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Barkey M, Büchner R, Wester A, Pritzl SD, Makarenko M, Wang Q, Weber T, Trauner D, Maier SA, Fratalocchi A, Lohmüller T, Tittl A. Pixelated High- Q Metasurfaces for in Situ Biospectroscopy and Artificial Intelligence-Enabled Classification of Lipid Membrane Photoswitching Dynamics. ACS NANO 2024; 18:11644-11654. [PMID: 38653474 PMCID: PMC11080459 DOI: 10.1021/acsnano.3c09798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/21/2024] [Accepted: 03/28/2024] [Indexed: 04/25/2024]
Abstract
Nanophotonic devices excel at confining light into intense hot spots of electromagnetic near fields, creating exceptional opportunities for light-matter coupling and surface-enhanced sensing. Recently, all-dielectric metasurfaces with ultrasharp resonances enabled by photonic bound states in the continuum (BICs) have unlocked additional functionalities for surface-enhanced biospectroscopy by precisely targeting and reading out the molecular absorption signatures of diverse molecular systems. However, BIC-driven molecular spectroscopy has so far focused on end point measurements in dry conditions, neglecting the crucial interaction dynamics of biological systems. Here, we combine the advantages of pixelated all-dielectric metasurfaces with deep learning-enabled feature extraction and prediction to realize an integrated optofluidic platform for time-resolved in situ biospectroscopy. Our approach harnesses high-Q metasurfaces specifically designed for operation in a lossy aqueous environment together with advanced spectral sampling techniques to temporally resolve the dynamic behavior of photoswitchable lipid membranes. Enabled by a software convolutional neural network, we further demonstrate the real-time classification of the characteristic cis and trans membrane conformations with 98% accuracy. Our synergistic sensing platform incorporating metasurfaces, optofluidics, and deep learning reveals exciting possibilities for studying multimolecular biological systems, ranging from the behavior of transmembrane proteins to the dynamic processes associated with cellular communication.
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Affiliation(s)
- Martin Barkey
- Chair
in Hybrid Nanosystems, Nano-Institute Munich, Faculty of Physics, Ludwig-Maximilians-Universtität München, Königinstraße 10, 80539 München, Germany
| | - Rebecca Büchner
- Chair
in Hybrid Nanosystems, Nano-Institute Munich, Faculty of Physics, Ludwig-Maximilians-Universtität München, Königinstraße 10, 80539 München, Germany
- Nanophotonic
Systems Laboratory, ETH Zürich, 8092 Zürich, Switzerland
| | - Alwin Wester
- Chair
in Hybrid Nanosystems, Nano-Institute Munich, Faculty of Physics, Ludwig-Maximilians-Universtität München, Königinstraße 10, 80539 München, Germany
| | - Stefanie D. Pritzl
- Chair
for Photonics and Optoelectronics, Nano-Institute Munich, Faculty
of Physics, Ludwig-Maximilians-Universtität
München, Königinstraße
10, 80539 München, Germany
- Department
of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Maksim Makarenko
- PRIMALIGHT,
Faculty of Electrical Engineering, King
Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Qizhou Wang
- PRIMALIGHT,
Faculty of Electrical Engineering, King
Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Thomas Weber
- Chair
in Hybrid Nanosystems, Nano-Institute Munich, Faculty of Physics, Ludwig-Maximilians-Universtität München, Königinstraße 10, 80539 München, Germany
| | - Dirk Trauner
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United
States
| | - Stefan A. Maier
- Chair
in Hybrid Nanosystems, Nano-Institute Munich, Faculty of Physics, Ludwig-Maximilians-Universtität München, Königinstraße 10, 80539 München, Germany
- School of
Physics and Astronomy, Monash University, Wellington Road, Clayton, VIC 3800, Australia
- The Blackett
Laboratory, Department of Physics, Imperial
College London, London, SW7 2AZ, United Kingdom
| | - Andrea Fratalocchi
- PRIMALIGHT,
Faculty of Electrical Engineering, King
Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Theobald Lohmüller
- Chair
for Photonics and Optoelectronics, Nano-Institute Munich, Faculty
of Physics, Ludwig-Maximilians-Universtität
München, Königinstraße
10, 80539 München, Germany
| | - Andreas Tittl
- Chair
in Hybrid Nanosystems, Nano-Institute Munich, Faculty of Physics, Ludwig-Maximilians-Universtität München, Königinstraße 10, 80539 München, Germany
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2
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Yu YJ, Tian JL, Zheng T, Kuang HX, Li ZR, Hao CJ, Xiang MD, Li ZC. Perturbation of lipid metabolism in 3T3-L1 at different stages of preadipocyte differentiation and new insights into the association between changed metabolites and adipogenesis promoted by TBBPA or TBBPS. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133183. [PMID: 38070267 DOI: 10.1016/j.jhazmat.2023.133183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/28/2023] [Accepted: 12/03/2023] [Indexed: 02/08/2024]
Abstract
Tetrabromobisphenol A (TBBPA) and tetrabromobisphenol S (TBBPS) are widely distributed brominated flame retardants. While TBBPA has been demonstrated to stimulate adipogenesis, TBBPS is also under suspicion for potentially inducing comparable effects. In this study, we conducted a non-targeted metabolomics to examine the metabolic changes in 3T3-L1 cells exposed to an environmentally relevant dose of TBBPA or TBBPS. Our findings revealed that 0.1 µM of both TBBPA and TBBPS promoted the adipogenesis of 3T3-L1 preadipocytes. Multivariate analysis showed significant increases in glycerophospholipids, sphingolipids, and steroids relative levels in 3T3-L1 cells exposed to TBBPA or TBBPS at the final stage of preadipocyte differentiation. Metabolites set composed of glycerophospholipids was found to be highly effective predictors of adipogenesis in 3T3-L1 cells exposed to TBBPA or TBBPS (revealed from the receiver operating characteristic curve with an area under curve > 0.90). The results from metabolite set enrichment analysis suggested both TBBPA and TBBPS exposures significantly perturbed steroid biosynthesis in adipocytes. Moreover, TBBPS additionally disrupted the sphingolipid metabolism in the adipocytes. Our study presents new insights into the obesogenic effects of TBBPS and provides valuable information about the metabolites associated with adipogenesis induced by TBBPA or TBBPS.
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Affiliation(s)
- Yun-Jiang Yu
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, Guangdong 510655, China
| | - Jing-Lin Tian
- Vascular Disease Research Center, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Tong Zheng
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, Guangdong 510655, China
| | - Hong-Xuan Kuang
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, Guangdong 510655, China
| | - Zong-Rui Li
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, Guangdong 510655, China
| | - Chao-Jie Hao
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, Guangdong 510655, China
| | - Ming-Deng Xiang
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, Guangdong 510655, China
| | - Zhen-Chi Li
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong 518055, China.
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Buckner DK, Anderson MJ, Wisnosky S, Alvarado W, Nuevo M, Williams AJ, Ricco AJ, Anamika, Debic S, Friend L, Hoac T, Jahnke L, Radosevich L, Williams R, Wilhelm MB. Quantifying Global Origin-Diagnostic Features and Patterns in Biotic and Abiotic Acyclic Lipids for Life Detection. ASTROBIOLOGY 2024; 24:1-35. [PMID: 38150549 DOI: 10.1089/ast.2023.0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Lipids are a geologically robust class of organics ubiquitous to life as we know it. Lipid-like soluble organics are synthesized abiotically and have been identified in carbonaceous meteorites and on Mars. Ascertaining the origin of lipids on Mars would be a profound astrobiological achievement. We enumerate origin-diagnostic features and patterns in two acyclic lipid classes, fatty acids (i.e., carboxylic acids) and acyclic hydrocarbons, by collecting and analyzing molecular data reported in over 1500 samples from previously published studies of terrestrial and meteoritic organics. We identify 27 combined (15 for fatty acids, 12 for acyclic hydrocarbons) molecular patterns and structural features that can aid in distinguishing biotic from abiotic synthesis. Principal component analysis (PCA) demonstrates that multivariate analyses of molecular features (16 for fatty acids, 14 for acyclic hydrocarbons) can potentially indicate sample origin. Terrestrial lipids are dominated by longer straight-chain molecules (C4-C34 fatty acids, C14-C46 acyclic hydrocarbons), with predominance for specific branched and unsaturated isomers. Lipid-like meteoritic soluble organics are shorter, with random configurations. Organic solvent-extraction techniques are most commonly reported, motivating the design of our novel instrument, the Extractor for Chemical Analysis of Lipid Biomarkers in Regolith (ExCALiBR), which extracts lipids while preserving origin-diagnostic features that can indicate biogenicity.
