1
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Mielke S, Sorkin R, Klein J. Effect of cholesterol on the mechanical stability of gel-phase phospholipid bilayers studied by AFM force spectroscopy. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:77. [PMID: 37672138 DOI: 10.1140/epje/s10189-023-00338-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/24/2023] [Indexed: 09/07/2023]
Abstract
The remarkably low sliding friction of articular cartilage in the major joints such as hips and knees, which is crucial for its homeostasis and joint health, has been attributed to lipid bilayers forming lubricious boundary layers at its surface. The robustness of such layers, and thus their lubrication efficiency at joint pressures, depends on the lipids forming them, including cholesterol which is a ubiquitous component, and which may act to strengthen of weaken the bilayer. In this work, a systematic study using an atomic force microscope (AFM) was carried out to understand the effect of cholesterol on the nanomechanical stability of two saturated phospholipids, DSPC (1,2-distearoyl-sn-glycero-3-phosphatidlycholine) and DPPC (1,2-dipalmitoyl-sn-glycero- phosphatidylcholine), that differ in acyl chain lengths. Measurements were carried out both in water and in phosphate buffer solution (PBS). The nanomechanical stability of the lipid bilayers was quantitatively evaluated by measuring the breakthrough force needed to puncture the bilayer by the AFM tip. The molar fractions of cholesterol incorporated in the bilayers were 10% and 40%. We found that for both DSPC and DPPC, cholesterol significantly decreases the mechanical stability of the bilayers in solid-ordered (SO) phase. In accordance with the literature, the strengthening effect of salt on the lipid bilayers was also observed. For DPPC with 10 mol % cholesterol, the effect of tip properties and the experimental procedure parameters on the breakthrough forces were also studied. Tip radius (2-42 nm), material (Si, Si3N4, Au) and loading rate (40-1000 nm/s) were varied systematically. The values of the breakthrough forces measured were not significantly affected by any of these parameters, showing that the weakening effect of cholesterol does not result from such changes in experimental conditions. As we have previously demonstrated that mechanical robustness improves the tribological performance of lipid layers, this study helps to shed light on the mechanism of physiological lubrication. Nanoindentation of SDPC bilayers.
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Affiliation(s)
- Salomé Mielke
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Raya Sorkin
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel.
| | - Jacob Klein
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 76100, Rehovot, Israel.
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2
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Rostami N, Faridghiasi F, Ghebleh A, Noei H, Samadzadeh M, Gomari MM, Tajiki A, Abdouss M, Aminoroaya A, Kumari M, Heidari R, Uversky VN, Smith BR. Design, Synthesis, and Comparison of PLA-PEG-PLA and PEG-PLA-PEG Copolymers for Curcumin Delivery to Cancer Cells. Polymers (Basel) 2023; 15:3133. [PMID: 37514522 PMCID: PMC10385204 DOI: 10.3390/polym15143133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/17/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Curcumin (CUR) has potent anticancer activities, and its bioformulations, including biodegradable polymers, are increasingly able to improve CUR's solubility, stability, and delivery to cancer cells. In this study, copolymers comprising poly (L-lactide)-poly (ethylene glycol)-poly (L-lactide) (PLA-PEG-PLA) and poly (ethylene glycol)-poly (L-lactide)-poly (ethylene glycol) (PEG-PLA-PEG) were designed and synthesized to assess and compare their CUR-delivery capacity and inhibitory potency on MCF-7 breast cancer cells. Molecular dynamics simulations and free energy analysis indicated that PLA-PEG-PLA has a higher propensity to interact with the cell membrane and more negative free energy, suggesting it is the better carrier for cell membrane penetration. To characterize the copolymer synthesis, Fourier transform-infrared (FT-IR) and proton nuclear magnetic resonance (1H-NMR) were employed, copolymer size was measured using dynamic light scattering (DLS), and their surface charge was determined by zeta potential analysis. Characterization indicated that the ring-opening polymerization (ROP) reaction was optimal for synthesizing high-quality polymers. Microspheres comprising the copolymers were then synthesized successfully. Of the two formulations, PLA-PEG-PLA experimentally exhibited better results, with an initial burst release of 17.5%, followed by a slow, constant release of the encapsulated drug up to 80%. PLA-PEG-PLA-CUR showed a significant increase in cell death in MCF-7 cancer cells (IC50 = 23.01 ± 0.85 µM) based on the MTT assay. These data were consistent with gene expression studies of Bax, Bcl2, and hTERT, which showed that PLA-PEG-PLA-CUR induced apoptosis more efficiently in these cells. Through the integration of nano-informatics and in vitro approaches, our study determined that PLA-PEG-PLA-CUR is an optimal system for delivering curcumin to inhibit cancer cells.
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Affiliation(s)
- Neda Rostami
- Department of Chemistry, Amirkabir University of Technology, Tehran 1591634311, Iran
| | - Farzaneh Faridghiasi
- Department of Tissue Engineering and Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Aida Ghebleh
- School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan 8174673461, Iran
| | - Hadi Noei
- Department of Medical Biology and Genetics, Faculty of Medicine, Istinye University, Istanbul 34010, Turkey
| | - Meisam Samadzadeh
- Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Istinye University, Istanbul 34010, Turkey
| | - Mohammad Mahmoudi Gomari
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Alireza Tajiki
- Department of Chemistry, Amirkabir University of Technology, Tehran 1591634311, Iran
| | - Majid Abdouss
- Department of Chemistry, Amirkabir University of Technology, Tehran 1591634311, Iran
| | - Alireza Aminoroaya
- Department of Biomedical Engineering and Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Manisha Kumari
- Department of Biomedical Engineering and Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Reza Heidari
- Research Center for Cancer Screening and Epidemiology, AJA University of Medical Sciences, Tehran 1411718541, Iran
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Bryan R Smith
- Department of Biomedical Engineering and Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
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3
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Meng X, Liu H, Zhao N, Yang Y, Zhao K, Dai Y. Molecular Dynamics Study of the Effect of Charge and Glycosyl on Superoxide Anion Distribution near Lipid Membrane. Int J Mol Sci 2023; 24:10926. [PMID: 37446103 DOI: 10.3390/ijms241310926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
To examine the effects of membrane charge, the electrolyte species and glycosyl on the distribution of negatively charged radical of superoxide anion (·O2-) around the cell membrane, different phospholipid bilayer systems containing ·O2- radicals, different electrolytes and phospholipid bilayers were constructed through Charmm-GUI and Amber16. These systems were equilibrated with molecular dynamics by using Gromacs 5.0.2 to analyze the statistical behaviors of ·O2- near the lipid membrane under different conditions. It was found that in the presence of potassium rather than sodium, the negative charge of the phospholipid membrane is more likely to rarefy the superoxide anion distribution near the membrane surface. Further, the presence of glycosyl significantly reduced the density of ·O2- near the phospholipid bilayer by 78.3% compared with that of the neutral lipid membrane, which may have a significant contribution to reducing the lipid peroxidation from decreasing the ·O2- density near the membrane.
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Affiliation(s)
- Xuan Meng
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Huiyu Liu
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Ning Zhao
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Yajun Yang
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Kai Zhao
- Hebei Kingsci Pharmaceutical Technology Co., Ltd., Shijiazhuang 050035, China
- Jangxi Ourshi Pharmaceutical Co., Ltd., Xinyu 338012, China
| | - Yujie Dai
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
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4
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Banerjee KK, Maity P, Das S, Karmakar S. Effect of cholesterol on the ion-membrane interaction: Zeta potential and dynamic light scattering study. Chem Phys Lipids 2023; 254:105307. [PMID: 37182823 DOI: 10.1016/j.chemphyslip.2023.105307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/11/2023] [Indexed: 05/16/2023]
Abstract
Cholesterol in a bio-membrane plays a significant role in many cellular event and is known to regulate the functional activity of protein and ion channel. In this study we report a significant effect of cholesterol on the ion-membrane interaction. We prepare large unilamellar vesicles, composed of zwitterionic lipid DOPC and anionic lipid DOPG with different cholesterol concentration. Electrostatics of anionic membranes containing cholesterol in the presence of NaCl has systematically been explored using dynamic light scattering and zeta potential. Negative zeta potential of the membrane decreases its negative value with increasing ion concentration for all cholesterol concentrations. However, zeta potential itself decreases with increasing cholesterol content even in the absence of monovalent ions. Electrostatic behaviour of the membrane is determined from well-known Gouy Chapmann model. Negative surface charge density of the membrane decreases with increasing cholesterol content. Binding constant, estimated from the electrostatic double layer theory, is found to increase significantly in the presence of cholesterol. Comparison of electrostatic parameters of the membrane in the presence and absence of cholesterol suggests that cholesterol significantly alter the electrostatic behaviour of the membrane.
