase lipids in the electroporation of binary giant unilamellar vesicles (GUVs), composed from DPPC (gel-phase) and DPhPC (fluid-phase) lipids (molar ratio 8:2 and 2:8). We have observed that the exposure to electric pulses leads to expel of fluid-phase lipids and concomitant decrease in GUV size, whereas the gel-phase domains become buckled. Based on experiments on pure fluid-phase and gel-phase GUVs, we have found that fluid-phase lipids can be expelled by electrical forces and the highly viscous gel-phase lipids cannot. Moreover, our analyses suggest that pore formation occurs primarily in fluid-phase domains and that the pore size is similar in all GUVs containing fluid-phase lipids, irrespective of the gel-phase percentage.
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21
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Electropore Formation in Mechanically Constrained Phospholipid Bilayers. J Membr Biol 2017; 251:237-245. [DOI: 10.1007/s00232-017-0002-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 11/06/2017] [Indexed: 01/10/2023]
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22
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Perrier DL, Rems L, Boukany PE. Lipid vesicles in pulsed electric fields: Fundamental principles of the membrane response and its biomedical applications. Adv Colloid Interface Sci 2017; 249:248-271. [PMID: 28499600 DOI: 10.1016/j.cis.2017.04.016] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/24/2017] [Accepted: 04/25/2017] [Indexed: 01/04/2023]
Abstract
The present review focuses on the effects of pulsed electric fields on lipid vesicles ranging from giant unilamellar vesicles (GUVs) to small unilamellar vesicles (SUVs), from both fundamental and applicative perspectives. Lipid vesicles are the most popular model membrane systems for studying biophysical and biological processes in living cells. Furthermore, as vesicles are made from biocompatible and biodegradable materials, they provide a strategy to create safe and functionalized drug delivery systems in health-care applications. Exposure of lipid vesicles to pulsed electric fields is a common physical method to transiently increase the permeability of the lipid membrane. This method, termed electroporation, has shown many advantages for delivering exogenous molecules including drugs and genetic material into vesicles and living cells. In addition, electroporation can be applied to induce fusion between vesicles and/or cells. First, we discuss in detail how research on cell-size GUVs as model cell systems has provided novel insight into the basic mechanisms of cell electroporation and associated phenomena. Afterwards, we continue with a thorough overview how electroporation and electrofusion have been used as versatile methods to manipulate vesicles of all sizes in different biomedical applications. We conclude by summarizing the open questions in the field of electroporation and possible future directions for vesicles in the biomedical field.
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23
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Rems L. Applicative Use of Electroporation Models. ADVANCES IN BIOMEMBRANES AND LIPID SELF-ASSEMBLY 2017. [DOI: 10.1016/bs.abl.2017.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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24
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Trick JL, Chelvaniththilan S, Klesse G, Aryal P, Wallace EJ, Tucker SJ, Sansom MSP. Functional Annotation of Ion Channel Structures by Molecular Simulation. Structure 2016; 24:2207-2216. [PMID: 27866853 PMCID: PMC5145807 DOI: 10.1016/j.str.2016.10.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 08/12/2016] [Accepted: 10/12/2016] [Indexed: 01/30/2023]
Abstract
Ion channels play key roles in cell membranes, and recent advances are yielding an increasing number of structures. However, their functional relevance is often unclear and better tools are required for their functional annotation. In sub-nanometer pores such as ion channels, hydrophobic gating has been shown to promote dewetting to produce a functionally closed (i.e., non-conductive) state. Using the serotonin receptor (5-HT3R) structure as an example, we demonstrate the use of molecular dynamics to aid the functional annotation of channel structures via simulation of the behavior of water within the pore. Three increasingly complex simulation analyses are described: water equilibrium densities; single-ion free-energy profiles; and computational electrophysiology. All three approaches correctly predict the 5-HT3R crystal structure to represent a functionally closed (i.e., non-conductive) state. We also illustrate the application of water equilibrium density simulations to annotate different conformational states of a glycine receptor.