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Affiliation(s)
- Denise K Buckner
- Department of Geological Sciences, University of Florida, Gainesville, Florida, USA
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Morgan J Anderson
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
- Axient Corporation, Huntsville, Alabama, USA
| | - Sydney Wisnosky
- Axient Corporation, Huntsville, Alabama, USA
- Department of Biology, University of Miami, Coral Gables, Florida, USA
| | - Walter Alvarado
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
| | - Michel Nuevo
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Amy J Williams
- Department of Geological Sciences, University of Florida, Gainesville, Florida, USA
| | - Antonio J Ricco
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
- Electrical Engineering-Integrated Circuits Laboratory, Stanford University, Stanford, California, USA
| | - Anamika
- Department of Space Studies, University of North Dakota, Grand Forks, North Dakota, USA
| | - Sara Debic
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Trinh Hoac
- Axient Corporation, Huntsville, Alabama, USA
| | - Linda Jahnke
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | | | - Ross Williams
- Civil & Environmental Engineering & Earth Sciences, Notre Dame University, Notre Dame, Indiana, USA
| | - Mary Beth Wilhelm
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
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Zhang J, Kriebel CN, Wan Z, Shi M, Glaubitz C, He X. Automated Fragmentation Quantum Mechanical Calculation of 15N and 13C Chemical Shifts in a Membrane Protein. J Chem Theory Comput 2023; 19:7405-7422. [PMID: 37788419 DOI: 10.1021/acs.jctc.3c00621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
In this work, we developed an accurate and cost-effective automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method to calculate the chemical shifts of 15N and 13C of membrane proteins. The convergence of the AF-QM/MM method was tested using Krokinobacter eikastus rhodopsin 2 as a test case. When the distance threshold of the QM region is equal to or larger than 4.0 Å, the results of the AF-QM/MM calculations are close to convergence. In addition, the effects of selected density functionals, basis sets, and local chemical environment of target atoms on the chemical shift calculations were systematically investigated. Our results demonstrate that the predicted chemical shifts are more accurate when important environmental factors including cross-protomer interactions, lipid molecules, and solvent molecules are taken into consideration, especially for the 15N chemical shift prediction. Furthermore, with the presence of sodium ions in the environment, the chemical shift of residues, retinal, and retinal Schiff base are affected, which is consistent with the results of the solid-state nuclear magnetic resonance (NMR) experiment. Upon comparing the performance of various density functionals (namely, B3LYP, B3PW91, M06-2X, M06-L, mPW1PW91, OB95, and OPBE), the results show that mPW1PW91 is a suitable functional for the 15N and 13C chemical shift prediction of the membrane proteins. Meanwhile, we find that the improved accuracy of the 13Cβ chemical shift calculations can be achieved by the employment of the triple-ζ basis set. However, the employment of the triple-ζ basis set does not improve the accuracy of the 15N and 13Cα chemical shift calculations nor does the addition of a diffuse function improve the overall prediction accuracy of the chemical shifts. Our study also underscores that the AF-QM/MM method has significant advantages in predicting the chemical shifts of key ligands and nonstandard residues in membrane proteins than most widely used empirical models; therefore, it could be an accurate computational tool for chemical shift calculations on various types of biological systems.
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Affiliation(s)
- Jinhuan Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Clara Nassrin Kriebel
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Zheng Wan
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Man Shi
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Clemens Glaubitz
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200062, China
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Tempra C, Brkljača Z, Vazdar M. Why do polyarginines adsorb at neutral phospholipid bilayers and polylysines do not? An insight from density functional theory calculations and molecular dynamics simulations. Phys Chem Chem Phys 2023; 25:27204-27214. [PMID: 37791394 DOI: 10.1039/d3cp02411c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Adsorption of cell-penetrating peptides (CPPs) at cellular membranes is the first and necessary step for their subsequent translocation across cellular membranes into the cytosol. It has been experimentally shown that CPPs rich in arginine (Arg) amino acid penetrate across phospholipid bilayers more effectively than their lysine (Lys) rich counterparts. In this work, we aim to understand the differences in the first translocation step, adsorption of Arg9 and Lys9 peptides at fully hydrated neutral phosphatidylcholine (PC) and phosphatidylethanolamine (PE) lipid bilayers and evaluate in detail the energetics of the process using molecular dynamics (MD) simulations and free energy calculations of adsorption of the single peptide. We show that the adsorption of Arg9 is energetically feasible, with the free energy of adsorption being ∼-5.0 kcal mol-1 at PC and ∼-5.5 kcal mol-1 at PE bilayers. In contrast, adsorption of Lys9 is not observed at PC bilayers, and their adsorption at PE bilayers is very weak, being ∼-0.5 kcal mol-1. We show by energy decomposition and analysis of peptide hydration along the membrane that significantly stronger electrostatic interactions of Arg9 with lipid phosphate groups, together with the greater loss of peptide hydration (and in turn stronger hydrophobic interactions) along the membrane translocation path, are the main driving factors governing the adsorption of Arg-rich peptides at neutral lipid bilayers in contrast to Lys-rich peptides. Finally, we also compare the energetics in lipid/bilayer systems with the density functional theory (DFT) calculations of the corresponding model systems in the continuum water model and reveal the energetic differences in different environments.
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Affiliation(s)
- Carmelo Tempra
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 16000 Prague, Czech Republic
| | - Zlatko Brkljača
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Mario Vazdar
- Department of Mathematics, Informatics, and Cybernetics, University of Chemistry and Technology, Technická 5, 16628 Prague, Czech Republic.
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Mitra S, Sharma VK, Ghosh SK. Effects of ionic liquids on biomembranes: A review on recent biophysical studies. Chem Phys Lipids 2023; 256:105336. [PMID: 37586678 DOI: 10.1016/j.chemphyslip.2023.105336] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/05/2023] [Accepted: 08/11/2023] [Indexed: 08/18/2023]
Abstract
Ionic liquids (ILs) have been emerged as a versatile class of compounds that can be easily tuned to achieve desirable properties for various applications. The ability of ILs to interact with biomembranes has attracted significant interest, as they have been shown to modulate membrane properties in ways that may have implications for various biological processes. This review provides an overview of recent studies that have investigated the interaction between ILs and biomembranes. We discuss the effects of ILs on the physical and chemical properties of biomembranes, including changes in membrane fluidity, permeability, and stability. We also explore the mechanisms underlying the interaction of ILs with biomembranes, such as electrostatic interactions, hydrogen bonding, and van der Waals forces. Additionally, we discuss the future prospects of this field.
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Affiliation(s)
- Saheli Mitra
- Department of Physics, School of Natural Sciences, Shiv Nadar Institution of Eminence, NH 91, Tehsil Dadri, G. B. Nagar, Uttar Pradesh 201314, India.
| | - Veerendra K Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India.
| | - Sajal K Ghosh
- Department of Physics, School of Natural Sciences, Shiv Nadar Institution of Eminence, NH 91, Tehsil Dadri, G. B. Nagar, Uttar Pradesh 201314, India.
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Wroński A, Dobrzyńska I, Sękowski S, Łuczaj W, Olchowik-Grabarek E, Skrzydlewska E. Cannabidiol and Cannabigerol Modify the Composition and Physicochemical Properties of Keratinocyte Membranes Exposed to UVA. Int J Mol Sci 2023; 24:12424. [PMID: 37569799 PMCID: PMC10418984 DOI: 10.3390/ijms241512424] [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: 07/05/2023] [Revised: 07/28/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
The action of UVA radiation (both that derived from solar radiation and that used in the treatment of skin diseases) modifies the function and composition of keratinocyte membranes. Therefore, this study aimed to assess the effects of phytocannabinoids (CBD and CBG), used singly and in combination, on the contents of phospholipids, ceramides, lipid rafts and sialic acid in keratinocyte membranes exposed to UVA radiation, together with their structure and functionality. The phytocannabinoids, especially in combination (CBD+CBG), partially prevented increased levels of phosphatidylinositols and sialic acid from occurring and sphingomyelinase activity after the UVA exposure of keratinocytes. This was accompanied by a reduction in the formation of lipid rafts and malondialdehyde, which correlated with the parameters responsible for the integrity and functionality of the keratinocyte membrane (membrane fluidity and permeability and the activity of transmembrane transporters), compared to UVA-irradiated cells. This suggests that the simultaneous use of two phytocannabinoids may have a protective effect on healthy cells, without significantly reducing the therapeutic effect of UV radiation used to treat skin diseases such as psoriasis.
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Affiliation(s)
- Adam Wroński
- Dermatological Specialized Center “DERMAL” NZOZ in Białystok, Nowy Swiat 17/5, 15-453 Białystok, Poland;
| | - Izabela Dobrzyńska
- Laboratory of Bioanalysis, Faculty of Chemistry, University in Białystok, Ciołkowskiego 1K, 15-245 Białystok, Poland;
| | - Szymon Sękowski
- Laboratory of Molecular Biophysics, Department of Microbiology and Biotechnology, Faculty of Biology, University in Białystok, Ciołkowskiego 1J, 15-245 Białystok, Poland; (S.S.); (E.O.-G.)
| | - Wojciech Łuczaj
- Department of Analytical Chemistry, Medical University of Białystok, Mickiewicza 2D, 15-222 Białystok, Poland;
| | - Ewa Olchowik-Grabarek
- Laboratory of Molecular Biophysics, Department of Microbiology and Biotechnology, Faculty of Biology, University in Białystok, Ciołkowskiego 1J, 15-245 Białystok, Poland; (S.S.); (E.O.-G.)
| | - Elżbieta Skrzydlewska
- Department of Analytical Chemistry, Medical University of Białystok, Mickiewicza 2D, 15-222 Białystok, Poland;
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Krzyzanowski N, Porcar L, Perez-Salas U. A Small-Angle Neutron Scattering, Calorimetry and Densitometry Study to Detect Phase Boundaries and Nanoscale Domain Structure in a Binary Lipid Mixture. MEMBRANES 2023; 13:323. [PMID: 36984710 PMCID: PMC10051979 DOI: 10.3390/membranes13030323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
Techniques that can probe nanometer length scales, such as small-angle neutron scattering (SANS), have become increasingly popular to detect phase separation in membranes. But to extract the phase composition and domain structure from the SANS traces, complementary information is needed. Here, we present a SANS, calorimetry and densitometry study of a mixture of two saturated lipids that exhibits solidus-liquidus phase coexistence: 1,2-dipalmitoyl-d62-sn-glycero-3-phosphocholine (dDPPC, tail-deuterated DPPC) and 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC). With calorimetry, we investigated the phase diagram for this system and found that the boundary traces for both multilamellar vesicles (MLVs) as well as 50 nm unilamellar vesicles overlap. Because the solidus boundary was mostly inaccessible by calorimetry, we investigated it by both SANS and molecular volume measurements for a 1:1 dDPPC:DLPC lipid mixture. From the temperature behavior of the molecular volume for the 1:1 dDPPC:DLPC mixture, as well as the individual molecular volume of each lipid species, we inferred that the liquidus phase consists of only fluid-state lipids while the solidus phase consists of lipids that are in gel-like states. Using this solidus-liquidus phase model, the SANS data were analyzed with an unrestricted shape model analysis software: MONSA. The resulting fits show irregular domains with dendrite-like features as those previously observed on giant unilamellar vesicles (GUVs). The surface pair correlation function describes a characteristic domain size for the minority phase that decreases with temperature, a behavior found to be consistent with a concomitant decrease in membrane mismatch between the liquidus and solidus phases.