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Affiliation(s)
- Kalyan Kumar Banerjee
- Soft matter and Biophysics Laboratory, Department of Physics, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata 700032, India
| | - Pabitra Maity
- Soft matter and Biophysics Laboratory, Department of Physics, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata 700032, India
| | - Surajit Das
- Soft matter and Biophysics Laboratory, Department of Physics, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata 700032, India
| | - Sanat Karmakar
- Soft matter and Biophysics Laboratory, Department of Physics, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata 700032, India.
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Chattopadhyay M, Krok E, Orlikowska-Rzeznik H, Piatkowski L. Cooperativity between sodium ions and water molecules facilitates lipid mobility in model cell membranes. Chem Sci 2023; 14:4002-4011. [PMID: 37063804 PMCID: PMC10094088 DOI: 10.1039/d2sc06836b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Cellular membranes are surrounded by an aqueous buffer solution containing various ions, which influence the hydration layer of the lipid head groups. At the same time, water molecules hydrating the lipids play a major role in facilitating the organisation and dynamics of membrane lipids. Employing fluorescence microscopy imaging and fluorescence recovery after photobleaching measurements, we demonstrate that the cooperativity between water and sodium (Na+) ions is crucial to maintain lipid mobility upon the removal of the outer hydration layer of the lipid membrane. Under similar hydration conditions, lipid diffusion ceases in the absence of Na+ ions. We find that Na+ ions (and similarly K+ ions) strengthen the water clathrate cage around the lipid phosphocholine headgroup and thus prevent its breaking upon removal of bulk water. Intriguingly, Ca2+ and Mg2+ do not show this effect. In this article, we provide a detailed molecular-level picture of ion specific dependence of lipid mobility and membrane hydration properties.
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Affiliation(s)
| | - Emilia Krok
- Institute of Physics, Poznan University of Technology Piotrowo 3 60-965 Poznan Poland
| | | | - Lukasz Piatkowski
- Institute of Physics, Poznan University of Technology Piotrowo 3 60-965 Poznan Poland
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6
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Abdel-Gawad WM, Abdelmohsen M, Gaber MH, Khalil WMA, Abu-Elmagd MSM. Molecular dynamics simulation of phosphatidylcholine membrane in low ionic strengths of sodium chloride. J Biomol Struct Dyn 2023; 41:13891-13901. [PMID: 36812302 DOI: 10.1080/07391102.2023.2183040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 02/14/2023] [Indexed: 02/24/2023]
Abstract
The one-microsecond molecular dynamics simulations of a membrane-protein complex investigate the influence of the aqueous sodium chloride solutions on the structure and dynamics of a palmitoyl-oleoyl-phosphatidylcholine bilayer membrane. The simulations were performed on five different concentrations (40, 150, 200, 300, and 400 mM) in addition to a salt-free system by using the charmm36 force field for all atoms. Four biophysical parameters, (membrane thicknesses of annular and bulk lipids, and the area per lipid of both leaflets), were computed separately. Nevertheless, the area per lipid was expressed by using the Voronoi algorithm. All time-independent analyses were carried out for the last 400 ns trajectories. Different concentrations revealed dissimilar membrane dynamics before equilibration. The biophysical properties of the membrane (thickness, area-per-lipid, and order parameter) have non-significant changes with increasing ionic strength, however, the 150 mM system had exceptional behavior. Sodium cations were dynamically penetrating the membrane forming weak coordinate bonds with single or multiple lipids. Nevertheless, the binding constant was unaffected by the cation concentration. The electrostatic and Van der Waals energies of lipid-lipid interactions were influenced by the ionic strength. On the other hand, the Fast Fourier Transform was performed to figure out the dynamics at the membrane-protein interface. The nonbonding energies of membrane-protein interactions and order parameters explained the differences in the synchronization pattern. All results were consensus with experimental and theoretical works.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Mahmoud Abdelmohsen
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
- Mathematics and Engineering Physics Department, The Higher Institute of Engineering, Shorouk Academy, El-Shorouk City, Cairo, Egypt
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7
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Nachliel E, Gutman M. Reaction within the coulomb-cage; science in retrospect. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184071. [PMID: 36244436 DOI: 10.1016/j.bbamem.2022.184071] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 08/01/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
The Coulomb-cage is defined as the space where the electrostatic interaction between two bodies is more intensive than the thermal energy (kBT). For small molecule, the Coulomb-cage is a small sphere, extending only few water molecules towards the bulk and its radius is sensitive to the ionic strength of the solution. For charged proteins or membranal structures, the Coulomb-cage can engulf large fraction of the surface and provides a preferred pathway for ion propagation along the surface. Similarly, electrostatic potential at the inner space of a channel can form preferential trajectories passage for ions. The dynamics of ions inside the Coulomb-cage of ions was formulated by the studies of proton-anion recombination of excited photoacids. In the present article, we recount the study of intra- Coulomb-cage reaction taking place on the surface of macro-molecular bodies like micelles, membranes, proteins and intra-protein cavities. The study progressed stepwise, tracing the dynamics of a proton ejected from a photo-acid molecule located at defined sites (on membrane, inter-membrane space, active site of enzyme, inside Large Pore Channels etc.). Accumulation of experimental observations encouraged us to study of the reaction mechanism by molecular dynamics simulations of ions within the Coulomb-cage of proteins surface or inside large pores. The intra-Coulomb-cage proton transfer events follows closely the fine structure of the electrostatic field inside the cage and reflects the shape of nearby dielectric boundaries, the temporal ordering of the solvent molecules and the structural fluctuations of the charged side chains. The article sums some 40 years of research, which in retrospect clarifies the intra-Coulomb-cage reaction mechanism.
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Affiliation(s)
- E Nachliel
- Laser Laboratory for Fast Reactions, Dep. Of Biochemistry and Molecular Biology, Life Sciences, Tel Aviv University, Israel
| | - M Gutman
- Laser Laboratory for Fast Reactions, Dep. Of Biochemistry and Molecular Biology, Life Sciences, Tel Aviv University, Israel.
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8
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Sharma VK, Gupta J, Mamontov E. Lateral diffusion of lipids in the DMPG membrane across the anomalous melting regime: effects of NaCl. SOFT MATTER 2022; 19:57-68. [PMID: 36458871 DOI: 10.1039/d2sm01425d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The anionic dimyristoyl phosphatidylglycerol (DMPG) membrane in solvents with a low ionic strength is known to exhibit an unusually wide melting regime between the gel and fluid phase characterized by various anomalous macroscopic characteristics, such as low turbidity and high electrical conductivity and viscosity. A recent neutron spin echo study [Kelley, E. G. et al., Struct. Dyn., 7 (2020) 054704] revealed that during the extended melting phase transition the DMPG membrane becomes softer and exhibits faster collective bending fluctuation compared to the higher temperature fluid phase. In contrast, in the present work, using incoherent quasielastic neutron scattering through the anomalous phase transition regime we find that single-particle lateral and internal lipid motions in the DMPG membrane show regular temperature dependence, with no enhanced dynamics evident in the anomalous melting regime. Further, we find that incorporation of NaCl in DMPG suppresses the anomalous extended melting regime, concurrently enhancing the single-particle lipid dynamics, both the lateral diffusivity and (to a lesser extent) the internal lipid motion. This seems rather counterintuitive and in variance with the dynamic suppression effect exerted by a salt on a zwitterionic membrane. However, since incorporation of a salt in anionic DMPG leads to enhanced cooperativity, the disrupted cooperativity in the salt-free DMPG is associated with the baseline lipid dynamics that is suppressed to begin with, whereas addition of salt partially restores the cooperativity, thus enhancing lipid dynamics compared to the salt-free baseline DMPG membrane state. These results provide new insights into the ion-membrane interaction and divulge a correlation between microscopic dynamics and the structure of the lipid bilayer.
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Affiliation(s)
- V K Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - J Gupta
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - E Mamontov
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
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9
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Hu P, Shao J, Qian G, Adeleye AS, Hao T. Removal of tetracycline by aerobic granular sludge from marine aquaculture wastewater: A molecular dynamics investigation. BIORESOURCE TECHNOLOGY 2022; 355:127286. [PMID: 35545206 DOI: 10.1016/j.biortech.2022.127286] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Although biological treatment of marine aquaculture wastewater is promising, the fundamental principles driving the adsorption of tetracycline to microbial cell membrane are not well understood. Using a combination of experiments and molecular dynamics (MD) simulations, the mechanism underlying the biological removal of tetracycline from seawater was investigated. More than 90% tetracycline removal was achieved in an aerobic granular sludge system, with degradation accounting for 30% of total removal. A model of the tetracycline-dipalmitoylphosphatidylcholine lipid bilayers was established to elucidate the transport mechanism of tetracycline from bulk solution to microorganisms' cell membrane. 62% of the driving force for tetracycline adsorption on the cell membrane originated from electrostatic attraction. The electrophilic groups on tetracycline (amino and aromatic groups) were attracted to the phosphate groups in the cell membrane. Sodium ions, which are abundant in seawater, decreased the interaction energy between tetracycline and the cell membrane.