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Affiliation(s)
- Jemma L Trick
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Sivapalan Chelvaniththilan
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Gianni Klesse
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Prafulla Aryal
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK; OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, UK
| | | | - Stephen J Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK; OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, UK.
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25
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Hoiles W, Gupta R, Cornell B, Cranfield C, Krishnamurthy V. The Effect of Tethers on Artificial Cell Membranes: A Coarse-Grained Molecular Dynamics Study. PLoS One 2016; 11:e0162790. [PMID: 27736860 PMCID: PMC5063460 DOI: 10.1371/journal.pone.0162790] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 08/29/2016] [Indexed: 11/18/2022] Open
Abstract
Tethered bilayer lipid membranes (tBLMs) provide a stable platform for modeling the dynamics and order of biological membranes where the tethers mimic the cytoskeletal supports present in biological cell membranes. In this paper coarse-grained molecular dynamics (CGMD) is applied to study the effects of tethers on lipid membrane properties. Using results from the CGMD model and the overdamped Fokker-Planck equation, we show that the diffusion tensor and particle density of water in the tBLM is spatially dependent. Further, it is shown that the membrane thickness, lipid diffusion, defect density, free energy of lipid flip-flop, and membrane dielectric permittivity are all dependent on the tether density. The numerically computed results from the CGMD model are in agreement with the experimentally measured results from tBLMs containing different tether densities and lipids derived from Archaebacteria. Additionally, using experimental measurements from Escherichia coli bacteria and Saccharomyces Cerevisiae yeast tethered membranes, we illustrate how previous molecular dynamics results can be combined with the proposed model to estimate the dielectric permittivity and defect density of these membranes as a function of tether density.
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Affiliation(s)
- William Hoiles
- Department of Electrical and Computer Engineering, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Rini Gupta
- Department of Electrical and Computer Engineering, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Bruce Cornell
- Director of Science and Technology, Surgical Diagnostics Pty Ltd., Unit 6 30-32 Barcoo Street, Roseville, New South Wales, 2069, Australia
| | - Charles Cranfield
- School of Life Sciences, University of Technology Sydney, Broadway, New South Wales, Australia
| | - Vikram Krishnamurthy
- Electrical and Computer Engineering, Cornell University, New York, New York, United States of America
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26
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Golberg A, Sack M, Teissie J, Pataro G, Pliquett U, Saulis G, Stefan T, Miklavcic D, Vorobiev E, Frey W. Energy-efficient biomass processing with pulsed electric fields for bioeconomy and sustainable development. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:94. [PMID: 27127539 PMCID: PMC4848877 DOI: 10.1186/s13068-016-0508-z] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/13/2016] [Indexed: 05/24/2023]
Abstract
Fossil resources-free sustainable development can be achieved through a transition to bioeconomy, an economy based on sustainable biomass-derived food, feed, chemicals, materials, and fuels. However, the transition to bioeconomy requires development of new energy-efficient technologies and processes to manipulate biomass feed stocks and their conversion into useful products, a collective term for which is biorefinery. One of the technological platforms that will enable various pathways of biomass conversion is based on pulsed electric fields applications (PEF). Energy efficiency of PEF treatment is achieved by specific increase of cell membrane permeability, a phenomenon known as membrane electroporation. Here, we review the opportunities that PEF and electroporation provide for the development of sustainable biorefineries. We describe the use of PEF treatment in biomass engineering, drying, deconstruction, extraction of phytochemicals, improvement of fermentations, and biogas production. These applications show the potential of PEF and consequent membrane electroporation to enable the bioeconomy and sustainable development.
