1
|
Kitaoka H, Yokoyama Y, Sakka T, Nishi N. Salting-out and Competitive Adsorption of Ethanol into Lipid Bilayer Membranes: Conflicting Effects of Salts on Ethanol-Membrane Interactions Studied by Molecular Dynamics Simulations. J Phys Chem B 2024. [PMID: 39046846 DOI: 10.1021/acs.jpcb.4c03399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Small amphiphilic molecules, such as ethanol, disturb the structure of lipid bilayer membranes to increase the membrane permeability, which is important for applications such as drug delivery, disinfection, and fermentation. To investigate how and the extent to which coexisting salts affect membrane disturbance, we performed molecular dynamics (MD) simulations on lipid bilayer membranes composed of zwitterionic lipids in aqueous ethanol solutions containing 0-631 mM NaCl, KCl, and KI salts. The addition of salts at low concentrations induced cationic adsorption on the lipid membrane, which competes with ethanol adsorption, thereby reducing the hydrogen bonds between ethanol and lipid molecules. This competitive adsorption mitigated the membrane disturbance and decreased the permeation of ethanol molecules into the membrane. In contrast, higher salt concentrations enhanced the membrane disturbance and permeability, which was caused by the salting-out of ethanol from the aqueous phase to the lipid bilayer. These conflicting effects appearing at different concentrations were stronger with the chloride salts than with the iodide salt. Among the two chloride salts, NaCl and KCl, the latter showed a greater enhancement in ethanol permeation at high concentrations. This seeming anti-Hofmeister salting-out behavior resulted from greater Na+ adsorption, preventing the ethanol-lipid interactions.
Collapse
Affiliation(s)
- Haru Kitaoka
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Yuko Yokoyama
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- iCaNS, Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tetsuo Sakka
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- iCaNS, Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Naoya Nishi
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- iCaNS, Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| |
Collapse
|
2
|
Mallick S, Agmon N. Lateral diffusion of ions near membrane surface. Phys Chem Chem Phys 2024; 26:19433-19449. [PMID: 38973628 DOI: 10.1039/d3cp04112c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Biological membranes isolate living cells from their environment, while allowing selective molecular transport between the inner and outer realms. For example, Na+ and K+ permeability through ionic channels contributes to neural conduction. Whether the ionic currents arise directly from cations in the bulk, or from the interface, is currently unclear. There are only scant results concerning lateral diffusion of ions on aquated membrane surfaces (and strong belief that this occurs through binding to a diffusing lipid). We performed classical molecular dynamics (MD) simulations of monovalent ions, Na+, K+, and Cl-, near the surface of the zwitterionic palmitoyl-oleoyl-phosphatidylcholine (POPC) membrane. Realistic force-fields for lipids (Amber's Lipid17 and Lipid21) and water (TIP4P-Ew) are tested for the mass and charge densities and the electrostatic potential across the membrane. These calculations reveal that the chloride can bind to the choline moiety through an intervening water molecule by forming a CH⋯OH hydrogen bond, while cations bind to both the phosphatic and carbonyl oxygens of phosphatidylcholine moieties. Upon transitioning from the bulk to the interface, a cation sheds some of its hydration water, which are replaced by headgroup atoms. Notably, an interfacial cation can bind 1-4 headgroup atoms, which is a key to understanding its surface hopping mechanism. We find that cation binding to three headgroup atoms immobilizes it, while binding to four energizes it. Consequently, the lateral cation diffusion rate is only 15-25 times slower than in the bulk, and 4-5 times faster than lipid self-diffusion. K+ diffusion is notably more anomalous than Na+, switching from sub- to super-diffusion after about 2 ns.
Collapse
Affiliation(s)
- Subhasish Mallick
- The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
| | - Noam Agmon
- The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
| |
Collapse
|
3
|
Villalaín J. Location and interaction of idebenone and mitoquinone in a membrane similar to the inner mitochondrial membrane. Comparison with ubiquinone 10. Free Radic Biol Med 2024; 222:211-222. [PMID: 38908803 DOI: 10.1016/j.freeradbiomed.2024.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/10/2024] [Accepted: 06/19/2024] [Indexed: 06/24/2024]
Abstract
Oxygen is essential for aerobic life on earth but it is also the origin of harmful reactive oxygen species (ROS). Ubiquinone is par excellence the endogenous cellular antioxidant, but a very hydrophobic one. Because of that, other molecules have been envisaged, such as idebenone (IDE) and mitoquinone (MTQ), molecules having the same redox active benzoquinone moiety but higher solubility. We have used molecular dynamics to determine the location and interaction of these molecules, both in their oxidized and reduced forms, with membrane lipids in a membrane similar to that of the mitochondria. Both IDE and reduced IDE (IDOL) are situated near the membrane interface, whereas both MTQ and reduced MTQ (MTQOL) locate in a position adjacent to the phospholipid hydrocarbon chains. The quinone moieties of both ubiquinone 10 (UQ10) and reduced UQ10 (UQOL10) in contraposition to the same moieties of IDE, IDOL, MTQ and MTQOL, located near the membrane interphase, whereas the isoprenoid chains remained at the middle of the hydrocarbon chains. These molecules do not aggregate and their functional quinone moieties are located in the membrane at different depths but near the hydrophobic phospholipid chains whereby protecting them from ROS harmful effects.
Collapse
Affiliation(s)
- José Villalaín
- Institute of Research, Development, and Innovation in Healthcare Biotechnology (IDiBE), Universidad "Miguel Hernández", E-03202, Elche, Alicante, Spain.
| |
Collapse
|
4
|
Lyu Y, Chen S, Zhao Y, Yuan H, Zhang C, Zhang C, Meng Q. Effect of GM1 concentration change on plasma membrane: molecular dynamics simulation and analysis. Phys Chem Chem Phys 2024; 26:12552-12563. [PMID: 38595108 DOI: 10.1039/d3cp06161b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Ganglioside GM1 is a class of glycolipids predominantly located in the nervous system. Comprising a ceramide anchor and an oligosaccharide chain containing sialic acid, GM1 plays a pivotal role in various cellular processes, including signal transduction, cell adhesion, and membrane organization. Moreover, GM1 has been implicated in the pathogenesis of several neurological disorders, such as Parkinson's disease, Alzheimer's disease, and stroke. In this study, by creating a neural cell model membrane simulation system and employing rigorous molecular models, we utilize a coarse-grained molecular dynamics approach to explore the structural and dynamic characteristics of multi-component neuronal plasma membranes at varying GM1 ganglioside concentrations. The simulation results reveal that as GM1 concentration increases, a greater number of hydrogen bonds form between GM1 molecules, resulting in the formation of larger clusters, which leads to reduced membrane fluidity, increased lipid ordering, decreased membrane thickness and surface area and higher levels of GM1 dissociation. Through a meticulous analysis, while considering GM1's structural attributes, we offer valuable insights into the structural and dynamic traits of the cell membrane. This study provides a robust methodology for exploring membrane characteristics and enhances our comprehension of GM1 molecules, serving as a resource for both experimental and computational researchers in this field.
Collapse
Affiliation(s)
- Yongkang Lyu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, People's Republic of China.
| | - Shuo Chen
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, People's Republic of China.
| | - Yu Zhao
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, People's Republic of China.
| | - Hongxiu Yuan
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, People's Republic of China.
| | - Chenyang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, People's Republic of China.
| | - Changzhe Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, People's Republic of China.
| | - Qingtian Meng
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, People's Republic of China.
| |
Collapse
|
5
|
Birtles D, Abbas W, Lee J. Bis(Monoacylglycero)Phosphate Promotes Membrane Fusion Facilitated by the SARS-CoV-2 Fusion Domain. J Phys Chem B 2024; 128:2675-2683. [PMID: 38466655 DOI: 10.1021/acs.jpcb.3c07863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Membrane fusion is a critical component of the viral lifecycle. For SARS-CoV-2, fusion is facilitated by the spike glycoprotein and can take place via either the plasma membrane or the endocytic pathway. The fusion domain (FD), which is found within the spike glycoprotein, is primarily responsible for the initiation of fusion as it embeds itself within the target cell's membrane. A preference for SARS-CoV-2 to fuse at low pH akin to the environment of the endocytic pathway has already been established; however, the impact of the target cell's lipid composition on the FD has yet to be explored. Here, we have shown that the SARS-CoV-2 FD preferentially initiates fusion at the late endosomal membrane over the plasma membrane, on the basis of lipid composition alone. A positive, fusogenic relationship with anionic lipids from the plasma membrane (POPS: 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine) and endosomal membrane (BMP: bis(monoacylglycero)phosphate) was established, with a large preference demonstrated for the latter. When comparing the binding affinity and secondary structure of the FD in the presence of different anionic lipids, little deviation was evident while the charge was maintained. However, it was discovered that BMP had a subtle, negative impact on lipid packing in comparison to that of POPS. Furthermore, an inverse relationship between lipid packing and the fusogenecity of the SARS-CoV-2 FD was witnessed. In conclusion, the SARS-CoV-2 FD preferentially initiates fusion at a membrane resembling that of the late endosomal compartment, predominately due to the presence of BMP and its impact on lipid packing.