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Affiliation(s)
- Natalie Krzyzanowski
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60608, USA
| | - Lionel Porcar
- Large Scale Structures Group, Institut Laue-Langevin, CEDEX 9, 38042 Grenoble, France
| | - Ursula Perez-Salas
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60608, USA
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9
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Priyanka U, Lens PNL. Enhanced production of amylase, pyruvate and phenolic compounds from glucose by light-driven Aspergillus niger-CuS nanobiohybrids. JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY (OXFORD, OXFORDSHIRE : 1986) 2023; 98:602-614. [PMID: 37066082 PMCID: PMC10087041 DOI: 10.1002/jctb.7153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/29/2022] [Accepted: 06/08/2022] [Indexed: 06/19/2023]
Abstract
BACKGROUND The demand for value-added compounds such as amylase, pyruvate and phenolic compounds produced by biological methods has prompted the rapid development of advanced technologies for their enhanced production. Nanobiohybrids (NBs) make use of both the microbial properties of whole-cell microorganisms and the light-harvesting efficiency of semiconductors. Photosynthetic NBs were constructed that link the biosynthetic pathways of Aspergillus niger with CuS nanoparticles. RESULTS In this work, NB formation was confirmed by negative values of the interaction energy, i.e., 2.31 × 108 to -5.52 × 108 kJ mol-1 for CuS-Che NBs, whereas for CuS-Bio NBs the values were -2.31 × 108 to -4.62 × 108 kJ mol-1 for CuS-Bio NBs with spherical nanoparticle interaction. For CuS-Bio NBs with nanorod interaction, it ranged from -2.3 × 107 to -3.47 × 107 kJ mol-1 . Further, the morphological changes observed by scanning electron microscopy showed the presence of the elements Cu and S in the energy-dispersive X-ray spectra and the presence of CuS bonds in Fourier transform infrared spectroscopy indicate NB formation. In addition, the quenching effect in photoluminescence studies confirmed NB formation. Production yields of amylase, phenolic compounds and pyruvate amounted to 11.2 μmol L-1, 52.5 μmol L-1 and 28 nmol μL-1, respectively, in A. niger-CuS Bio NBs on the third day of incubation in the bioreactor. Moreover, A niger cells-CuS Bio NBs had amino acids and lipid yields of 6.2 mg mL-1 and 26.5 mg L-1, respectively. Furthermore, probable mechanisms for the enhanced production of amylase, pyruvate and phenolic compounds are proposed. CONCLUSION Aspergillus niger-CuS NBs were used for the production of the amylase enzyme and value-added compounds such as pyruvate and phenolic compounds. Aspergillus niger-CuS Bio NBs showed a greater efficiency compared to A. niger-CuS Che NBs as the biologically produced CuS nanoparticles had a higher compatibility with A. niger cells. © 2022 The Authors. Journal of Chemical Technology and Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry (SCI).
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Affiliation(s)
- Uddandarao Priyanka
- Department of Microbiology and Ryan InstituteNational University of IrelandGalwayIreland
| | - Piet NL Lens
- Department of Microbiology and Ryan InstituteNational University of IrelandGalwayIreland
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10
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Tzortzini E, Corey RA, Kolocouris A. Comparative Study of Receptor-, Receptor State-, and Membrane-Dependent Cholesterol Binding Sites in A 2A and A 1 Adenosine Receptors Using Coarse-Grained Molecular Dynamics Simulations. J Chem Inf Model 2023; 63:928-949. [PMID: 36637988 DOI: 10.1021/acs.jcim.2c01181] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We used coarse-grained molecular dynamics (CG MD) simulations to study protein-cholesterol interactions for different activation states of the A2A adenosine receptor (A2AR) and the A1 adenosine receptor (A1R) and predict new cholesterol binding sites indicating amino acid residues with a high residence time in three biologically relevant membranes. Compared to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)-cholesterol and POPC-phosphatidylinositol-bisphosphate (PIP2)-cholesterol, the plasma mimetic membrane best described the cholesterol binding sites previously detected for the inactive state of A2AR and revealed the binding sites with long-lasting amino acid residues. We observed that using the plasma mimetic membrane and plotting residues with cholesterol residence time ≥2 μs, our CG MD simulations captured most obviously the cholesterol-protein interactions. For the inactive A2AR, we identified one more binding site in which cholesterol is bound to residues with a long residence time compared to the previously detected, for the active A1R, three binding sites, and for the inactive A1R, two binding sites. We calculated that for the active states, cholesterol binds to residues with a much longer residence time compared to the inactive state for both A2AR and A1R. The stability of the identified binding sites to A1R or A2AR with CG MD simulations was additionally investigated with potential of mean force calculations using umbrella sampling. We observed that the binding sites with residues to which cholesterol has a long residence time in A2AR have shallow binding free energy minima compared to the related binding sites in A1R, suggesting a stronger binding for cholesterol to A1R. The differences in binding sites in which cholesterol is stabilized and interacts with residues with a long residence time between active and inactive states of A1R and A2AR can be important for differences in functional activity and orthosteric agonist or antagonist affinity and can be used for the design of allosteric modulators, which can bind through lipid pathways. We observed a stronger binding for cholesterol to A1R (i.e., generally higher association rates) compared to A2AR, which remains to be demonstrated. For the active states, cholesterol binds to residues with much longer residence times compared to the inactive state for both A2AR and A1R. Taken together, binding sites of active A1R may be considered as promising allosteric targets.
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Affiliation(s)
- Efpraxia Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771Athens, Greece
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771Athens, Greece
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11
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Bouquiaux C, Castet F, Champagne B. Influence of the Nature of the Lipid Building Blocks on the Second-Order Nonlinear Optical Responses of an Embedded Di-8-ANEPPS Probe. J Phys Chem B 2023; 127:528-541. [PMID: 36606294 DOI: 10.1021/acs.jpcb.2c08093] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The extensive collection of lipids found in cell membranes is justified by the fact that each lipid contributes to their overall structure, dynamics, and properties and so to the biological processes taking place within them. It also showcases that, in order to deepen our understanding of membranes, we need to have a tool to differentiate lipid bilayers of varying composition. In this work, we investigate a suite of single-component saturated glycerophospholipids varying only in their headgroup structure by analyzing the second harmonic generation (SHG) nonlinear optical (NLO) response of a probe, di-8-ANEPPS, embedded into the membranes. The seven hydrophilic heads chosen (phosphatidylcholine (PC), phosphatidylethanolamine (PE), diaglycerol (GL), phosphatidylserine (PS), phosphatidylglycerol (PG), phosphatidylinositol (PI), and phosphatidyc acid (PA)) represent all the major headgroups that are part of mammalian plasma membranes and provide an assortment of neutral, zwiterrionic, and charged species. First, molecular dynamics simulations revealed that the lipidic arrangement is strongly sensitive to the nature of the hydrophilic head and less to the variety in the hydrophobic region. Membranes exhibiting drastically opposite structural properties can be pointed out: 1,2-dihexadecanoyl-rac-glycerol (DPGL) is the thickest and most ordered and aligned system, whereas 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) (DPPG) is thinnest and least ordered and aligned system. The structural analyses are then confronted with the molecular NLO responses, β, computed at the time-dependent density functional theory (TDDFT) level. As the orientation of the chromophore is impacted by the various degrees of order within the lipid bilayers, the diagonal component of the β tensor parallel to the bilayer normal, βZZZ, is as well. In the end, this computational approach provides insights into the link between lipid building blocks and the NLO responses of the embedded dye.
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Affiliation(s)
- Charlotte Bouquiaux
- University of Namur, Theoretical Chemistry Lab, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, rue de Bruxelles, 61, B-5000Namur, Belgium
| | - Frédéric Castet
- University of Bordeaux, Institut des Sciences Moléculaires, UMR 5255 CNRS, cours de la Libération 351, F-33405 CedexTalence, France
| | - Benoît Champagne
- University of Namur, Theoretical Chemistry Lab, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, rue de Bruxelles, 61, B-5000Namur, Belgium
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12
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Percivalle NM, Carofiglio M, Conte M, Rosso G, Bentivogli A, Mesiano G, Vighetto V, Cauda V. Artificial and Naturally Derived Phospholipidic Bilayers as Smart Coatings of Solid-State Nanoparticles: Current Works and Perspectives in Cancer Therapy. Int J Mol Sci 2022; 23:ijms232415815. [PMID: 36555455 PMCID: PMC9779745 DOI: 10.3390/ijms232415815] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/24/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Recent advances in nanomedicine toward cancer treatment have considered exploiting liposomes and extracellular vesicles as effective cargos to deliver therapeutic agents to tumor cells. Meanwhile, solid-state nanoparticles are continuing to attract interest for their great medical potential thanks to their countless properties and possible applications. However, possible drawbacks arising from the use of nanoparticles in nanomedicine, such as the nonspecific uptake of these materials in healthy organs, their aggregation in biological environments and their possible immunogenicity, must be taken into account. Considering these limitations and the intrinsic capability of phospholipidic bilayers to act as a biocompatible shield, their exploitation for effectively encasing solid-state nanoparticles seems a promising strategy to broaden the frontiers of cancer nanomedicine, also providing the possibility to engineer the lipid bilayers to further enhance the therapeutic potential of such nanotools. This work aims to give a comprehensive overview of the latest developments in the use of artificial liposomes and naturally derived extracellular vesicles for the coating of solid-state nanoparticles for cancer treatment, starting from in vitro works until the up-to-date advances and current limitations of these nanopharmaceutics in clinical applications, passing through in vivo and 3D cultures studies.