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Affiliation(s)
- Peng Hu
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Jingyi Shao
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Guangsheng Qian
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Adeyemi S Adeleye
- Department of Civil and Environmental Engineering, University of California, Irvine, CA 92697-2175, USA
| | - Tianwei Hao
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China.
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10
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Frigini EN, Porasso RD. Effect of Ionic Strength on Ibuprofenate Adsorption on a Lipid Bilayer of Dipalmitoylphosphatidylcholine from Molecular Dynamics Simulations. J Phys Chem B 2022; 126:1941-1950. [PMID: 35226503 DOI: 10.1021/acs.jpcb.1c09301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this work, the free energy change in the process of transferring ibuprofenate from the bulk solution to the center of a model of the dipalmitoylphosphatidylcholine bilayer at different NaCl concentrations was calculated. Two minima were found in the free energy profile: a local minimum, located in the vicinity of the membrane, and the global free energy minimum, found near the headgroup region. The downward shift of free energy minima with increasing NaCl concentration is consistent with the results of previous works. Conversely, the upward shift of the free energy maximum with increasing ionic strength is due to the competition of sodium ions and lipids molecules to coordinate with ibuprofenate and neutralize its charge. In addition, normal molecular dynamics simulations were performed to study the effects of the ibuprofenate on the lipid bilayer and in the presence of a high ibuprofenate concentration. The effect of ionic strength on the properties of the lipid bilayer and on lipid-drug interactions was analyzed. The area per lipid shrinking with increasing ionic strength, volume of lipids, and thickness of the bilayer is consistent with the experimental results. At a very high ibuprofenate concentration, the lipid bilayer dehydrates, and it consequently transforms into the gel phase, thus blocking the permeation.
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Affiliation(s)
- Ezequiel N Frigini
- Instituto de Matemáticas Aplicada San Luis, CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Avenida Ejército de los Andes 950, 5700 San Luis, Argentina
| | - Rodolfo D Porasso
- Instituto de Matemáticas Aplicada San Luis, CONICET, Facultad de Ciencias Físico Matemáticas y Naturales, Universidad Nacional de San Luis, Avenida Ejército de los Andes 950, 5700 San Luis, Argentina
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11
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Jang J, Kim S, Eom K. NaCl increases the dielectric constant of nanoconfined water in phospholipid multilamellar vesicle by enhancing intermolecular orientation correlation rather than rotational freedom of individual molecules. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Frigini EN, López Cascales JJ, Porasso RD. Influence of Lipid Composition on the Insertion Process of Glyphosate into Membranes: A Thermodynamic Study. J Phys Chem B 2021; 125:184-192. [PMID: 33375787 DOI: 10.1021/acs.jpcb.0c09561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, molecular dynamics simulations were applied to investigate the influence of lipid composition of the model membrane on the insertion of glyphosate (in its charged state, GLYP2-). The profiles of free energy, entropy and enthalpy were obtained through umbrella sampling calculations, for lipid bilayers composed by only 1,2-dipalmitoyl-sn-glycerol-3-phosphocholine (DPPC), only 1,2-dipalmitoyl-sn-glycerol-3-phosphoserine (DPPS) or a symmetric binary mixture of DPPC and DPPS. In general, the location, the values of minima and maxima of the free energy, and the trend of free energy profiles are influenced by the lipid composition of the lipid bilayer. The driving force in the glyphosate insertion process depends on the lipid composition of the membrane model. If the lipid bilayer is composed solely of DPPS or DPPC, GLYP2- insertion is driven by a favorable enthalpic change. However, if the membrane is composed of a mixture of both lipids, this process is driven by a favorable entropic change. In the lipid bilayer containing DPPS, the glyphosate was found to penetrate hydrated and coordinated with Na+ ions, in contrast to the pure zwitterionic lipid bilayer which penetrated only hydrated. This effect is independent of the concentration of sodium ions present in the bulk solution.
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Affiliation(s)
- Ezequiel N Frigini
- Instituto de Matemáticas Aplicada San Luis (IMASL), CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Avenue Ejército de los Andes 950, 5700 San Luis, Argentina
| | - J J López Cascales
- Universidad Politécnica de Cartagena, Grupo de Bioinformática y Macromoléculas (BioMac), Área de Química Física, Aulario II, Campus de Alfonso XIII, 30203 Cartagena, Murcia, Spain
| | - Rodolfo D Porasso
- Instituto de Matemáticas Aplicada San Luis (IMASL), CONICET, Facultad de Ciencias Física Matemáticas y Naturales, Universidad Nacional de San Luis, Avenue Ejército de los Andes 950, 5700 San Luis, Argentina
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13
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Smith MD, Smith JC. Effects of sodium and calcium chloride ionic stresses on model yeast membranes revealed by molecular dynamics simulation. Chem Phys Lipids 2020; 233:104980. [PMID: 33038307 DOI: 10.1016/j.chemphyslip.2020.104980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 09/27/2020] [Accepted: 09/28/2020] [Indexed: 11/25/2022]
Abstract
As efforts to move a renewable economy grow, it will be necessary to make use of microbial conversion strategies for the production of novel materials or the upgrading of waste to high-value products. One critical technical challenge currently limiting waste upgrading remains the difficulty in obtaining single-pot conversion techniques where physical, chemical, and biological conversion are performed in a single step. To overcome this challenge, a detailed understanding of how different stresses impact microbial membrane stability will be necessary. Using all-atom molecular dynamics simulations, we examine the impacts of moderate concentrations of NaCl and CaCl2on a model yeast plasma membrane. Weak, though statistically significant, changes in membrane morphology and dynamics functions are observed that are consistent with swelling and stiffening. Additionally, an examination of the ion-lipid contacts and the behavior of water at the water-membrane interface suggests that the impacts of these common salts may, in part, be mediated through changes to water-membrane hydrogen-bonding and hydration water dynamics.
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Affiliation(s)
- Micholas Dean Smith
- Department of Biochemistry, Molecular & Cellular Biology, The University of Tennessee, Knoxville, Knoxville, TN, United States; UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, United States.
| | - Jeremy C Smith
- Department of Biochemistry, Molecular & Cellular Biology, The University of Tennessee, Knoxville, Knoxville, TN, United States; UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, United States
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14
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Deplazes E, Tafalla BD, Cranfield CG, Garcia A. Role of Ion-Phospholipid Interactions in Zwitterionic Phospholipid Bilayer Ion Permeation. J Phys Chem Lett 2020; 11:6353-6358. [PMID: 32687371 DOI: 10.1021/acs.jpclett.0c01479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Despite the central role of Na+ and K+ in physiological processes, it is still unclear whether they interact or alter the physical properties of simple zwitterionic phospholipid bilayers at physiologically relevant concentrations. Here we report a difference in membrane permeability between Na+ and K+, as measured with electrical impedance spectroscopy and tethered bilayer lipid membranes. We reveal that the differences in membrane permeability originate from distinct ion coordination by carbonyl oxygens at the phospholipid-water interface, altering the propensity for bilayer pore formation. Molecular dynamics simulations showed differences in the coordination of Na+ and K+ at the phospholipid-water interface of zwitterionic phospholipid bilayers. The ability of Na+ to conscript more phospholipids with a greater number of coordinating interactions causes a higher localized energy barrier for pore formation. These results provide evidence that ion-specific interactions at the phospholipid-water interface can modulate the physical properties of zwitterionic phospholipid bilayers.