Collapse
Affiliation(s)
- Daniel Birtles
- Department of Chemistry and Biochemistry, University of Maryland, College Park 20742, Maryland, United States
| | - Wafa Abbas
- Department of Chemistry and Biochemistry, University of Maryland, College Park 20742, Maryland, United States
| | - Jinwoo Lee
- Department of Chemistry and Biochemistry, University of Maryland, College Park 20742, Maryland, United States
| |
Collapse
|
6
|
Villalaín J. Phospholipid binding of the dengue virus envelope E protein segment containing the conserved His residue. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184198. [PMID: 37437754 DOI: 10.1016/j.bbamem.2023.184198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/16/2023] [Accepted: 07/05/2023] [Indexed: 07/14/2023]
Abstract
Flaviviruses encompass many important human pathogens, including Dengue, Zika, West Nile, Yellow fever, Japanese encephalitis, and Tick-borne encephalitis viruses as well as several emerging viruses that affect millions of people worldwide. They enter cells by endocytosis, fusing their membrane with the late endosomal one in a pH-dependent manner, so membrane fusion is one of the main targets for obtaining new antiviral inhibitors. The envelope E protein, a class II membrane fusion protein, is responsible for fusion and contains different domains involved in the fusion mechanism, including the fusion peptide. However, other segments, apart from the fusion peptide, have been implicated in the mechanism of membrane fusion, in particular a segment containing a His residue supposed to act as a specific pH sensor. We have used atomistic molecular dynamics to study the binding of the envelope E protein segment containing the conserved His residue in its three different tautomer forms with a complex membrane mimicking the late-endosomal one. We show that this His-containing segment is capable of spontaneous membrane binding, preferentially binds electronegatively charged phospholipids and does not bind cholesterol. Since Flaviviruses have caused epidemics in the past, continue to do so and will undoubtedly continue to do so, this specific segment could characterise a new target that would allow finding effective antiviral molecules against DENV virus in particular and Flaviviruses in general.
Collapse
Affiliation(s)
- José Villalaín
- Institute of Research, Development, and Innovation in Healthcare Biotechnology (IDiBE), Universitas "Miguel Hernández", E-03202 Elche, Alicante, Spain.
| |
Collapse
|
7
|
Jain H, Karathanou K, Bondar AN. Graph-Based Analyses of Dynamic Water-Mediated Hydrogen-Bond Networks in Phosphatidylserine: Cholesterol Membranes. Biomolecules 2023; 13:1238. [PMID: 37627303 PMCID: PMC10452392 DOI: 10.3390/biom13081238] [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: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Phosphatidylserine lipids are anionic molecules present in eukaryotic plasma membranes, where they have essential physiological roles. The altered distribution of phosphatidylserine in cells such as apoptotic cancer cells, which, unlike healthy cells, expose phosphatidylserine, is of direct interest for the development of biomarkers. We present here applications of a recently implemented Depth-First-Search graph algorithm to dissect the dynamics of transient water-mediated lipid clusters at the interface of a model bilayer composed of 1-palmytoyl-2-oleoyl-sn-glycero-2-phosphatidylserine (POPS) and cholesterol. Relative to a reference POPS bilayer without cholesterol, in the POPS:cholesterol bilayer there is a somewhat less frequent sampling of relatively complex and extended water-mediated hydrogen-bond networks of POPS headgroups. The analysis protocol used here is more generally applicable to other lipid:cholesterol bilayers.
Collapse
Affiliation(s)
- Honey Jain
- Faculty of Physics, University of Bucharest, Atomiștilor 405, 077125 Măgurele, Romania
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | | | - Ana-Nicoleta Bondar
- Faculty of Physics, University of Bucharest, Atomiștilor 405, 077125 Măgurele, Romania
- IAS-5/INM-9, Forschungszentrum Jülich, Institute of Computational Biomedicine, Wilhelm-Johnen Straße, 52428 Jülich, Germany
| |
Collapse
|
8
|
Cui Z, Jiao Y, Pu L, Chen J, Liu M, Tang JZ, Wang G. The Interaction Mechanism of Intramuscular Gene Delivery Materials with Cell Membranes. J Funct Biomater 2023; 14:jfb14040219. [PMID: 37103309 PMCID: PMC10144004 DOI: 10.3390/jfb14040219] [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: 02/17/2023] [Revised: 03/25/2023] [Accepted: 04/08/2023] [Indexed: 04/28/2023] Open
Abstract
It has been confirmed that skeletal muscle cells have the capability to receive foreign plasmid DNA (pDNA) and express functional proteins. This provides a promisingly applicable strategy for safe, convenient, and economical gene therapy. However, intramuscular pDNA delivery efficiency was not high enough for most therapeutic purposes. Some non-viral biomaterials, especially several amphiphilic triblock copolymers, have been shown to significantly improve intramuscular gene delivery efficiency, but the detailed process and mechanism are still not well understood. In this study, the molecular dynamics simulation method was applied to investigate the structure and energy changes of the material molecules, the cell membrane, and the DNA molecules at the atomic and molecular levels. From the results, the interaction process and mechanism of the material molecules with the cell membrane were revealed, and more importantly, the simulation results almost completely matched the previous experimental results. This study may help us design and optimize better intramuscular gene delivery materials for clinical applications.
Collapse
Affiliation(s)
- Zhanpeng Cui
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu 610064, China
| | - Yang Jiao
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu 610064, China
| | - Linyu Pu
- School of Materials and Chemistry, Southwest University of Science and Technology, Mianyang 621010, China
| | - Jianlin Chen
- School of Laboratory Medicine, Chengdu Medical College, Chengdu 610500, China
| | - Ming Liu
- Department of Medical Oncology/Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - James Zhenggui Tang
- Research Institute of Healthcare Science, Faculty of Science & Engineering, University of Wolverhampton, Wolverhampton WV1 1SB, UK
| | - Gang Wang
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu 610064, China
| |
Collapse
|
9
|
Villalaín J. LABYRINTHOPEPTIN A2 DISRUPTS RAFT DOMAINS. Chem Phys Lipids 2023; 253:105303. [PMID: 37061155 DOI: 10.1016/j.chemphyslip.2023.105303] [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: 01/25/2023] [Revised: 03/21/2023] [Accepted: 04/11/2023] [Indexed: 04/17/2023]
Abstract
Labyrinthopeptins constitute a class of ribosomal synthesized peptides belonging to the type III family of lantibiotics. They exist in different variants and display broad antiviral activities as well as show antiallodynic activity. Although their mechanism of action is not understood, it has been described that Labyrinthopeptins interact with membrane phospholipids modulating its biophysical properties and point out to membrane destabilization as its main point of action. We have used all-atom molecular dynamics to study the location of labyrinthopeptin A2 in a complex membrane as well as the existence of specific interactions with membrane lipids. Our results indicate that labyrinthopeptin A2, maintaining its globular structure, tends to be placed at the membrane interface, mainly between the phosphate atoms of the phospholipids and the oxygen atom of cholesterol modulating the biophysical properties of the membrane lipids. Outstandingly, we have found that labyrinthopeptin A2 tends to be preferentially surrounded by sphingomyelin while excluding cholesterol. The bioactive properties of labyrinthopeptin A2 could be attributed to the specific disorganization of raft domains in the membrane and the concomitant disruption of the overall membrane organization. These results support the improvement of Labyrinthopeptins as therapeutic molecules, opening up new opportunities for future medical advances.