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13
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Knittel CH, Devaraj NK. Bioconjugation Strategies for Revealing the Roles of Lipids in Living Cells. Acc Chem Res 2022; 55:3099-3109. [PMID: 36215688 DOI: 10.1021/acs.accounts.2c00511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The structural boundaries of living cells are composed of numerous membrane-forming lipids. Lipids not only are crucial for the cellular compartmentalization but also are involved in cell signaling as well as energy storage. Abnormal lipid levels have been linked to severe human diseases such as cancer, multiple sclerosis, neurodegenerative diseases, as well as lysosomal storage disorders. Given their biological significance, there is immense interest in studying lipids and their effect on cells. However, limiting factors include the low solubility of lipids, their structural complexity, and the challenge of using genetic techniques to directly manipulate lipid structure. Current methods to study lipids rely mostly on lipidomics, which analyzes the composition of lipid extracts using mass spectrometry. Although, these efforts have successfully catalogued and profiled a great number of lipids in cells, many aspects about their exact functional role and subcellular distribution remain enigmatic.In this Account, we outline how our laboratory developed and applied different bioconjugation strategies to study the role of lipids and lipid modifications in cells. Inspired by our ongoing work on developing lipid bioconjugation strategies to generate artificial cell membranes, we developed a ceramide synthesis method in live cells using a salicylaldehyde ester that readily reacts with sphingosine in form of a traceless ceramide ligation. Our study not only confirmed existing knowledge about the association of ceramides with cell death, but also gave interesting new findings about the structure-function relationship of ceramides in apoptosis. Our initial efforts led us to investigate probes that detect endogenous sphingolipids using live cell imaging. We describe the development of a fluorogenic probe that reacts chemoselectively with sphingosine in living cells, enabling the detection of elevated endogenous levels of this biomarker in human disease. Building on our interest in the fluorescence labeling of lipids, we have also explored the use of bioorthogonal reactions to label chemically synthesized lipid probes. We discuss the development of photocaged dihydrotetrazine lipids, where the initiation of the bioorthogonal reaction can be triggered by visible light, allowing for live cell modification of membranes with spatiotemporal control.Finally, proteins are often post-translationally modified by lipids, which have important effects on protein subcellular localization and function. Controlling lipid modifications with small molecule probes could help reveal the function of lipid post-translational modifications and could potentially inspire novel therapeutic strategies. We describe how our previous studies on synthetic membrane formation inspired us to develop an amphiphilic cysteine derivative that depalmitoylates membrane-bound S-acylated proteins in live cells. Ultimately, we applied this amphiphile mediated depalmitoylation (AMD) in studies investigating the palmitoylation of cancer relevant palmitoylated proteins in healthy and diseased cells.
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Affiliation(s)
- Caroline H Knittel
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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14
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Schiaffarino O, Valdivieso González D, García-Pérez IM, Peñalva DA, Almendro-Vedia VG, Natale P, López-Montero I. Mitochondrial membrane models built from native lipid extracts: Interfacial and transport properties. Front Mol Biosci 2022; 9:910936. [PMID: 36213125 PMCID: PMC9538489 DOI: 10.3389/fmolb.2022.910936] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 09/02/2022] [Indexed: 12/03/2022] Open
Abstract
The mitochondrion is an essential organelle enclosed by two membranes whose functionalities depend on their very specific protein and lipid compositions. Proteins from the outer mitochondrial membrane (OMM) are specialized in mitochondrial dynamics and mitophagy, whereas proteins of the inner mitochondrial membrane (IMM) have dedicated functions in cellular respiration and apoptosis. As for lipids, the OMM is enriched in glycerophosphatidyl choline but cardiolipin is exclusively found within the IMM. Though the lipid topology and distribution of the OMM and IMM are known since more than four decades, little is known about the interfacial and dynamic properties of the IMM and OMM lipid extracts. Here we build monolayers, supported bilayers and giant unilamellar vesicles (GUVs) of native OMM and IMM lipids extracts from porcine heart. Additionally, we perform a comparative analysis on the interfacial, phase immiscibility and mechanical properties of both types of extract. Our results show that IMM lipids form more expanded and softer membranes than OMM lipids, allowing a better understanding of the physicochemical and biophysical properties of mitochondrial membranes.
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Affiliation(s)
- Olivia Schiaffarino
- Departamento Química Física, Universidad Complutense de Madrid, Madrid, Spain
| | - David Valdivieso González
- Departamento Química Física, Universidad Complutense de Madrid, Madrid, Spain
- Instituto de Investigación Biomédica Hospital Doce de Octubre (imas12), Madrid, Spain
| | | | - Daniel A. Peñalva
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB), ConsejoNacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | - Víctor G. Almendro-Vedia
- Instituto de Investigación Biomédica Hospital Doce de Octubre (imas12), Madrid, Spain
- Departamento de Farmacia Galénica y Tecnología Alimentaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Paolo Natale
- Departamento Química Física, Universidad Complutense de Madrid, Madrid, Spain
- Instituto de Investigación Biomédica Hospital Doce de Octubre (imas12), Madrid, Spain
- *Correspondence: Iván López-Montero, ; Paolo Natale,
| | - Iván López-Montero
- Departamento Química Física, Universidad Complutense de Madrid, Madrid, Spain
- Instituto de Investigación Biomédica Hospital Doce de Octubre (imas12), Madrid, Spain
- Instituto Pluridisciplinar, Universidad Complutense de Madrid, Madrid, Spain
- *Correspondence: Iván López-Montero, ; Paolo Natale,
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15
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Maier AG, van Ooij C. The role of cholesterol in invasion and growth of malaria parasites. Front Cell Infect Microbiol 2022; 12:984049. [PMID: 36189362 PMCID: PMC9522969 DOI: 10.3389/fcimb.2022.984049] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/15/2022] [Indexed: 11/24/2022] Open
Abstract
Malaria parasites are unicellular eukaryotic pathogens that develop through a complex lifecycle involving two hosts, an anopheline mosquito and a vertebrate host. Throughout this lifecycle, the parasite encounters widely differing conditions and survives in distinct ways, from an intracellular lifestyle in the vertebrate host to exclusively extracellular stages in the mosquito. Although the parasite relies on cholesterol for its growth, the parasite has an ambiguous relationship with cholesterol: cholesterol is required for invasion of host cells by the parasite, including hepatocytes and erythrocytes, and for the development of the parasites in those cells. However, the parasite is unable to produce cholesterol itself and appears to remove cholesterol actively from its own plasma membrane, thereby setting up a cholesterol gradient inside the infected host erythrocyte. Overall a picture emerges in which the parasite relies on host cholesterol and carefully controls its transport. Here, we describe the role of cholesterol at the different lifecycle stages of the parasites.
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Affiliation(s)
- Alexander G. Maier
- Research School of Biology, The Australian National University, Canberra ACT, Australia
- *Correspondence: Alexander G. Maier, ; Christiaan van Ooij,
| | - Christiaan van Ooij
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
- *Correspondence: Alexander G. Maier, ; Christiaan van Ooij,
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16
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Trautenberg LC, Brankatschk M, Shevchenko A, Wigby S, Reinhardt K. Ecological lipidology. eLife 2022; 11:79288. [PMID: 36069772 PMCID: PMC9451535 DOI: 10.7554/elife.79288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Dietary lipids (DLs), particularly sterols and fatty acids, are precursors for endogenous lipids that, unusually for macronutrients, shape cellular and organismal function long after ingestion. These functions – cell membrane structure, intracellular signalling, and hormonal activity – vary with the identity of DLs, and scale up to influence health, survival, and reproductive fitness, thereby affecting evolutionary change. Our Ecological Lipidology approach integrates biochemical mechanisms and molecular cell biology into evolution and nutritional ecology. It exposes our need to understand environmental impacts on lipidomes, the lipid specificity of cell functions, and predicts the evolution of lipid-based diet choices. Broad interdisciplinary implications of Ecological Lipidology include food web alterations, species responses to environmental change, as well as sex differences and lifestyle impacts on human nutrition, and opportunities for DL-based therapies.
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Affiliation(s)
| | - Marko Brankatschk
- Biotechnology Center (BIOTEC), Technische Universität Dresden, Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Stuart Wigby
- Applied Zoology, Technische Universität Dresden, Dresden, Germany.,Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Klaus Reinhardt
- Applied Zoology, Technische Universität Dresden, Dresden, Germany
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17
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Mari SA, Pluhackova K, Pipercevic J, Leipner M, Hiller S, Engel A, Müller DJ. Gasdermin-A3 pore formation propagates along variable pathways. Nat Commun 2022; 13:2609. [PMID: 35545613 PMCID: PMC9095878 DOI: 10.1038/s41467-022-30232-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 04/22/2022] [Indexed: 12/31/2022] Open
Abstract
Gasdermins are main effectors of pyroptosis, an inflammatory form of cell death. Released by proteolysis, the N-terminal gasdermin domain assembles large oligomers to punch lytic pores into the cell membrane. While the endpoint of this reaction, the fully formed pore, has been well characterized, the assembly and pore-forming mechanisms remain largely unknown. To resolve these mechanisms, we characterize mouse gasdermin-A3 by high-resolution time-lapse atomic force microscopy. We find that gasdermin-A3 oligomers assemble on the membrane surface where they remain attached and mobile. Once inserted into the membrane gasdermin-A3 grows variable oligomeric stoichiometries and shapes, each able to open transmembrane pores. Molecular dynamics simulations resolve how the membrane-inserted amphiphilic β-hairpins and the structurally adapting hydrophilic head domains stabilize variable oligomeric conformations and open the pore. The results show that without a vertical collapse gasdermin pore formation propagates along a set of multiple parallel but connected reaction pathways to ensure a robust cellular response.
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Affiliation(s)
- Stefania A Mari
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland
| | - Kristyna Pluhackova
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland.
| | | | - Matthew Leipner
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland
| | | | - Andreas Engel
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland.
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18
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Kubiszewski-Jakubiak S, Worch R. Unique properties of Coronaviridae single-pass transmembrane domain regions as an adaptation to diverse membrane systems. Virology 2022; 570:1-8. [PMID: 35306415 PMCID: PMC8922268 DOI: 10.1016/j.virol.2022.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 11/25/2022]
Abstract
Enveloped viruses such as Coronaviridae (CoV) enter the host cell by fusing the viral envelope directly with the plasma membrane (PM) or with the membrane of the endosome. Replication of the CoV genome takes place in membrane compartments formed by rearrangement of the endoplasmic reticulum (ER) membrane network. Budding of these viruses occurs from the ER-Golgi intermediate compartment (ERGIC). The relationship between proteins and various membranes is crucial for the replication cycle of CoVs. The role of transmembrane domains (TMDs) and pre-transmembrane domains (pre-TMD) of viral proteins in this process is gaining more recognition. Here we present a thorough analysis of physico-chemical parameters, such as accessible surface area (ASA), average hydrophobicity (Hav), and contribution of specific amino acids in TMDs and pre-TMDs of single-span membrane proteins of human viruses. We focus on unique properties of these elements in CoV and postulate their role in adaptation to diverse host membranes and regulation of retention of membrane proteins during replication.