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Affiliation(s)
- Evelyne Deplazes
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | | | - Charles G Cranfield
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Alvaro Garcia
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
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15
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Pires F, Magalhães-Mota G, Geraldo VPN, Ribeiro PA, Oliveira ON, Raposo M. The impact of blue light in monolayers representing tumorigenic and nontumorigenic cell membranes containing epigallocatechin-3-gallate. Colloids Surf B Biointerfaces 2020; 193:111129. [PMID: 32502833 DOI: 10.1016/j.colsurfb.2020.111129] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 04/21/2020] [Accepted: 05/11/2020] [Indexed: 02/08/2023]
Abstract
Natural products such as epigallocatechin-3-gallate (EGCG) have been suggested for complementary treatments of cancer, since they lower toxic side effects of anticancer drugs, and possess anti-inflammatory and antioxidant properties that inhibit carcinogenesis. Their effects on cancer cells depend on interactions with the membrane, which is the motivation to investigate Langmuir monolayers as simplified membrane models. In this study, EGCG was incorporated in zwitterionic dipalmitoyl phosphatidyl choline (DPPC) and anionic dipalmitoyl phosphatidyl serine (DPPS) Langmuir monolayers to simulate healthy and cancer cells membranes, respectively. EGCG induces condensation in surface pressure isotherms for both DPPC and DPPS monolayers, interacting mainly via electrostatic forces and hydrogen bonding with the choline and phosphate groups of the phospholipids, according to data from polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS). Both monolayers become more compressible upon interaction with EGCG, which may be correlated to the synergy between EGCG and anticancer drugs reported in the literature. The interaction with EGCG is stronger for DPPC, leading to stronger morphological changes in Brewster angle microscopy (BAM) images and higher degree of condensation in the surface pressure isotherms. The changes induced by blue irradiation on DPPC and DPPS monolayers were largely precluded when EGCG was incorporated, thus confirming its antioxidant capacity for both types of membrane.
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Affiliation(s)
- Filipa Pires
- CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Gonçalo Magalhães-Mota
- CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | | | - Paulo A Ribeiro
- CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | | | - Maria Raposo
- CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.
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16
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Han K, Gericke A, Pastor RW. Characterization of Specific Ion Effects on PI(4,5)P 2 Clustering: Molecular Dynamics Simulations and Graph-Theoretic Analysis. J Phys Chem B 2020; 124:1183-1196. [PMID: 31994887 PMCID: PMC7461730 DOI: 10.1021/acs.jpcb.9b10951] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Numerous cellular functions mediated by phosphatidylinositol (4,5)-bisphosphate (PI(4,5)P2; PIP2) involve clustering of the lipid as well as colocalization with other lipids. Although the cation-mediated electrostatic interaction is regarded as the primary clustering mechanism, the ion-specific nature of the intermolecular network formation makes it challenging to characterize the clusters. Here we use all-atom molecular dynamics (MD) simulations of PIP2 monolayers and graph-theoretic analysis to gain insight into the phenomenon. MD simulations reveal that the intermolecular interactions preferentially occur between specific cations and phosphate groups (P1, P4, and P5) of the inositol headgroup with better-matched kosmotropic/chaotropic characters consistent with the law of matching water affinities (LMWA). Ca2+ is strongly attracted to P4/P5, while K+ preferentially binds to P1; Na+ interacts with both P4/P5 and P1. These specific interactions lead to the characteristic clustering patterns. Specificially, the size distributions and structures of PIP2 clusters generated by kosmotropic cations Ca2+ and Na+ are bimodal, with a combination of small and large clusters, while there is little clustering in the presence of only chaotropic K+; the largest clusters are obtained in systems with all three cations. The small-world network (a model with both local and long-range connections) best characterizes the clusters, followed by the random and the scale-free networks. More generally, the present results interpreted within the LMWA are consistent with the relative eukaryotic intracellular concentrations Ca2+ ≪ Na+ < Mg2+ < K+; that is, concentrations of Ca2+ and Na+ must be low to prevent damaging aggregation of lipids, DNA, RNA and phosphate-containing proteins.
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Affiliation(s)
- Kyungreem Han
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Arne Gericke
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Richard W. Pastor
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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17
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Westerfield J, Gupta C, Scott HL, Ye Y, Cameron A, Mertz B, Barrera FN. Ions Modulate Key Interactions between pHLIP and Lipid Membranes. Biophys J 2019; 117:920-929. [PMID: 31422821 DOI: 10.1016/j.bpj.2019.07.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/05/2019] [Accepted: 07/22/2019] [Indexed: 02/04/2023] Open
Abstract
The pH-low insertion peptide (pHLIP) is used for targeted delivery of drug cargoes to acidic tissues such as tumors. The extracellular acidosis found in solid tumors triggers pHLIP to transition from a membrane-adsorbed state to fold into a transmembrane α-helix. Different factors influence the acidity required for pHLIP to insert into lipid membranes. One of them is the lipid headgroup composition, which defines the electrostatic profile of the membrane. However, the molecular interactions that drive the adsorption of pHLIP to the bilayer surface are poorly understood. In this study, we combine biophysical experiments and all-atom molecular dynamics simulations to understand the role played by electrostatics in the interaction between pHLIP and a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer. We observed that the solution ionic strength affects the structure of pHLIP at the membrane surface as well as the acidity needed for different steps in the membrane insertion process. In particular, our simulations revealed that an increase in ionic strength affected both pHLIP and the bilayer; the coordination of sodium ions with the C-terminus of pHLIP led to localized changes in helicity, whereas the coordination of sodium ions with the phosphate moiety of the phosphocholine headgroups had a condensing effect on our model bilayer. These results are relevant to our understanding of environmental influences on the ability of pHLIP to adsorb to the cell membrane and are useful in our fundamental understanding of the absorption of pH-responsive peptides and cell-penetrating peptides.
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Affiliation(s)
- Justin Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee
| | - Chitrak Gupta
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia
| | - Haden L Scott
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee
| | - Yujie Ye
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee
| | - Alayna Cameron
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee
| | - Blake Mertz
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia; WVU Cancer Institute, West Virginia University, Morgantown, West Virginia.
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee.
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18
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Deplazes E, White J, Murphy C, Cranfield CG, Garcia A. Competing for the same space: protons and alkali ions at the interface of phospholipid bilayers. Biophys Rev 2019; 11:483-490. [PMID: 31115866 DOI: 10.1007/s12551-019-00541-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/29/2019] [Indexed: 10/26/2022] Open
Abstract
Maintaining gradients of solvated protons and alkali metal ions such as Na+ and K+ across membranes is critical for cellular function. Over the last few decades, both the interactions of protons and alkali metal ions with phospholipid membranes have been studied extensively and the reported interactions of these ions with phospholipid headgroups are very similar, yet few studies have investigated the potential interdependence between proton and alkali metal ion binding at the water-lipid interface. In this short review, we discuss the similarities between the proton-membrane and alkali ion-membrane interactions. Such interactions include cation attraction to the phosphate and carbonyl oxygens of the phospholipid headgroups that form strong lipid-ion and lipid-ion-water complexes. We also propose potential mechanisms that may modulate the affinities of these cationic species to the water-phospholipid interfacial oxygen moieties. This review aims to highlight the potential interdependence between protons and alkali metal ions at the membrane surface and encourage a more nuanced understanding of the complex nature of these biologically relevant processes.
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Affiliation(s)
- Evelyne Deplazes
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia. .,School of Pharmacy and Biomedical Sciences, Curtin University, Perth, WA, 6845, Australia.
| | - Jacqueline White
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Christopher Murphy
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Charles G Cranfield
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Alvaro Garcia
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
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19
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Vashchenko O, Kasian N, Budianska L, Brodskii R, Bespalova I, Lisetski L. Adsorption of ions on model phospholipid membranes. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.11.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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20
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Meynaq MYK, Lindholm-Sethson B, Tesfalidet S. Interaction of anions with lipid cubic phase membranes, an electrochemical impedance study. J Colloid Interface Sci 2018; 528:263-270. [PMID: 29859451 DOI: 10.1016/j.jcis.2018.05.071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/18/2018] [Accepted: 05/21/2018] [Indexed: 11/30/2022]
Abstract
HYPOTHESIS Electrochemical impedance spectroscopy is useful to monitor anionic interactions with a Lipid Cubic Phase, as previously demonstrated for cationic interaction (Khani Meynaq et al., 2016). It was expected that the smaller hydrophilic anions, acetate and chloride, would interact differently than the large tryptophan anion with its hydrophobic tail. EXPERIMENT The impedance measurements enabled estimation of resistances and capacitances of a freestanding lipid cubic phase membrane at exposure to 4 and 40 mM solutions of NaCl, NaOAc and NaTrp. Small-angle X-ray scattering was used for cubic phase identification and to track structural changes within the cubic phase when exposed to the different electrolytes. FINDINGS The membrane resistance increases at exposure to the electrolytes in the order Cl- < OAc- < Trp-. The membrane resistance decreases with time at exposure to the hydrophilic anions and increases with time at Trp- exposure. The membrane capacitances were lower for NaTrp compared to NaCl and NaOAc at the corresponding concentrations which is consistent with the results from SAXRD. It is concluded that Trp- ions do not enter the aqueous channels of the cubic phase but are strongly adsorbed to the membrane/electrolyte interface leading to large alteration of the lipid phase structure and a high membrane resistance.