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Affiliation(s)
- Alexander Golberg
- />Porter School of Environmental Studies, Tel Aviv University, Tel Aviv, Israel
| | - Martin Sack
- />Institute for Pulsed Power and Microwave Technology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Justin Teissie
- />CNRS, Institut de Pharmacologie et de Biologie Structurale Université de Toulouse, Toulouse, France
| | - Gianpiero Pataro
- />Department of Industrial Engineering, University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano, SA Italy
| | - Uwe Pliquett
- />Institut für Bioprozeβ- und Analysenmeβtechnik e.V., Heilbad Heiligenstadt, Germany
| | - Gintautas Saulis
- />Department of Biology, Faculty of Natural Sciences, Vytautas Magnus University, Kaunas, Lithuania
| | - Töpfl Stefan
- />German Institute of Food Technologies, Quakenbrück, Germany
| | - Damijan Miklavcic
- />Faculty of Electrical Engineering, University of Ljubljana, Ljubljana, Slovenia
| | - Eugene Vorobiev
- />Departement de Genie Chimique, Centre de Recherche de Royallieu, Universite de Technologie de Compiegne, Compiegne, France
| | - Wolfgang Frey
- />Institute for Pulsed Power and Microwave Technology, Karlsruhe Institute of Technology, Karlsruhe, Germany
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27
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Čorović S, Mahnič-Kalamiza S, Miklavčič D. Education on electrical phenomena involved in electroporation-based therapies and treatments: a blended learning approach. Biomed Eng Online 2016; 15:36. [PMID: 27056369 PMCID: PMC4823865 DOI: 10.1186/s12938-016-0152-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 03/30/2016] [Indexed: 11/28/2022] Open
Abstract
Background Electroporation-based applications require multidisciplinary expertise and collaboration of experts with different professional backgrounds in engineering and science. Beginning in 2003, an international scientific workshop and postgraduate course electroporation based technologies and treatments (EBTT) has been organized at the University of Ljubljana to facilitate transfer of knowledge from leading experts to researches, students and newcomers in the field of electroporation. In this paper we present one of the integral parts of EBTT: an e-learning practical work we developed to complement delivery of knowledge via lectures and laboratory work, thus providing a blended learning approach on electrical phenomena involved in electroporation-based therapies and treatments. Methods The learning effect was assessed via a pre- and post e-learning examination test composed of 10 multiple choice questions (i.e. items). The e-learning practical work session and both of the e-learning examination tests were carried out after the live EBTT lectures and other laboratory work. Statistical analysis was performed to compare and evaluate the learning effect measured in two groups of students: (1) electrical engineers and (2) natural scientists (i.e. medical doctors, biologists and chemists) undergoing the e-learning practical work in 2011–2014 academic years. Item analysis was performed to assess the difficulty of each item of the examination test. Results The results of our study show that the total score on the post examination test significantly improved and the item difficulty in both experimental groups decreased. The natural scientists reached the same level of knowledge (no statistical difference in total post-examination test score) on the post-course test take, as do electrical engineers, although the engineers started with statistically higher total pre-test examination score, as expected. Conclusions The main objective of this study was to investigate whether the educational content the e-learning practical work presented to the students with different professional backgrounds enhanced their knowledge acquired via lectures during EBTT. We compared the learning effect assessed in two experimental groups undergoing the e-learning practical work: electrical engineers and natural scientists. The same level of knowledge on the post-course examination was reached in both groups. The results indicate that our e-learning platform supported by blended learning approach provides an effective learning tool for populations with mixed professional backgrounds and thus plays an important role in bridging the gap between scientific domains involved in electroporation-based technologies and treatments. Electronic supplementary material The online version of this article (doi:10.1186/s12938-016-0152-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Selma Čorović
- Faculty of Electrical Engineering, University of Ljubljana, Tržaška c. 25, 1000, Ljubljana, Slovenia.
