1
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Chatterjee H, Mahapatra AJ, Zacharias M, Sengupta N. Helical reorganization in the context of membrane protein folding: Insights from simulations with bacteriorhodopsin (BR) fragments. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184333. [PMID: 38740122 DOI: 10.1016/j.bbamem.2024.184333] [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: 02/07/2024] [Revised: 04/20/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024]
Abstract
Membrane protein folding is distinct from folding of soluble proteins. Conformational acquisition in major membrane protein subclasses can be delineated into insertion and folding processes. An exception to the "two stage" folding, later developed to "three stage" folding, is observed within the last two helices in bacteriorhodopsin (BR), a system that serves as a model membrane protein. We employ a reductionist approach to understand interplay of molecular factors underlying the apparent defiance. Leveraging available solution NMR structures, we construct, sample in silico, and analyze partially (PIn) and fully inserted (FIn) BR membrane states. The membrane lateral C-terminal helix (CH) in PIn is markedly prone to transient structural distortions over microsecond timescales; a disorder prone region (DPR) is thereby identified. While clear transmembrane propensities are not acquired, the distortions induce alterations in local membrane curvature and area per lipid. Importantly, energetic decompositions reveal that overall, the N-terminal helix (NH) is thermodynamically more stable in the PIn. Higher overall stability of the FIn arises from favorable interactions between the NH and the CH. Our results establish lack of spontaneous transition of the PIn to the FIn, and attributes their partitioning to barriers that exceed those accessible with thermal fluctuations. This work paves the way for further detailed studies aimed at determining the thermo-kinetic roles of the initial five helices, or complementary external factors, in complete helical folding and insertion in BR. We comment that complementing such efforts with the growing field of machine learning assisted energy landscape searches may offer unprecedented insights.
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Affiliation(s)
- Hindol Chatterjee
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Anshuman J Mahapatra
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Martin Zacharias
- Center for Functional Protein Assemblies, TUM School of Natural Sciences Technical University Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany.
| | - Neelanjana Sengupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India.
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2
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Cao Y, Gao C, Yang L, Zhou P, Sun D. Molecular simulation on the interaction between trehalose and asymmetric lipid bilayer mimicking the membrane of human red blood cells. Cryobiology 2024; 115:104898. [PMID: 38663665 DOI: 10.1016/j.cryobiol.2024.104898] [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: 01/10/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 05/05/2024]
Abstract
Trehalose is widely acknowledged for its ability to stabilize plasma membranes during dehydration. However, the exact mechanism by which trehalose interacts with lipid bilayers remains presently unclear. In this study, we conducted atomistic molecular dynamic simulations on asymmetric model bilayers that mimic the membrane of human red blood cells at various trehalose and water contents. We considered three different hydration levels mimicking the full hydration to desiccation scenarios. Results indicate that the asymmetric distribution of lipids did not significantly influence the computed structural characteristics at full and low hydration. At dehydration, however, the order parameter obtained from the symmetric bilayer is significantly higher compared to those obtained from asymmetric ones. Analysis of hydrogen bonds revealed that the protective ability of trehalose is well described by the water replacement hypothesis at full and low hydration, while at dehydration other interaction mechanisms associated with trehalose exclusion from the bilayer may involve. In addition, we found that trehalose exclusion is not attributed to sugar saturation but rather to the reduction in hydration levels. It can be concluded that the protective effect of trehalose is not only related to the hydration level of the bilayer, but also closely tied to the asymmetric distribution of lipids within each leaflet.
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Affiliation(s)
- Yu Cao
- Department of Refrigeration & Cryogenics Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Cai Gao
- Department of Refrigeration & Cryogenics Engineering, Hefei University of Technology, Hefei, 230009, China.
| | - Lei Yang
- Department of Refrigeration & Cryogenics Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Pei Zhou
- Department of Refrigeration & Cryogenics Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Dongfang Sun
- Department of Refrigeration & Cryogenics Engineering, Hefei University of Technology, Hefei, 230009, China.
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3
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Xu J, Karra V, Large DE, Auguste DT, Hung FR. Understanding the Mechanical Properties of Ultradeformable Liposomes Using Molecular Dynamics Simulations. J Phys Chem B 2023; 127:9496-9512. [PMID: 37879075 PMCID: PMC10641833 DOI: 10.1021/acs.jpcb.3c04386] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/19/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023]
Abstract
Improving drug delivery efficiency to solid tumor sites is a central challenge in anticancer therapeutic research. Our previous experimental study (Guo et al., Nat. Commun. 2018, 9, 130) showed that soft, elastic liposomes had increased uptake and accumulation in cancer cells and tumors in vitro and in vivo respectively, relative to rigid particles. As a first step toward understanding how liposomes' molecular structure and composition modulates their elasticity, we performed all-atom and coarse-grained classical molecular dynamics (MD) simulations of lipid bilayers formed by mixing a long-tailed unsaturated phospholipid with a short-tailed saturated lipid with the same headgroup. The former types of phospholipids considered were 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-dipalmitoleoyl-sn-glycero-3-phosphocholine (termed here DPMPC). The shorter saturated lipids examined were 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC), 1,2-didecanoyl-sn-glycero-3-phosphocholine (DDPC), 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). Several lipid concentrations and surface tensions were considered. Our results show that DOPC or DPMPC systems having 25-35 mol % of the shortest lipids DHPC or DDPC are the least rigid, having area compressibility moduli KA that are ∼10% smaller than the values observed in pure DOPC or DPMPC bilayers. These results agree with experimental measurements of the stretching modulus and lysis tension in liposomes with the same compositions. These mixed systems also have lower areas per lipid and form more uneven x-y interfaces with water, the tails of both primary and secondary lipids are more disordered, and the terminal methyl groups in the tails of the long lipid DOPC or DPMPC wriggle more in the vertical direction, compared to pure DOPC or DPMPC bilayers or their mixtures with the longer saturated lipid DLPC or DMPC. These observations confirm our hypothesis that adding increasing concentrations of the short unsaturated lipid DHPC or DDPC to DOPC or DPMPC bilayers alters lipid packing and thus makes the resulting liposomes more elastic and less rigid. No formation of lipid nanodomains was noted in our simulations, and no clear trends were observed in the lateral diffusivities of the lipids as the concentration, type of secondary lipid, and surface tension were varied.
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Affiliation(s)
- Jiaming Xu
- Department
of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Vyshnavi Karra
- Department
of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Danielle E. Large
- Department
of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Debra T. Auguste
- Department
of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
- Department
of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Francisco R. Hung
- Department
of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
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4
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Tripathy M, Srivastava A. Lipid packing in biological membranes governs protein localization and membrane permeability. Biophys J 2023; 122:2727-2743. [PMID: 37254482 PMCID: PMC10397809 DOI: 10.1016/j.bpj.2023.05.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/18/2023] [Accepted: 05/25/2023] [Indexed: 06/01/2023] Open
Abstract
Plasma membrane (PM) heterogeneity has long been implicated in various cellular functions. However, mechanistic principles governing functional regulations of lipid environment are not well understood due to the inherent complexities associated with the relevant length and timescales that limit both direct experimental measurements and their interpretation. In this context, computer simulations hold immense potential to investigate molecular-level interactions and mechanisms that lead to PM heterogeneity and its functions. Herein, we investigate spatial and dynamic heterogeneity in model membranes with coexisting liquid ordered and liquid disordered phases and characterize the membrane order in terms of the local topological changes in lipid environment using the nonaffine deformation framework. Furthermore, we probe the packing defects in these membranes, which can be considered as the conjugate of membrane order assessed in terms of the nonaffine parameter. In doing so, we formalize the connection between membrane packing and local membrane order and use that to explore the mechanistic principles behind their functions. Our observations suggest that heterogeneity in mixed phase membranes is a consequence of local lipid topology and its temporal evolution, which give rise to disparate lipid packing in ordered and disordered domains. This in turn governs the distinct nature of packing defects in these domains that can play a crucial role in preferential localization of proteins in mixed phase membranes. Furthermore, we observe that lipid packing also leads to contrasting distribution of free volume in the membrane core region in ordered and disordered membranes, which can lead to distinctive membrane permeability of small molecules. Our results, thus, indicate that heterogeneity in mixed phase membranes closely governs the membrane functions that may emerge from packing-related basic design principles.
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Affiliation(s)
- Madhusmita Tripathy
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, Bangalore, Karnataka, India.
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, Bangalore, Karnataka, India.
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5
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Kalutskii MA, Galimzyanov TR, Pinigin KV. Determination of elastic parameters of lipid membranes from simulation under varied external pressure. Phys Rev E 2023; 107:024414. [PMID: 36932616 DOI: 10.1103/physreve.107.024414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Many cellular processes such as endocytosis, exocytosis, and vesicle trafficking involve membrane deformations, which can be analyzed in the framework of the elastic theories of lipid membranes. These models operate with phenomenological elastic parameters. A connection between these parameters and the internal structure of lipid membranes can be provided by three-dimensional (3D) elastic theories. Considering a membrane as a 3D layer, Campelo et al. [F. Campelo et al., Adv. Colloid Interface Sci. 208, 25 (2014)10.1016/j.cis.2014.01.018] developed a theoretical basis for the calculation of elastic parameters. In this work we generalize and improve this approach by considering a more general condition of global incompressibility instead of local incompressibility. Crucially, we find an important correction to the theory of Campelo et al., which if not taken into account leads to a significant miscalculation of elastic parameters. With the total volume conservation taken into account, we derive an expression for the local Poisson's ratio, which determines how the local volume changes upon stretching and permits a more precise determination of elastic parameters. Also, we substantially simplify the procedure by calculating the derivatives of the moments of the local tension with respect to stretching instead of calculating the local stretching modulus. We obtain a relation between the Gaussian curvature modulus as a function of stretching and the bending modulus, showing that these two elastic parameters are not independent, as was previously assumed. The proposed algorithm is applied to membranes composed of pure dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), and their mixture. The following elastic parameters of these systems are obtained: the monolayer bending and stretching moduli, spontaneous curvature, neutral surface position, and local Poisson's ratio. It is shown that the bending modulus of the DPPC/DOPC mixture follows a more complex trend than predicted by the classical Reuss averaging, which is often employed in theoretical frameworks.