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21
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Rezaei Sani SM, Akhavan M, Jalili S. Salt-induced effects on natural and inverse DPPC lipid membranes: Molecular dynamics simulation. Biophys Chem 2018; 239:7-15. [DOI: 10.1016/j.bpc.2018.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/22/2018] [Accepted: 04/22/2018] [Indexed: 11/29/2022]
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22
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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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23
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Abstract
Biomembranes assemble and operate at the interface with electrolyte solutions. Interactions between ions in solutions and the lipid affect the membrane structure, dynamics and electrostatic potential. In this article, I review some of the experimental and computational methods that are used to study membrane–ions interactions. Experimental methods that account for membrane–ion interactions directly and indirectly are presented first. Then, studies in which molecular dynamics simulations were used to gain an understanding of membrane–ion interactions are surveyed. Finally, the current view on membrane–ion interactions and their significance is briefly discussed.
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Affiliation(s)
- Ran Friedman
- Department of Chemistry and Biomedical Sciences and Centre of Excellence "Biomaterials Chemistry", Linnæus University, Kalmar, Sweden.
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24
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Kinetics of DNA condensation with DPPC: effect of calcium and sodium cations. CHEMICAL PAPERS 2017. [DOI: 10.1007/s11696-017-0340-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Martí J. Free-energy surfaces of ionic adsorption in cholesterol-free and cholesterol-rich phospholipid membranes. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1391383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Jordi Martí
- Department of Physics, Technical University of Catalonia-Barcelona Tech, Barcelona, Spain
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26
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Kruczek J, Saunders M, Khosla M, Tu Y, Pandit SA. Molecular dynamics simulations of ether- and ester-linked phospholipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2297-2307. [PMID: 28882547 DOI: 10.1016/j.bbamem.2017.08.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/28/2017] [Accepted: 08/30/2017] [Indexed: 10/18/2022]
Abstract
Dissimilarities in the bulk structure of bilayers composed of ether- vs ester-linked lipids are well-established; however, the atomistic interactions responsible for these differences are not well known. These differences are important in understanding of why archaea have a different bilayer composition than the other domains of life and why humans have larger concentrations of plasmalogens in specialized membranes? In this paper, we simulate two lipid bilayers, the ester linked dipalmitoylphosphatidylcholine (DPPC) and the ether lined dihexadecylphosphatidylcholine (DHPC), to study these variations. The structural analysis of the bilayers reveals that DPPC is more compressible than DHPC. A closer examination of dipole potential shows DHPC, despite having a smaller dipole potential of the bilayer, has a higher potential barrier than DPPC at the surface. Analysis of water order and dynamics suggests DHPC has a more ordered, less mobile layer of water in the headgroup. These results seem to resolve the issue as to whether the decrease in permeability of DHPC is due to of differences in minimum area per lipid (A0) or diffusion coefficient of water in the headgroup region (Dhead) (Guler et al., 2009) since we have shown significant changes in the order and mobility of water in that region.
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Affiliation(s)
- James Kruczek
- Department of Physics, University of South Florida, Tampa, FL 33620, United States.
| | - Matthew Saunders
- Department of Physics, University of South Florida, Tampa, FL 33620, United States
| | - Meghna Khosla
- Department of Physics, University of South Florida, Tampa, FL 33620, United States
| | - Yicheng Tu
- Department of Computer Science and Engineering, University of South Florida, Tampa, FL 33620, United States
| | - Sagar A Pandit
- Department of Physics, University of South Florida, Tampa, FL 33620, United States.
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27
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Soares TA, Vanni S, Milano G, Cascella M. Toward Chemically Resolved Computer Simulations of Dynamics and Remodeling of Biological Membranes. J Phys Chem Lett 2017; 8:3586-3594. [PMID: 28707901 DOI: 10.1021/acs.jpclett.7b00493] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Cellular membranes are fundamental constituents of living organisms. Apart from defining the boundaries of the cells, they are involved in a wide range of biological functions, associated with both their structural and the dynamical properties. Biomembranes can undergo large-scale transformations when subject to specific environmental changes, including gel-liquid phase transitions, change of aggregation structure, formation of microtubules, or rupture into vesicles. All of these processes are dependent on a delicate interplay between intermolecular forces, molecular crowding, and entropy, and their understanding requires approaches that are able to capture and rationalize the details of all of the involved interactions. Molecular dynamics-based computational models at atom-level resolution are, in principle, the best way to perform such investigations. Unfortunately, the relevant spatial and time dimensionalities involved in membrane remodeling phenomena would require computational costs that are today unaffordable on a routinely basis. Such hurdles can be removed by coarse-graining the representations of the individual molecular components of the systems. This procedure anyway reduces the possibility of describing the chemical variations in the lipid mixtures composing biological membranes. New hybrid particle field multiscale approaches offer today a promising alternative to the more traditional particle-based simulations methods. By combining chemically distinguishable molecular representations with mesoscale-based computationally affordable potentials, they appear as one of the most promising ways to keep an accurate description of the chemical complexity of biological membranes and, at the same time, cover the required scales to describe remodeling events.
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Affiliation(s)
- Thereza A Soares
- Department of Fundamental Chemistry, Federal University of Pernambuco, Cidade Universitária , Recife PE 50740-560, Brazil
| | - Stefano Vanni
- Department of Biology, University of Fribourg , 1700 Fribourg, Switzerland
| | - Giuseppe Milano
- Dipartimento di Chimica e Biologia, Università di Salerno , Via Giovanni Paolo II, 132, I-84084 Fisciano, Italy
| | - Michele Cascella
- Department of Chemistry and Centre for Theoretical and Computational Chemistry (CTCC) , Sem Saelands vei 26, 0371 Oslo, Norway
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28
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Vashchenko OV, Sadchenko AO, Budianska LV, Lisetski LN. The combined effects of nitrates on multibilayer lipid membranes: Thermodynamic effects. Biophysics (Nagoya-shi) 2017. [DOI: 10.1134/s0006350917020282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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29
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Trick JL, Song C, Wallace EJ, Sansom MSP. Voltage Gating of a Biomimetic Nanopore: Electrowetting of a Hydrophobic Barrier. ACS NANO 2017; 11:1840-1847. [PMID: 28141923 DOI: 10.1021/acsnano.6b07865] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
It is desirable that nanopores that are components of biosensors are gated, i.e., capable of controllable switching between closed (impermeable) and open (permeable) states. A central hydrophobic barrier within a nanopore may act as a voltage-dependent gate via electrowetting, i.e., changes in nanopore surface wettability by application of an electric field. We use "computational electrophysiology" simulations to demonstrate and characterize electrowetting of a biomimetic nanopore containing a hydrophobic gate. We show that a hydrophobic gate in a model β-barrel nanopore can be functionally opened by electrowetting at voltages that do not electroporate lipid bilayers. During the process of electrowetting, voltage-induced alignment of water dipoles occurs within the hydrophobic gate region of the nanopore, with water entry preceding permeation of ions through the opened nanopore. When the ionic imbalance that generates a transbilayer potential is dissipated, water is expelled from the hydrophobic gate and the nanopore recloses. The open nanopore formed by electrowetting of a "featureless" β-barrel is anionic selective due to the transmembrane dipole potential resulting from binding of Na+ ions to the headgroup regions of the surrounding lipid bilayer. Thus, hydrophobic barriers can provide voltage-dependent gates in designed biomimetic nanopores. This extends our understanding of hydrophobic gating in synthetic and biological nanopores, providing a framework for the design of functional nanopores with tailored gating functionality.
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Affiliation(s)
- Jemma L Trick
- Department of Biochemistry, University of Oxford , Oxford OX1 3QU, U.K
| | - Chen Song
- Department of Biochemistry, University of Oxford , Oxford OX1 3QU, U.K
| | - E Jayne Wallace
- Oxford Nanopore Technologies Ltd., Edmund Cartwright House , 4 Robert Robinson Avenue, Oxford Science Park, Oxford OX4 4GA, U.K
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford , Oxford OX1 3QU, U.K
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30
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Kruczek J, Chiu SW, Jakobsson E, Pandit SA. Effects of Lithium and Other Monovalent Ions on Palmitoyl Oleoyl Phosphatidylcholine Bilayer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:1105-1115. [PMID: 28076953 DOI: 10.1021/acs.langmuir.6b04166] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Interactions of monovalent salts with lipid membranes are explored with molecular dynamics (MD) simulations. The simulations included the monovalent ions Na+ and K+, for their importance in physiology, Li+ for its small size and importance in several medical conditions including bipolar disorder, and Rb+ for its large size. All simulations included Cl- as counterions. One bilayer was simulated without salt as a control. Palmitoyl oleoyl phosphatidylcholine (POPC) bilayers experienced reductions in area per lipid with the addition of salt; the smaller the ion the smaller the area, with the exception of Li+. Li+ exhibited unique binding affinities between phosphates and sn-2 carbonyls that lowered the order of the top part of sn-2 chain, which increased the area per lipid, compared to other ionic simulations. Further, we observe that monovalent salts alter bilayer properties through structural changes and not so much through the changes in surface potential.