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19
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Larsen A, John L, Sansom M, Corey R. Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us? Biosci Rep 2022; 42:BSR20211406. [PMID: 35297484 PMCID: PMC9008707 DOI: 10.1042/bsr20211406] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 12/04/2022] Open
Abstract
Peripheral membrane proteins (PMPs) can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding domains are typically solved in a soluble form, sometimes with a lipid or lipid headgroup at the binding site. To provide a detailed molecular view of PMP interactions with the membrane, computational methods such as molecular dynamics (MD) simulations can be applied. Here, we outline recent attempts to characterise these binding interactions, focusing on both intracellular proteins, such as phosphatidylinositol phosphate (PIP)-binding domains, and extracellular proteins such as glycolipid-binding bacterial exotoxins. We compare methods used to identify and analyse lipid-binding sites from simulation data and highlight recent work characterising the energetics of these interactions using free energy calculations. We describe how improvements in methodologies and computing power will help MD simulations to continue to contribute to this field in the future.
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Affiliation(s)
| | - Laura H. John
- Department of Biochemistry, University of Oxford, Oxford, U.K
| | | | - Robin A. Corey
- Department of Biochemistry, University of Oxford, Oxford, U.K
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20
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Song W, Corey RA, Ansell TB, Cassidy CK, Horrell MR, Duncan AL, Stansfeld PJ, Sansom MSP. PyLipID: A Python Package for Analysis of Protein-Lipid Interactions from Molecular Dynamics Simulations. J Chem Theory Comput 2022; 18:1188-1201. [PMID: 35020380 PMCID: PMC8830038 DOI: 10.1021/acs.jctc.1c00708] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Indexed: 12/11/2022]
Abstract
Lipids play important modulatory and structural roles for membrane proteins. Molecular dynamics simulations are frequently used to provide insights into the nature of these protein-lipid interactions. Systematic comparative analysis requires tools that provide algorithms for objective assessment of such interactions. We introduce PyLipID, a Python package for the identification and characterization of specific lipid interactions and binding sites on membrane proteins from molecular dynamics simulations. PyLipID uses a community analysis approach for binding site detection, calculating lipid residence times for both the individual protein residues and the detected binding sites. To assist structural analysis, PyLipID produces representative bound lipid poses from simulation data, using a density-based scoring function. To estimate residue contacts robustly, PyLipID uses a dual-cutoff scheme to differentiate between lipid conformational rearrangements while bound from full dissociation events. In addition to the characterization of protein-lipid interactions, PyLipID is applicable to analysis of the interactions of membrane proteins with other ligands. By combining automated analysis, efficient algorithms, and open-source distribution, PyLipID facilitates the systematic analysis of lipid interactions from large simulation data sets of multiple species of membrane proteins.
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Affiliation(s)
- Wanling Song
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
- Rahko,
Clifton House, 46 Clifton
Terrace, Finsbury Park, London N4 3JP, United Kingdom
| | - Robin A. Corey
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - T. Bertie Ansell
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - C. Keith Cassidy
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Michael R. Horrell
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Anna L. Duncan
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Phillip J. Stansfeld
- School
of Life Sciences & Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Mark S. P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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21
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Modak B, Girkar S, Narayan R, Kapoor S. Mycobacterial Membranes as Actionable Targets for Lipid-Centric Therapy in Tuberculosis. J Med Chem 2022; 65:3046-3065. [PMID: 35133820 DOI: 10.1021/acs.jmedchem.1c01870] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Infectious diseases remain significant health concerns worldwide, and resistance is particularly common in patients with tuberculosis caused by Mycobacterium tuberculosis. The development of anti-infectives with novel modes of action may help overcome resistance. In this regard, membrane-active agents, which modulate membrane components essential for the survival of pathogens, present attractive antimicrobial agents. Key advantages of membrane-active compounds include their ability to target slow-growing or dormant bacteria and their favorable pharmacokinetics. Here, we comprehensively review recent advances in the development of membrane-active chemotypes that target mycobacterial membranes and discuss clinically relevant membrane-active antibacterial agents that have shown promise in counteracting bacterial infections. We discuss the relationship between the membrane properties and the synthetic requirements within the chemical scaffold, as well as the limitations of current membrane-active chemotypes. This review will lay the chemical groundwork for the development of membrane-active antituberculosis agents and will foster the discovery of more effective antitubercular agents.
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Affiliation(s)
- Biswabrata Modak
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Siddhali Girkar
- School of Chemical and Materials Sciences, Indian Institute of Technology Goa, Goa 403110, India
| | - Rishikesh Narayan
- School of Chemical and Materials Sciences, Indian Institute of Technology Goa, Goa 403110, India
| | - 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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22
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Olchawa MM, Herrnreiter AM, Skumatz CMB, Krzysztynska-Kuleta OI, Mokrzynski KT, Burke JM, Sarna TJ. The Inhibitory Effect of Blue Light on Phagocytic Activity by ARPE-19 Cells. Photochem Photobiol 2022; 98:1110-1121. [PMID: 35067943 DOI: 10.1111/php.13596] [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: 11/05/2021] [Revised: 01/12/2022] [Accepted: 01/18/2022] [Indexed: 11/30/2022]
Abstract
Chronic exposure of the retina to short wavelength visible light is a risk factor in pathogenesis of age-related macular degeneration. The proper functioning and survival of photoreceptors depends on efficient phagocytosis of photoreceptor outer segments (POS) by retinal pigment epithelium. The purpose of this study was to analyze the phagocytic activity of blue light-treated ARPE-19 cells, and to examine whether the observed effects could be related to altered levels of POS phagocytosis receptor proteins and/or to oxidation of cellular proteins and lipids. POS phagocytosis was measured by flow cytometry. Phagocytosis receptor proteins αv and β5 integrin subunits and Mer tyrosine kinase (MerTK) were quantified by western blotting. The intact functional heterodimer αvβ5 was quantified by immunoprecipitation followed by immunoblotting. Cellular protein and lipid hydroperoxides were analyzed by coumarin boronic acid probe and iodometric assay, respectively. Cell irradiation induced reversible inhibition of specific phagocytosis and transient reductions in phagocytosis receptor proteins. Full recovery of functional heterodimer was apparent. Significant photooxidation of cellular proteins and lipids was observed. The results indicate that transient inhibition of specific phagocytosis by blue light could be related to the reduction in phagocytosis receptor proteins. Such changes may arise from oxidative modifications of cell phagocytic machinery components.
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Affiliation(s)
- Magdalena M Olchawa
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland.,Department of Ophthalmology, Eye Institute, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Anja M Herrnreiter
- Department of Ophthalmology, Eye Institute, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Christine M B Skumatz
- Department of Ophthalmology, Eye Institute, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.,Department of Ophthalmology and Visual Sciences, Eye Institute, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Olga I Krzysztynska-Kuleta
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Krystian T Mokrzynski
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Janice M Burke
- Department of Ophthalmology, Eye Institute, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.,Emeritus Professor of Ophthalmology
| | - Tadeusz J Sarna
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
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23
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Banerjee S, Lyubchenko YL. Topographically smooth and stable supported lipid bilayer for high-resolution AFM studies. Methods 2022; 197:13-19. [PMID: 33609699 PMCID: PMC8371085 DOI: 10.1016/j.ymeth.2021.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 01/03/2023] Open
Abstract
The cellular membrane has been identified to play a critical role in various biological processes including the assembly of biological systems. Membranes are complex, primarily two-dimensional assemblies with varied lipid compositions depending on the particular region of the cell. Supported lipid bilayers are considered as appropriate models for physio-chemical studies of membranes including numerous single molecule techniques. Atomic force microscopy (AFM) as a topographic technique is a fully appropriate single molecule technique capable of direct observation of molecular processes on membranes. However, reliable experimental AFM studies require the preparation of the bilayer with a sub-nanometer smooth morphology, which remains stable over long-time observation. Here we present the methodology, which allows one to prepare a smooth, stable, structurally homogeneous lipid bilayer without the presence of any trapped vesicles. We described the application of such lipid bilayers to probe time-dependent early stages of aggregation of monomeric amyloid proteins. Importantly, the proposed methodology can be extended to bilayers with various compositions, by incorporating different lipids for on-membrane aggregation study including cholesterol. Furthermore, this methodology development allowed us to monitor the aggregation of amyloid protein at its physiologically relevant low protein concentration. The flexibility of altering the membrane composition allows to identify the specific role of a particular lipid towards the aggregation kinetics, revealing the plausible mechanism of disease development.
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24
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Xue K, Movellan KT, Zhang XC, Najbauer EE, Forster MC, Becker S, Andreas LB. Towards a native environment: structure and function of membrane proteins in lipid bilayers by NMR. Chem Sci 2021; 12:14332-14342. [PMID: 34880983 PMCID: PMC8580007 DOI: 10.1039/d1sc02813h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/07/2021] [Indexed: 01/17/2023] Open
Abstract
Solid-state NMR (ssNMR) is a versatile technique that can be used for the characterization of various materials, ranging from small molecules to biological samples, including membrane proteins. ssNMR can probe both the structure and dynamics of membrane proteins, revealing protein function in a near-native lipid bilayer environment. The main limitation of the method is spectral resolution and sensitivity, however recent developments in ssNMR hardware, including the commercialization of 28 T magnets (1.2 GHz proton frequency) and ultrafast MAS spinning (<100 kHz) promise to accelerate acquisition, while reducing sample requirement, both of which are critical to membrane protein studies. Here, we review recent advances in ssNMR methodology used for structure determination of membrane proteins in native and mimetic environments, as well as the study of protein functions such as protein dynamics, and interactions with ligands, lipids and cholesterol.