| | - Samo Mahnič-Kalamiza
- Faculty of Electrical Engineering, University of Ljubljana, Tržaška c. 25, 1000, Ljubljana, Slovenia
| | - Damijan Miklavčič
- Faculty of Electrical Engineering, University of Ljubljana, Tržaška c. 25, 1000, Ljubljana, Slovenia
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Casciola M, Tarek M. A molecular insight into the electro-transfer of small molecules through electropores driven by electric fields. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2278-2289. [PMID: 27018309 DOI: 10.1016/j.bbamem.2016.03.022] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 03/21/2016] [Accepted: 03/21/2016] [Indexed: 11/26/2022]
Abstract
The transport of chemical compounds across the plasma membrane into the cell is relevant for several biological and medical applications. One of the most efficient techniques to enhance this uptake is reversible electroporation. Nevertheless, the detailed molecular mechanism of transport of chemical species (dyes, drugs, genetic materials, …) following the application of electric pulses is not yet fully elucidated. In the past decade, molecular dynamics (MD) simulations have been conducted to model the effect of pulsed electric fields on membranes, describing several aspects of this phenomenon. Here, we first present a comprehensive review of the results obtained so far modeling the electroporation of lipid membranes, then we extend these findings to study the electrotransfer across lipid bilayers subject to microsecond pulsed electric fields of Tat11, a small hydrophilic charged peptide, and of siRNA. We use in particular a MD simulation protocol that allows to characterize the transport of charged species through stable pores. Unexpectedly, our results show that for an electroporated bilayer subject to transmembrane voltages in the order of 500mV, i.e. consistent with experimental conditions, both Tat11 and siRNA can translocate through nanoelectropores within tens of ns. We discuss these results in comparison to experiments in order to rationalize the mechanism of drug uptake by cells. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Maura Casciola
- Université de Lorraine, UMR 7565, F-54506 Vandoeuvre les Nancy, France; Department of Information Engineering, Electronics and Telecommunications (D.I.E.T), Sapienza University of Rome, 00184 Rome, Italy; Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, 00161 Rome, Italy
| | - Mounir Tarek
- Université de Lorraine, UMR 7565, F-54506 Vandoeuvre les Nancy, France; CNRS, UMR 7565, F-54506 Vandoeuvre les Nancy, France.
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29
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Velikonja A, Kramar P, Miklavčič D, Maček Lebar A. Specific electrical capacitance and voltage breakdown as a function of temperature for different planar lipid bilayers. Bioelectrochemistry 2016; 112:132-7. [PMID: 26948707 DOI: 10.1016/j.bioelechem.2016.02.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 02/15/2016] [Accepted: 02/23/2016] [Indexed: 12/16/2022]
Abstract
The breakdown voltage and specific electrical capacitance of planar lipid bilayers formed from lipids isolated from the membrane of archaeon Aeropyrum pernix K1 as a function of temperature were studied and compared with data obtained previously in MD simulation studies. Temperature dependence of breakdown voltage and specific electrical capacitance was measured also for dipalmitoylphosphatidylcholine (DPPC) bilayers and bilayers formed from mixture of diphytanoylphosphocholine (DPhPC) and DPPC in ratio 80:20. The breakdown voltage of archaeal lipids planar lipid bilayers is more or less constant until 50°C, while at higher temperatures a considerable drop is observed, which is in line with the results from MD simulations. The breakdown voltage of DPPC planar lipid bilayer at melting temperature is considerably higher than in the gel phase. Specific electrical capacitance of planar lipid bilayers formed from archaeal lipids is approximately constant for temperatures up to 40°C and then gradually decreases. The difference with MD simulation predictions is discussed. Specific electrical capacitance of DPPC planar lipid bilayers in fluid phase is 1.75 times larger than that of the gel phase and it follows intermediated phases before phase transition. Increase in specific electrical capacitance while approaching melting point of DPPC is visible also for DPhPC:DPPC mixture.