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Affiliation(s)
- James Kruczek
- Department of Physics, University of South Florida , Tampa, Florida 33620, United States
| | | | | | - Sagar A Pandit
- Department of Physics, University of South Florida , Tampa, Florida 33620, United States
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31
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Effect of Sodium and Chloride Binding on a Lecithin Bilayer. A Molecular Dynamics Study. MEMBRANES 2017; 7:membranes7010005. [PMID: 28125062 PMCID: PMC5371966 DOI: 10.3390/membranes7010005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 01/12/2017] [Accepted: 01/14/2017] [Indexed: 01/17/2023]
Abstract
The effect of ion binding on the structural, mechanical, dynamic and electrostatic properties of a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer in a 0.5 M aqueous NaCl solution is investigated using classical atomistic molecular dynamics simulation with different force-field descriptions for ion-ion and ion-lipid interactions. Most importantly, the repulsive Lennard-Jones parameters for the latter were modified, such that approximately similar binding of cations and anions to the lipid membrane is achieved. This was done to qualitatively improve the apparent ion-lipid binding constants obtained from simulations with the original force field (Berger lipids and GROMOS87 ions in combination with the SPC water model) in comparison to experimental data. Furthermore, various parameters characterizing membrane structure, elasticity, order and dynamics are analyzed. It is found that ion binding as observed in simulations involving the modified in comparison to the original force-field description leads to: (i) a smaller salt-induced change in the area per lipid, which is in closer agreement with the experiment; (ii) a decrease in the area compressibility and bilayer thickness to values comparable to a bilayer in pure water; (iii) lipid deuterium order parameters and lipid diffusion coefficients on nanosecond timescales that are very similar to the values for a membrane in pure water. In general, salt effects on the structural properties of a POPC bilayer in an aqueous sodium-chloride solution appear to be reproduced reasonably well by the new force-field description. An analysis of membrane-membrane disjoining pressure suggests that the smaller salt-induced change in area per lipid induced by the new force-field description is not due to the alteration of membrane-associated net charge, but must rather be understood as a consequence of ion-specific effects on the arrangement of lipid molecules.
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32
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Gonzalez MA, Barriga HMG, Richens JL, Law RV, O'Shea P, Bresme F. How does ytterbium chloride interact with DMPC bilayers? A computational and experimental study. Phys Chem Chem Phys 2017; 19:9199-9209. [DOI: 10.1039/c7cp01400g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lanthanide salts have been studied for many years, primarily in Nuclear Magnetic Resonance (NMR) experiments of mixed lipid–protein systems and more recently to study lipid flip-flop in model membrane systems.
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Affiliation(s)
| | | | | | - Robert V. Law
- Department of Chemistry
- Imperial College London
- London
- UK
| | - Paul O'Shea
- Department of Chemistry
- Imperial College London
- London
- UK
- School of Life Sciences
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33
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Adams EM, Casper CB, Allen HC. Effect of cation enrichment on dipalmitoylphosphatidylcholine (DPPC) monolayers at the air-water interface. J Colloid Interface Sci 2016; 478:353-64. [DOI: 10.1016/j.jcis.2016.06.016] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/02/2016] [Accepted: 06/03/2016] [Indexed: 01/07/2023]
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34
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Duro N, Gjika M, Siddiqui A, Scott HL, Varma S. POPC Bilayers Supported on Nanoporous Substrates: Specific Effects of Silica-Type Surface Hydroxylation and Charge Density. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:6766-6774. [PMID: 27283467 DOI: 10.1021/acs.langmuir.6b01155] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Recent advances in nanotechnology bring to the forefront a new class of extrinsic constraints for remodeling lipid bilayers. In this next-generation technology, membranes are supported over nanoporous substrates. The nanometer-sized pores in the substrate are too small for bilayers to follow the substrate topology; consequently, the bilayers hang over the pores. Experiments demonstrate that nanoporous substrates remodel lipid bilayers differently from continuous substrates. The underlying molecular mechanisms, however, remain largely undetermined. Here we use molecular dynamics (MD) simulations to probe the effects of silica-type hydroxylation and charge densities on adsorbed palmitoyl-oleoylphosphatidylcholine (POPC) bilayers. We find that a 50% porous substrate decorated with a surface density of 4.6 hydroxyls/nm(2) adsorbs a POPC bilayer at a distance of 4.5 Å, a result consistent with neutron reflectivity experiments conducted on topologically similar silica constructs under highly acidic conditions. Although such an adsorption distance suggests that the interaction between the bilayer and the substrate will be buffered by water molecules, we find that the substrate does interact directly with the bilayer. The substrate modifies several properties of the bilayer-it dampens transverse lipid fluctuations, reduces lipid diffusion rates, and modifies transverse charge densities significantly. Additionally, it affects lipid properties differently in the two leaflets. Compared to substrates functionalized with sparser surface hydroxylation densities, this substrate adheres to bilayers at smaller distances and also remodels POPC more extensively, suggesting a direct correspondence between substrate hydrophilicity and membrane properties. A partial deprotonation of surface hydroxyls, as expected of a silica substrate under mildly acidic conditions, however, produces an inverse effect: it increases the substrate-bilayer distance, which we attribute to the formation of an electric double layer over the negatively charged substrate, and restores, at least partially, leaflet asymmetry and headgroup orientations. Overall, this study highlights the intrinsic complexity of lipid-substrate interactions and suggests the prospect of making two surface attributes-dipole densities and charge densities-work antagonistically toward remodeling lipid bilayer properties.
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Affiliation(s)
- Nalvi Duro
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida , Tampa, Florida 33620, United States
| | - Marion Gjika
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida , Tampa, Florida 33620, United States
| | - Ahnaf Siddiqui
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida , Tampa, Florida 33620, United States
| | - H Larry Scott
- Department of Physics, Illinois Institute of Technology , Chicago, Illinois 60616, United States
| | - Sameer Varma
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida , Tampa, Florida 33620, United States
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35
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Melcr J, Bonhenry D, Timr Š, Jungwirth P. Transmembrane Potential Modeling: Comparison between Methods of Constant Electric Field and Ion Imbalance. J Chem Theory Comput 2016; 12:2418-25. [DOI: 10.1021/acs.jctc.5b01202] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Josef Melcr
- Institute of Organic
Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
| | - Daniel Bonhenry
- Institute of Organic
Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
| | - Štěpán Timr
- Institute of Organic
Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic
Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
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36
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Maximally asymmetric transbilayer distribution of anionic lipids alters the structure and interaction with lipids of an amyloidogenic protein dimer bound to the membrane surface. Chem Phys Lipids 2016; 196:33-51. [PMID: 26827904 DOI: 10.1016/j.chemphyslip.2016.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 12/23/2022]
Abstract
We used molecular dynamics simulations to explore the effects of asymmetric transbilayer distribution of anionic phosphatidylserine (PS) lipids on the structure of a protein on the membrane surface and subsequent protein-lipid interactions. Our simulation systems consisted of an amyloidogenic, beta-sheet rich dimeric protein (D42) absorbed to the phosphatidylcholine (PC) leaflet, or protein-contact PC leaflet, of two membrane systems: a single-component PC bilayer and double PC/PS bilayers. The latter comprised of a stable but asymmetric transbilayer distribution of PS in the presence of counterions, with a 1-component PC leaflet coupled to a 1-component PS leaflet in each bilayer. The maximally asymmetric PC/PS bilayer had a non-zero transmembrane potential (TMP) difference and higher lipid order packing, whereas the symmetric PC bilayer had a zero TMP difference and lower lipid order packing under physiologically relevant conditions. Analysis of the adsorbed protein structures revealed weaker protein binding, more folding in the N-terminal domain, more aggregation of the N- and C-terminal domains and larger tilt angle of D42 on the PC leaflet surface of the PC/PS bilayer versus the PC bilayer. Also, analysis of protein-induced membrane structural disruption revealed more localized bilayer thinning in the PC/PS versus PC bilayer. Although the electric field profile in the non-protein-contact PS leaflet of the PC/PS bilayer differed significantly from that in the non-protein-contact PC leaflet of the PC bilayer, no significant difference in the electric field profile in the protein-contact PC leaflet of either bilayer was evident. We speculate that lipid packing has a larger effect on the surface adsorbed protein structure than the electric field for a maximally asymmetric PC/PS bilayer. Our results support the mechanism that the higher lipid packing in a lipid leaflet promotes stronger protein-protein but weaker protein-lipid interactions for a dimeric protein on membrane surfaces.