Collapse
Affiliation(s)
- José Villalaín
- Institute of Research, Development, and Innovation in Healthcare Biotechnology (IDiBE), Universidad "Miguel Hernández", E-03202 Elche-Alicante, Spain.
| |
Collapse
|
10
|
Villalaín J. SARS-CoV-2 Protein S Fusion Peptide Is Capable of Wrapping Negatively-Charged Phospholipids. MEMBRANES 2023; 13:344. [PMID: 36984731 PMCID: PMC10057416 DOI: 10.3390/membranes13030344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 06/18/2023]
Abstract
COVID-19, caused by SARS-CoV-2, which is a positive-sense, single-stranded RNA enveloped virus, emerged in late 2019 and was declared a worldwide pandemic in early 2020 causing more than 600 million infections so far and more than 6 million deaths in the world. Although new vaccines have been implemented, the pandemic continues to impact world health dramatically. Membrane fusion, critical for the viral entry into the host cell, is one of the main targets for the development of novel antiviral therapies to combat COVID-19. The S2 subunit of the viral S protein, a class I membrane fusion protein, contains the fusion domain which is directly implicated in the fusion mechanism. The knowledge of the membrane fusion mechanism at the molecular level will undoubtedly result in the development of effective antiviral strategies. We have used all-atom molecular dynamics to analyse the binding of the SARS-CoV-2 fusion peptide to specific phospholipids in model membranes composed of only one phospholipid plus cholesterol in the presence of either Na+ or Ca2+. Our results show that the fusion peptide is capable of binding to the membrane, that its secondary structure does not change significantly upon binding, that it tends to preferentially bind electronegatively charged phospholipids, and that it does not bind cholesterol at all. Understanding the intricacies of the membrane fusion mechanism and the molecular interactions involved will lead us to the development of antiviral molecules that will allow a more efficient battle against these viruses.
Collapse
Affiliation(s)
- José Villalaín
- Institute of Research, Development, and Innovation in Healthcare Biotechnology (IDiBE), Universitas "Miguel Hernández", E-03202 Elche, Spain
| |
Collapse
|
11
|
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.
Collapse
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
| | | | | | | |
Collapse
|
12
|
Villalaín J. Bergamottin: location, aggregation and interaction with the plasma membrane. J Biomol Struct Dyn 2023; 41:12026-12037. [PMID: 36602143 DOI: 10.1080/07391102.2022.2164521] [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: 10/15/2022] [Accepted: 12/27/2022] [Indexed: 01/06/2023]
Abstract
Bioactive furanocoumarins, a group of natural secondary metabolites common in higher plants, are recognized for their benefits to human health and have been shown to have numerous biological properties. However, the knowledge of its biomolecular mechanism is not known. One of the main furanocoumarins is bergamottin (BGM), which is characterized by a planar three-ringed structure and a hydrocarbon chain, which give BGM its high lipid/water partition coefficient. Because of that, and although the biological mechanism of BGM is not known, BGM bioactive properties could be ascribed to its potential to interact with the biological membrane, modulating its structure, changing its dynamics and at the same time that it might interact with lipids. For our goal, we have applied molecular dynamics to determine the position of BGM in a complex membrane and discern the possibility of certain interactions with membrane lipids. Our findings establish that BGM tends to locate in the middle of the hydrocarbon layer of the membrane, inserts in between the hydrocarbon chains of the phospholipids in an oblique position with respect to the membrane plane, increasing the fluidity of the membrane. Significantly, BGM tends to be surrounded by POPC molecules but exclude the molecule of CHOL. Outstandingly, BGM molecules associate spontaneously creating aggregates, which does not preclude them from interacting with and inserting into the membrane. The bioactive properties of BGM could be ascribed to its membranotropic effects and support the improvement of these molecules as therapeutic molecules, giving place to new opportunities for potential medical improvements.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- José Villalaín
- Institute of Research, Development, and Innovation in Healthcare Biotechnology (IDiBE), Universidad "Miguel Hernández", Elche-Alicante, Spain
| |
Collapse
|
13
|
Avalos-Padilla Y, Georgiev VN, Ewins E, Robinson T, Orozco E, Lipowsky R, Dimova R. Stepwise remodeling and subcompartment formation in individual vesicles by three ESCRT-III proteins. iScience 2022; 26:105765. [PMID: 36590172 PMCID: PMC9800321 DOI: 10.1016/j.isci.2022.105765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/21/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
The endosomal sorting complex required for transport (ESCRT) is a multi-protein machinery involved in several membrane remodeling processes. Different approaches have been used to resolve how ESCRT proteins scission membranes. However, the underlying mechanisms generating membrane deformations are still a matter of debate. Here, giant unilamellar vesicles, microfluidic technology, and micropipette aspiration are combined to continuously follow the ESCRT-III-mediated membrane remodeling on the single-vesicle level for the first time. With this approach, we identify different mechanisms by which a minimal set of three ESCRT-III proteins from Entamoeba histolytica reshape the membrane. These proteins modulate the membrane stiffness and spontaneous curvature to regulate bud size and generate intraluminal vesicles even in the absence of ATP. We demonstrate that the bud stability depends on the protein concentration and membrane tension. The approaches introduced here should open the road to diverse applications in synthetic biology for establishing artificial cells with several membrane compartments.
Collapse
Affiliation(s)
- Yunuen Avalos-Padilla
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany,Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, ES-08028 Barcelona, Spain,Barcelona Institute for Global Health (ISGlobal, Hospital Clínic-Universitat de Barcelona), Rosselló 149-153, ES-08036 Barcelona, Spain
| | - Vasil N. Georgiev
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany
| | - Eleanor Ewins
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany
| | - Tom Robinson
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, CINVESTAV IPN, 07360 Ciudad de México, México
| | - Reinhard Lipowsky
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany,Corresponding author
| |
Collapse
|
14
|
Villalaín J. Interaction of Lassa virus fusion and membrane proximal peptides with late endosomal membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184031. [PMID: 35964711 DOI: 10.1016/j.bbamem.2022.184031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/15/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Mammarenaviruses include many significant worldwide-widespread human pathogens, among them Lassa virus (LASV), having a dramatic morbidity and mortality rate. They are a potential high-risk menace to the worldwide public health since there are no treatments and there is a high possibility of animal-to-human and human-to-human viral transmission. These viruses enter into the cells by endocytosis fusing its membrane envelope with the late endosomal membrane thanks to the glycoprotein GP2, a membrane fusion protein of class I. This protein contains different domains, among them the N-terminal fusion peptide (NFP), the internal fusion loop (IFL), the membrane proximal external region (MPER) and the transmembrane domain (TMD). All these domains are implicated in the membrane fusion process. In this work, we have used an all-atom molecular dynamics study to know the binding of these protein domains with a complex membrane mimicking the late endosome one. We show that the NFP/IFL domain is capable of spontaneously inserting into the membrane without a significant change of secondary structure, the MPER domain locates at the bilayer interface with an orientation parallel to the membrane surface and tends to interact with other MPER domains, and the TMD domain tilts inside the bilayer. Moreover, they predominantly interact with negatively charged phospholipids. Overall, these membrane-interacting domains would characterise a target that would make possible to find effective antiviral molecules against LASV in particular and Mammarenaviruses in general.
Collapse
Affiliation(s)
- José Villalaín
- Institute of Research, Development, and Innovation in Healthcare Biotechnology (IDiBE), Universitas "Miguel Hernández", E-03202 Elche-Alicante, Spain.
| |
Collapse
|
15
|
Villalaín J. Procyanidin C1 Location, Interaction, and Aggregation in Two Complex Biomembranes. MEMBRANES 2022; 12:membranes12070692. [PMID: 35877895 PMCID: PMC9319219 DOI: 10.3390/membranes12070692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 01/25/2023]
Abstract
Procyanidins are known for their many benefits to human health and show a plethora of biological effects. One of the most important procyanidin is the procyanidin trimer C1 (PC1). Due to its relatively high lipid–water partition coefficient, the properties of PC1 could be attributed to its capability to interact with the biomembrane, to modulate its structure and dynamics, and to interact with lipids and proteins, however, its biological mechanism is not known. We have used all-atom molecular dynamics in order to determine the position of PC1 in complex membranes and the presence of its specific interactions with membrane lipids, having simulated a membrane mimicking the plasma membrane and another mimicking the mitochondrial membrane. PC1 has a tendency to be located at the membrane interphase, with part of the molecule exposed to the water solvent and part of it reaching the first carbons of the hydrocarbon chains. It has no preferred orientation, and it completely excludes the CHOL molecule. Remarkably, PC1 has a tendency to spontaneously aggregate, forming high-order oligomers. These data suggest that its bioactive properties could be attributed to its membranotropic effects, which therefore supports the development of these molecules as therapeutic molecules, which would open new opportunities for future medical advances.
