1
|
Sikdar S, Banerjee M, Vemparala S. Role of Disulphide Bonds in Membrane Partitioning of a Viral Peptide. J Membr Biol 2022; 255:129-142. [PMID: 35218393 PMCID: PMC8881898 DOI: 10.1007/s00232-022-00218-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/02/2022] [Indexed: 01/22/2023]
Abstract
The importance of disulphide bond in mediating viral peptide entry into host cells is well known. In the present work, we elucidate the role of disulphide (SS) bond in partitioning mechanism of membrane-active Hepatitis A Virus-2B (HAV-2B) peptide, which harbours three cysteine residues promoting formation of multiple SS-bonded states. The inclusion of SS-bond not only results in a compact conformation but also induces distorted α-helical hairpin geometry in comparison to SS-free state. Owing to these, the hydrophobic residues get buried, restricting the insertion of SS-bonded HAV-2B peptide into lipid packing defects and thus the partitioning of the peptide is completely or partly abolished. In this way, the disulphide bond can potentially regulate the partitioning of HAV-2B peptide such that the membrane remodelling effects of this viral peptide are significantly reduced. The current findings may have potential implications in drug designing, targeting the HAV-2B protein by promoting disulphide bond formation within its membrane-active region.
Collapse
Affiliation(s)
- Samapan Sikdar
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai, 600113, India. .,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Manidipa Banerjee
- Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, Hauz Khas, New Delhi, 110016, India.
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai, 600113, India. .,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| |
Collapse
|
2
|
Sikdar S, Banerjee M, Vemparala S. Effect of cholesterol on the membrane partitioning dynamics of hepatitis A virus-2B peptide. SOFT MATTER 2021; 17:7963-7977. [PMID: 34378608 DOI: 10.1039/d1sm01019k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Understanding viral peptide detection and partitioning and the subsequent host membrane composition-based response is essential for gaining insights into the viral mechanism. Here, we probe the crucial role of the presence of membrane lipid packing defects, depending on the membrane composition, in allowing the viral peptide belonging to C-terminal Hepatitis A Virus-2B (HAV-2B) to detect, attach and subsequently partition into host cell membrane mimics. Using molecular dynamics simulations, we conclusively show that the hydrophobic residues in the viral peptide detect transiently present lipid packing defects, insert themselves into such defects, form anchor points and facilitate the partitioning of the peptide, thereby inducing membrane disruption. We also show that the presence of cholesterol significantly alters such lipid packing defects, both in size and in number, thus mitigating the partitioning of the membrane active viral peptide into cholesterol-rich membranes. Our results are in excellent agreement with previously published experimental data and further explain the role of lipid defects in understanding such data. These results show differential ways in which the presence and absence of cholesterol can alter the permeability of the host membranes to the membrane active peptide component of HAV-2B virus, via lipid packing defects, and can possibly be a part of the general membrane detection mechanism for viroporins.
Collapse
Affiliation(s)
- Samapan Sikdar
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India.
| | | | | |
Collapse
|
3
|
Gupta R, Badhe Y, Rai B, Mitragotri S. Molecular mechanism of the skin permeation enhancing effect of ethanol: a molecular dynamics study. RSC Adv 2020; 10:12234-12248. [PMID: 35497613 PMCID: PMC9050718 DOI: 10.1039/d0ra01692f] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 03/16/2020] [Indexed: 02/01/2023] Open
Abstract
Ethanol is widely used in various pharmaceutical and cosmetic formulations in order to enhance skin penetration of active ingredients. While it is well known that ethanol partitions into the skin and enhances the permeation of both polar and nonpolar molecules, the exact mechanisms by which it enhances skin permeability are not fully understood. Several mechanisms have been proposed including lipid extraction from the stratum corneum (SC), fluidisation of SC lipid bilayer, alteration of SC protein conformation and enhancement of the drug solubility in the SC lipids. In this study, we performed molecular dynamics (MD) simulations of SC lipid bilayers comprised of an equimolar mixture of ceramides, cholesterol and free fatty acid in the presence of aqueous mixtures of ethanol. Various unrestrained MD simulations were performed in the presence of aqueous ethanol solution at molar ratios (x) ranging from x = 0 to x = 1. It was found that ethanol enhances bilayer permeability by dual actions (a) extraction of the skin lipids and (b) enhancing the mobility of lipid chains. Ethanol's permeation enhancing effect arises from its superior ability to form hydrogen bonds with headgroup atoms of skin lipids. Further, the free energy of extraction of ceramides (CER) and fatty acids (FFA) from the lipid bilayer was studied using umbrella sampling