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37
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Casper CB, Verreault D, Adams EM, Hua W, Allen HC. Surface Potential of DPPC Monolayers on Concentrated Aqueous Salt Solutions. J Phys Chem B 2016; 120:2043-52. [PMID: 26761608 DOI: 10.1021/acs.jpcb.5b10483] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Clayton B. Casper
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dominique Verreault
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Ellen M. Adams
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Wei Hua
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Heather C. Allen
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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38
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Pasenkiewicz-Gierula M, Baczynski K, Markiewicz M, Murzyn K. Computer modelling studies of the bilayer/water interface. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2305-2321. [PMID: 26825705 DOI: 10.1016/j.bbamem.2016.01.024] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/18/2016] [Accepted: 01/21/2016] [Indexed: 01/24/2023]
Abstract
This review summarises high resolution studies on the interface of lamellar lipid bilayers composed of the most typical lipid molecules which constitute the lipid matrix of biomembranes. The presented results were obtained predominantly by computer modelling methods. Whenever possible, the results were compared with experimental results obtained for similar systems. The first and main section of the review is concerned with the bilayer-water interface and is divided into four subsections. The first describes the simplest case, where the interface consists only of lipid head groups and water molecules and focuses on interactions between the lipid heads and water molecules; the second describes the interface containing also mono- and divalent ions and concentrates on lipid-ion interactions; the third describes direct inter-lipid interactions. These three subsections are followed by a discussion on the network of direct and indirect inter-lipid interactions at the bilayer interface. The second section summarises recent computer simulation studies on the interactions of antibacterial membrane active compounds with various models of the bacterial outer membrane. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Marta Pasenkiewicz-Gierula
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Krzysztof Baczynski
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Michal Markiewicz
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Krzysztof Murzyn
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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39
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Yang J, Bonomi M, Calero C, Martí J. Free energy landscapes of sodium ions bound to DMPC–cholesterol membrane surfaces at infinite dilution. Phys Chem Chem Phys 2016; 18:9036-41. [DOI: 10.1039/c5cp05527j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Typical configuration of two DMPC lipids and one cholesterol molecule solvating one sodium ion, together with two additional water molecules.
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Affiliation(s)
- Jing Yang
- Department of Physics
- Technical University of Catalonia-Barcelona Tech
- 08034 Barcelona
- Spain
| | | | - Carles Calero
- Center for Polymer Studies and Department of Physics
- Boston University
- Boston
- USA
| | - Jordi Martí
- Department of Physics
- Technical University of Catalonia-Barcelona Tech
- 08034 Barcelona
- Spain
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40
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Cordomí A, Edholm O, Perez JJ. Effect of Force Field Parameters on Sodium and Potassium Ion Binding to Dipalmitoyl Phosphatidylcholine Bilayers. J Chem Theory Comput 2015; 5:2125-34. [PMID: 26613152 DOI: 10.1021/ct9000763] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The behavior of electrolytes in molecular dynamics simulations of zwitterionic phospholipid bilayers is very sensitive to the force field parameters used. Here, several 200 ns molecular dynamics of simulations of dipalmitoyl phosphotidylcholine (PC) bilayers in 0.2 M sodium or potassium chloride using various common force field parameters for the cations are presented. All employed parameter sets give a larger number of Na(+) ions than K(+) ions that bind to the lipid heads, but depending on the parameter choice quite different results are seen. A wide range of coordination numbers for the Na(+) and K(+) ions is also observed. These findings have been analyzed and compared to published experimental data. Some simulations produce aggregates of potassium chloride, indicating (in accordance with published simulations) that these force fields do not reproduce the delicate balance between salt and solvated ions. The differences between the force fields can be characterized by one single parameter, the electrostatic radius of the ion, which is correlated to σMO (M represents Na(+)/K(+)), the Lennard-Jones radius. When this parameter exceeds a certain threshold, binding to the lipid heads is no longer observed. One would, however, need more accurate experimental data to judge or rank the different force fields precisely. Still, reasons for the poor performance of some of the parameter sets are clearly demonstrated, and a quality control procedure is provided.
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Affiliation(s)
- Arnau Cordomí
- Department d'Enginyeria Química, Technical University of Catalonia (UPC), Avenue Diagonal 647, 08028 Barcelona, Spain, and, Theoretical Biological Physics, Royal Institute of Technology (KTH), SE-10691 Stockholm, Sweden
| | - Olle Edholm
- Department d'Enginyeria Química, Technical University of Catalonia (UPC), Avenue Diagonal 647, 08028 Barcelona, Spain, and, Theoretical Biological Physics, Royal Institute of Technology (KTH), SE-10691 Stockholm, Sweden
| | - Juan J Perez
- Department d'Enginyeria Química, Technical University of Catalonia (UPC), Avenue Diagonal 647, 08028 Barcelona, Spain, and, Theoretical Biological Physics, Royal Institute of Technology (KTH), SE-10691 Stockholm, Sweden
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41
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Ulmschneider JP, Ulmschneider MB. United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field. J Chem Theory Comput 2015; 5:1803-13. [PMID: 26610004 DOI: 10.1021/ct900086b] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have developed a new united-atom set of lipid force field parameters for dipalmitoylphosphatidylcholine (DPPC) lipid bilayers that can be combined with the all-atom optimized potentials for liquid simulations (OPLS-AA) protein force field. For this, all torsions have been refitted for a nonbonded 1-4 scale factor of 0.5, which is the standard in OPLS-AA. Improved van der Waals parameters have been obtained for the acyl lipid tails by matching simulation results of bulk pentadecane against recently improved experimental measurements. The charge set has been adjusted from previous lipid force fields to allow for an identical treatment of the alkoxy ester groups. This reduces the amount of parameters required for the model. Simulation of DPPC bilayers in the tension-free NPT ensemble at 50 °C gives the correct area per lipid of 62.9 ± 0.1 Å(2), which compares well with the recently refined experimental value of 63.0 Å(2). Electron density profiles and deuterium order parameters are similarly well reproduced. The new parameters will allow for improved simulation results in microsecond scale peptide partitioning simulations, which have proved problematic with prior parametrizations.
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Affiliation(s)
- Jakob P Ulmschneider
- IWR, University of Heidelberg, Heidelberg, Germany, and Department of Chemistry, University of Utrecht, Utrecht, The Netherlands
| | - Martin B Ulmschneider
- IWR, University of Heidelberg, Heidelberg, Germany, and Department of Chemistry, University of Utrecht, Utrecht, The Netherlands
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42
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Hua W, Verreault D, Allen HC. Solvation of Calcium-Phosphate Headgroup Complexes at the DPPC/Aqueous Interface. Chemphyschem 2015; 16:3910-5. [PMID: 26486616 DOI: 10.1002/cphc.201500720] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Wei Hua
- Department of Chemistry & Biochemistry; The Ohio State University; 100 West 18th Avenue Columbus OH 43210 USA
| | - Dominique Verreault
- Department of Chemistry & Biochemistry; The Ohio State University; 100 West 18th Avenue Columbus OH 43210 USA
| | - Heather C. Allen
- Department of Chemistry & Biochemistry; The Ohio State University; 100 West 18th Avenue Columbus OH 43210 USA
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43
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Mao L, Yang L, Zhang Q, Jiang H, Yang H. Effects of ion interactions with a cholesterol-rich bilayer. Biochem Biophys Res Commun 2015; 468:125-9. [PMID: 26529547 DOI: 10.1016/j.bbrc.2015.10.149] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 10/27/2015] [Indexed: 11/24/2022]
Abstract
Previous molecular dynamics (MD) simulations of ion-lipid interactions have focused on pure phospholipid bilayers. Many functional microdomains in membranes have a complex composition of cholesterol and phospholipids. Here, we reveal the distinctiveness of the interactions and the effects of the ions on a cholesterol-rich bilayer by performing MD simulations of a cholesterol-rich bilayer with a Na(+)/K(+) mixture or a Na(+)/K(+)/Ca(2+)/Mg(2+) mixture. The simulations reveal that Ca(2+) maintains its dominant role in the interaction with the cholesterol-rich bilayer, but the binding affinity of Mg(2+) to the cholesterol-rich bilayer is even weaker than the affinities of Na(+) and K(+), whereas its interaction with pure phospholipid bilayers is strong and is only slightly weaker than that of Ca(2+). Additionally, it was found that the presence of additional divalent cations induces the headgroups of phospholipids to be more perpendicular to the membrane surface, reducing the lateral movement of lipids and slightly altering the ordering and packing of the cholesterol-rich bilayer, different from divalent cations, which strongly influence that ordering and packing of pure phospholipid bilayers. Therefore, this study indicates that cholesterol in the membrane could affect the interactions between membrane and cations. The findings could be helpful in understanding the biological processes relevant to regulation of cations in cholesterol-rich regions.