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Affiliation(s)
- Aljaž Velikonja
- University of Ljubljana, Faculty of Electrical Engineering, Slovenia
| | - Peter Kramar
- University of Ljubljana, Faculty of Electrical Engineering, Slovenia
| | - Damijan Miklavčič
- University of Ljubljana, Faculty of Electrical Engineering, Slovenia
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English NJ, Waldron CJ. Perspectives on external electric fields in molecular simulation: progress, prospects and challenges. Phys Chem Chem Phys 2016; 17:12407-40. [PMID: 25903011 DOI: 10.1039/c5cp00629e] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this review, the application of a wide variety of external electric fields in molecular simulation shall be discussed, including time-varying and electromagnetic, as well as the utility and potential impact and prospects for exploitation of such simulations for real-world and industrial end use. In particular, non-equilibrium molecular dynamics will be discussed, as well as challenges in addressing adequate thermostatting and scaling field amplitudes to more experimentally relevant levels. Attention shall be devoted to recent progress and advances in external fields in ab initio molecular simulation and dynamics, as well as elusive challenges thereof (and, to some extent, for molecular dynamics from empirical potentials), such as timescales required to observe low-frequency and intensity field effects. The challenge of deterministic molecular dynamics in external fields in sampling phase space shall be discussed, along with prospects for application of fields in enhanced-sampling simulations. Finally, the application of external electric fields to a wide variety of aqueous, nanoscale and biological systems will be discussed, often motivated by the possibility of exploitation in real-world applications, which serve to underpin our molecular-level understanding of field effects in terms of microscopic mechanisms, and possibly with a view to control thereof.
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Affiliation(s)
- Niall J English
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland.
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31
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Kirsch SA, Böckmann RA. Membrane pore formation in atomistic and coarse-grained simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:2266-2277. [PMID: 26748016 DOI: 10.1016/j.bbamem.2015.12.031] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 12/23/2015] [Accepted: 12/24/2015] [Indexed: 12/26/2022]
Abstract
Biological cells and their organelles are protected by ultra thin membranes. These membranes accomplish a broad variety of important tasks like separating the cell content from the outer environment, they are the site for cell-cell interactions and many enzymatic reactions, and control the in- and efflux of metabolites. For certain physiological functions e.g. in the fusion of membranes and also in a number of biotechnological applications like gene transfection the membrane integrity needs to be compromised to allow for instance for the exchange of polar molecules across the membrane barrier. Mechanisms enabling the transport of molecules across the membrane involve membrane proteins that form specific pores or act as transporters, but also so-called lipid pores induced by external fields, stress, or peptides. Recent progress in the simulation field enabled to closely mimic pore formation as supposed to occur in vivo or in vitro. Here, we review different simulation-based approaches in the study of membrane pores with a focus on lipid pore properties such as their size and energetics, poration mechanisms based on the application of external fields, charge imbalances, or surface tension, and on pores that are induced by small molecules, peptides, and lipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Sonja A Kirsch
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
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Majhi AK, Kanchi S, Venkataraman V, Ayappa KG, Maiti PK. Estimation of activation energy for electroporation and pore growth rate in liquid crystalline and gel phases of lipid bilayers using molecular dynamics simulations. SOFT MATTER 2015; 11:8632-8640. [PMID: 26372335 DOI: 10.1039/c5sm02029h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Molecular dynamics simulations of electroporation in POPC and DPPC lipid bilayers have been carried out at different temperatures ranging from 230 K to 350 K for varying electric fields. The dynamics of pore formation, including threshold field, pore initiation time, pore growth rate, and pore closure rate after the field is switched off, was studied in both the gel and liquid crystalline (Lα) phases of the bilayers. Using an Arrhenius model of pore initiation kinetics, the activation energy for pore opening was estimated to be 25.6 kJ mol(-1) and 32.6 kJ mol(-1) in the Lα phase of POPC and DPPC lipids respectively at a field strength of 0.32 V nm(-1). The activation energy decreases to 24.2 kJ mol(-1) and 23.7 kJ mol(-1) respectively at a higher field strength of 1.1 V nm(-1). At temperatures below the melting point, the activation energy in the gel phase of POPC and DPPC increases to 28.8 kJ mol(-1) and 34.4 kJ mol(-1) respectively at the same field of 1.1 V nm(-1). The pore closing time was found to be higher in the gel than in the Lα phase. The pore growth rate increases linearly with temperature and quadratically with field, consistent with viscosity limited growth models.