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Affiliation(s)
- Kai Xue
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Kumar Tekwani Movellan
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Xizhou Cecily Zhang
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Eszter E Najbauer
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Marcel C Forster
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Stefan Becker
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Loren B Andreas
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
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25
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Agarwala PK, Aneja R, Kapoor S. Lipidomic landscape in cancer: Actionable insights for membrane-based therapy and diagnoses. Med Res Rev 2021; 42:983-1018. [PMID: 34719798 DOI: 10.1002/med.21868] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 08/18/2021] [Accepted: 10/24/2021] [Indexed: 01/17/2023]
Abstract
Cancer cells display altered cellular lipid metabolism, including disruption in endogenous lipid synthesis, storage, and exogenous uptake for membrane biogenesis and functions. Altered lipid metabolism and, consequently, lipid composition impacts cellular function by affecting membrane structure and properties, such as fluidity, rigidity, membrane dynamics, and lateral organization. Herein, we provide an overview of lipid membranes and how their properties affect cellular functions. We also detail how the rewiring of lipid metabolism impacts the lipidomic landscape of cancer cell membranes and influences the characteristics of cancer cells. Furthermore, we discuss how the altered cancer lipidome provides cues for developing lipid-inspired innovative therapeutic and diagnostic strategies while improving our limited understanding of the role of lipids in cancer initiation and progression. We also present the arcade of membrane characterization techniques to cement their relevance in cancer diagnosis and monitoring of treatment response.
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Affiliation(s)
- Prema K Agarwala
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Ritu Aneja
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India.,Depertment of Biofunctional Science and Technology, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
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26
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Pal S, Chattopadhyay A. Hydration Dynamics in Biological Membranes: Emerging Applications of Terahertz Spectroscopy. J Phys Chem Lett 2021; 12:9697-9709. [PMID: 34590862 DOI: 10.1021/acs.jpclett.1c02576] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Water drives the spontaneous self-assembly of lipids and proteins into quasi two-dimensional biological membranes that act as catalytic scaffolds for numerous processes central to life. However, the functional relevance of hydration in membrane biology is only beginning to be addressed, predominantly because of challenges associated with direct measurements of hydration microstructure and dynamics in a biological milieu. Our recent work on the novel interplay of membrane electrostatics and crowding in shaping membrane hydration dynamics utilizing terahertz (THz) spectroscopy represents an important step in this context. In this Perspective, we provide a glimpse into the ever-broadening functional landscape of hydration dynamics in biological membranes in the backdrop of the unique physical chemistry of water molecules. We further highlight the immense (and largely untapped) potential of the THz toolbox in addressing contemporary problems in membrane biology, while emphasizing the adaptability of the analytical framework reported recently by us to such studies.
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Affiliation(s)
- Sreetama Pal
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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27
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Catalano C, AL Mughram MH, Guo Y, Kellogg GE. 3D interaction homology: Hydropathic interaction environments of serine and cysteine are strikingly different and their roles adapt in membrane proteins. Curr Res Struct Biol 2021; 3:239-256. [PMID: 34693344 PMCID: PMC8517007 DOI: 10.1016/j.crstbi.2021.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/23/2021] [Accepted: 09/23/2021] [Indexed: 12/12/2022] Open
Abstract
Atomic-resolution protein structural models are prerequisites for many downstream activities like structure-function studies or structure-based drug discovery. Unfortunately, this data is often unavailable for some of the most interesting and therapeutically important proteins. Thus, computational tools for building native-like structural models from less-than-ideal experimental data are needed. To this end, interaction homology exploits the character, strength and loci of the sets of interactions that define a structure. Each residue type has its own limited set of backbone angle-dependent interaction motifs, as defined by their environments. In this work, we characterize the interactions of serine, cysteine and S-bridged cysteine in terms of 3D hydropathic environment maps. As a result, we explore several intriguing questions. Are the environments different between the isosteric serine and cysteine residues? Do some environments promote the formation of cystine S-S bonds? With the increasing availability of structural data for water-insoluble membrane proteins, are there environmental differences for these residues between soluble and membrane proteins? The environments surrounding serine and cysteine residues are dramatically different: serine residues are about 50% solvent exposed, while cysteines are only 10% exposed; the latter are more involved in hydrophobic interactions although there are backbone angle-dependent differences. Our analysis suggests that one driving force for -S-S- bond formation is a rather substantial increase in burial and hydrophobic interactions in cystines. Serine and cysteine become less and more, respectively, solvent-exposed in membrane proteins. 3D hydropathic environment maps are an evolving structure analysis tool showing promise as elements in a new protein structure prediction paradigm.
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Affiliation(s)
- Claudio Catalano
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Mohammed H. AL Mughram
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Youzhong Guo
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Glen E. Kellogg
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA
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28
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Şterbuleac D. Molecular dynamics: a powerful tool for studying the medicinal chemistry of ion channel modulators. RSC Med Chem 2021; 12:1503-1518. [PMID: 34671734 PMCID: PMC8459385 DOI: 10.1039/d1md00140j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 07/21/2021] [Indexed: 01/10/2023] Open
Abstract
Molecular dynamics (MD) simulations allow researchers to investigate the behavior of desired biological targets at ever-decreasing costs with ever-increasing precision. Among the biological macromolecules, ion channels are remarkable transmembrane proteins, capable of performing special biological processes and revealing a complex regulatory matrix, including modulation by small molecules, either endogenous or exogenous. Recently, given the developments in ion channel structure determination and accessibility of bio-computational techniques, MD and related tools are becoming increasingly popular in the intense research area regarding ligand-channel interactions. This review synthesizes and presents the most important fields of MD involvement in investigating channel-molecule interactions, including, but not limited to, deciphering the binding modes of ligands to their ion channel targets and the mechanisms through which chemical compounds exert their effect on channel function. Special attention is devoted to the importance of more elaborate methods, such as free energy calculations, while principles regarding drug design and discovery are highlighted. Several technical aspects involving the creation and simulation of channel-molecule MD systems (ligand parameterization, proper membrane setup, system building, etc.) are also presented.
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Affiliation(s)
- Daniel Şterbuleac
- Department of Health and Human Development, "Ştefan cel Mare" University of Suceava Str. Universităţii 13, 720229, E Building Suceava Romania
- Department of Forestry and Environmental Protection, "Ştefan cel Mare" University of Suceava Str. Universităţii 13, 720229, E Building Suceava Romania
- Integrated Center for Research, Development and Innovation in Advanced Materials, Nanotechnologies and Distributed Systems for Fabrication and Control (MANSiD), "Ştefan cel Mare" University of Suceava Str. Universităţii 13 720229 Suceava Romania
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29
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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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30
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Ferraz L, Sauer M, Sousa MJ, Branduardi P. The Plasma Membrane at the Cornerstone Between Flexibility and Adaptability: Implications for Saccharomyces cerevisiae as a Cell Factory. Front Microbiol 2021; 12:715891. [PMID: 34434179 PMCID: PMC8381377 DOI: 10.3389/fmicb.2021.715891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/19/2021] [Indexed: 11/23/2022] Open
Abstract
In the last decade, microbial-based biotechnological processes are paving the way toward sustainability as they implemented the use of renewable feedstocks. Nonetheless, the viability and competitiveness of these processes are often limited due to harsh conditions such as: the presence of feedstock-derived inhibitors including weak acids, non-uniform nature of the substrates, osmotic pressure, high temperature, extreme pH. These factors are detrimental for microbial cell factories as a whole, but more specifically the impact on the cell’s membrane is often overlooked. The plasma membrane is a complex system involved in major biological processes, including establishing and maintaining transmembrane gradients, controlling uptake and secretion, intercellular and intracellular communication, cell to cell recognition and cell’s physical protection. Therefore, when designing strategies for the development of versatile, robust and efficient cell factories ready to tackle the harshness of industrial processes while delivering high values of yield, titer and productivity, the plasma membrane has to be considered. Plasma membrane composition comprises diverse macromolecules and it is not constant, as cells adapt it according to the surrounding environment. Remarkably, membrane-specific traits are emerging properties of the system and therefore it is not trivial to predict which membrane composition is advantageous under certain conditions. This review includes an overview of membrane engineering strategies applied to Saccharomyces cerevisiae to enhance its fitness under industrially relevant conditions as well as strategies to increase microbial production of the metabolites of interest.
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Affiliation(s)
- Luís Ferraz
- Center of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
| | - Michael Sauer
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Maria João Sousa
- Center of Molecular and Environmental Biology, University of Minho, Braga, Portugal
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
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31
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Chiricozzi E. Plasma membrane glycosphingolipid signaling: a turning point. Glycoconj J 2021; 39:99-105. [PMID: 34398373 PMCID: PMC8979859 DOI: 10.1007/s10719-021-10008-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 06/16/2021] [Accepted: 06/25/2021] [Indexed: 11/29/2022]
Abstract
Plasma membrane interaction is highly recognized as an essential step to start the intracellular events in response to extracellular stimuli. The ways in which these interactions take place are less clear and detailed. Over the last decade my research has focused on developing the understanding of the glycosphingolipids-protein interaction that occurs at cell surface. By using chemical synthesis and biochemical approaches we have characterized some fundamental interactions that are key events both in the immune response and in the maintenance of neuronal homeostasis. In particular, for the first time it has been demonstrated that a glycolipid, present on the outer side of the membrane, the long-chain lactosylceramide, is able to directly modulate a cytosolic protein. But the real conceptual change was the demonstration that the GM1 oligosaccharide chain is able, alone, to replicate numerous functions of GM1 ganglioside and to directly interact with plasma membrane receptors by activating specific cellular signaling. In this conceptual shift, the development and application of multidisciplinary techniques in the field of biochemistry, from chemical synthesis to bioinformatic analysis, as well as discussions with several national and international colleagues have played a key role.
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Affiliation(s)
- Elena Chiricozzi
- Department of Medical Biotechnology and Translational Medicine, University of Milano, Milano, Italy.