Collapse
Affiliation(s)
- José Villalaín
- Institute of Research, Development, and Innovation in Healthcare Biotechnology (IDiBE), Universidad Miguel Hernández, E-03202 Elche, Spain
| |
Collapse
|
16
|
Nasrollahpour M, Vafaee M, Razzaghi S. Structural and Dynamical Properties of Palmitoyl-Oleoyl Phosphatidylserine Lipid Nanotubes Containing Cholesterols and PEGylated Dioleoyl Phosphatidylethanolamine: A Coarse-Grained Molecular Dynamics Simulation. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.117848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
17
|
Antila HS, Kav B, Miettinen MS, Martinez-Seara H, Jungwirth P, Ollila OHS. Emerging Era of Biomolecular Membrane Simulations: Automated Physically-Justified Force Field Development and Quality-Evaluated Databanks. J Phys Chem B 2022. [DOI: 10.1021/acs.jpcb.2c01954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hanne S. Antila
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Batuhan Kav
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum
Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany
| | - Markus S. Miettinen
- Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
- Department of Chemistry, University of Bergen, 5020 Bergen, Norway
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic
| | - O. H. Samuli Ollila
- Institute of Biotechonology, University of Helsinki, Helsinki 00014, Finland
| |
Collapse
|
18
|
Villalaín J. Envelope E protein of dengue virus and phospholipid binding to the late endosomal membrane. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183889. [PMID: 35167815 DOI: 10.1016/j.bbamem.2022.183889] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/11/2022] [Accepted: 02/07/2022] [Indexed: 02/06/2023]
Abstract
Flaviviruses include many significant human pathogens, comprising dengue, West Nile, Yellow fever, Japanese encephalitis, Zika and tick-borne encephalitis viruses and many others, affecting millions of people in the world. These viruses have produced important epidemics in the past, they continue to do it and they will undoubtedly continue to do so in the future. Flaviviruses enter into the cells via receptor-mediated endocytosis by fusing its membrane with the endosomal membrane in a pH-dependent manner with the help of the envelope E protein, a prototypical class II membrane fusion protein. The envelope E protein has a conserved fusion peptide at its distal end, which is responsible in the first instance of inserting the protein into the host membrane. Since the participation of other segments of the E protein in the fusion process should not be ruled out, we have used atomistic molecular dynamics to study the binding of the distal end of domain II of the envelope E protein from Dengue virus (DENV) with a complex membrane similar to the late-endosome one. Our work shows that not only the fusion peptide participates directly in the fusion, but also two other sequences of the protein, next to the fusion peptide it in the three-dimensional structure, are jointly wrapped in the fusion process. Overall, these three sequences represent a new target that would make it possible to obtain effective antivirals against DENV in particular and Flaviviruses in general.
Collapse
Affiliation(s)
- José Villalaín
- Institute of Research, Development, and Innovation in Healthcare Biotechnology (IDiBE), Universitas "Miguel Hernández", E-03202 Elche-Alicante, Spain.
| |
Collapse
|
19
|
Karathanou K, Bondar AN. Algorithm to catalogue topologies of dynamic lipid hydrogen-bond networks. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183859. [PMID: 34999081 DOI: 10.1016/j.bbamem.2022.183859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/21/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
Lipid membrane interfaces host reactions essential for the functioning of cells. The hydrogen-bonding environment at the membrane interface is particularly important for binding of proteins, drug molecules, and ions. We present here the implementation and applications of a depth-first search algorithm that analyzes dynamic lipid interaction networks. Lipid hydrogen-bond networks sampled transiently during simulations of lipid bilayers are clustered according to main types of topologies that characterize three-dimensional arrangements of lipids connected to each other via short water bridges. We characterize the dynamics of hydrogen-bonded lipid clusters in simulations of model POPE and POPE:POPG membranes that are often used for bacterial membrane proteins, in a model of the Escherichia coli membrane with six different lipid types, and in POPS membranes. We find that all lipids sample dynamic hydrogen-bonded networks with linear, star, or circular arrangements of the lipid headgroups, and larger networks with combinations of these three types of topologies. Overall, linear lipid-water bridges tend to be short. Water-mediated lipid clusters in all membranes with PE lipids tend to be somewhat small, with about four lipids in all membranes studied here. POPS membranes allow circular arrangements of three POPS lipids to be sampled frequently, and complex arrangements of linear, star, and circular paths may also be sampled. These findings suggest a molecular picture of the membrane interface whereby lipid molecules transiently connect in clusters with somewhat small spatial extension.
Collapse
Affiliation(s)
- Konstantina Karathanou
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany; University of Bucharest, Faculty of Physics, Str. Atomiştilor 405, Bucharest-Măgurele 077125, Romania; Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany.
| |
Collapse
|
20
|
Kerr D, Gong Z, Suwatthee T, Luoma A, Roy S, Scarpaci R, Hwang HL, Henderson JM, Cao KD, Bu W, Lin B, Tietjen GT, Steck TL, Adams EJ, Lee KYC. How Tim proteins differentially exploit membrane features to attain robust target sensitivity. Biophys J 2021; 120:4891-4902. [PMID: 34529946 PMCID: PMC8595564 DOI: 10.1016/j.bpj.2021.09.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 07/24/2021] [Accepted: 09/08/2021] [Indexed: 12/17/2022] Open
Abstract
Immune surveillance cells such as T cells and phagocytes utilize integral plasma membrane receptors to recognize surface signatures on triggered and activated cells such as those in apoptosis. One such family of plasma membrane sensors, the transmembrane immunoglobulin and mucin domain (Tim) proteins, specifically recognize phosphatidylserine (PS) but elicit distinct immunological responses. The molecular basis for the recognition of lipid signals on target cell surfaces is not well understood. Previous results suggest that basic side chains present at the membrane interface on the Tim proteins might facilitate association with additional anionic lipids including but not necessarily limited to PS. We, therefore, performed a comparative quantitative analysis of the binding of the murine Tim1, Tim3, and Tim4, to synthetic anionic phospholipid membranes under physiologically relevant conditions. X-ray reflectivity and vesicle binding studies were used to compare the water-soluble domain of Tim3 with results previously obtained for Tim1 and Tim4. Although a calcium link was essential for all three proteins, the three homologs differed in how they balance the hydrophobic and electrostatic interactions driving membrane association. The proteins also varied in their sensing of phospholipid chain unsaturation and showed different degrees of cooperativity in their dependence on bilayer PS concentration. Surprisingly, trace amounts of anionic phosphatidic acid greatly strengthened the bilayer association of Tim3 and Tim4, but not Tim1. A novel mathematical model provided values for the binding parameters and illuminated the complex interplay among ligands. In conclusion, our results provide a quantitative description of the contrasting selectivity used by three Tim proteins in the recognition of phospholipids presented on target cell surfaces. This paradigm is generally applicable to the analysis of the binding of peripheral proteins to target membranes through the heterotropic cooperative interactions of multiple ligands.
Collapse
Affiliation(s)
- Daniel Kerr
- Program in Biophysical Sciences, Institute for Biophysical Dynamics, Chicago, Illinois; Department of Chemistry, Chicago, Illinois; James Franck Institute, Chicago, Illinois
| | - Zhiliang Gong
- Department of Chemistry, Chicago, Illinois; James Franck Institute, Chicago, Illinois
| | | | | | - Sobhan Roy
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Renee Scarpaci
- City University of New York City College, New York, New York
| | - Hyeondo Luke Hwang
- Department of Chemistry, Chicago, Illinois; James Franck Institute, Chicago, Illinois
| | - J Michael Henderson
- Department of Chemistry, Chicago, Illinois; James Franck Institute, Chicago, Illinois
| | - Kathleen D Cao
- Department of Chemistry, Chicago, Illinois; James Franck Institute, Chicago, Illinois
| | - Wei Bu
- NSF's ChemMatCARS, The University of Chicago, Chicago, Illinois
| | - Binhua Lin
- James Franck Institute, Chicago, Illinois; NSF's ChemMatCARS, The University of Chicago, Chicago, Illinois
| | - Gregory T Tietjen
- Department of Surgery, Section of Transplant and Immunology and Department of Biomedical Engineering, Yale University, New Haven, Connecticut
| | - Theodore L Steck
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Erin J Adams
- Program in Biophysical Sciences, Institute for Biophysical Dynamics, Chicago, Illinois; Committee on Immunology, Chicago, Illinois; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Ka Yee C Lee
- Program in Biophysical Sciences, Institute for Biophysical Dynamics, Chicago, Illinois; Department of Chemistry, Chicago, Illinois; James Franck Institute, Chicago, Illinois.