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Affiliation(s)
- Maksim A Kalutskii
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, Moscow 119071, Russia
- Department of Theoretical Physics and Quantum Technologies, National University of Science and Technology "MISiS," 4 Leninskiy Prospekt, 119049 Moscow, Russia
| | - Timur R Galimzyanov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, Moscow 119071, Russia
- Department of Theoretical Physics and Quantum Technologies, National University of Science and Technology "MISiS," 4 Leninskiy Prospekt, 119049 Moscow, Russia
| | - Konstantin V Pinigin
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, Moscow 119071, Russia
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6
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Aguilar-Pineda JA, Febres-Molina C, Cordova-Barrios CC, Campos-Olazával LM, Del-Carpio-Martinez BA, Ayqui-Cueva F, Gamero-Begazo PL, Gómez B. Study of the Rv1417 and Rv2617c Membrane Proteins and Their Interactions with Nicotine Derivatives as Potential Inhibitors of Erp Virulence-Associated Factor in Mycobacterium tuberculosis: An In Silico Approach. Biomolecules 2023; 13:biom13020248. [PMID: 36830617 PMCID: PMC9953637 DOI: 10.3390/biom13020248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/30/2022] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
The increasing emergence of Mycobacterium tuberculosis (Mtb) strains resistant to traditional anti-tuberculosis drugs has alarmed health services worldwide. The search for new therapeutic targets and effective drugs that counteract the virulence and multiplication of Mtb represents a challenge for the scientific community. Several studies have considered the erp gene a possible therapeutic target in the last two decades, since its disruption negatively impacts Mtb multiplication. This gene encodes the exported repetitive protein (Erp), which is located in the cell wall of Mtb. In vitro studies have shown that the Erp protein interacts with two putative membrane proteins, Rv1417 and Rv2617c, and the impairment of their interactions can decrease Mtb replication. In this study, we present five nicotine analogs that can inhibit the formation of heterodimers and trimers between these proteins. Through DFT calculations, molecular dynamics, docking, and other advanced in silico techniques, we have analyzed the molecular complexes, and show the effect these compounds have on protein interactions. The results show that four of these analogs can be possible candidates to counteract the pathogenicity of Mtb. This study aims to combine research on the Erp protein as a therapeutic target in the search for new drugs that serve to create new therapies against tuberculosis disease.
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Affiliation(s)
- Jorge Alberto Aguilar-Pineda
- Centro de Investigación en Ingeniería Molecular—CIIM, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
| | - Camilo Febres-Molina
- Centro de Investigación en Ingeniería Molecular—CIIM, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
- Doctorado en Fisicoquímica Molecular, Facultad de Ciencias Exactas, Universidad Andres Bello, Santiago de Chile 8370134, Chile
| | - Cinthia C. Cordova-Barrios
- Departamento de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
| | - Lizbeth M. Campos-Olazával
- Facultad de Arquitectura e Ingeniería Civil y del Ambiente, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
| | - Bruno A. Del-Carpio-Martinez
- Centro de Investigación en Ingeniería Molecular—CIIM, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
| | - Flor Ayqui-Cueva
- Centro de Investigación en Ingeniería Molecular—CIIM, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
| | - Pamela L. Gamero-Begazo
- Centro de Investigación en Ingeniería Molecular—CIIM, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
- Doctorado en Fisicoquímica Molecular, Facultad de Ciencias Exactas, Universidad Andres Bello, Santiago de Chile 8370134, Chile
| | - Badhin Gómez
- Centro de Investigación en Ingeniería Molecular—CIIM, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
- Departamento de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
- Correspondence: ; Tel.: +51-982895967
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7
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Krivić H, Himbert S, Rheinstädter MC. Perspective on the Application of Erythrocyte Liposome-Based Drug Delivery for Infectious Diseases. MEMBRANES 2022; 12:1226. [PMID: 36557133 PMCID: PMC9785899 DOI: 10.3390/membranes12121226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Nanoparticles are explored as drug carriers with the promise for the treatment of diseases to increase the efficacy and also reduce side effects sometimes seen with conventional drugs. To accomplish this goal, drugs are encapsulated in or conjugated to the nanocarriers and selectively delivered to their targets. Potential applications include immunization, the delivery of anti-cancer drugs to tumours, antibiotics to infections, targeting resistant bacteria, and delivery of therapeutic agents to the brain. Despite this great promise and potential, drug delivery systems have yet to be established, mainly due to their limitations in physical instability and rapid clearance by the host's immune response. Recent interest has been taken in using red blood cells (RBC) as drug carriers due to their naturally long circulation time, flexible structure, and direct access to many target sites. This includes coating of nanoparticles with the membrane of red blood cells, and the fabrication and manipulation of liposomes made of the red blood cells' cytoplasmic membrane. The properties of these erythrocyte liposomes, such as charge and elastic properties, can be tuned through the incorporation of synthetic lipids to optimize physical properties and the loading efficiency and retention of different drugs. Specificity can be established through the anchorage of antigens and antibodies in the liposomal membrane to achieve targeted delivery. Although still at an early stage, this erythrocyte-based platform shows first promising results in vitro and in animal studies. However, their full potential in terms of increased efficacy and side effect minimization still needs to be explored in vivo.
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Affiliation(s)
- Hannah Krivić
- Department of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Sebastian Himbert
- Department of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Maikel C. Rheinstädter
- Department of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, ON L8S 4M1, Canada
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8
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Pinigin KV. Determination of Elastic Parameters of Lipid Membranes with Molecular Dynamics: A Review of Approaches and Theoretical Aspects. MEMBRANES 2022; 12:membranes12111149. [PMID: 36422141 PMCID: PMC9692374 DOI: 10.3390/membranes12111149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 05/12/2023]
Abstract
Lipid membranes are abundant in living organisms, where they constitute a surrounding shell for cells and their organelles. There are many circumstances in which the deformations of lipid membranes are involved in living cells: fusion and fission, membrane-mediated interaction between membrane inclusions, lipid-protein interaction, formation of pores, etc. In all of these cases, elastic parameters of lipid membranes are important for the description of membrane deformations, as these parameters determine energy barriers and characteristic times of membrane-involved phenomena. Since the development of molecular dynamics (MD), a variety of in silico methods have been proposed for the determination of elastic parameters of simulated lipid membranes. These MD methods allow for the consideration of details unattainable in experimental techniques and represent a distinct scientific field, which is rapidly developing. This work provides a review of these MD approaches with a focus on theoretical aspects. Two main challenges are identified: (i) the ambiguity in the transition from the continuum description of elastic theories to the discrete representation of MD simulations, and (ii) the determination of intrinsic elastic parameters of lipid mixtures, which is complicated due to the composition-curvature coupling effect.
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Affiliation(s)
- Konstantin V Pinigin
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia
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9
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Adhyapak P, Dong W, Dasgupta S, Dutta A, Duan M, Kapoor S. Lipid Clustering in Mycobacterial Cell Envelope Layers Governs Spatially Resolved Solvation Dynamics. Chem Asian J 2022; 17:e202200146. [PMID: 35419975 DOI: 10.1002/asia.202200146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/30/2022] [Indexed: 11/06/2022]
Abstract
The mycobacterial cell envelope acts as a multilayered barrier to drugs. However, the role of lipid composition in the properties of different mycobacterial membranes, otherwise dictating their interactions with drugs, is poorly understood. In this study, we found that hydration states, solvation relaxation kinetics, rotational lipid mobility, and lateral lipid diffusion differed between inner and outer mycobacterial membranes. Molecular modeling showed that lipid clustering patterns governed membrane dynamics in the different layers of the cell envelope. By regulating membrane properties, lipid composition and structure modulated water abundance and interactions with lipid head groups. These findings can help deepen our understanding of the physical chemistry underlying membrane structure and function, as well as the interaction of mycobacterial membranes with drugs and host membranes.
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Affiliation(s)
- Pranav Adhyapak
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Wanqian Dong
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
| | - Souradip Dasgupta
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Anindya Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Mojie Duan
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, 400076, India.,Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, 739-8528, Japan
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10
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Ilangumaran Ponmalar I, Swain J, Basu JK. Escherichia coli response to subinhibitory concentrations of colistin: insights from a study of membrane dynamics and morphology. Biomater Sci 2022; 10:2609-2617. [PMID: 35411890 DOI: 10.1039/d2bm00037g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Prevalence of widespread bacterial infections brings forth a critical need to understand the molecular mechanisms of the antibiotics as well as the bacterial response to those antibiotics. Improper use of antibiotics, which can be in sub-lethal concentrations is one among the multiple reasons for acquiring antibiotic resistance which makes it vital to understand the bacterial response towards sub-lethal concentrations of antibiotics. In this work, we have used colistin, a well-known membrane active antibiotic used to treat severe bacterial infections and explored the impact of its sub-minimum inhibitory concentration (MIC) on the lipid membrane dynamics and morphological changes of E. coli. Upon investigation of live cell membrane properties such as lipid dynamics using fluorescence correlation spectroscopy, we observed that colistin disrupts the lipid membrane at sub-MIC by altering the lipid diffusivity. Interestingly, filamentation-like cell elongation was observed upon colistin treatment which led to further exploration of surface morphology with the help of atomic force spectroscopy. The changes in the surface roughness upon colistin treatment provides additional insight on the colistin-membrane interaction corroborating with the altered lipid diffusion. Although altered lipid dynamics could be attributed to an outcome of lipid rearrangement due to direct disruption by antibiotic molecules on the membrane or an indirect consequence of disruptions in lipid biosynthetic pathways, we were able to ascertain that altered bacterial membrane dynamics is due to direct disruptions. Our results provide a broad overview on the consequence of the cyclic polypeptide colistin on membrane-specific lipid dynamics and morphology of a live Gram-negative bacterial cell.
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Affiliation(s)
| | - Jitendriya Swain
- Department of Physics, Indian Institute of Science, Bengaluru 560012, India.
| | - Jaydeep K Basu
- Department of Physics, Indian Institute of Science, Bengaluru 560012, India.
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11
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Karal MAS, Mokta NA, Levadny V, Belaya M, Ahmed M, Ahamed MK, Ahammed S. Effects of cholesterol on the size distribution and bending modulus of lipid vesicles. PLoS One 2022; 17:e0263119. [PMID: 35089965 PMCID: PMC8797199 DOI: 10.1371/journal.pone.0263119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 01/12/2022] [Indexed: 11/19/2022] Open
Abstract
The influence of cholesterol fraction in the membranes of giant unilamellar vesicles (GUVs) on their size distributions and bending moduli has been investigated. The membranes of GUVs were synthesized by a mixture of two elements: electrically neutral lipid 1, 2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and cholesterol and also a mixture of three elements: electrically charged lipid 1,2-dioleoyl-sn-glycero-3-phospho-(1′-rac-glycerol) (DOPG), DOPC and cholesterol. The size distributions of GUVs have been presented by a set of histograms. The classical lognormal distribution is well fitted to the histograms, from where the average size of vesicle is obtained. The increase of cholesterol content in the membranes of GUVs increases the average size of vesicles in the population. Using the framework of Helmholtz free energy of the system, the theory developed by us is extended to explain the experimental results. The theory determines the influence of cholesterol on the bending modulus of membranes from the fitting of the proper histograms. The increase of cholesterol in GUVs increases both the average size of vesicles in population and the bending modulus of membranes.