simulations. The free energy of extraction of CER was found to be much higher compared to FFA for all ethanol concentrations which shows that CER are difficult to extract as compared to FFA. Finally, the permeation of benzoic acid drug molecules through the skin lipid bilayer is shown in presence of ethanol molecules. It was found that ethanol selectively targets the FFA of the skin lipid bilayer and extracts it out of the lipid bilayer within few microseconds. Further, ethanol penetrates inside the lipid layer and creates the channels from which drug molecules can easily cross the lipid layer. Our observations (both in unrestrained and umbrella sampling simulations) are consistent with the experimental findings reported in the literature. The simulation methodology could be used for design and testing of permeation enhancers (acting on skin SC lipid lamella) for topical and transdermal drug delivery applications. Concentration dependent action of mechanism of ethanol on skin SC lipid barrier.![]()
Collapse
Affiliation(s)
- Rakesh Gupta
- Physical Science Research Area
- Tata Research Development and Design Centre
- TCS Research
- Tata Consultancy Services
- Pune – 411013
| | - Yogesh Badhe
- Physical Science Research Area
- Tata Research Development and Design Centre
- TCS Research
- Tata Consultancy Services
- Pune – 411013
| | - Beena Rai
- Physical Science Research Area
- Tata Research Development and Design Centre
- TCS Research
- Tata Consultancy Services
- Pune – 411013
| | - Samir Mitragotri
- School of Engineering and Applied Sciences
- Wyss Institute
- Harvard University
- USA
| |
Collapse
|
4
|
Lovely CB. Animal models of gene-alcohol interactions. Birth Defects Res 2019; 112:367-379. [PMID: 31774246 DOI: 10.1002/bdr2.1623] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 11/09/2019] [Indexed: 12/16/2022]
Abstract
Most birth defects arise from complex interactions between multiple genetic and environmental factors. However, our current understanding of how these interactions and their contributions affect birth defects remains incomplete. Human studies are limited in their ability to identify the fundamental causes of birth defects due to ethical and practical limitations. Animal models provide a great number of resources not available to human studies and they have been critical in advancing our understanding of birth defects and the complex interactions that underlie them. In this review, we discuss the use of animal models in the context of gene-environment interactions that underlie birth defects. We focus on alcohol which is the most common environmental factor associated with birth defects. Prenatal alcohol exposure leads to a wide range of cognitive impairments and structural deficits broadly termed fetal alcohol spectrum disorders (FASD). We discuss the broad impact of prenatal alcohol exposure on the developing embryo and elaborate on the current state of gene-alcohol interactions. Additionally, we discuss how animal models have informed our understanding of the genetics of FASD. Ultimately, these topics will provide insight into the use of animal models in understanding gene-environment interactions and their subsequent impact on birth defects.
Collapse
Affiliation(s)
- Charles Benjamin Lovely
- Department of Biochemistry and Molecular Genetics, Alcohol Research Center, University of Louisville, Louisville, Kentucky
| |
Collapse
|
5
|
Oakes V, Domene C. Capturing the Molecular Mechanism of Anesthetic Action by Simulation Methods. Chem Rev 2018; 119:5998-6014. [DOI: 10.1021/acs.chemrev.8b00366] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Victoria Oakes
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Carmen Domene
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| |
Collapse
|
6
|
Polley A. Partition of common anesthetic molecules in the liquid disordered phase domain of a composite multicomponent membrane. Phys Rev E 2018; 98:012409. [PMID: 30110859 DOI: 10.1103/physreve.98.012409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Indexed: 01/04/2023]
Abstract
Despite a vast clinical application of anesthetics, the molecular level of understanding of general anesthesia is far from our reach. Using atomistic molecular dynamics simulation, we study the effects of common anesthetics: ethanol, chloroform, and methanol in the fully hydrated symmetric multicomponent lipid bilayer membrane comprised of an unsaturated palmitoyl-oleoyl-phosphatidyl-choline (POPC), a saturated palmitoyl-sphingomyelin, and cholesterol, which exhibits phase coexistence of liquid-ordered (l_{o})-liquid-disordered (l_{d}) phase domains. We find that the mechanical and physical properties such as the thickness and rigidity of the membrane are reduced while the lateral expansion of the membrane is exhibited in the presence of anesthetic molecules. Our simulation shows both lateral and transverse heterogeneity of the anesthetics in the composite multicomponent lipid membrane. Both ethanol and chloroform partition in the POPC-rich l_{d} phase domain, while methanol is distributed in both l_{o}-l_{d} phase domains. Chloroform can penetrate deep into the membrane, while methanol partitions mostly at the water layer closed to the head group and ethanol at the neck of the lipids in the membrane.