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Affiliation(s)
- Amit Kumar Majhi
- Department of Physics, Indian Institute of Science, Bangalore, India.
| | - Subbarao Kanchi
- Department of Physics, Indian Institute of Science, Bangalore, India.
| | - V Venkataraman
- Department of Physics, Indian Institute of Science, Bangalore, India.
| | - K G Ayappa
- Department of Chemical Engineering, Center for Biosystems Science and Engineering, Bangalore, India.
| | - Prabal K Maiti
- Department of Physics, Indian Institute of Science, Bangalore, India.
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Polak A, Velikonja A, Kramar P, Tarek M, Miklavčič D. Electroporation threshold of POPC lipid bilayers with incorporated polyoxyethylene glycol (C12E8). J Phys Chem B 2014; 119:192-200. [PMID: 25495217 DOI: 10.1021/jp509789m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Electroporation relates to a phenomenon in which cell membranes are permeabilized after being exposed to high electric fields. On the molecular level, the mechanism is not yet fully elucidated, although a considerable body of experiments and molecular dynamic (MD) simulations were performed on model membranes. Here we present the results of a combined theoretical and experimental investigation of electroporation of palmitoy-oleoyl-phosphatidylcholine (POPC) bilayers with incorporated polyoxyethylene glycol (C12E8) surfactants. The experimental results show a slight increase of the capacitance and a 22% decrease of the voltage breakdown upon addition of C12E8 to pure POPC bilayers. These results were qualitatively confirmed by the MD simulations. They later revealed that the polyoxyethylene glycol molecules play a major role in the formation of hydrophilic pores in the bilayers above the electroporation threshold. The headgroup moieties of the latter are indeed embedded in the interior of the bilayer, which favors formation of water wires that protrude into its hydrophobic core. When the water wires extend across the whole bilayer, they form channels stabilized by the C12E8 head groups. These hydrophilic channels can transport ions across the membrane without the need of major lipid head-group rearrangements.
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Affiliation(s)
- Andraž Polak
- University of Ljubljana , Faculty of Electrical Engineering, Tržaška cesta 25, SI-1000 Ljubljana, Slovenia
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Abstract
Electroporation has been used extensively to transfer DNA to bacteria, yeast, and mammalian cells in culture for the past 30 years. Over this time, numerous advances have been made, from using fields to facilitate cell fusion, delivery of chemotherapeutic drugs to cells and tissues, and most importantly, gene and drug delivery in living tissues from rodents to man. Electroporation uses electrical fields to transiently destabilize the membrane allowing the entry of normally impermeable macromolecules into the cytoplasm. Surprisingly, at the appropriate field strengths, the application of these fields to tissues results in little, if any, damage or trauma. Indeed, electroporation has even been used successfully in human trials for gene delivery for the treatment of tumors and for vaccine development. Electroporation can lead to between 100 and 1000-fold increases in gene delivery and expression and can also increase both the distribution of cells taking up and expressing the DNA as well as the absolute amount of gene product per cell (likely due to increased delivery of plasmids into each cell). Effective electroporation depends on electric field parameters, electrode design, the tissues and cells being targeted, and the plasmids that are being transferred themselves. Most importantly, there is no single combination of these variables that leads to greatest efficacy in every situation; optimization is required in every new setting. Electroporation-mediated in vivo gene delivery has proven highly effective in vaccine production, transgene expression, enzyme replacement, and control of a variety of cancers. Almost any tissue can be targeted with electroporation, including muscle, skin, heart, liver, lung, and vasculature. This chapter will provide an overview of the theory of electroporation for the delivery of DNA both in individual cells and in tissues and its application for in vivo gene delivery in a number of animal models.