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Affiliation(s)
- Mohammad Abu Sayem Karal
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
- * E-mail:
| | - Nadia Akter Mokta
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Victor Levadny
- Theoretical Problem Center of Physico-Chemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
| | - Marina Belaya
- Department of Mathematics of Russian State University for the Humanities, Moscow, Russia
| | - Marzuk Ahmed
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Md. Kabir Ahamed
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Shareef Ahammed
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
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12
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Caparotta M, Puiatti M, Masone D. Artificial stabilization of the fusion pore by intra-organelle styrene-maleic acid copolymers. SOFT MATTER 2021; 17:8314-8321. [PMID: 34550159 DOI: 10.1039/d1sm00978h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Styrene-maleic acid copolymers have become an advantageous detergent-free alternative for membrane protein isolation. Since their discovery, experimental membrane protein extraction and purification by keeping intact their lipid environment has become significantly easier. With the aim of identifying new applications of these interesting copolymers, their molecular binding and functioning mechanisms have recently become intense objects of study. In this work, we describe the use of styrene-maleic acid copolymers as an artificial tool to stabilize the fusion pore. We show that when these copolymers circumscribe the water channel that defines the fusion pore, they keep it from shrinking and closing. We describe how only intra-organelle copolymers have stabilizing capabilities while extra-organelle ones have negligible or even contrary effects on the fusion pore life-time.
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Affiliation(s)
- Marcelo Caparotta
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500, Mendoza, Argentina
| | - Marcelo Puiatti
- Instituto de Investigaciones en Físico-Química de Córdoba (INFIQC) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba (UNC), 5016, Córdoba, Argentina
| | - Diego Masone
- Facultad de Ingeniería, Universidad Nacional de Cuyo (UNCuyo), 5500, Mendoza, Argentina
- Instituto de Histología y Embriología de Mendoza (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500, Mendoza, Argentina.
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Bouquiaux C, Castet F, Champagne B. Unravelling the Effects of Cholesterol on the Second-Order Nonlinear Optical Responses of Di-8-ANEPPS Dye Embedded in Phosphatidylcholine Lipid Bilayers. J Phys Chem B 2021; 125:10195-10212. [PMID: 34491062 DOI: 10.1021/acs.jpcb.1c05630] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Cholesterol is known for its role in maintaining the correct fluidity and rigidity of the animals cell membranes and thus their functions. Assessing the content and the role of cholesterol in lipid bilayers is therefore of crucial importance for a deeper understanding and control of membrane functioning. In this computational work, we investigate bilayers built from three types of glycerophospholipid phosphatidylcholine (PC) lipids, namely dipalmitoylphosphatidylcholine (DPPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and dioleoylphosphatidylcholine (DOPC), and containing different amounts of cholesterol by analyzing the second-harmonic generation (SHG) nonlinear optical (NLO) response of a probe molecule, di-8-ANEPPS, inserted into the membranes. This molecular property presents the advantage to be specific to interfacial regions such as lipid bilayers. To unravel these effects, Molecular Dynamics (MD) simulations have been performed on both DPPC and DOPC lipids by varying the cholesterol mole fraction (from 0 to 0.66), while POPC was only considered as a pure bilayer. In the case of the structural properties of the bilayers, all the analyses converge toward the same conclusion: as the mole fraction of cholesterol increases, the systems become more rigid, confirming the condensing effect of cholesterol. In addition, the chromophore is progressively more aligned with respect to the normal to the bilayer. On the contrary, addition of unsaturation disorders the lipid bilayers, with barely no impact on the alignment of the chromophore. Then, using the frames obtained from the MD simulations, the first hyperpolarizability β of the dye in its environment has been computed at the TDDFT level. On the one hand, the addition of cholesterol induces a progressive increase of the diagonal component the β tensor parallel to the bilayer normal. On the other hand, larger β values have been calculated for the unsaturated than for the saturated lipid systems. In summary, this study illustrates the relationship between the composition and structure of the bilayers and the NLO responses of the embedded dye.
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Affiliation(s)
- Charlotte Bouquiaux
- Theoretical Chemistry Lab, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, University of Namur, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Frédéric Castet
- , Institut des Sciences Moléculaires, UMR 5255 CNRS, University of Bordeaux, cours de la Libération 351, F-33405 Talence Cedex, France
| | - Benoît Champagne
- Theoretical Chemistry Lab, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, University of Namur, rue de Bruxelles, 61, B-5000 Namur, Belgium
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Karal MAS, Ahamed MK, Ahmed M, Mahbub ZB. Recent developments in the kinetics of ruptures of giant vesicles under constant tension. RSC Adv 2021; 11:29598-29619. [PMID: 35479542 PMCID: PMC9040846 DOI: 10.1039/d1ra04647k] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/17/2021] [Indexed: 01/03/2023] Open
Abstract
External tension in membranes plays a vital role in numerous physiological and physicochemical phenomena. In this review, recent developments in the constant electric- and mechanical-tension-induced rupture of giant unilamellar vesicles (GUVs) are considered. We summarize the results relating to the kinetics of GUV rupture as a function of membrane surface charge, ions in the bathing solution, lipid composition, cholesterol content in the membrane, and osmotic pressure. The mechanical stability and line tension of the membrane under these conditions are discussed. The membrane tension due to osmotic pressure and the critical tension of rupture for various membrane compositions are also discussed. The results and their analysis provide a biophysical description of the kinetics of rupture, along with insight into biological processes. Future directions and possible developments in this research area are included.
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Affiliation(s)
- Mohammad Abu Sayem Karal
- Department of Physics, Bangladesh University of Engineering and Technology Dhaka-1000 Bangladesh +880-2-58613046 +880-2-9665613
| | - Md Kabir Ahamed
- Department of Physics, Bangladesh University of Engineering and Technology Dhaka-1000 Bangladesh +880-2-58613046 +880-2-9665613
| | - Marzuk Ahmed
- Department of Physics, Bangladesh University of Engineering and Technology Dhaka-1000 Bangladesh +880-2-58613046 +880-2-9665613
| | - Zaid Bin Mahbub
- Department of Mathematics and Physics, North South University Dhaka-1229 Bangladesh
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15
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Kondela T, Dushanov E, Vorobyeva M, Mamatkulov K, Drolle E, Soloviov D, Hrubovčák P, Kholmurodov K, Arzumanyan G, Leonenko Z, Kučerka N. Investigating the competitive effects of cholesterol and melatonin in model lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183651. [PMID: 34023300 DOI: 10.1016/j.bbamem.2021.183651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 10/21/2022]
Abstract
We have studied the impact of cholesterol and/or melatonin on the static and dynamical properties of bilayers made of DPPC or DOPC utilizing neutron scattering techniques, Raman spectroscopy and molecular dynamics simulations. While differing in the amplitude of the effect due to cholesterol or melatonin when comparing their interactions with the two lipids, their addition ensued recognizable changes to both types of bilayers. As expected, based on the two-component systems of lipid/cholesterol or lipid/melatonin studied previously, we show the impact of cholesterol and melatonin being opposite and competitive in the case of three-component systems of lipid/cholesterol/melatonin. The effect of cholesterol appears to prevail over that of melatonin in the case of structural properties of DPPC-based bilayers, which can be explained by its interactions targeting primarily the saturated lipid chains. The dynamics of hydrocarbon chains represented by the ratio of trans/gauche conformers reveals the competitive effect of cholesterol and melatonin being somewhat more balanced. The additive yet opposing effects of cholesterol and melatonin have been observed also in the case of structural properties of DOPC-based bilayers. We report that cholesterol induced an increase in bilayer thickness, while melatonin induced a decrease in bilayer thickness in the three-component systems of DOPC/cholesterol/melatonin. Commensurately, by evaluating the projected area of DOPC, we demonstrate a lipid area decrease with an increasing concentration of cholesterol, and a lipid area increase with an increasing concentration of melatonin. The demonstrated condensing effect of cholesterol and the fluidizing effect of melatonin appear in an additive manner upon their mutual presence.
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Affiliation(s)
- Tomáš Kondela
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russian Federation; Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynska dolina, Bratislava 842 48, Slovakia
| | - Ermuhammad Dushanov
- Laboratory of Radiation Biology, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russian Federation; Department of Biophysics, Dubna State University, Universitetskaya 19, Dubna, Moscow Region 141980, Russian Federation
| | - Maria Vorobyeva
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russian Federation
| | - Kahramon Mamatkulov
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russian Federation
| | - Elizabeth Drolle
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Dmytro Soloviov
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russian Federation; Faculty of Physics, Taras Shevchenko National University of Kyiv, Hlushkova Ave. 4, Kyiv 03127, Ukraine
| | - Pavol Hrubovčák
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russian Federation; Department of Condensed Matter Physics, P. J. Šafárik University, Park Angelinum 9, Košice 04154, Slovakia
| | - Kholmirzo Kholmurodov
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russian Federation; Department of Chemistry, New Technologies and Materials, Dubna State University, Universitetskaya 19, Dubna, Moscow Region 141980, Russian Federation
| | - Grigory Arzumanyan
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russian Federation
| | - Zoya Leonenko
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada; Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario, Canada
| | - Norbert Kučerka
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russian Federation; Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, Bratislava 832 32, Slovakia.
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16
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Sarkar MK, Karal MAS, Ahmed M, Ahamed MK, Ahammed S, Sharmin S, Shibly SUA. Effects of osmotic pressure on the irreversible electroporation in giant lipid vesicles. PLoS One 2021; 16:e0251690. [PMID: 33989363 PMCID: PMC8121316 DOI: 10.1371/journal.pone.0251690] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/03/2021] [Indexed: 02/06/2023] Open
Abstract
Irreversible electroporation (IRE) is a nonthermal tumor/cell ablation technique in which a series of high-voltage short pulses are used. As a new approach, we aimed to investigate the rupture of giant unilamellar vesicles (GUVs) using the IRE technique under different osmotic pressures (Π), and estimated the membrane tension due to Π. Two categories of GUVs were used in this study. One was prepared with a mixture of dioleoylphosphatidylglycerol (DOPG), dioleoylphosphatidylcholine (DOPC) and cholesterol (chol) for obtaining more biological relevance while other with a mixture of DOPG and DOPC, with specific molar ratios. We determined the rate constant (kp) of rupture of DOPG/DOPC/chol (46/39/15)-GUVs and DOPG/DOPC (40/60)-GUVs induced by constant electric tension (σc) under different Π. The σc dependent kp values were fitted with a theoretical equation, and the corresponding membrane tension (σoseq) at swelling equilibrium under Π was estimated. The estimated membrane tension agreed well with the theoretical calculation within the experimental error. Interestingly, the values of σoseq were almost same for both types of synthesized GUVs under same osmotic pressure. We also examined the sucrose leakage, due to large osmotic pressure-induced pore formation, from the inside of DOPG/DOPC/chol(46/39/15)-GUVs. The estimated membrane tension due to large Π at which sucrose leaked out was very similar to the electric tension at which GUVs were ruptured without Π. We explained the σc and Π induced pore formation in the lipid membranes of GUVs.