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32
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Kim DH, Triet HM, Ryu SH. Regulation of EGFR activation and signaling by lipids on the plasma membrane. Prog Lipid Res 2021; 83:101115. [PMID: 34242725 DOI: 10.1016/j.plipres.2021.101115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/02/2021] [Accepted: 07/01/2021] [Indexed: 12/12/2022]
Abstract
Lipids on the plasma membrane are not only components of the membrane biophysical structures but also regulators of receptor functions. Recently, the critical roles of lipid-protein interactions have been intensively highlighted. Epidermal growth factor receptor (EGFR) is one of the most extensively studied receptors exhibiting various lipid interactions, including interactions with phosphatidylcholine, phosphatidylserine, phosphatidylinositol phosphate, cholesterol, gangliosides, and palmitate. Here, we review recent findings on how direct interaction with these lipids regulates EGFR activation and signaling, providing unprecedented insight into the comprehensive roles of various lipids in the control of EGFR functions. Finally, the current limitations in investigating lipid-protein interactions and novel technologies to potentially overcome these limitations are discussed.
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Affiliation(s)
- Do-Hyeon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Hong Minh Triet
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Sung Ho Ryu
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
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33
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Chen S, Dai X, Yang D, Dong B. Effects of sludge age on anaerobic acidification of waste activated sludge: Volatile fatty acids production and phosphorus release. J Environ Sci (China) 2021; 105:11-21. [PMID: 34130828 DOI: 10.1016/j.jes.2020.12.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 06/12/2023]
Abstract
Effects of sludge age on volatile fatty acids (VFAs) production and Phosphorus (P) release during anaerobic acidification of waste activated sludge (WAS) were investigated. Sequencing batch reactors (SBR) fed with simulating domestic sewage were applied to produce WAS of different sludge ages, and batch tests were used for anaerobic acidification. The maximum dissolved total organic carbon, release of PO43+-P, and accumulation of acetate (C2), propionate (C3), butyrate (C4), and valerate (C5) decreased by 56.2%, 55.8%, 52.6%, 43.7%, 82.4% and 84.8%, respectively, as the sludge age of WAS increased from 5 to 40 days. Limited degradation of protein played a dominating role in decreasing DTOC and VFAs production. Moreover, the increase in molecular weight of organics and organic nitrogen content in the supernatant after acidification suggested that the refractory protein in WAS increased as sludge age extended. Although the production of C2, C3, C4, and C5 from WAS decreased as the sludge age increased, the proportions of C2 and C3 in VFAs increased, which might be due to the declined production of C5 from protein and the faded genus Dechlorobacter. Keeping sludge age of WAS at a relatively low level (<10 days) is more appropriate for anaerobic acidification of WAS as internal carbon sources and P resource.
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Affiliation(s)
- Sisi Chen
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xiaohu Dai
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Dianhai Yang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Bin Dong
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
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34
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The Mystery of Red Blood Cells Extracellular Vesicles in Sleep Apnea with Metabolic Dysfunction. Int J Mol Sci 2021; 22:ijms22094301. [PMID: 33919065 PMCID: PMC8122484 DOI: 10.3390/ijms22094301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 12/12/2022] Open
Abstract
Sleep is very important for overall health and quality of life, while sleep disorder has been associated with several human diseases, namely cardiovascular, metabolic, cognitive, and cancer-related alterations. Obstructive sleep apnea (OSA) is the most common respiratory sleep-disordered breathing, which is caused by the recurrent collapse of the upper airway during sleep. OSA has emerged as a major public health problem and increasing evidence suggests that untreated OSA can lead to the development of various diseases including neurodegenerative diseases. In addition, OSA may lead to decreased blood oxygenation and fragmentation of the sleep cycle. The formation of free radicals or reactive oxygen species (ROS) can emerge and react with nitric oxide (NO) to produce peroxynitrite, thereby diminishing the bioavailability of NO. Hypoxia, the hallmark of OSA, refers to a decline of tissue oxygen saturation and affects several types of cells, playing cell-to-cell communication a vital role in the outcome of this interplay. Red blood cells (RBCs) are considered transporters of oxygen and nutrients to the tissues, and these RBCs are important interorgan communication systems with additional functions, including participation in the control of systemic NO metabolism, redox regulation, blood rheology, and viscosity. RBCs have been shown to induce endothelial dysfunction and increase cardiac injury. The mechanistic links between changes of RBC functional properties and cardiovascular are largely unknown. Extracellular vesicles (EVs) are secreted by most cell types and released in biological fluids both under physiological and pathological conditions. EVs are involved in intercellular communication by transferring complex cargoes including proteins, lipids, and nucleic acids from donor cells to recipient cells. Advancing our knowledge about mechanisms of RBC-EVs formation and their pathophysiological relevance may help to shed light on circulating EVs and to translate their application to clinical practice. We will focus on the potential use of RBC-EVs as valuable diagnostic and prognostic biomarkers and state-specific cargoes, and possibilities as therapeutic vehicles for drug and gene delivery. The use of RBC-EVs as a precision medicine for the diagnosis and treatment of the patient with sleep disorder will improve the prognosis and the quality of life in patients with cardiovascular disease (CVD).
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35
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Hongo Y, Kaida K, Komuta Y, Takazaki H, Yamazaki K, Suzuki K. Cholesterol-added antigens can enhance antiglycolipid antibody activity: Application to antibody testing. J Neuroimmunol 2021; 356:577580. [PMID: 33933819 DOI: 10.1016/j.jneuroim.2021.577580] [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: 03/16/2021] [Revised: 04/13/2021] [Accepted: 04/17/2021] [Indexed: 10/21/2022]
Abstract
We analysed the effect of adding cholesterol to glycolipid antigens on antibody activity with enzyme-linked immunosorbent assay in 123 subjects consisting of 96 patients with Guillain-Barré syndrome, 25 Miller Fisher syndrome, and two Bickerstaff brainstem encephalitis. The use of cholesterol-added GM1 antigens increased anti-GM1 activity in 11 out of 23 anti-GM1-positive patients and resulted in six out of 100 anti-GM1-negative patients becoming anti-GM1-positive. Enhancement of anti-GM1 activity by cholesterol addition was significantly associated with antecedent gastrointestinal infection. The use of cholesterol-added glycolipid antigens can increase the detection rate of anti-glycolipid antibodies and accurately evaluate the anti-glycolipid antibody activity in vivo.
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Affiliation(s)
- Yu Hongo
- Department of Neurology, National Defense Medical College, Tokorozawa, Japan
| | - Kenichi Kaida
- Department of Neurology, National Defense Medical College, Tokorozawa, Japan; Department of Neurology, Saitama Medical Center, Saitama Medical University, Kawagoe, Japan.
| | - Yukari Komuta
- Department of Neurology, National Defense Medical College, Tokorozawa, Japan
| | - Hiroshi Takazaki
- Department of Neurology, National Defense Medical College, Tokorozawa, Japan
| | - Keishi Yamazaki
- Department of Neurology, National Defense Medical College, Tokorozawa, Japan
| | - Kazushi Suzuki
- Department of Neurology, National Defense Medical College, Tokorozawa, Japan
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36
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Abstract
Glycosphingolipids are a structurally diverse class of lipids that regulate plasma membrane protein function. Rizzo et al (2021) now show that GOLPH3 promotes intra-Golgi transport of several enzymes that function at branching points of sphingolipid biosynthesis. By regulating the cellular sphingolipidome, GOLPH3 promotes growth factor signaling and cell proliferation, which may explain its oncogenic properties.
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Affiliation(s)
- Wilhelm Palm
- German Cancer Research Center (DKFZ), Heidelberg, Germany
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Moreno MJ, Teles Martins PA, Bernardino EF, Abel B, Ambudkar SV. Characterization of the Lipidome and Biophysical Properties of Membranes from High Five Insect Cells Expressing Mouse P-Glycoprotein. Biomolecules 2021; 11:biom11030426. [PMID: 33799403 PMCID: PMC8001469 DOI: 10.3390/biom11030426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 12/31/2022] Open
Abstract
The lipid composition of biomembranes influences the properties of the lipid bilayer and that of the proteins. In this study, the lipidome and the lipid/protein ratio of membranes from High Five™ insect cells overexpressing mouse P-glycoprotein was characterized. This provides a better understanding of the lipid environment in which P-glycoprotein is embedded, and thus of its functional and structural properties. The relative abundance of the distinct phospholipid classes and their acyl chain composition was characterized. A mass ratio of 0.57 ± 0.11 phospholipids to protein was obtained. Phosphatidylethanolamines are the most abundant phospholipids, followed by phosphatidylcholines. Membranes are also enriched in negatively charged lipids (phosphatidylserines, phosphatidylinositols and phosphatidylglycerols), and contain small amounts of sphingomyelins, ceramides and monoglycosilatedceramides. The most abundant acyl chains are monounsaturated, with significant amounts of saturated chains. The characterization of the phospholipids by HPLC-MS allowed identification of the combination of acyl chains, with palmitoyl-oleoyl being the most representative for all major phospholipid classes except for phosphatidylserines, which are mostly saturated. A mixture of POPE:POPC:POPS in the ratio 45:35:20 is proposed for the preparation of simple representative model membranes. The adequacy of the model membranes was further evaluated by characterizing their surface potential and fluidity.
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Affiliation(s)
- Maria João Moreno
- Coimbra Chemistry Center, Chemistry Department, FCTUC, University of Coimbra, 3004-535 Coimbra, Portugal; (P.A.T.M.); (E.F.B.)
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal
- Correspondence:
| | | | - Eva F. Bernardino
- Coimbra Chemistry Center, Chemistry Department, FCTUC, University of Coimbra, 3004-535 Coimbra, Portugal; (P.A.T.M.); (E.F.B.)
| | - Biebele Abel
- Laboratory of Cell Biology, CCR, National Cancer Institute, NIH, Bethesda, MD 20892, USA; (B.A.); (S.V.A.)
| | - Suresh V. Ambudkar
- Laboratory of Cell Biology, CCR, National Cancer Institute, NIH, Bethesda, MD 20892, USA; (B.A.); (S.V.A.)