| |
Collapse
|
21
|
Zhang L. Interaction of Human β Defensin Type 3 (hBD-3) with Different PIP2-Containing Membranes, a Molecular Dynamics Simulation Study. J Chem Inf Model 2021; 61:4670-4686. [PMID: 34473496 DOI: 10.1021/acs.jcim.1c00805] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Human β defensin type 3 (hBD-3) is a cysteine-rich small antibacterial peptide. It belongs to the human innate immune system. hBD-3 has six cysteine residues, which form three pairs of disulfide bonds, and those bonds break in the reducing condition. It is known that hBD-3 can interact with bacterial membrane, and even eukaryotic cell membrane, which has a low concentration of phosphatidylinositol 4,5-bisphosphate (PIP2) lipids. PIP2 is a vital component in cell membranes and has been found to play important roles during antimicrobial peptide (AMP) interaction with membranes. To understand the functional mechanism of hBD-3 interacting with PIP2-containing membranes, the binding structures of hBD-3 on 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers mixed with 10% of PIP2 were predicted using two kinds of methods. The first one is by placing the hBD-3 monomer in different orientations above the POPC + 10%PIP2 membrane to set up five different initial simulation systems and performing long-term simulations on each to predict the most stable binding structure. It was found that hBD-3 analogue binds on the mixed lipid membrane on the two loop regions. The second method is by running long-term simulations on one or nine hBD-3 dimers binding on POPC mixed with 10%PIP2 lipid bilayer starting from the solid-state NMR (ssNMR)-suggested orientation. The dimer dissociated, and the most stable binding of hBD-3 in wild-type on the mixed membrane is also through the two loop regions, which agrees with the prediction from both the first method and the lipid self-assembly result. The PIP2 lipids can form long-lasting hydrogen bonds with positively charged residues such as Arg and Lys on hBD-3, thus forming clusters with hBD-3. As a comparison, hBD-3 dimers binding with a combined bilayer having 1,2-palmitoyl-oleoyl-sn-glycero-3-phosphoserine (POPS) on the upper and POPC on the lower leaflets and the combined POPS + POPC bilayer mixing with 10%PIP2 were also studied. The long-term simulation result shows that hBD-3 can bind with the heads of negatively charged POPS and PIP2 lipids and form hydrogen bonds. The stable binding sites of hBD-3 on PIP2 or POPS mixed bilayers are still on the two loop regions. On the combined POPS + POPC mixed with 10%PIP2 bilayer, the binding of hBD-3 with PIP2 lipids became less stable and fewer because of the competition of binding with the POPS lipids. Besides that, binding with hBD-3 can decrease the membrane thickness of the POPC + PIP2, POPS + POPC, and POPS + POPC + PIP2 bilayers and make POPS and PIP2 lipids more flexible based on the order parameter calculations. Our results supply molecular insight on AMP binding with different membranes and can help understand the functional mechanism of hBD-3 disrupting PIP2-containing membranes.
Collapse
Affiliation(s)
- Liqun Zhang
- Department of Chemical Engineering, Tennessee Technological University, Cookeville, Tennessee 38505, United States
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Yee SM, Gillams RJ, McLain SE, Lorenz CD. Effects of lipid heterogeneity on model human brain lipid membranes. SOFT MATTER 2021; 17:126-135. [PMID: 33155582 DOI: 10.1039/d0sm01766c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cell membranes naturally contain a heterogeneous lipid distribution. However, homogeneous bilayers are commonly preferred and utilised in computer simulations due to their relative simplicity, and the availability of lipid force field parameters. Recently, experimental lipidomics data for the human brain cell membranes under healthy and Alzheimer's disease (AD) conditions were investigated, since disruption to the lipid composition has been implicated in neurodegenerative disorders, including AD [R. B. Chan et al., J. Biol. Chem., 2012, 287, 2678-2688]. In order to observe the effects of lipid complexity on the various bilayer properties, molecular dynamics simulations were used to study four membranes with increasing heterogeneity: a pure POPC membrane, a POPC and cholesterol membrane in a 1 : 1 ratio (POPC-CHOL), and to our knowledge, the first realistic models of a healthy brain membrane and an Alzheimer's diseased brain membrane. Numerous structural, interfacial, and dynamical properties, including the area per lipid, interdigitation, dipole potential, and lateral diffusion of the two simple models, POPC and POPC-CHOL, were analysed and compared to those of the complex brain models consisting of 27 lipid components. As the membranes gain heterogeneity, a number of alterations were found in the structural and dynamical properties, and more significant differences were observed in the lateral diffusion. Additionally, we observed snorkeling behaviour of the lipid tails that may play a role in the permeation of small molecules across biological membranes. In this work, atomistic description of realistic brain membrane models is provided, which can add insight towards the permeability and transport pathways of small molecules across these membrane barriers.
Collapse
Affiliation(s)
- Sze May Yee
- Department of Physics, King's College London, London WC2R 2LS, UK.
| | - Richard J Gillams
- School of Electronics and Computer Science, and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Sylvia E McLain
- Department of Chemistry, School of Life Sciences, University of Sussex, Brighton BN1 9RH, UK
| | | |
Collapse
|
24
|
Aggregation of 25-hydroxycholesterol in a complex biomembrane. Differences with cholesterol. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183413. [PMID: 32721397 DOI: 10.1016/j.bbamem.2020.183413] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 12/16/2022]
Abstract
25-Hydroxycholesterol (25HC), one of the most important oxysterol molecules, can be used by cells to fight bacterial and viral infections but the mechanism that defines its biological effects are unknown. Using molecular dynamics, we have aimed to describe the orientation and location of 25HC in the membrane as well as the interactions it might have with lipids. We have studied two complex model membrane systems, one similar to the late endosome membrane and the other one to the plasma membrane. Our results reinforce that 25HC is inserted in the membrane in a relative stable location similar to but not identical to cholesterol. 25HC fluctuates in the membrane to a much greater degree than cholesterol, but the effect of 25HC on the phospholipid order parameters is not significantly different. One of the most notable facts about 25HC is that, unlike cholesterol, this molecule tends to aggregate, forming dimers, trimers and higher-order aggregates. These aggregates are formed spontaneously through the formation of hydrogen bonds between the two 25HC atoms, the formation of hydrogen bonds being independent of the studied system. Remarkably, no contacts or hydrogen bonds are observed between 25HC and cholesterol molecules, as well as between cholesterol molecules themselves at any time. It would be conceivable that 25HC, by forming high order aggregates without significantly altering the membrane properties, would modify the way proteins interact with the membrane and henceforth form a true innate antiviral molecule.
Collapse
|
25
|
Mohideen N, Weiner MD, Feigenson GW. Bilayer compositional asymmetry influences the nanoscopic to macroscopic phase domain size transition. Chem Phys Lipids 2020; 232:104972. [PMID: 32941827 DOI: 10.1016/j.chemphyslip.2020.104972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/18/2020] [Accepted: 09/04/2020] [Indexed: 10/23/2022]
Abstract
The eukaryotic plasma membrane (PM) exhibits lipid mixing heterogeneities known as lipid rafts. These lipid rafts, the result of liquid-liquid phase separation, can be modeled by coexisting liquid ordered (Lo) and liquid disordered (Ld) domains. Four-lipid component systems with a high-melting lipid, a nanodomain-inducing low-melting lipid, a macrodomain-inducing low-melting lipid, and cholesterol (chol) can give rise to domains of different sizes. These four-component systems have been characterized in experiments, yet there are few studies that model the asymmetric distribution of lipids actually found in the PM. We used molecular dynamics (MD) simulations to analyze the transition from nanoscopic to macroscopic domains in symmetric and in asymmetric model membranes. Using coarse-grained MD simulations, we found that asymmetry promotes macroscopic domain growth in a case where symmetric systems exhibit nanoscopic domains. Also, macroscopic domain formation in symmetric systems is highly dependent on registration of like phases in the cytoplasmic and exoplasmic leaflets. Using united-atom MD simulations, we found that symmetric Lo domains are only slightly more ordered than asymmetric Lo domains. We also found that large Lo domains in our asymmetric systems induce a slight chain ordering in the apposed cytoplasmic regions. The chol fractions of phase-separated Lo and Ld domains of the exoplasmic leaflet were unchanged whether the system was symmetric or asymmetric.