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Affiliation(s)
- Malay Kumar Sarkar
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
- Department of Arts and Sciences, Ahsanullah University of Science and Technology, Dhaka, Bangladesh
| | - Mohammad Abu Sayem Karal
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
- * E-mail:
| | - Marzuk Ahmed
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Md. Kabir Ahamed
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Shareef Ahammed
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Sabrina Sharmin
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
- Department of Arts and Sciences, Ahsanullah University of Science and Technology, Dhaka, Bangladesh
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17
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Arulkumaran N, Lanphere C, Gaupp C, Burns JR, Singer M, Howorka S. DNA Nanodevices with Selective Immune Cell Interaction and Function. ACS NANO 2021; 15:4394-4404. [PMID: 33492943 DOI: 10.1021/acsnano.0c07915] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA nanotechnology produces precision nanostructures of defined chemistry. Expanding their use in biomedicine requires designed biomolecular interaction and function. Of topical interest are DNA nanostructures that function as vaccines with potential advantages over nonstructured nucleic acids in terms of serum stability and selective interaction with human immune cells. Here, we describe how compact DNA nanobarrels bind with a 400-fold selectivity via membrane anchors to white blood immune cells over erythrocytes, without affecting cell viability. The selectivity is based on the preference of the cholesterol lipid anchor for the more fluid immune cell membranes compared to the lower membrane fluidity of erythrocytes. Compacting DNA into the nanostructures gives rise to increased serum stability. The DNA barrels furthermore functionally modulate white blood cells by suppressing the immune response to pro-inflammatory endotoxin lipopolysaccharide. This is likely due to electrostatic or steric blocking of toll-like receptors on white blood cells. Our findings on immune cell-specific DNA nanostructures may be applied for vaccine development, immunomodulatory therapy to suppress septic shock, or the targeting of bioactive substances to immune cells.
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Affiliation(s)
- Nishkantha Arulkumaran
- Division of Medicine, Bloomsbury Institute of Intensive Care Medicine, University College London, London WC1E 6BT, United Kingdom
| | - Conor Lanphere
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Charlotte Gaupp
- Division of Medicine, Bloomsbury Institute of Intensive Care Medicine, University College London, London WC1E 6BT, United Kingdom
| | - Jonathan R Burns
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Mervyn Singer
- Division of Medicine, Bloomsbury Institute of Intensive Care Medicine, University College London, London WC1E 6BT, United Kingdom
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
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18
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Ermilova I, Swenson J. DOPC versus DOPE as a helper lipid for gene-therapies: molecular dynamics simulations with DLin-MC3-DMA. Phys Chem Chem Phys 2020; 22:28256-28268. [PMID: 33295352 DOI: 10.1039/d0cp05111j] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ionizable lipids are important compounds of modern therapeutic lipid nano-particles (LNPs). One of the most promising ionizable lipids (or amine lipids) is DLin-MC3-DMA. Depending on their pharmaceutical application these LNPs can also contain various helper lipids, such as phospho- and pegylated lipids, cholesterol and nucleic acids as a cargo. Due to their complex compositions the structures of these therapeutics have not been refined properly. Therefore, the role of each lipid in the pharmacological properties of LNPs has not been determined. In this work an atomistic model for the neutral form of DLin-MC3-DMA was derived and all-atom molecular dynamics (MD) simulations were carried out in order to investigate the effect of the phospholipid headgroup on the possible properties of the shell-membranes of LNPs. Bilayers containing either DOPC or DOPE lipids at two different ratios of DLin-MC3-DMA (5 mol% and 15 mol%) were constructed and simulated at neutral pH 7.4. The results from the analysis of MD trajectories revealed that DOPE lipid headgroups associated strongly with lipid tails and carbonyl oxygens of DLin-MC3-DMA, while for DOPC lipid headgroups no significant associations were observed. Furthermore, the strong associations between DOPE and DLin-MC3-DMA result in the positioning of DLin-MC3-DMA at the surface of the membrane. Such an interplay between the lipids slows down the lateral diffusion of all simulated bilayers, where a more dramatic decrease of the diffusion rate is observed in membranes with DOPE. This can explain the low water penetration of lipid bilayers with phosphatidylethanolamines and, probably, can relate to the bad transfection properties of LNPs with DOPE and DLin-MC3-DMA.
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Affiliation(s)
- Inna Ermilova
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden.
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19
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Gusmira A, Takemura K, Lee SY, Inaba T, Hanawa-Suetsugu K, Oono-Yakura K, Yasuhara K, Kitao A, Suetsugu S. Regulation of caveolae through cholesterol-depletion-dependent tubulation mediated by PACSIN2. J Cell Sci 2020; 133:jcs246785. [PMID: 32878944 DOI: 10.1242/jcs.246785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/24/2020] [Indexed: 01/09/2023] Open
Abstract
The membrane-shaping ability of PACSIN2 (also known as syndapin II), which is mediated by its F-BAR domain, has been shown to be essential for caveolar morphogenesis, presumably through the shaping of the caveolar neck. Caveolar membranes contain abundant cholesterol. However, the role of cholesterol in PACSIN2-mediated membrane deformation remains unclear. Here, we show that the binding of PACSIN2 to the membrane can be negatively regulated by cholesterol. We prepared reconstituted membranes based on the lipid composition of caveolae. The reconstituted membrane with cholesterol had a weaker affinity for the F-BAR domain of PACSIN2 than a membrane without cholesterol. Consistent with this, upon depletion of cholesterol from the plasma membrane, PACSIN2 localized at tubules that had caveolin-1 at their tips, suggesting that cholesterol inhibits membrane tubulation mediated by PACSIN2. The tubules induced by PACSIN2 could be representative of an intermediate of caveolae endocytosis. Consistent with this, the removal of caveolae from the plasma membrane upon cholesterol depletion was diminished in the PACSIN2-deficient cells. These data suggest that PACSIN2-mediated caveolae internalization is dependent on the amount of cholesterol, providing a mechanism for cholesterol-dependent regulation of caveolae.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Aini Gusmira
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Kazuhiro Takemura
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Shin Yong Lee
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Takehiko Inaba
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Kyoko Hanawa-Suetsugu
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Kayoko Oono-Yakura
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Kazuma Yasuhara
- Division of Material Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Shiro Suetsugu
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
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20
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Zu Z, Lin EC, Louie EA, Xu J, Li H, Xie J, Lankford CL, Chekmenev EY, Swanson SD, Does MD, Gore JC, Gochberg DF. Relayed nuclear Overhauser enhancement sensitivity to membrane Cho phospholipids. Magn Reson Med 2020; 84:1961-1976. [PMID: 32243662 PMCID: PMC8238412 DOI: 10.1002/mrm.28258] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/17/2020] [Accepted: 02/26/2020] [Indexed: 12/20/2022]
Abstract
PURPOSE Phospholipids are key constituents of cell membranes and serve vital functions in the regulation of cellular processes; thus, a method for in vivo detection and characterization could be valuable for detecting changes in cell membranes that are consequences of either normal or pathological processes. Here, we describe a new method to map the distribution of partially restricted phospholipids in tissues. METHODS The phospholipids were measured by signal changes caused by relayed nuclear Overhauser enhancement-mediated CEST between the phospholipid Cho headgroup methyl protons and water at around -1.6 ppm from the water resonance. The biophysical basis of this effect was examined by controlled manipulation of head group, chain length, temperature, degree of saturation, and presence of cholesterol. Additional experiments were performed on animal tumor models to evaluate potential applications of this novel signal while correcting for confounding contributions. RESULTS Negative relayed nuclear Overhauser dips in Z-spectra were measured from reconstituted Cho phospholipids with cholesterol but not for other Cho-containing metabolites or proteins. Significant contrast was found between tumor and contralateral normal tissue signals in animals when comparing both the measured saturation transfer signal and a more specific imaging metric. CONCLUSION We demonstrated specific relayed nuclear Overhauser effects in partially restricted phospholipid phantoms and similar effects in solid brain tumors after correcting for confounding signal contributions, suggesting possible translational applications of this novel molecular imaging method, which we name restricted phospholipid transfer.
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Affiliation(s)
- Zhongliang Zu
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, Tennessee
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Eugene C. Lin
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, Tennessee
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Elizabeth A. Louie
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, Tennessee
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Junzhong Xu
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, Tennessee
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
- Deparment of Physics and Astronomy, Vanderbilt University, Nashville, Tennessee
| | - Hua Li
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, Tennessee
- Deparment of Physics and Astronomy, Vanderbilt University, Nashville, Tennessee
| | - Jingping Xie
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, Tennessee
| | - Christopher L. Lankford
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, Tennessee
| | - Eduard Y. Chekmenev
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, Tennessee
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
| | - Scott D. Swanson
- Department of Radiology, University of Michigan, Ann Arbor, Michigan
| | - Mark D. Does
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, Tennessee
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
- Department of Electrical Engineering, Vanderbilt University, Nashville, Tennessee
| | - John C. Gore
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, Tennessee
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
- Deparment of Physics and Astronomy, Vanderbilt University, Nashville, Tennessee
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee
| | - Daniel F. Gochberg
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, Tennessee
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
- Deparment of Physics and Astronomy, Vanderbilt University, Nashville, Tennessee
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21
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Kelley EG, Butler PD, Ashkar R, Bradbury R, Nagao M. Scaling relationships for the elastic moduli and viscosity of mixed lipid membranes. Proc Natl Acad Sci U S A 2020; 117:23365-23373. [PMID: 32883879 PMCID: PMC7519290 DOI: 10.1073/pnas.2008789117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The elastic and viscous properties of biological membranes play a vital role in controlling cell functions that require local reorganization of the membrane components as well as dramatic shape changes such as endocytosis, vesicular trafficking, and cell division. These properties are widely acknowledged to depend on the unique composition of lipids within the membrane, yet the effects of lipid mixing on the membrane biophysical properties remain poorly understood. Here, we present a comprehensive characterization of the structural, elastic, and viscous properties of fluid membranes composed of binary mixtures of lipids with different tail lengths. We show that the mixed lipid membrane properties are not simply additive quantities of the single-component analogs. Instead, the mixed membranes are more dynamic than either of their constituents, quantified as a decrease in their bending modulus, area compressibility modulus, and viscosity. While the enhanced dynamics are seemingly unexpected, we show that the measured moduli and viscosity for both the mixed and single-component bilayers all scale with the area per lipid and collapse onto respective master curves. This scaling links the increase in dynamics to mixing-induced changes in the lipid packing and membrane structure. More importantly, the results show that the membrane properties can be manipulated through lipid composition the same way bimodal blends of surfactants, liquid crystals, and polymers are used to engineer the mechanical properties of soft materials, with broad implications for understanding how lipid diversity relates to biomembrane function.