Collapse
Affiliation(s)
- Anirban Polley
- Department of Chemical Engineering, Columbia University, New York City, New York 10027, USA
| |
Collapse
|
7
|
Draberova L, Paulenda T, Halova I, Potuckova L, Bugajev V, Bambouskova M, Tumova M, Draber P. Ethanol Inhibits High-Affinity Immunoglobulin E Receptor (FcεRI) Signaling in Mast Cells by Suppressing the Function of FcεRI-Cholesterol Signalosome. PLoS One 2015; 10:e0144596. [PMID: 26658290 PMCID: PMC4686000 DOI: 10.1371/journal.pone.0144596] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 11/21/2015] [Indexed: 12/12/2022] Open
Abstract
Ethanol has multiple effects on biochemical events in a variety of cell types, including the high-affinity immunoglobulin E receptor (FcεRI) signaling in antigen-activated mast cells. However, the underlying molecular mechanism remains unknown. To get better understanding of the effect of ethanol on FcεRI-mediated signaling we examined the effect of short-term treatment with non-toxic concentrations of ethanol on FcεRI signaling events in mouse bone marrow-derived mast cells. We found that 15 min exposure to ethanol inhibited antigen-induced degranulation, calcium mobilization, expression of proinflammatory cytokine genes (tumor necrosis factor-α, interleukin-6, and interleukin-13), and formation of reactive oxygen species in a dose-dependent manner. Removal of cellular cholesterol with methyl-β-cyclodextrin had a similar effect and potentiated some of the inhibitory effects of ethanol. In contrast, exposure of the cells to cholesterol-saturated methyl-β-cyclodextrin abolished in part the inhibitory effect of ethanol on calcium response and production of reactive oxygen species, supporting lipid-centric theories of ethanol action on the earliest stages of mast cell signaling. Further studies showed that exposure to ethanol and/or removal of cholesterol inhibited early FcεRI activation events, including tyrosine phosphorylation of the FcεRI β and γ subunits, SYK kinases, LAT adaptor protein, phospholipase Cγ, STAT5, and AKT and internalization of aggregated FcεRI. Interestingly, ethanol alone, and particularly in combination with methyl-β-cyclodextrin, enhanced phosphorylation of negative regulatory tyrosine 507 of LYN kinase. Finally, we found that ethanol reduced passive cutaneous anaphylactic reaction in mice, suggesting that ethanol also inhibits FcεRI signaling under in vivo conditions. The combined data indicate that ethanol interferes with early antigen-induced signaling events in mast cells by suppressing the function of FcεRI-cholesterol signalosomes at the plasma membrane.
Collapse
Affiliation(s)
- Lubica Draberova
- Laboratory of Signal Transduction, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- * E-mail: (LD); (PD)
| | - Tomas Paulenda
- Laboratory of Signal Transduction, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Ivana Halova
- Laboratory of Signal Transduction, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Lucie Potuckova
- Laboratory of Signal Transduction, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Viktor Bugajev
- Laboratory of Signal Transduction, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Monika Bambouskova
- Laboratory of Signal Transduction, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Magda Tumova
- Laboratory of Signal Transduction, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Petr Draber
- Laboratory of Signal Transduction, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- * E-mail: (LD); (PD)
| |
Collapse
|
8
|
Baul U, Kuroda K, Vemparala S. Interaction of multiple biomimetic antimicrobial polymers with model bacterial membranes. J Chem Phys 2015; 141:084902. [PMID: 25173040 DOI: 10.1063/1.4893440] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using atomistic molecular dynamics simulations, interaction of multiple synthetic random copolymers based on methacrylates on prototypical bacterial membranes is investigated. The simulations show that the cationic polymers form a micellar aggregate in water phase and the aggregate, when interacting with the bacterial membrane, induces clustering of oppositely charged anionic lipid molecules to form clusters and enhances ordering of lipid chains. The model bacterial membrane, consequently, develops lateral inhomogeneity in membrane thickness profile compared to polymer-free system. The individual polymers in the aggregate are released into the bacterial membrane in a phased manner and the simulations suggest that the most probable location of the partitioned polymers is near the 1-palmitoyl-2-oleoyl-phosphatidylglycerol (POPG) clusters. The partitioned polymers preferentially adopt facially amphiphilic conformations at lipid-water interface, despite lacking intrinsic secondary structures such as α-helix or β-sheet found in naturally occurring antimicrobial peptides.