Collapse
Affiliation(s)
- Naveen Mohideen
- Cornell University Department of Physics, 117 Clark Hall, Ithaca, New York, 14853, United States; Johns Hopkins University Department of Molecular Biophysics, 101 Jenkins Hall, 3400 N. Charles Street, Baltimore, Maryland, 21218, United States.
| | - Michael D Weiner
- Cornell University Department of Physics, 117 Clark Hall, Ithaca, New York, 14853, United States; Georgia Institute of Technology Partnership for an Advanced Computing Environment, 756 W. Peachtree St. NW, Atlanta, Georgia, 30332, United States.
| | - Gerald W Feigenson
- Cornell University Department of Molecular Biology and Genetics, Room 201 215 Tower Rd. Ithaca, New York, 14853, United States.
| |
Collapse
|
26
|
Chetty R, Singh M. In-vitro interaction of cerium oxide nanoparticles with hemoglobin, insulin, and dsDNA at 310.15 K: Physicochemical, spectroscopic and in-silico study. Int J Biol Macromol 2020; 156:1022-1044. [PMID: 32171830 DOI: 10.1016/j.ijbiomac.2020.03.067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 03/08/2020] [Accepted: 03/10/2020] [Indexed: 01/05/2023]
Abstract
Lanthanide nanoparticles and nanorods especially their biocompatible oxide forms like cerium oxide nanoparticles (CNPs) with therapeutic applications are used to cure neurological oxidative stresses. Thus it tempts to study their biocompatible aspects by interactions with several biologically significant molecules. In-Vitro interactions of 15-240 μM CNPs with water, Phosphate buffered saline (PBS), DMEM media, Insulin (Ins) hemoglobin (Hb) and ds-DNA at 37 °C were studied. Their physicochemical properties study by Borosil Mansingh Survismeter (BMS) showed the first order interaction with the protein-protein structure breaking behaviour of CNPs with Hb, Ins, and DNA. Zeta potential measurements of CNPs in different biological medium show a net increase in negative charge magnitude with good colloidal stability. Kb = 4 × 106 mM-1 of CNPs-DNA infer noncovalent interactions. Circular dichroism and FTIR revealed a loss of secondary conformation with increasing CNPs concentration. In-silico molecular docking depicts CNP interaction via conventional hydrogen bonding, carbon hydrogen bonding and electrostatic interactions at the minor groove of DNA. The study reports in-dept unfolding functional mechanism investigated by physicochemical, spectroscopic, and In-Silico approaches of protein on interactions with CNPs for safer-by-design use in medicine and pharmaceutics. Fundamentally the CeO2 in ~62% and Ce2O3 in ~38% with Ce4+ and Ce3+ oxidation potentials develop a unique case of electronic configurations with 4f05d06s0 and 4f15d06s0 electrons respectively which these studies a novel one.
Collapse
Affiliation(s)
- Rajlakshmi Chetty
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, India
| | - Man Singh
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, India.
| |
Collapse
|
27
|
Bouquiaux C, Tonnelé C, Castet F, Champagne B. Second-Order Nonlinear Optical Properties of an Amphiphilic Dye Embedded in a Lipid Bilayer. A Combined Molecular Dynamics–Quantum Chemistry Study. J Phys Chem B 2020; 124:2101-2109. [DOI: 10.1021/acs.jpcb.9b10988] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Charlotte Bouquiaux
- Theoretical Chemistry Laboratory, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, University of Namur, Rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Claire Tonnelé
- University of Bordeaux, Institut des Sciences Moléculaires, UMR 5255 CNRS, Cours de la Libération 351, F-33405 Talence Cedex, France
| | - Frédéric Castet
- University of Bordeaux, Institut des Sciences Moléculaires, UMR 5255 CNRS, Cours de la Libération 351, F-33405 Talence Cedex, France
| | - Benoît Champagne
- Theoretical Chemistry Laboratory, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, University of Namur, Rue de Bruxelles, 61, B-5000 Namur, Belgium
| |
Collapse
|
28
|
Galiano V, Encinar JA, Villalaín J. Location, Orientation and Aggregation of Bardoxolone-ME, CDDO-ME, in a Complex Phospholipid Bilayer Membrane. J Membr Biol 2020; 253:115-128. [PMID: 31965219 DOI: 10.1007/s00232-020-00106-5] [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: 09/04/2019] [Accepted: 01/09/2020] [Indexed: 11/29/2022]
Abstract
Bardoxolone methyl (CDDO-Me), a synthetic derivative of the naturally occurring triterpenoid oleanolic acid, displays strong antioxidant, anticancer and anti-inflammatory activities, according to different bibliographical sources. However, the understanding of its molecular mechanism is missing. Furthermore, CDDO-Me has displayed a significant cytotoxicity against various types of cancer cells. CDDO-Me has a noticeable hydrophobic character and several of its effects could be attributed to its ability to be incorporated inside the biological membrane and therefore modify its structure and specifically interact with its components. In this study, we have used full-atom molecular dynamics to determine the location, orientation and interactions of CDDO-Me in phospholipid model membranes. Our results support the location of CDDO-Me in the middle of the membrane, it specifically orients so that the cyano group lean towards the phospholipid interface and it specifically interacts with particular phospholipids. Significantly, in the membrane the CDDO-Me molecules specifically interact with POPE and POPS. Moreover, CDDO-Me does not aggregates in the membrane but it forms a complex conglomerate in solution. The formation of a complex aggregate in solution might hamper its biological activity and therefore it should be taken into account when intended to be used in clinical assays. This work should aid in the development of these molecules opening new avenues for future therapeutic developments.
Collapse
Affiliation(s)
- Vicente Galiano
- Physics and Computer Architecture Department, Desarrollo e Innovación en Biotecnología Sanitaria (IDiBE), Universitas "Miguel Hernández", 03202, Elche-Alicante, Spain
| | - José A Encinar
- Instituto de Biología Molecular y Celular (IBMC), Desarrollo e Innovación en Biotecnología Sanitaria (IDiBE), Universitas "Miguel Hernández", 03202, Elche-Alicante, Spain.,Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria (IDiBE), Universitas "Miguel Hernández", 03202, Elche-Alicante, Spain
| | - José Villalaín
- Instituto de Biología Molecular y Celular (IBMC), Desarrollo e Innovación en Biotecnología Sanitaria (IDiBE), Universitas "Miguel Hernández", 03202, Elche-Alicante, Spain. .,Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria (IDiBE), Universitas "Miguel Hernández", 03202, Elche-Alicante, Spain.
| |
Collapse
|
29
|
Melcr J, Ferreira TM, Jungwirth P, Ollila OHS. Improved Cation Binding to Lipid Bilayers with Negatively Charged POPS by Effective Inclusion of Electronic Polarization. J Chem Theory Comput 2019; 16:738-748. [PMID: 31762275 DOI: 10.1021/acs.jctc.9b00824] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Phosphatidylserine (PS) lipids are important signaling molecules and the most common negatively charged lipids in eukaryotic membranes. The signaling can be often regulated by calcium, but its interactions with PS headgroups are not fully understood. Classical molecular dynamics (MD) simulations can potentially give detailed description of lipid-ion interactions, but the results strongly depend on the used force field. Here, we apply the electronic continuum correction (ECC) to the Amber Lipid17 parameters of 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine (POPS) lipid to improve its interactions with K+, Na+, and Ca2+ ions. The partial charges of the headgroup, glycerol backbone, and carbonyls of POPS, bearing a unit negative charge, were scaled with a factor of 0.75, derived for monovalent ions, and the Lennard-Jones σ parameters of the same segments were scaled with a factor of 0.89. The resulting ECC-POPS model gives more realistic interactions with Na+ and Ca2+ cations than the original Amber Lipid17 parameters when validated using headgroup order parameters and the "electrometer concept". In ECC-lipids simulations, populations of complexes of Ca2+ cations with more than two PS lipids are negligible, and interactions of Ca2+ cations with only carboxylate groups are twice more likely than with only phosphate groups, while interactions with carbonyls almost entirely involve other groups as well. Our results pave the way for more realistic MD simulations of biomolecular systems with anionic membranes, allowing signaling processes involving PS and Ca2+ to be elucidated.