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Affiliation(s)
- Elizabeth G Kelley
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899;
| | - Paul D Butler
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716
- Department of Chemistry, The University of Tennessee, Knoxville, TN 37996
| | - Rana Ashkar
- Physics Department, Virginia Tech, Blacksburg, VA 20461
- Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 20461
| | - Robert Bradbury
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
- Center for Exploration of Energy and Matter, Indiana University, Bloomington, IN 47408
| | - Michihiro Nagao
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
- Center for Exploration of Energy and Matter, Indiana University, Bloomington, IN 47408
- Department of Physics and Astronomy, University of Delaware, Newark, DE 19716
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22
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Karal MAS, Ahamed MK, Mokta NA, Ahmed M, Ahammed S. Influence of cholesterol on electroporation in lipid membranes of giant vesicles. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:361-370. [PMID: 32535676 DOI: 10.1007/s00249-020-01443-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/19/2020] [Accepted: 06/08/2020] [Indexed: 12/16/2022]
Abstract
Irreversible electroporation (IRE) is primarily a nonthermal ablative technology that uses a series of high-voltage and ultra-short pulses with high-frequency electrical energy to induce cell death. This paper presents the influence of cholesterol on the IRE-induced probability of pore formation and the rate constant of pore formation in giant unilamellar vesicles (GUVs). The GUVs are prepared by a mixture of dioleoylphosphatidylglycerol (DOPG), dioleoylphosphatidylcholine (DOPC) and cholesterol using the natural swelling method. An IRE signal of frequency 1.1 kHz is applied to the membranes of GUVs. The probability of pore formation and the rate constant of pore formation events are obtained using statistical analysis from several single GUVs. The time-dependent fraction of intact GUVs among all those examined is fitted to a single exponential decay function from where the rate constant of pore formation is calculated. The probability of pore formation and the rate constant of pore formation decreases with an increase in cholesterol content in the membranes of GUVs. Theoretical equations are fitted to the tension-dependent rate constant of pore formation and to the probability of pore formation, which allows us to obtain the line tension of membranes. The obtained line tension increases with an increase in cholesterol in the membranes. The increase in the energy barrier of the prepore state, due to the increase of cholesterol in membranes, is the main factor explaining the decrease in the rate constant of pore formation.
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Affiliation(s)
- Mohammad Abu Sayem Karal
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh.
| | - Md Kabir Ahamed
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh
| | - Nadia Akter Mokta
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh
| | - Marzuk Ahmed
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh
| | - Shareef Ahammed
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh
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23
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Yang A, Moore TC, Iacovella CR, Thompson M, Moore DJ, McCabe C. Examining Tail and Headgroup Effects on Binary and Ternary Gel-Phase Lipid Bilayer Structure. J Phys Chem B 2020; 124:3043-3053. [PMID: 32196346 DOI: 10.1021/acs.jpcb.0c00490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The structural properties of two- and three-component gel-phase bilayers were studied using molecular dynamics simulations. The bilayers contain distearoylphosphatidylcholine (DSPC) phospholipids mixed with alcohols and/or fatty acids of varying tail lengths, with carbon chain lengths of 12, 16, and 24 studied. Changes in both headgroup chemistry and tail length are found to affect the balance between steric repulsion and van der Waals attraction within the bilayers, manifesting in different bilayer structural properties. Lipid components are found to be located at different depths within the bilayer depending on both chain length and headgroup chemistry. The highest bilayer ordering and lowest area per tail are found in systems with medium-length tails. While longer tails can enhance van der Waals attractions, the increased tail-length asymmetry is found to induce disorder and reduce tail packing. Bulkier headgroups further increase steric repulsion, as reflected in increased component offsets and reduced tail packing. These findings help explain how bilayer composition affects the structure of gel-phase bilayers.
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Affiliation(s)
- Alexander Yang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States.,Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Timothy C Moore
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States.,Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Christopher R Iacovella
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States.,Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Michael Thompson
- GlaxoSmithKline Consumer Health Care, 184 Liberty Corner Road, Suite 200, Warren, New Jersey 07059, United States
| | - David J Moore
- GlaxoSmithKline Consumer Health Care, 184 Liberty Corner Road, Suite 200, Warren, New Jersey 07059, United States
| | - Clare McCabe
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States.,Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, Tennessee 37212, United States.,Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
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24
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Loschwitz J, Olubiyi OO, Hub JS, Strodel B, Poojari CS. Computer simulations of protein-membrane systems. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:273-403. [PMID: 32145948 PMCID: PMC7109768 DOI: 10.1016/bs.pmbts.2020.01.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The interactions between proteins and membranes play critical roles in signal transduction, cell motility, and transport, and they are involved in many types of diseases. Molecular dynamics (MD) simulations have greatly contributed to our understanding of protein-membrane interactions, promoted by a dramatic development of MD-related software, increasingly accurate force fields, and available computer power. In this chapter, we present available methods for studying protein-membrane systems with MD simulations, including an overview about the various all-atom and coarse-grained force fields for lipids, and useful software for membrane simulation setup and analysis. A large set of case studies is discussed.
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Affiliation(s)
- Jennifer Loschwitz
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Olujide O Olubiyi
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany
| | - Birgit Strodel
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Chetan S Poojari
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany.
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25
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Bux K, Moin ST. Solvation of cholesterol in different solvents: a molecular dynamics simulation study. Phys Chem Chem Phys 2020; 22:1154-1167. [PMID: 31848548 DOI: 10.1039/c9cp05303d] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
To the best of our knowledge, molecular dynamics simulations of an isolated cholesterol immersed in four different solvents of varying polarity, such as water, methanol, dimethyl sulfoxide and benzene, were reported for the first time to gain insights into the structural and dynamical properties. The study was mainly focused on the evaluation of solvation of cholesterol with respect to its hydrophilic and hydrophobic structural components in the form of respective functional groups interacting with the solvents. Structural evaluations suggested that both hydrophilic and hydrophobic groups of cholesterol were interacting with the solvents, in particular methanol and dimethyl sulfoxide, which presented both types of interactions that are polar and non-polar. On the other hand, the highly polar water and non-polar benzene demonstrated extreme solvation behavior, since water was involved only in hydrogen bonding to the solute hydroxyl group and non-polar benzene formed strong van der Waals interactions only. Furthermore, the hydrophobic effect of cholesterol was also analyzed mainly in polar solvents, as the effect was more pronounced in the polar environment thereby preventing the solvent mobility in the solvation layer(s). The dynamical properties in terms of lateral diffusion and hydrogen bond dynamics as well as free energies of solvation also corroborated the findings based on the structural data and the hydrophobic character of cholesterol was later quantified by the computation of the averaged solvent accessible surface area. The polarity effect of the solvents on the aggregation property of cholesterol was further investigated, which is of big concern from the clinical point of view due to its major role in cardiovascular ailments. It was another major finding of the present study that aggregation was shown to be facilitated by highly polar solvents like water.
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Affiliation(s)
- Khair Bux
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Science, University of Karachi, Karachi-75270, Pakistan.
| | - Syed Tarique Moin
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Science, University of Karachi, Karachi-75270, Pakistan.
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26
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Usuda H, Hishida M, Kelley EG, Yamamura Y, Nagao M, Saito K. Interleaflet coupling of n-alkane incorporated bilayers. Phys Chem Chem Phys 2020; 22:5418-5426. [PMID: 31904060 DOI: 10.1039/c9cp06059f] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The relationship between the membrane bending modulus (κ) and compressibility modulus (KA) depends on the extent of coupling between the two monolayers (leaflets). Using neutron spin echo (NSE) spectroscopy, we investigate the effects of n-alkanes on the interleaflet coupling of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayers. Structural studies with small-angle X-ray and neutron scattering (SAXS and SANS) showed that the bilayer thickness increased with increasing n-alkane length, while NSE suggested that the bilayers became softer. Additional measurements of the membrane thickness fluctuations with NSE suggested that the changes in elastic moduli were due to a decrease in coupling between the leaflets upon addition of the longer n-alkanes. The decreased coupling with elongating n-alkane length was explained based on the n-alkane distribution within the bilayers characterized by SANS measurement of bilayers composed of protiated DPPC and deuterated n-alkanes. A higher fraction of the incorporated long n-alkanes were concentrated at the central plane of the bilayers and decreased the physical interaction between the leaflets. Using NSE and SANS, we successfully correlated changes in the mesoscopic collective dynamics and microscopic membrane structure upon incorporation of n-alkanes.
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Affiliation(s)
- Hatsuho Usuda
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan.
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27
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Lemma T, Marques Ruiz GC, Oliveira ON, Constantino CJ. The pesticide picloram affects biomembrane models made with Langmuir monolayers. Colloids Surf B Biointerfaces 2019; 181:953-958. [DOI: 10.1016/j.colsurfb.2019.06.060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/18/2019] [Accepted: 06/25/2019] [Indexed: 11/15/2022]
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28
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
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29
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Yadav DK, Kumar S, Choi EH, Chaudhary S, Kim MH. Molecular dynamic simulations of oxidized skin lipid bilayer and permeability of reactive oxygen species. Sci Rep 2019; 9:4496. [PMID: 30872693 PMCID: PMC6418262 DOI: 10.1038/s41598-019-40913-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 02/26/2019] [Indexed: 12/30/2022] Open
Abstract
Lipid peroxidation by reactive oxygen species (ROS) during oxidative stress is non-enzymatic damage that affects the integrity of biological membrane, and alters the fluidity and permeability. We conducted molecular dynamic simulation studies to evaluate the structural properties of the bilayer after lipid peroxidation and to measure the permeability of distinct ROS. The oxidized membrane contains free fatty acid, ceramide, cholesterol, and 5α-hydroperoxycholesterol (5α-CH). The result of unconstrained molecular dynamic simulations revealed that lipid peroxidation causes area-per-lipid of the bilayer to increase and bilayer thickness to decrease. The simulations also revealed that the oxidized group of 5α-CH (-OOH) moves towards the aqueous layer and its backbone tilts causing lateral expansion of the bilayer membrane. These changes are detrimental to structural and functional properties of the membrane. The measured free energy profile for different ROS (H2O2, HO2, HO, and O2) across the peroxidized lipid bilayer showed that the increase in lipid peroxidation resulted in breaching barrier decrease for all species, allowing easy traversal of the membrane. Thus, lipid peroxidation perturbs the membrane barrier and imposes oxidative stress resulting into apoptosis. The collective insights increase the understanding of oxidation stress at the atomic level.