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Affiliation(s)
- Jennifer L Young
- Department of Pediatrics, University of Rochester, Rochester, NY, USA
| | - David A Dean
- Departments of Pediatrics and Biomedical Engineering, University of Rochester, Rochester, NY, USA
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Polak A, Tarek M, Tomšič M, Valant J, Ulrih NP, Jamnik A, Kramar P, Miklavčič D. Electroporation of archaeal lipid membranes using MD simulations. Bioelectrochemistry 2014; 100:18-26. [DOI: 10.1016/j.bioelechem.2013.12.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 12/24/2013] [Accepted: 12/31/2013] [Indexed: 12/13/2022]
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Mahnič-Kalamiza S, Vorobiev E, Miklavčič D. Electroporation in food processing and biorefinery. J Membr Biol 2014; 247:1279-304. [PMID: 25287023 DOI: 10.1007/s00232-014-9737-x] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 09/25/2014] [Indexed: 12/12/2022]
Abstract
Electroporation is a method of treatment of plant tissue that due to its nonthermal nature enables preservation of the natural quality, colour and vitamin composition of food products. The range of processes where electroporation was shown to preserve quality, increase extract yield or optimize energy input into the process is overwhelming, though not exhausted; e.g. extraction of valuable compounds and juices, dehydration, cryopreservation, etc. Electroporation is--due to its antimicrobial action--a subject of research as one stage of the pasteurization or sterilization process, as well as a method of plant metabolism stimulation. This paper provides an overview of electroporation as applied to plant materials and electroporation applications in food processing, a quick summary of the basic technical aspects on the topic, and a brief discussion on perspectives for future research and development in the field. The paper is a review in the very broadest sense of the word, written with the purpose of orienting the interested newcomer to the field of electroporation applications in food technology towards the pertinent, highly relevant and more in-depth literature from the respective subdomains of electroporation research.
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Affiliation(s)
- Samo Mahnič-Kalamiza
- Centre de Recherches de Royallieu, University of Technology of Compiègne, BP 20529, 60205, Compiègne Cedex, France,
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Fernández ML, Reigada R. Effects of dimethyl sulfoxide on lipid membrane electroporation. J Phys Chem B 2014; 118:9306-12. [PMID: 25035931 DOI: 10.1021/jp503502s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pores can be generated in lipid membranes by the application of an external electric field or by the addition of particular chemicals such as dimethyl sulfoxide (DMSO). Molecular dynamics (MD) has been shown to be a useful tool for unveiling many aspects of pore formation in lipid membranes in both situations. By means of MD simulations, we address the formation of electropores in cholesterol-containing lipid bilayers under the influence of DMSO. We show how a combination of physical and chemical mechanisms leads to more favorable conditions for generating membrane pores and, in particular, how the addition of DMSO to the medium significantly reduces the minimum electric field required to electroporate a lipid membrane. The strong alteration of membrane transversal properties and the energetic stabilization of the hydrophobic pore stage by DMSO provide the physicochemical mechanisms that explain this effect.
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Affiliation(s)
- M Laura Fernández
- Laboratorio de Sistemas Complejos, Departamento de Computación, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , Buenos Aires, Argentina
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Polak A, Tarek M, Tomšič M, Valant J, Ulrih NP, Jamnik A, Kramar P, Miklavčič D. Structural properties of archaeal lipid bilayers: small-angle X-ray scattering and molecular dynamics simulation study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:8308-8315. [PMID: 25000416 DOI: 10.1021/la5014208] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Aeropyrum pernix is an aerobic hyperthermophilic archaeon that grows in harsh environmental conditions and as such possesses unique structural and metabolic features. Its membrane interfaces with the extreme environment and is the first line of defense from external factors. Therefore, lipids composing this membrane have special moieties that increase its stability. The membrane of A. pernix is composed predominantly of two polar lipids 2,3-di-O-sesterterpanyl-sn-glicerol-1-phospho-1'(2'-O-α-D-glucosyl)-myo-inositol (AGI) and 2,3-di-O-sesterterpanyl-sn-glicerol-1-phospho-myo-inositol (AI). Both have methyl branches in their lipid tails and ether linkages and carbohydrates in their headgroup. These moieties significantly affect the structure and dynamics of the bilayer. To provide a molecular level insight into these characteristics, we used here Molecular Dynamics (MD) simulations of lipid bilayers of composition similar to those of the archaeal membranes. First, we show that the electron density profiles along the normal to the bilayers derived from the simulations are in good agreement with the profiles obtained by the small-angle X-ray scattering (SAXS) technique, which provides confidence in the force fields used. Analyses of the simulation data show that the archaeal lipid bilayers are less hydrated than conventional phosphatidylcholine (PC) lipids and that their structure is not affected by the salt present in the surrounding solution. Furthermore, the lateral pressure in their hydrophobic core, due to the presence of the branched tails, is much higher than that at PC-based lipid bilayers. Both the methyl branched tails and the special headgroup moieties contribute to slow drastically the lateral diffusion of the lipids. Furthermore, we found that the lipid head groups associate via hydrogen bonding, which affects their reorientational dynamics. All together, our data provide links between the microscopic properties of these membranes and their overall stability in harsh environments.