Collapse
Affiliation(s)
- Upayan Baul
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
| | - Kenichi Kuroda
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, Ann Arbor, Michigan 48109, USA
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
| |
Collapse
|
9
|
Thind R, O'Neill DW, Del Regno A, Notman R. Ethanol induces the formation of water-permeable defects in model bilayers of skin lipids. Chem Commun (Camb) 2015; 51:5406-9. [DOI: 10.1039/c4cc08527b] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We observe that ethanol can induce the formation of water-permeable defects in model bilayers of skin lipids and propose this as a new mechanism of action of ethanol as a membrane modulator.
Collapse
Affiliation(s)
- R. Thind
- Department of Chemistry and Centre for Scientific Computing
- University of Warwick
- Coventry
- UK
| | - D. W. O'Neill
- Department of Chemistry and Centre for Scientific Computing
- University of Warwick
- Coventry
- UK
| | - A. Del Regno
- Department of Chemistry and Centre for Scientific Computing
- University of Warwick
- Coventry
- UK
| | - R. Notman
- Department of Chemistry and Centre for Scientific Computing
- University of Warwick
- Coventry
- UK
| |
Collapse
|
10
|
Róg T, Vattulainen I. Cholesterol, sphingolipids, and glycolipids: what do we know about their role in raft-like membranes? Chem Phys Lipids 2014; 184:82-104. [PMID: 25444976 DOI: 10.1016/j.chemphyslip.2014.10.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 10/24/2014] [Accepted: 10/25/2014] [Indexed: 12/14/2022]
Abstract
Lipids rafts are considered to be functional nanoscale membrane domains enriched in cholesterol and sphingolipids, characteristic in particular of the external leaflet of cell membranes. Lipids, together with membrane-associated proteins, are therefore considered to form nanoscale units with potential specific functions. Although the understanding of the structure of rafts in living cells is quite limited, the possible functions of rafts are widely discussed in the literature, highlighting their importance in cellular functions. In this review, we discuss the understanding of rafts that has emerged based on recent atomistic and coarse-grained molecular dynamics simulation studies on the key lipid raft components, which include cholesterol, sphingolipids, glycolipids, and the proteins interacting with these classes of lipids. The simulation results are compared to experiments when possible.
Collapse
Affiliation(s)
- Tomasz Róg
- Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, Tampere, Finland; MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark.
| |
Collapse
|
11
|
McCarthy N, Eberhart JK. Gene-ethanol interactions underlying fetal alcohol spectrum disorders. Cell Mol Life Sci 2014; 71:2699-706. [PMID: 24554057 PMCID: PMC11114006 DOI: 10.1007/s00018-014-1578-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 01/14/2014] [Accepted: 01/27/2014] [Indexed: 12/16/2022]
Abstract
Fetal alcohol spectrum disorders (FASD) is an umbrella term that describes a diverse set of ethanol-induced defects. The phenotypic variation is generated by numerous factors, including timing and dosage of ethanol exposure as well as genetic background. We are beginning to learn about how the concentration, duration, and timing of ethanol exposure mediate variability within ethanol teratogenesis. However, little is known about the genetic susceptibilities in FASD. Studies of FASD animal models are beginning to implicate a number of susceptibility genes that are involved in various pathways. Here we review the current literature that focuses on the genetic predispositions in FASD.
Collapse
Affiliation(s)
- Neil McCarthy
- Molecular Biosciences, Waggoner Center for Alcohol and Addiction Research, Institute for Cellular and Molecular Biology, University of Texas at Austin,
Austin, TX 78713
USA
| | - Johann K. Eberhart
- Molecular Biosciences, Waggoner Center for Alcohol and Addiction Research, Institute for Cellular and Molecular Biology, University of Texas at Austin,
Austin, TX 78713
USA
| |
Collapse
|
12
|
Setiawan I, Blanchard GJ. Ethanol-induced perturbations to planar lipid bilayer structures. J Phys Chem B 2014; 118:537-46. [PMID: 24372563 DOI: 10.1021/jp410305m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We report on the formation of planar lipid bilayer structures on mica where the bilayer contains the phosphocholine 1,2-dioleoyl-sn-phosphatidylcholine (DOPC), cholesterol, sphingomyelin and sulforhodamine-tagged-1,2-dioleoyl-sn-phosphatidylethanolamine (SR-DOPE). Phase separation is seen for the cholesterol domains within the bilayer structure, and exposure of this supported bilayer to controlled concentrations of ethanol reveals organizational changes on both the micrometer- and molecular-length scales. We report steady state fluorescence imaging, fluorescence lifetime imaging, and fluorescence anisotropy decay imaging for these bilayers. These data are complementary to existing information on the interactions of lipid bilayers with ethanol and point to subtle but important changes in the molecular-scale organization of these structures.
Collapse
Affiliation(s)
- Iwan Setiawan
- Department of Chemistry, Michigan State University , 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | | |
Collapse
|