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Affiliation(s)
- Dharmendra Kumar Yadav
- Gachon Institute of Pharmaceutical Science & Department of Pharmacy, College of Pharmacy, Gachon University, Incheon, 406-799, South Korea.
| | - Surendra Kumar
- Gachon Institute of Pharmaceutical Science & Department of Pharmacy, College of Pharmacy, Gachon University, Incheon, 406-799, South Korea
| | - Eun-Ha Choi
- Plasma Bioscience Research Center/PDP Research Center, Kwangwoon University, Nowon-Gu, Seoul, 139-791, Korea
| | - Sandeep Chaudhary
- Laboratory of Organic and Medicinal Chemistry, Department of Chemistry, Malaviya National Institute of Technology, Jaipur, 302017, India
| | - Mi-Hyun Kim
- Gachon Institute of Pharmaceutical Science & Department of Pharmacy, College of Pharmacy, Gachon University, Incheon, 406-799, South Korea.
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30
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Cao Z, Zhang X, Wang C, Liu L, Zhao L, Wang J, Zhou Y. Different effects of cholesterol on membrane permeation of arginine and tryptophan revealed by bias-exchange metadynamics simulations. J Chem Phys 2019; 150:084106. [PMID: 30823753 DOI: 10.1063/1.5082351] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Experiments have shown that cholesterol influences the membrane permeability of small molecules, amino acids, and cell-penetrating peptides. However, their exact translocation mechanisms under the influence of cholesterol remain poorly understood. Given the practical importance of cell-penetrating peptides and the existence of varied cholesterol contents in different cell types, it is necessary to examine the permeation of amino acids in cholesterol-containing membranes at atomic level of details. Here, bias-exchange metadynamics simulations were employed to investigate the molecular mechanism of the membrane permeation of two amino acids Arg and Trp important for cell-penetrating peptides in the presence of different concentrations of cholesterol. We found that the free energy barrier of Arg+ (the protonated form) permeation increased linearly as the cholesterol concentration increased, whereas the barrier of Trp permeation had a rapid increase from 0 mol. % to 20 mol. % cholesterol-containing membranes and nearly unchanged from 20 mol. % to 40 mol. % cholesterol-containing membranes. Arg0 becomes slightly more stable than Arg+ at the center of the dipalmitoylphosphatidylcholine (DPPC) membrane with 40 mol. % cholesterol concentrations. As a result, Arg+ has a similar permeability as Trp at 0 mol. % and 20 mol. % cholesterol, but a significantly lower permeability than Trp at 40 mol. % cholesterol. This difference is caused by the gradual reduction of water defects for Arg+ as the cholesterol concentration increases but lack of water defects for Trp in cholesterol-containing membranes. Strong but different orientation dependence between Arg+ and Trp permeations is observed. These results provide an improved microscopic understanding of amino-acid permeation through cholesterol-containing DPPC membrane systems.
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Affiliation(s)
- Zanxia Cao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Xiumei Zhang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Chunling Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Lei Liu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Liling Zhao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Yaoqi Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
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31
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Shimanouchi T, Kitagawa Y, Kimura Y. Application of liposome membrane as the reaction field: A case study using the Horner-Wadsworth-Emmons reaction. J Biosci Bioeng 2019; 128:198-202. [PMID: 30827857 DOI: 10.1016/j.jbiosc.2019.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 10/27/2022]
Abstract
The properties of the liposome membrane as a reaction field were investigated by focusing on the Horner-Wadsworth-Emmons reaction as a case study. Use of the liposomes existing in the gel phase resulted in the enhanced activity of the substrates and furnished the products with same E/Z stereoselectivity as in the liposome-free system. The membrane environment in the gel phase most likely assisted the formation of adducts that induced selective generation of the E-isomer. The possible role of liposomes is to assist the proton removal from the reactant, rather than providing the basic interfacial environment.
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Affiliation(s)
- Toshinori Shimanouchi
- Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-Naka, Okayama 700-8530, Japan
| | - Yuki Kitagawa
- Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-Naka, Okayama 700-8530, Japan
| | - Yukitaka Kimura
- Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-Naka, Okayama 700-8530, Japan.
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32
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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.
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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
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33
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Hantal G, Fábián B, Sega M, Jójárt B, Jedlovszky P. Effect of general anesthetics on the properties of lipid membranes of various compositions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1861:594-609. [PMID: 30571949 DOI: 10.1016/j.bbamem.2018.12.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/05/2018] [Accepted: 12/13/2018] [Indexed: 10/27/2022]
Abstract
Computer simulations of four lipid membranes of different compositions, namely neat DPPC and PSM, and equimolar DPPC-cholesterol and PSM-cholesterol mixtures, are performed in the presence and absence of the general anesthetics diethylether and sevoflurane both at 1 and 600 bar. The results are analyzed in order to identify membrane properties that are potentially related to the molecular mechanism of anesthesia, namely that change in the same way in any membrane with any anesthetics, and change oppositely with increasing pressure. We find that the lateral lipid density satisfies both criteria: it is decreased by anesthetics and increased by pressure. This anesthetic-induced swelling is attributed to only those anesthetic molecules that are located close to the boundary of the apolar phase. This lateral expansion is found to lead to increased lateral mobility of the lipids, an effect often thought to be related to general anesthesia; to an increased fraction of the free volume around the outer preferred position of anesthetics; and to the decrease of the lateral pressure in the nearby range of the ester and amide groups, a region into which anesthetic molecules already cannot penetrate. All these changes are reverted by the increase of pressure. Another important finding of this study is that cholesterol has an opposite effect on the membrane properties than anesthetics, and, correspondingly, these changes are less marked in the presence of cholesterol. Therefore, changes in the membrane that can lead to general anesthesia are expected to occur in the membrane domains of low cholesterol content.
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Affiliation(s)
- György Hantal
- Faculty of Physics, University of Vienna, Sensengasse 8/9, A-1090 Vienna, Austria
| | - Balázs Fábián
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szt. Gellért tér 4, H-1111 Budapest, Hungary; Institut UTINAM (CNRS UMR 6213), Université Bourgogne Franche-Comté, 16 route de Gray, F-25030 Besançon, France
| | - Marcello Sega
- Faculty of Physics, University of Vienna, Sensengasse 8/9, A-1090 Vienna, Austria
| | - Balázs Jójárt
- Institute of Food Engineering, University of Szeged, Moszkvai krt 5-7, H-6725 Szeged, Hungary
| | - Pál Jedlovszky
- Department of Chemistry, Eszterházy Károly University, Leányka utca 6, H-3300 Eger, Hungary.
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34
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Leeb F, Maibaum L. Spatially Resolving the Condensing Effect of Cholesterol in Lipid Bilayers. Biophys J 2018; 115:2179-2188. [PMID: 30447996 DOI: 10.1016/j.bpj.2018.10.024] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 10/15/2018] [Accepted: 10/24/2018] [Indexed: 11/15/2022] Open
Abstract
We study the effect of cholesterol on the structure of dipalmitoylphosphatidylcholine phospholipid bilayers. Using extensive molecular dynamics computer simulations at atomistic resolution, we observe and quantify several structural changes upon increasing cholesterol content that are collectively known as the condensing effect: a thickening of the bilayer, an increase in lipid tail order, and a decrease in lateral area. We also observe a change in leaflet interdigitation and a lack thereof in the distributions of dipalmitoylphosphatidylcholine headgroup orientations. These results, obtained over a wide range of cholesterol mole fractions, are then used to calibrate the analysis of phospholipid properties in bilayers containing a single cholesterol molecule per leaflet, which we perform in a spatially resolved way. We find that a single cholesterol molecule affects phospholipids in its first and second solvation shells, which puts the range of this effective interaction to be on the order of 1-2 nm. We also observe a tendency of phospholipids to orient their polar headgroups toward the cholesterol, which provides additional support for the umbrella model of bilayer organization.
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Affiliation(s)
- Felix Leeb
- Department of Chemistry, University of Washington, Seattle, Washington
| | - Lutz Maibaum
- Department of Chemistry, University of Washington, Seattle, Washington.
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35
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Borisova-Mubarakshina MM, Ivanov BN, Orekhova NI, Osochuk SS. Antioxidant Properties of Plastoquinone and Prospects of its Practical Application. Biophysics (Nagoya-shi) 2018. [DOI: 10.1134/s0006350918060040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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36
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Parameterization of a coarse-grained model of cholesterol with point-dipole electrostatics. J Comput Aided Mol Des 2018; 32:1259-1271. [DOI: 10.1007/s10822-018-0164-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022]
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37
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Kumar S, Yadav DK, Choi EH, Kim MH. Insight from Molecular dynamic simulation of reactive oxygen species in oxidized skin membrane. Sci Rep 2018; 8:13271. [PMID: 30185881 PMCID: PMC6125594 DOI: 10.1038/s41598-018-31609-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 08/10/2018] [Indexed: 11/08/2022] Open
Abstract
Non-enzymatic lipid peroxidation of the skin-lipid bilayer causes perturbations that affect the biomembrane structure, function, and permeability of reactive oxygen species (ROS). In the present study, we employed molecular dynamics simulations to study the effect of lipid peroxidation on the bilayer structural properties and permeability of various ROS. The oxidized skin-lipid bilayer was composed of ceramide, cholesterol, free fatty acid, and 5α-hydroperoxycholesterol (5α-CH). The simulation showed that, upon oxidation, the oxidized group (-OOH) of 5α-CH migrates towards the aqueous phase and the backbone of 5α-CH tilts, which causes the membrane to expand laterally. Measurements of the permeability of all ROS along the oxidized skin-lipid bilayer revealed a decreased breaching barrier for all the species as the degree of peroxidation increased, with a resulting easy passage across the membrane. The insights from the simulations indicate that lipid peroxidation might perturb the membrane barrier, thereby inflicting oxidative stress that leads to apoptosis. This study helps to understand oxidative stress at the atomic level. To our knowledge, this is the first reported molecular dynamics simulation study on oxidized skin-lipid bilayer and permeability of ROS.
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Affiliation(s)
- Surendra Kumar
- Gachon Institute of Pharmaceutical Science & Department of Pharmacy, College of Pharmacy, Gachon University, 191, Hambakmoeiro, Yeonsu-gu, Incheon, 406-799, Korea
| | - Dharmendra Kumar Yadav
- Gachon Institute of Pharmaceutical Science & Department of Pharmacy, College of Pharmacy, Gachon University, 191, Hambakmoeiro, Yeonsu-gu, Incheon, 406-799, Korea.
| | - Eun-Ha Choi
- Plasma Bioscience Research Center/PDP Research Center, Kwangwoon University, Nowon-Gu, Seoul, 139-791, Korea
| | - Mi-Hyun Kim
- Gachon Institute of Pharmaceutical Science & Department of Pharmacy, College of Pharmacy, Gachon University, 191, Hambakmoeiro, Yeonsu-gu, Incheon, 406-799, Korea.