Collapse
Affiliation(s)
- Josef Melcr
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 542/2 , CZ-16610 Prague 6 , Czech Republic.,Groningen Biomolecular Sciences and Biotechnology Institute and The Zernike Institute for Advanced Materials , University of Groningen , 9747 AG Groningen , The Netherlands
| | - Tiago M Ferreira
- NMR Group-Institut for Physics , Martin-Luther University Halle-Wittenberg , 06120 Halle , Germany
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 542/2 , CZ-16610 Prague 6 , Czech Republic
| | - O H Samuli Ollila
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 542/2 , CZ-16610 Prague 6 , Czech Republic.,Institute of Biotechnology , University of Helsinki , Helsinki FI-00014 , Finland
| |
Collapse
|
30
|
Antila H, Buslaev P, Favela-Rosales F, Ferreira TM, Gushchin I, Javanainen M, Kav B, Madsen JJ, Melcr J, Miettinen MS, Määttä J, Nencini R, Ollila OHS, Piggot TJ. Headgroup Structure and Cation Binding in Phosphatidylserine Lipid Bilayers. J Phys Chem B 2019; 123:9066-9079. [DOI: 10.1021/acs.jpcb.9b06091] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hanne Antila
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Pavel Buslaev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Russia
| | - Fernando Favela-Rosales
- Departamento de Investigación, Tecnológico Nacional de México, Campus Zacatecas Occidente, C. P. 99102 Zacatecas, México
| | - Tiago M. Ferreira
- NMR Group - Institute for Physics, Martin-Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Russia
| | - Matti Javanainen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16610 Prague 6, Czech Republic
| | - Batuhan Kav
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Jesper J. Madsen
- Department of Chemistry, The University of Chicago, 60637 Chicago, Illinois, United States of America
- Department of Global Health, College of Public Health, University of South Florida, 33612 Tampa, Florida, United States of America
| | - Josef Melcr
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16610 Prague 6, Czech Republic
- Groningen Biomolecular Sciences and Biotechnology Institute and The Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Markus S. Miettinen
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Jukka Määttä
- Department of Chemistry and Materials Science, Aalto University, 00076 Espoo, Finland
| | - Ricky Nencini
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16610 Prague 6, Czech Republic
| | - O. H. Samuli Ollila
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16610 Prague 6, Czech Republic
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Thomas J. Piggot
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| |
Collapse
|
31
|
Cho HJ, Yoon H, Lee HH. Phosphatidylserine-induced dissociation of the heterodimeric PstB2p/Pbi1p complex in yeast phosphatidylserine trafficking system. Biochem Biophys Res Commun 2019; 517:285-290. [DOI: 10.1016/j.bbrc.2019.07.066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 07/18/2019] [Indexed: 10/26/2022]
|
32
|
Flood E, Boiteux C, Lev B, Vorobyov I, Allen TW. Atomistic Simulations of Membrane Ion Channel Conduction, Gating, and Modulation. Chem Rev 2019; 119:7737-7832. [DOI: 10.1021/acs.chemrev.8b00630] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Emelie Flood
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Céline Boiteux
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Bogdan Lev
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Igor Vorobyov
- Department of Physiology & Membrane Biology/Department of Pharmacology, University of California, Davis, 95616, United States
| | - Toby W. Allen
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| |
Collapse
|
33
|
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.
Collapse
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.
| |
Collapse
|
34
|
Shahane G, Ding W, Palaiokostas M, Orsi M. Physical properties of model biological lipid bilayers: insights from all-atom molecular dynamics simulations. J Mol Model 2019; 25:76. [PMID: 30806797 DOI: 10.1007/s00894-019-3964-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/07/2019] [Indexed: 02/04/2023]
Abstract
The physical properties of lipid bilayers are sensitive to the specific type and composition of the lipids that make up the many different types of cell membranes. Studying model bilayers of representative heterogeneous compositions can provide key insights into membrane functionality. In this work, we use atomistic molecular dynamics simulations to characterize key properties in a number of bilayer membranes of varying composition. We first examine basic properties, such as lipid area, volume, and bilayer thickness, of simple, homogeneous bilayers comprising several lipid types, which are prevalent in biological membranes. Such lipids are then used in simulations of heterogeneous systems representative of bacterial, mammalian, and cancer membranes. Our analysis is especially focused on depth-dependent, transmembrane profiles; in particular, we calculate lateral pressure and dipole potential profiles, two fundamental properties which play key roles in a large number of biological functions.
Collapse
Affiliation(s)
- Ganesh Shahane
- Institute of Bioengineering, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Wei Ding
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Michail Palaiokostas
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Mario Orsi
- Department of Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK.
| |
Collapse
|
35
|
Leonard AN, Wang E, Monje-Galvan V, Klauda JB. Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes. Chem Rev 2019; 119:6227-6269. [DOI: 10.1021/acs.chemrev.8b00384] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
36
|
Moradi S, Nowroozi A, Shahlaei M. Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: a review study. RSC Adv 2019; 9:4644-4658. [PMID: 35520151 PMCID: PMC9060685 DOI: 10.1039/c8ra08441f] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 03/12/2019] [Accepted: 01/16/2019] [Indexed: 12/20/2022] Open
Abstract
This review gives an overview about the some of the most important possible analyzes, technical challenges, and existing protocols that can be performed on the biological membrane by the molecular dynamics simulation.
Collapse
Affiliation(s)
- Sajad Moradi
- Nano Drug Delivery Research Center
- Kermanshah University of Medical Sciences
- Kermanshah
- Iran
| | - Amin Nowroozi
- Pharmaceutical Sciences Research Center
- Faculty of Pharmacy
- Kermanshah University of Medical Sciences
- Kermanshah
- Iran
| | - Mohsen Shahlaei
- Medical Biology Research Center
- Kermanshah University of Medical Sciences
- Kermanshah
- Iran
| |
Collapse
|
37
|
Klauda JB. Perspective: Computational modeling of accurate cellular membranes with molecular resolution. J Chem Phys 2018; 149:220901. [DOI: 10.1063/1.5055007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Jeffery B. Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
- Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, USA
| |
Collapse
|
38
|
Villalaín J. Epigallocatechin-3-gallate location and interaction with late endosomal and plasma membrane model membranes by molecular dynamics. J Biomol Struct Dyn 2018; 37:3122-3134. [PMID: 30081748 DOI: 10.1080/07391102.2018.1508372] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Epigallocatechin-3-gallate (EGCG) is the most abundant polyphenol in green tea and it has been reported to have many beneficial properties against many different types of illnesses and infections. However, the exact mechanism/s underlying its biological effects are unknown. It has been previously shown that EGCG is capable of binding to and disrupting the membrane, so that some of its effects on biological systems could be ascribed to its capacity to incorporate into the biological membrane and modulate its structure. In this work, we have used atomistic molecular dynamics (MD) to discern the location and orientation of EGCG in model membranes and the possible existence of specific interactions with membrane lipids. For that goal, we have used in our simulation two complex model membranes, one resembling the plasma membrane (PM) and the other one the late endosome (LE) membrane. Our results support that EGCG tends to associate with the membrane and exists inside it in a relatively stable and steady location with a low propensity to be associated with other EGCG molecules. Interestingly, EGCG forms hydrogen bonds with POPC and POPE in the PM system but POPC and BMP and no POPE in the LE. These data suggest that the broad beneficial effects of EGCG could be mediated, at least in part, through its membranotropic effects and therefore membrane functioning. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- José Villalaín
- a Molecular and Cellular Biology Institute (IBMC) and Institute for Biotechnological Research, Development and Innovation (IDiBE) , Universitas "Miguel Hernández" , Alicante , Spain
| |
Collapse
|
39
|
Yousefpour A, Amjad-Iranagh S, Goharpey F, Modarress H. Effect of drug amlodipine on the charged lipid bilayer cell membranes DMPS and DMPS + DMPC: a molecular dynamics simulation study. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:939-950. [PMID: 29971510 DOI: 10.1007/s00249-018-1317-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 05/19/2018] [Accepted: 06/26/2018] [Indexed: 01/03/2023]
Abstract
In this work, the effects of the anti-hypertensive drug amlodipine in native and PEGylated forms on the malfunctioning of negatively charged lipid bilayer cell membranes constructed from DMPS or DMPS + DMPC were studied by molecular dynamics simulation. The obtained results indicate that amlodipine alone aggregates and as a result its diffusion into the membrane is retarded. In addition, due to their large size aggregates of the drug can damage the cell, rupturing the cell membrane. It is shown that PEGylation of amlodipine prevents this aggregation and facilitates its diffusion into the lipid membrane. The interaction of the drug with negatively charged membranes in the presence of an aqueous solution of NaCl, as the medium, is investigated and its effects on the membrane are considered by evaluating the structural properties of the membrane such as area per lipid, thickness, lipid chain order and electrostatic potential difference between bulk solution and lipid bilayer surface. The effect of these parameters on the diffusion of the drug into the cell is critically examined and discussed.