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Affiliation(s)
- Andraž Polak
- Faculty of Electrical Engineering, University of Ljubljana , Tržaška cesta 25, SI-1000 Ljubljana, Slovenia
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Gurtovenko AA, Lyulina AS. Electroporation of Asymmetric Phospholipid Membranes. J Phys Chem B 2014; 118:9909-18. [DOI: 10.1021/jp5028355] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrey A. Gurtovenko
- Institute
of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi
Prospect V.O. 31, St. Petersburg, 199004 Russia
- Faculty
of Physics, St. Petersburg State University, Ulyanovskaya str. 1, Petrodvorets, St. Petersburg, 198504 Russia
| | - Anastasia S. Lyulina
- Institute
of Physics, Nanotechnology and Telecommunications, St. Petersburg State Polytechnical University, Polytechnicheskaya str. 29, St. Petersburg, 195251 Russia
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Sridhara V, Joshi R. Evaluations of a mechanistic hypothesis for the influence of extracellular ions on electroporation due to high-intensity, nanosecond pulsing. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:1793-800. [DOI: 10.1016/j.bbamem.2014.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 03/17/2014] [Accepted: 03/18/2014] [Indexed: 10/25/2022]
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Bonhenry D, Tarek M, Dehez F. Effects of Phospholipid Composition on the Transfer of a Small Cationic Peptide Across a Model Biological Membrane. J Chem Theory Comput 2013; 9:5675-84. [PMID: 26592298 DOI: 10.1021/ct400576e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The transfer of a lysine amino acid analogue across phospholipid membrane models was investigated using molecular-dynamics simulations. The evolution of the protonation state of this small peptide as a function of its position inside the membrane was studied by determining the local pKa by means of free-energy calculations. Permeability and mean-first-passage time were evaluated and showed that the transfer occurs on the submillisecond time scale. Comparative studies were conducted to evaluate changes in the pKa arising from differences in the phospholipid chemical structure. We compared, hence, the effect of an ether vs an ester linkage of the lipid headgroup as well as linear vs branched lipid tails. The study reveals that protonated lysine residues can be buried further inside an ether lipid membrane than an ester lipid membrane, while branched lipids are found to stabilize less the charged form compared to their unbranched lipid chain counterparts.
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Affiliation(s)
- Daniel Bonhenry
- Université de Lorraine, SRSMC, UMR 7565 , Vandoeuvre-lès-Nancy, F-54500, France.,CNRS, SRSMC, UMR 7565 , Vandoeuvre-lès-Nancy, F-54500, France
| | - Mounir Tarek
- Université de Lorraine, SRSMC, UMR 7565 , Vandoeuvre-lès-Nancy, F-54500, France.,CNRS, SRSMC, UMR 7565 , Vandoeuvre-lès-Nancy, F-54500, France
| | - François Dehez
- Université de Lorraine, SRSMC, UMR 7565 , Vandoeuvre-lès-Nancy, F-54500, France.,CNRS, SRSMC, UMR 7565 , Vandoeuvre-lès-Nancy, F-54500, France
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