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38
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Elola MD, Rodriguez J. Influence of Cholesterol on the Dynamics of Hydration in Phospholipid Bilayers. J Phys Chem B 2018; 122:5897-5907. [PMID: 29742895 DOI: 10.1021/acs.jpcb.8b00360] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigate the dynamics of interfacial waters in dipalmitoylphosphatidylcholine (DPPC) bilayers upon the addition of cholesterol, by molecular dynamics simulations. Our data reveal that the inclusion of cholesterol modifies the membrane aqueous interfacial dynamics: waters diffuse faster, their rotational decay time is shorter, and the DPPC/water hydrogen bond dynamics relaxes faster than in the pure DPPC membrane. The observed acceleration of the translational water dynamics agrees with recent experimental results, in which, by means of NMR techniques, an increment of the surface water diffusivity is measured upon the addition of cholesterol. A microscopic analysis of the lipid/water hydrogen bond network at the interfacial region suggests that the mechanism underlying the observed water mobility enhancement is given by the rupture of a fraction of interlipid water bridge hydrogen bonds connecting two different DPPC molecules, concomitant to the formation of new lipid/solvent bonds, whose dynamics is faster than that of the former. The consideration of a simple two-state model for the decay of the hydrogen bond correlation function yielded excellent results, obtaining two well-separated characteristic time scales: a slow one (∼250 ps) associated with bonds linking two DPPC molecules, and a fast one (∼15 ps), related to DPPC/solvent bonds.
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Affiliation(s)
- M Dolores Elola
- Departamento de Física , Comisión Nacional de Energía Atómica , Av Libertador 8250, 1429 Buenos Aires , Argentina
| | - Javier Rodriguez
- Departamento de Física , Comisión Nacional de Energía Atómica , Av Libertador 8250, 1429 Buenos Aires , Argentina.,ECyT , UNSAM , Martín de Irigoyen 3100, 1650 San Martín, Provincia de Buenos Aires , Argentina
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39
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Barragán Vidal IA, Müller M. Generalization of the swelling method to measure the intrinsic curvature of lipids. J Chem Phys 2017; 147:224902. [PMID: 29246037 DOI: 10.1063/1.5001858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Via computer simulation of a coarse-grained model of two-component lipid bilayers, we compare two methods of measuring the intrinsic curvatures of the constituting monolayers. The first one is a generalization of the swelling method that, in addition to the assumption that the spontaneous curvature linearly depends on the composition of the lipid mixture, incorporates contributions from its elastic energy. The second method measures the effective curvature-composition coupling between the apposing leaflets of bilayer structures (planar bilayers or cylindrical tethers) to extract the spontaneous curvature. Our findings demonstrate that both methods yield consistent results. However, we highlight that the two-leaflet structure inherent to the latter method has the advantage of allowing measurements for mixed lipid systems up to their critical point of demixing as well as in the regime of high concentration (of either species).
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Affiliation(s)
- I A Barragán Vidal
- Institut für Theoretische Physik, Georg-August-Universität, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - M Müller
- Institut für Theoretische Physik, Georg-August-Universität, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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40
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Ivanova N, Ivanova A. Testing the limits of model membrane simulations-bilayer composition and pressure scaling. J Comput Chem 2017; 39:387-396. [DOI: 10.1002/jcc.25117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/07/2017] [Accepted: 11/06/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Nikoleta Ivanova
- Faculty of Chemistry and Pharmacy, 1 James Bourchier Blvd; University of Sofia; Sofia 1164 Bulgaria
| | - Anela Ivanova
- Faculty of Chemistry and Pharmacy, 1 James Bourchier Blvd; University of Sofia; Sofia 1164 Bulgaria
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41
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Zaki AM, Carbone P. How the Incorporation of Pluronic Block Copolymers Modulates the Response of Lipid Membranes to Mechanical Stress. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:13284-13294. [PMID: 29084428 DOI: 10.1021/acs.langmuir.7b02244] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We employ atomistic molecular dynamics simulations to investigate the effect that the incorporation of the nonionic amphiphilic copolymer known as Pluronic L64 has on the mechanical stability of a DPPC membrane. The simulations reveal that the incorporation of the polymer chains leads to membranes that can sustain increasing mechanical stresses. Analysis of mechanical, structural, and dynamic properties of the membrane shows that the polymer chains interact strongly with the lipids in the vicinity, restraining their mobility and imparting better mechanical stability to the membrane. The hybrid membranes under tension remain thicker, more ordered, and stiffer in comparison to their lipid analogues. Trans-bilayer lipid movements (flip-flop) are observed and appear to be triggered by the presence of the polymer chains. A careful analysis of the pore formation under high tensions reveals two distinctive mechanisms that depend on the distribution of the hydrophilic polymer blocks in the bilayer. Finally, the rate of growth of the formed membrane defects is slowed down in the presence of polymers. These findings show that Pluronic block copolymers could be exploited for the formation of optimized hybrid nanodevices with controlled elastic and dynamic properties.
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Affiliation(s)
- Afroditi Maria Zaki
- School of Chemical Engineering and Analytical Science, The University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
| | - Paola Carbone
- School of Chemical Engineering and Analytical Science, The University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
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42
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Herrera F, Sevrain CM, Jaffrès PA, Couthon H, Grélard A, Dufourc EJ, Chantôme A, Potier-Cartereau M, Vandier C, Bouchet AM. Singular Interaction between an Antimetastatic Agent and the Lipid Bilayer: The Ohmline Case. ACS OMEGA 2017; 2:6361-6370. [PMID: 30023517 PMCID: PMC6045331 DOI: 10.1021/acsomega.7b00936] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/08/2017] [Indexed: 06/08/2023]
Abstract
SK3 channels are abnormaly expressed in metastatic cells, and Ohmline (OHM), an ether lipid, has been shown to reduce the activity of SK3 channels and the migration capacity of cancer cells. OHM incorporation into the plasma membrane is proposed to dissociate the protein complex formed between SK3 and Orai1, a potassium and a calcium channel, respectively, and would lead to a modification in the lipid environment of both the proteins. Here, we report the synthesis of deuterated OHM that affords the determination, through solid-state NMR, of its entire partitioning into membranes mimicking the SK3 environment. Use of deuterated lipids affords the demonstration of an OHM-induced membrane disordering, which is dose-dependent and increases with increasing amounts of cholesterol (CHOL). Molecular dynamics simulations comfort the disordering action and show that OHM interacts with the carbonyl and phosphate groups of stearoylphosphatidylcholine and sphingomyelin and to a minor extent with CHOL. OHM is thus proposed to remove the CHOL OH moieties away from their main binding sites, forcing a new rearrangement with other lipid groups. Such an interaction takes its origin at the lipid-water interface, but it propagates toward the entire lipid molecules and leads to a cooperative destabilization of the lipid acyl chains, that is, membrane disordering. The consequences of this reorganization of the lipid phases are discussed in the context of the OHM-induced inhibition of SK3 channels.
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Affiliation(s)
- Fernando
E. Herrera
- Physics
Department, Universidad Nacional del Litoral,
Ciudad Universitaria, 3000 Santa Fe, Argentina
| | - Charlotte M. Sevrain
- Université
de Brest, CEMCA, UMR CNRS 6521, IBSAM, 6, Avenue Victor le Gorgeu, 29238 Brest, France
- Network
and Cancer-Canceropole Grand Ouest, (IC-CGO), Maison de la Recherche
en Santé, 63 Quai
Magellan, 44000 Nantes, France
| | - Paul-Alain Jaffrès
- Université
de Brest, CEMCA, UMR CNRS 6521, IBSAM, 6, Avenue Victor le Gorgeu, 29238 Brest, France
- Network
and Cancer-Canceropole Grand Ouest, (IC-CGO), Maison de la Recherche
en Santé, 63 Quai
Magellan, 44000 Nantes, France
| | - Hélène Couthon
- Université
de Brest, CEMCA, UMR CNRS 6521, IBSAM, 6, Avenue Victor le Gorgeu, 29238 Brest, France
- Network
and Cancer-Canceropole Grand Ouest, (IC-CGO), Maison de la Recherche
en Santé, 63 Quai
Magellan, 44000 Nantes, France
| | - Axelle Grélard
- Université
Bordeaux, Institute of Chemistry & Biology of Membranes &
Nanoobjects, UMR5248 CNRS, Allée de Geoffroy St Hilaire Bât B14 Pessac, 33600 Bordeaux, France
| | - Erick J. Dufourc
- Université
Bordeaux, Institute of Chemistry & Biology of Membranes &
Nanoobjects, UMR5248 CNRS, Allée de Geoffroy St Hilaire Bât B14 Pessac, 33600 Bordeaux, France
| | - Aurélie Chantôme
- Network
and Cancer-Canceropole Grand Ouest, (IC-CGO), Maison de la Recherche
en Santé, 63 Quai
Magellan, 44000 Nantes, France
- Université
François Rabelais de Tours, Nutrition, Croissance et Cancer, Inserm UMR1069, 10 Boulevard Tonnellé Bât. Dutrochet, 2ème étage, 37032 Tours, France
| | - Marie Potier-Cartereau
- Network
and Cancer-Canceropole Grand Ouest, (IC-CGO), Maison de la Recherche
en Santé, 63 Quai
Magellan, 44000 Nantes, France
- Université
François Rabelais de Tours, Nutrition, Croissance et Cancer, Inserm UMR1069, 10 Boulevard Tonnellé Bât. Dutrochet, 2ème étage, 37032 Tours, France
| | - Christophe Vandier
- Network
and Cancer-Canceropole Grand Ouest, (IC-CGO), Maison de la Recherche
en Santé, 63 Quai
Magellan, 44000 Nantes, France
- Université
François Rabelais de Tours, Nutrition, Croissance et Cancer, Inserm UMR1069, 10 Boulevard Tonnellé Bât. Dutrochet, 2ème étage, 37032 Tours, France
| | - Ana M. Bouchet
- Network
and Cancer-Canceropole Grand Ouest, (IC-CGO), Maison de la Recherche
en Santé, 63 Quai
Magellan, 44000 Nantes, France
- Université
François Rabelais de Tours, Nutrition, Croissance et Cancer, Inserm UMR1069, 10 Boulevard Tonnellé Bât. Dutrochet, 2ème étage, 37032 Tours, France
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43
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Thoms VL, Hormel TT, Reyer MA, Parthasarathy R. Tension Independence of Lipid Diffusion and Membrane Viscosity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:12510-12515. [PMID: 28984459 DOI: 10.1021/acs.langmuir.7b02917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The diffusion of biomolecules at lipid membranes is governed by the viscosity of the underlying two-dimensionally fluid lipid bilayer. For common three-dimensional fluids, viscosity can be modulated by hydrostatic pressure, and pressure-viscosity data have been measured for decades. Remarkably, the two-dimensional analogue of this relationship, the dependence of molecular mobility on tension, has to the best of our knowledge never been measured for lipid bilayers, limiting our understanding of cellular mechanotransduction as well as the fundamental fluid mechanics of membranes. Here we report both molecular-scale and mesoscopic measures of fluidity in giant lipid vesicles as a function of mechanical tension applied using micropipette aspiration. Both molecular-scale data, from fluorescence recovery after photobleaching, and micron-scale data, from tracking the diffusion of phase-separated domains, show a surprisingly weak dependence of viscosity on tension, in contrast to predictions of recent molecular dynamics simulations, highlighting fundamental gaps in our understanding of membrane fluidity.