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Affiliation(s)
- Lingxue Mao
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Linlin Yang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Qiansen Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hualiang Jiang
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Huaiyu Yang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, 555 Zuchongzhi Road, Shanghai 201203, China.
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44
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Yang J, Calero C, Bonomi M, Martí J. Specific Ion Binding at Phospholipid Membrane Surfaces. J Chem Theory Comput 2015; 11:4495-9. [DOI: 10.1021/acs.jctc.5b00540] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jing Yang
- Department
of Physics and Nuclear Engineering, Technical University of Catalonia-Barcelona Tech, B4-B5 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain
| | - Carles Calero
- Center
for Polymer Studies and Department of Physics, Boston University, 590
Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Massimiliano Bonomi
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Jordi Martí
- Department
of Physics and Nuclear Engineering, Technical University of Catalonia-Barcelona Tech, B4-B5 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain
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45
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Wiącek AE, Adryańczyk E. Interfacial Properties of Phosphatidylcholine-based Dispersed Systems. Ind Eng Chem Res 2015. [DOI: 10.1021/acs.iecr.5b01429] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Agnieszka Ewa Wiącek
- Department of Interfacial
Phenomena, Faculty of Chemistry, Maria Curie-Skłodowska University, 20031 Lublin, Poland
| | - Emilian Adryańczyk
- Department of Interfacial
Phenomena, Faculty of Chemistry, Maria Curie-Skłodowska University, 20031 Lublin, Poland
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46
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van Eerden FJ, de Jong DH, de Vries AH, Wassenaar TA, Marrink SJ. Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1319-30. [PMID: 25749153 DOI: 10.1016/j.bbamem.2015.02.025] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 02/16/2015] [Accepted: 02/24/2015] [Indexed: 11/17/2022]
Abstract
The thylakoid membrane is mainly composed of non-common lipids, so called galactolipids. Despite the importance of these lipids for the function of the photosynthetic reaction centers, the molecular organization of these membranes is largely unexplored. Here we use multiscale molecular dynamics simulations to characterize the thylakoid membrane of both cyanobacteria and higher plants. We consider mixtures of up to five different galactolipids plus phosphatidylglycerol to represent these complex membranes. We find that the different lipids generally mix well, although nanoscale heterogeneities are observed especially in case of the plant membrane. The fluidity of the cyanobacterial membrane is markedly reduced compared to the plant membrane, even considering elevated temperatures at which thermophilic cyanobacteria are found. We also find that the plant membrane more readily undergoes a phase transformation to an inverted hexagonal phase. We furthermore characterized the conformation and dynamics of the cofactors plastoquinone and plastoquinol, revealing of the fast flip-flop rates for the non-reduced form. Together, our results provide a molecular view on the dynamical organization of the thylakoid membrane.
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Affiliation(s)
- Floris J van Eerden
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
| | - Djurre H de Jong
- Institut für Physikalische Chemie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Alex H de Vries
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Tsjerk A Wassenaar
- Computational Biology, Department of Biology, University of Erlangen-Nürnberg, Staudtstr. 5, 91052 Erlangen Germany
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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47
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Harland B, Lee WH, Brownell WE, Sun SX, Spector AA. The potential and electric field in the cochlear outer hair cell membrane. Med Biol Eng Comput 2015; 53:405-13. [PMID: 25687712 DOI: 10.1007/s11517-015-1248-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 02/02/2015] [Indexed: 10/24/2022]
Abstract
Outer hair cell electromechanics, critically important to mammalian active hearing, is driven by the cell membrane potential. The membrane protein prestin is a crucial component of the active outer hair cell's motor. The focus of the paper is the analysis of the local membrane potential and electric field resulting from the interaction of electric charges involved. Here the relevant charges are the ions inside and outside the cell, lipid bilayer charges, and prestin-associated charges (mobile-transferred by the protein under the action of the applied field, and stationary-relatively unmoved by the field). The electric potentials across and along the membrane are computed for the case of an applied DC-field. The local amplitudes and phases of the potential under different frequencies are analyzed for the case of a DC + AC-field. We found that the effect of the system of charges alters the electric potential and internal field, which deviate significantly from their traditional linear and constant distributions. Under DC + AC conditions, the strong frequency dependence of the prestin mobile charge has a relatively small effect on the amplitude and phase of the resulting potential. The obtained results can help in a better understanding and experimental verification of the mechanism of prestin performance.
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Affiliation(s)
- Ben Harland
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
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48
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Role of electrolyte in the occurrence of the voltage induced phase transitions in a dioleoyl phosphatidylcholine monolayer on Hg. Electrochim Acta 2015. [DOI: 10.1016/j.electacta.2014.12.077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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49
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Zarzycki P. Interfacial water screens the protein-induced transmembrane voltage. J Phys Chem B 2015; 119:1474-82. [PMID: 25563965 DOI: 10.1021/jp509329u] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transmembrane proteins are crucial in cellular traffic, signal transduction, and energy storage in a form of transmembrane voltage. These proteins are stabilized by hydrophobic and hydrophilic interactions, in which cytoplasmic and exoplasmic water plays a special role. Water structural ordering generates the dipole potential that typically overcompensates for an intrinsic membrane-protein potential gradient, and thus it modifies and sustains an overall cellular electrostatics. Although the transmembrane voltage has been extensively studied, the dipole potential has attracted very little attention. Here, by using molecular dynamics, we examined water electrostatic response to the transmembrane charge, field, and potential asymmetry introduced by the presence of four integral membrane proteins: typical of inner (α-helix) and outer membrane (β-barrel). In all cases, the protein presence introduces electrostatic directionality in the transmembrane dipole field and voltage. In particular, water generates a deep potential sink if strongly polar residues are densely packed on one side of bilayer, as frequently occurs in a selectivity filter of the K(+) channel. We also found that protein secondary structure is less important than the polar residue distribution along the protein channel. Our findings are relevant for understanding the driving force behind biomembrane conductivity: the ability of biological water to electrostatically screen the transmembrane voltage.
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Affiliation(s)
- Piotr Zarzycki
- Institute of Physical Chemistry, Polish Academy of Sciences , Warsaw, Poland
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50
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Wang N, Zhou S, Kekenes-Huskey PM, Li B, McCammon JA. Poisson-Boltzmann versus Size-Modified Poisson-Boltzmann Electrostatics Applied to Lipid Bilayers. J Phys Chem B 2014; 118:14827-32. [PMID: 25426875 PMCID: PMC4280115 DOI: 10.1021/jp511702w] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
![]()
Mean-field
methods, such as the Poisson–Boltzmann equation
(PBE), are often used to calculate the electrostatic properties of
molecular systems. In the past two decades, an enhancement of the
PBE, the size-modified Poisson–Boltzmann equation (SMPBE),
has been reported. Here, the PBE and the SMPBE are reevaluated for
realistic molecular systems, namely, lipid bilayers, under eight different
sets of input parameters. The SMPBE appears to reproduce the molecular
dynamics simulation results better than the PBE only under specific
parameter sets, but in general, it performs no better than the Stern
layer correction of the PBE. These results emphasize the need for
careful discussions of the accuracy of mean-field calculations on
realistic systems with respect to the choice of parameters and call
for reconsideration of the cost-efficiency and the significance of
the current SMPBE formulation.
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Affiliation(s)
- Nuo Wang
- Department of Chemistry and Biochemistry, ‡Department of Mathematics, §Department of Pharmacology, ⊥Howard Hughes Medical Institute, University of California-San Diego , La Jolla, California 92093, United States
| | - Shenggao Zhou
- Department of Chemistry and Biochemistry, ‡Department of Mathematics, §Department of Pharmacology, ⊥Howard Hughes Medical Institute, University of California-San Diego , La Jolla, California 92093, United States
| | - Peter M Kekenes-Huskey
- Department of Chemistry and Biochemistry, ‡Department of Mathematics, §Department of Pharmacology, ⊥Howard Hughes Medical Institute, University of California-San Diego , La Jolla, California 92093, United States
| | - Bo Li
- Department of Chemistry and Biochemistry, ‡Department of Mathematics, §Department of Pharmacology, ⊥Howard Hughes Medical Institute, University of California-San Diego , La Jolla, California 92093, United States
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, ‡Department of Mathematics, §Department of Pharmacology, ⊥Howard Hughes Medical Institute, University of California-San Diego , La Jolla, California 92093, United States
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