Collapse
Affiliation(s)
- Abbas Yousefpour
- Department of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic), 424 Hafez Ave, Tehran, P.O. Box 15875-4413, Iran
| | - Sepideh Amjad-Iranagh
- Department of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic), 424 Hafez Ave, Tehran, P.O. Box 15875-4413, Iran
| | - Fatemeh Goharpey
- Department of Polymer Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran
| | - Hamid Modarress
- Department of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic), 424 Hafez Ave, Tehran, P.O. Box 15875-4413, Iran.
| |
Collapse
|
40
|
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.
Collapse
|
41
|
Dynamic Water Hydrogen-Bond Networks at the Interface of a Lipid Membrane Containing Palmitoyl-Oleoyl Phosphatidylglycerol. J Membr Biol 2018. [DOI: 10.1007/s00232-018-0023-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
42
|
A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids. Molecules 2017; 23:molecules23010077. [PMID: 29301229 PMCID: PMC6017617 DOI: 10.3390/molecules23010077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/26/2017] [Accepted: 12/28/2017] [Indexed: 11/18/2022] Open
Abstract
In all of the classical force fields, electrostatic interaction is simply treated and explicit electronic polarizability is neglected. The condensed-phase polarization, relative to the gas-phase charge distributions, is commonly accounted for in an average way by increasing the atomic charges, which remain fixed throughout simulations. Based on the lipid polarizable force field DMPC and following the same framework as Atomic Multipole Optimized Energetics for BiomoleculAr (AMOEBA) simulation, the present effort expands the force field to new anionic lipid models, in which the new lipids contain DMPG and POPS. The parameters are compatible with the AMOEBA force field, which includes water, ions, proteins, etc. The charge distribution of each atom is represented by the permanent atomic monopole, dipole and quadrupole moments, which are derived from the ab initio gas phase calculations. Many-body polarization including the inter- and intramolecular polarization is modeled in a consistent manner with distributed atomic polarizabilities. Molecular dynamics simulations of the two aqueous DMPG and POPS membrane bilayer systems, consisting of 72 lipids with water molecules, were then carried out to validate the force field parameters. Membrane width, area per lipid, volume per lipid, deuterium order parameters, electron density profile, electrostatic potential difference between the center of the bilayer and water are all calculated, and compared with limited experimental data.
Collapse
|
43
|
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.
Collapse
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
| |
Collapse
|
44
|
Graber ZT, Shi Z, Baumgart T. Cations induce shape remodeling of negatively charged phospholipid membranes. Phys Chem Chem Phys 2017; 19:15285-15295. [PMID: 28569910 PMCID: PMC5562360 DOI: 10.1039/c7cp00718c] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The divalent cation Ca2+ is a key component in many cell signaling and membrane trafficking pathways. Ca2+ signal transduction commonly occurs through interaction with protein partners. However, in this study we show a novel mechanism by which Ca2+ may impact membrane structure. We find an asymmetric concentration of Ca2+ across the membrane triggers deformation of membranes containing negatively charged lipids such as phosphatidylserine (PS) and phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2). Membrane invaginations in vesicles were observed forming away from the leaflet with higher Ca2+ concentration, showing that Ca2+ induces negative curvature. We hypothesize that the negative curvature is produced by Ca2+-induced clustering of PS and PI(4,5)P2. In support of this notion, we find that Ca2+-induced membrane deformation is stronger for membranes containing PI(4,5)P2, which is known to more readily cluster in the presence of Ca2+. The observed Ca2+-induced membrane deformation is strongly influenced by Na+ ions. A high symmetric [Na+] across the membrane reduces Ca2+ binding by electrostatic shielding, inhibiting Ca2+-induced membrane deformation. An asymmetric [Na+] across the membrane, however, can either oppose or support Ca2+-induced deformation, depending on the direction of the gradient in [Na+]. At a sufficiently high asymmetric Na+ concentration it can impact membrane structure in the absence of Ca2+. We propose that Ca2+ works in concert with curvature generating proteins to modulate membrane curvature and shape transitions. This novel structural impact of Ca2+ could be important for Ca2+-dependent cellular processes that involve the creation of membrane curvature, including exocytosis, invadopodia, and cell motility.
Collapse
Affiliation(s)
- Z T Graber
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.
| | | | | |
Collapse
|
45
|
Bera I, Klauda JB. Molecular Simulations of Mixed Lipid Bilayers with Sphingomyelin, Glycerophospholipids, and Cholesterol. J Phys Chem B 2017; 121:5197-5208. [DOI: 10.1021/acs.jpcb.7b00359] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Indrani Bera
- Department
of Chemical and Biomolecular Engineering and ‡Biophysics Program, University of Maryland, College Park, Maryland 20742, United States
| | - Jeffery B. Klauda
- Department
of Chemical and Biomolecular Engineering and ‡Biophysics Program, University of Maryland, College Park, Maryland 20742, United States
| |
Collapse
|
46
|
Qiang X, Wang X, Ji Y, Li S, He L. Liquid-crystal self-assembly of lipid membranes on solutions: A dissipative particle dynamic simulation study. POLYMER 2017. [DOI: 10.1016/j.polymer.2017.03.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
47
|
Non-thermal effects of microwave in sodium chloride aqueous solution: Insights from molecular dynamics simulations. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2016.11.126] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
48
|
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.
Collapse
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
| | | |
Collapse
|
49
|
Pineda De Castro LF, Dopson M, Friedman R. Biological Membranes in Extreme Conditions: Anionic Tetraether Lipid Membranes and Their Interactions with Sodium and Potassium. J Phys Chem B 2016; 120:10628-10634. [PMID: 27668511 DOI: 10.1021/acs.jpcb.6b06206] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Archaea such as Sulfolobus acidocaldarius tolerate extreme temperatures and high acidity and can grow in the presence of toxic metals and low concentrations of Na+ or K+. It is believed that their unique tetraether membranes protect them from harsh environments and allow their survival under such conditions. We used molecular dynamics simulations to study membranes comprising glycerol dialkylnonitol tetraether lipids, which are the main component of S. acidocaldarius membranes, in solutions containing different concentrations of NaCl and KCl or with Na+ or K+ counterions (trace cations, 0 M). Anionic binding sites on the membranes were almost 50% occupied in the presence of counterions. The free energy of cation-phosphate complexation and the residence times of ions near the membranes were found to be both ion- and concentration-dependent. Sodium ions had more favorable interactions with the membranes and a longer residence time, whereas higher cation concentrations led to shorter ion residence times. When only counterions were present in the solutions, large residence times suggested that the membrane may function as a cation-attracting reservoir. The results suggested that the ions can be easily transferred to the cytoplasm as needed, explaining the growth curves of S. acidocaldarius under different salinities and pH.
Collapse
Affiliation(s)
- Luis Felipe Pineda De Castro
- Computational Chemistry and Biochemistry Research Group (CCBG), Department of Chemistry and Biomedical Sciences, ‡Centre of Excellence "Biomaterials Chemistry", and §Linnaeus University Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnæus University , 391 82 Kalmar, Sweden
| | - Mark Dopson
- Computational Chemistry and Biochemistry Research Group (CCBG), Department of Chemistry and Biomedical Sciences, ‡Centre of Excellence "Biomaterials Chemistry", and §Linnaeus University Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnæus University , 391 82 Kalmar, Sweden
| | - Ran Friedman
- Computational Chemistry and Biochemistry Research Group (CCBG), Department of Chemistry and Biomedical Sciences, ‡Centre of Excellence "Biomaterials Chemistry", and §Linnaeus University Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnæus University , 391 82 Kalmar, Sweden
| |
Collapse
|
50
|
Zhang T, Cathcart MG, Vidalis AS, Allen HC. Cation effects on phosphatidic acid monolayers at various pH conditions. Chem Phys Lipids 2016; 200:24-31. [DOI: 10.1016/j.chemphyslip.2016.06.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 05/11/2016] [Accepted: 06/01/2016] [Indexed: 11/29/2022]
|