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Affiliation(s)
- Vincent L Thoms
- Department of Physics and Materials Science Institute, The University of Oregon , Eugene, Oregon 97403-1274, United States
| | - Tristan T Hormel
- Department of Physics and Materials Science Institute, The University of Oregon , Eugene, Oregon 97403-1274, United States
| | - Matthew A Reyer
- Department of Physics and Materials Science Institute, The University of Oregon , Eugene, Oregon 97403-1274, United States
| | - Raghuveer Parthasarathy
- Department of Physics and Materials Science Institute, The University of Oregon , Eugene, Oregon 97403-1274, United States
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44
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A Cholesterol-Based Allostery Model of T Cell Receptor Phosphorylation. Immunity 2017; 44:1091-101. [PMID: 27192576 DOI: 10.1016/j.immuni.2016.04.011] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 11/17/2015] [Accepted: 04/11/2016] [Indexed: 12/20/2022]
Abstract
Signaling through the T cell receptor (TCR) controls adaptive immune responses. Antigen binding to TCRαβ transmits signals through the plasma membrane to induce phosphorylation of the CD3 cytoplasmic tails by incompletely understood mechanisms. Here we show that cholesterol bound to the TCRβ transmembrane region keeps the TCR in a resting, inactive conformation that cannot be phosphorylated by active kinases. Only TCRs that spontaneously detached from cholesterol could switch to the active conformation (termed primed TCRs) and then be phosphorylated. Indeed, by modulating cholesterol binding genetically or enzymatically, we could switch the TCR between the resting and primed states. The active conformation was stabilized by binding to peptide-MHC, which thus controlled TCR signaling. These data are explained by a model of reciprocal allosteric regulation of TCR phosphorylation by cholesterol and ligand binding. Our results provide both a molecular mechanism and a conceptual framework for how lipid-receptor interactions regulate signal transduction.
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45
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Huang FY, Chiu CC. Interplay between alkyl chain asymmetry and cholesterol addition in the rigid ion pair amphiphile bilayer systems. J Chem Phys 2017; 146:035102. [PMID: 28109215 DOI: 10.1063/1.4974089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ion pair amphiphile (IPA), a molecular complex composed of a pair of cationic and anionic surfactants, has been proposed as a novel phospholipid substitute. Controlling the physical stability of IPA vesicles is important for its application developments such as cosmetic and drug deliveries. To investigate the effects of IPA alkyl chain combinations and the cholesterol additive on the structural and mechanical properties of IPA vesicular bilayers, we conducted a series of molecular dynamics studies on the hexadecyltrimethylammonium-dodecylsulfate (HTMA-DS) and dodecyltrimethylammonium-hexadecylsulfate (DTMA-HS) IPA bilayers with cholesterol. We found that both IPA bilayers are in the gel phase at 298 K, consistent with experimental observations. Compared with the HTMA-DS system, the DTMA-HS bilayer has more disordered alkyl chains in the hydrophobic region. When adding cholesterol, it induces alkyl chain ordering around its rigid sterol ring. Yet, cholesterol increases the molecular areas for all species and disturbs the molecular packing near the hydrophilic region and the bilayer core. Cholesterol also promotes the alkyl chain mismatch between the IPA moieties, especially for the DTMA-HS bilayer. The combined effects lead to non-monotonically enhancement of the membrane mechanical moduli for both IPA-cholesterol systems. Furthermore, cholesterol can form H-bonds with the alkylsulfate and thus enhance the contribution of alkylsulfate to the overall mechanical moduli. Combined results provide valuable molecular insights into the roles of each IPA component and the cholesterol on modulating the IPA bilayer properties.
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Affiliation(s)
- Fong-Yin Huang
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Chi-Cheng Chiu
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
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46
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Dynamic processes in biological membrane mimics revealed by quasielastic neutron scattering. Chem Phys Lipids 2017; 206:28-42. [DOI: 10.1016/j.chemphyslip.2017.05.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/22/2017] [Accepted: 05/25/2017] [Indexed: 12/15/2022]
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47
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Hartkamp R, Moore TC, Iacovella CR, Thompson MA, Bulsara PA, Moore DJ, McCabe C. Investigating the Structure of Multicomponent Gel-Phase Lipid Bilayers. Biophys J 2017; 111:813-823. [PMID: 27558724 DOI: 10.1016/j.bpj.2016.07.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/07/2016] [Accepted: 07/11/2016] [Indexed: 11/30/2022] Open
Abstract
Single- and multicomponent lipid bilayers of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC), 1,2-distearoyl-sn-glycero-3-phosphatidylcholine (DSPC), isostearyl isostearate, and heptadecanoyl heptadecanoate in the gel phase are studied via molecular dynamics simulations. It is shown that the structural properties of multicomponent bilayers can deviate strongly from the structures of their single-component counterparts. Specifically, the lipid mixtures are shown to adopt a compact packing by offsetting the positioning depths at which different lipid species are located in the bilayer. This packing mechanism affects the area per lipid, the bilayer height, and the chain tilt angles and has important consequences for other bilayer properties, such as interfacial hydrogen bonding and bilayer permeability. In particular, the simulations suggest that bilayers containing isostearyl isostearate or heptadecanoyl heptadecanoate are less permeable than pure 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine or DSPC bilayers. Furthermore, hydrogen-bond analysis shows that the residence times of lipid-water hydrogen bonds depend strongly on the bilayer composition, with longer residence times for bilayers that have a higher DSPC content. The findings illustrate and explain the fundamental differences between the properties of single- and multicomponent bilayers.
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Affiliation(s)
- Remco Hartkamp
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee
| | - Timothy C Moore
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee
| | - Christopher R Iacovella
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee
| | | | | | - David J Moore
- GlaxoSmithKline Consumer Healthcare, Warren, New Jersey
| | - Clare McCabe
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee.
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48
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Gillams RJ, Lorenz CD, McLain SE. Comparative atomic-scale hydration of the ceramide and phosphocholine headgroup in solution and bilayer environments. J Chem Phys 2017; 144:225101. [PMID: 27306021 DOI: 10.1063/1.4952444] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Previous studies have used neutron diffraction to elucidate the hydration of the ceramide and the phosphatidylcholine headgroup in solution. These solution studies provide bond-length resolution information on the system, but are limited to liquid samples. The work presented here investigates how the hydration of ceramide and phosphatidylcholine headgroups in a solution compares with that found in a lipid bilayer. This work shows that the hydration patterns seen in the solution samples provide valuable insight into the preferential location of hydrating water molecules in the bilayer. There are certain subtle differences in the distribution, which result from a combination of the lipid conformation and the lipid-lipid interactions within the bilayer environment. The lipid-lipid interactions in the bilayer will be dependent on the composition of the bilayer, whereas the restricted exploration of conformational space is likely to be applicable in all membrane environments. The generalized description of hydration gathered from the neutron diffraction studies thus provides good initial estimation for the hydration pattern, but this can be further refined for specific systems.
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Affiliation(s)
- Richard J Gillams
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Christian D Lorenz
- Department of Physics, King's College London, London WC2R 2LS, United Kingdom
| | - Sylvia E McLain
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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49
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Van der Paal J, Verheyen C, Neyts EC, Bogaerts A. Hampering Effect of Cholesterol on the Permeation of Reactive Oxygen Species through Phospholipids Bilayer: Possible Explanation for Plasma Cancer Selectivity. Sci Rep 2017; 7:39526. [PMID: 28059085 PMCID: PMC5216346 DOI: 10.1038/srep39526] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/23/2016] [Indexed: 11/08/2022] Open
Abstract
In recent years, the ability of cold atmospheric pressure plasmas (CAPS) to selectively induce cell death in cancer cells has been widely established. This selectivity has been assigned to the reactive oxygen and nitrogen species (RONS) created in CAPs. To provide new insights in the search for an explanation for the observed selectivity, we calculate the transfer free energy of multiple ROS across membranes containing a varying amount of cholesterol. The cholesterol fraction is investigated as a selectivity parameter because membranes of cancer cells are known to contain lower fractions of cholesterol compared to healthy cells. We find that cholesterol has a significant effect on the permeation of reactive species across a membrane. Indeed, depending on the specific reactive species, an increasing cholesterol fraction can lead to (i) an increase of the transfer free energy barrier height and width, (ii) the formation of a local free energy minimum in the center of the membrane and (iii) the creation of extra free energy barriers due to the bulky sterol rings. In the context of plasma oncology, these observations suggest that the increased ingress of RONS in cancer cells can be explained by the decreased cholesterol fraction of their cell membrane.
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Affiliation(s)
- Jonas Van der Paal
- Research group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk-Antwerp, Belgium
| | - Claudia Verheyen
- Research group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk-Antwerp, Belgium
| | - Erik C. Neyts
- Research group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk-Antwerp, Belgium
| | - Annemie Bogaerts
- Research group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk-Antwerp, Belgium
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50
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Hartkamp R, Moore TC, Iacovella CR, Thompson MA, Bulsara PA, Moore DJ, McCabe C. Structural Properties of Phospholipid-based Bilayers with Long-Chain Alcohol Molecules in the Gel Phase. J Phys Chem B 2016; 120:12863-12871. [DOI: 10.1021/acs.jpcb.6b10192] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Remco Hartkamp
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States
- Multiscale
Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Timothy C. Moore
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States
- Multiscale
Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Christopher R. Iacovella
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States
- Multiscale
Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Michael A. Thompson
- GlaxoSmithKline Consumer Healthcare, 184 Liberty Corner Road, Suite 200, Warren, New Jersey 07059, United States
| | - Pallav A. Bulsara
- GlaxoSmithKline Consumer Healthcare, 184 Liberty Corner Road, Suite 200, Warren, New Jersey 07059, United States
| | - David J. Moore
- GlaxoSmithKline Consumer Healthcare, 184 Liberty Corner Road, Suite 200, Warren, New Jersey 07059, United States
| | - Clare McCabe
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States
- Multiscale
Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37212, United States
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
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