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Winterstein LM, Kukovetz K, Hansen UP, Schroeder I, Van Etten JL, Moroni A, Thiel G, Rauh O. Distinct lipid bilayer compositions have general and protein-specific effects on K+ channel function. J Gen Physiol 2021; 153:211677. [PMID: 33439243 PMCID: PMC7809880 DOI: 10.1085/jgp.202012731] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/08/2020] [Indexed: 12/17/2022] Open
Abstract
It has become increasingly apparent that the lipid composition of cell membranes affects the function of transmembrane proteins such as ion channels. Here, we leverage the structural and functional diversity of small viral K+ channels to systematically examine the impact of bilayer composition on the pore module of single K+ channels. In vitro–synthesized channels were reconstituted into phosphatidylcholine bilayers ± cholesterol or anionic phospholipids (aPLs). Single-channel recordings revealed that a saturating concentration of 30% cholesterol had only minor and protein-specific effects on unitary conductance and gating. This indicates that channels have effective strategies for avoiding structural impacts of hydrophobic mismatches between proteins and the surrounding bilayer. In all seven channels tested, aPLs augmented the unitary conductance, suggesting that this is a general effect of negatively charged phospholipids on channel function. For one channel, we determined an effective half-maximal concentration of 15% phosphatidylserine, a value within the physiological range of aPL concentrations. The different sensitivity of two channel proteins to aPLs could be explained by the presence/absence of cationic amino acids at the interface between the lipid headgroups and the transmembrane domains. aPLs also affected gating in some channels, indicating that conductance and gating are uncoupled phenomena and that the impact of aPLs on gating is protein specific. In two channels, the latter can be explained by the altered orientation of the pore-lining transmembrane helix that prevents flipping of a phenylalanine side chain into the ion permeation pathway for long channel closings. Experiments with asymmetrical bilayers showed that this effect is leaflet specific and most effective in the inner leaflet, in which aPLs are normally present in plasma membranes. The data underscore a general positive effect of aPLs on the conductance of K+ channels and a potential interaction of their negative headgroup with cationic amino acids in their vicinity.
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Affiliation(s)
| | - Kerri Kukovetz
- Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Ulf-Peter Hansen
- Department of Structural Biology, Christian-Albrechts-Universität, Kiel, Germany
| | - Indra Schroeder
- Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - James L Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska Lincoln, Lincoln, NE
| | - Anna Moroni
- Department of Biosciences and Consiglio Nazionale delle Ricerche, Istituto di Biofisica Milano, Università degli Studi di Milano, Milano, Italy
| | - Gerhard Thiel
- Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Oliver Rauh
- Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
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Abstract
Glycosphingolipids are amphiphilic plasma membrane components formed by a glycan linked to a specific lipid moiety. In this chapter we report on these compounds, on their role played in our cells to maintain the correct cell biology.In detail, we report on their structure, on their metabolic processes, on their interaction with proteins and from this, their property to modulate positively in health and negatively in disease, the cell signaling and cell biology.
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Adigun OA, Nadeem M, Pham TH, Jewell LE, Cheema M, Thomas R. Recent advances in bio-chemical, molecular and physiological aspects of membrane lipid derivatives in plant pathology. PLANT, CELL & ENVIRONMENT 2021; 44:1-16. [PMID: 33034375 DOI: 10.1111/pce.13904] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 09/22/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
Plant pathogens pose a significant threat to the food industry and food security accounting for 10-40% crop losses annually on a global scale. Economic losses from plant diseases are estimated at $300B for major food crops and are associated with reduced food availability and accessibility and also high food costs. Although strategies exist to reduce the impact of diseases in plants, many of these introduce harmful chemicals to our food chain. Therefore, it is important to understand and utilize plants' immune systems to control plant pathogens to enable more sustainable agriculture. Lipids are core components of cell membranes and as such are part of the first line of defense against pathogen attack. Recent developments in omics technologies have advanced our understanding of how plant membrane lipid biosynthesis, remodelling and/or signalling modulate plant responses to infection. Currently, there is limited information available in the scientific literature concerning lipid signalling targets and their biochemical and physiological consequences in response to plant pathogens. This review focusses on the functions of membrane lipid derivatives and their involvement in plant responses to pathogens as biotic stressors. We describe major plant defense systems including systemic-acquired resistance, basal resistance, hypersensitivity and the gene-for-gene concept in this context.
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Affiliation(s)
- Oludoyin Adeseun Adigun
- School of Science and the Environment/Boreal Ecosystem Research Facility, Memorial University of Newfoundland, Corner Brook, Newfoundland and Labrador, A2H5G4, Canada
| | - Muhammad Nadeem
- School of Science and the Environment/Boreal Ecosystem Research Facility, Memorial University of Newfoundland, Corner Brook, Newfoundland and Labrador, A2H5G4, Canada
| | - Thu Huong Pham
- School of Science and the Environment/Boreal Ecosystem Research Facility, Memorial University of Newfoundland, Corner Brook, Newfoundland and Labrador, A2H5G4, Canada
| | - Linda Elizabeth Jewell
- St. John's Research and Development Centre, Agriculture and Agri-Food Canada, 204 Brookfield Rd, St. John's, Newfoundland and Labrador, A1E 6J5, Canada
| | - Mumtaz Cheema
- School of Science and the Environment/Boreal Ecosystem Research Facility, Memorial University of Newfoundland, Corner Brook, Newfoundland and Labrador, A2H5G4, Canada
| | - Raymond Thomas
- School of Science and the Environment/Boreal Ecosystem Research Facility, Memorial University of Newfoundland, Corner Brook, Newfoundland and Labrador, A2H5G4, Canada
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Fake It 'Till You Make It-The Pursuit of Suitable Membrane Mimetics for Membrane Protein Biophysics. Int J Mol Sci 2020; 22:ijms22010050. [PMID: 33374526 PMCID: PMC7793082 DOI: 10.3390/ijms22010050] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 12/13/2022] Open
Abstract
Membrane proteins evolved to reside in the hydrophobic lipid bilayers of cellular membranes. Therefore, membrane proteins bridge the different aqueous compartments separated by the membrane, and furthermore, dynamically interact with their surrounding lipid environment. The latter not only stabilizes membrane proteins, but directly impacts their folding, structure and function. In order to be characterized with biophysical and structural biological methods, membrane proteins are typically extracted and subsequently purified from their native lipid environment. This approach requires that lipid membranes are replaced by suitable surrogates, which ideally closely mimic the native bilayer, in order to maintain the membrane proteins structural and functional integrity. In this review, we survey the currently available membrane mimetic environments ranging from detergent micelles to bicelles, nanodiscs, lipidic-cubic phase (LCP), liposomes, and polymersomes. We discuss their respective advantages and disadvantages as well as their suitability for downstream biophysical and structural characterization. Finally, we take a look at ongoing methodological developments, which aim for direct in-situ characterization of membrane proteins within native membranes instead of relying on membrane mimetics.
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Influenza A H1 and H3 Transmembrane Domains Interact Differently with Each Other and with Surrounding Membrane Lipids. Viruses 2020; 12:v12121461. [PMID: 33348831 PMCID: PMC7765950 DOI: 10.3390/v12121461] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023] Open
Abstract
Hemagglutinin (HA) is a class I viral membrane fusion protein, which is the most abundant transmembrane protein on the surface of influenza A virus (IAV) particles. HA plays a crucial role in the recognition of the host cell, fusion of the viral envelope and the host cell membrane, and is the major antigen in the immune response during the infection. Mature HA organizes in homotrimers consisting of a sequentially highly variable globular head and a relatively conserved stalk region. Every HA monomer comprises a hydrophilic ectodomain, a pre-transmembrane domain (pre-TMD), a hydrophobic transmembrane domain (TMD), and a cytoplasmic tail (CT). In recent years the effect of the pre-TMD and TMD on the structure and function of HA has drawn some attention. Using bioinformatic tools we analyzed all available full-length amino acid sequences of HA from 16 subtypes across various host species. We calculated several physico-chemical parameters of HA pre-TMDs and TMDs including accessible surface area (ASA), average hydrophobicity (Hav), and the hydrophobic moment (µH). Our data suggests that distinct differences in these parameters between the two major phylogenetic groups, represented by H1 and H3 subtypes, could have profound effects on protein–lipid interactions, trimer formation, and the overall HA ectodomain orientation and antigen exposure.
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Miyamura H, Bergman RG, Raymond KN, Toste FD. Heterogeneous Supramolecular Catalysis through Immobilization of Anionic M4L6 Assemblies on Cationic Polymers. J Am Chem Soc 2020; 142:19327-19338. [DOI: 10.1021/jacs.0c09556] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hiroyuki Miyamura
- Chemical Sciences Division, Lawrence Berkeley National Laboratory and Department of Chemistry, University of California—Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Robert G. Bergman
- Chemical Sciences Division, Lawrence Berkeley National Laboratory and Department of Chemistry, University of California—Berkeley, Berkeley, California 94720, United States
| | - Kenneth N. Raymond
- Chemical Sciences Division, Lawrence Berkeley National Laboratory and Department of Chemistry, University of California—Berkeley, Berkeley, California 94720, United States
| | - F. Dean Toste
- Chemical Sciences Division, Lawrence Berkeley National Laboratory and Department of Chemistry, University of California—Berkeley, Berkeley, California 94720, United States
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45
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Zapata-Morin PA, Sierra-Valdez FJ, Ruiz-Suárez JC. The cut-off effect of n-alcohols in lipid rafts: A lipid-dependent phenomenon ☆. J Mol Graph Model 2020; 101:107732. [PMID: 32920240 DOI: 10.1016/j.jmgm.2020.107732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 10/23/2022]
Abstract
n-Aliphatic alcohols act as anesthetics only up to a certain chain length, beyond which its biological activity disappears. This is known as the 'cut-off' phenomenon. Although the most accepted explanation is based on action sites in membrane proteins, it is not well understood why alcohols alter their functions. The structural dependence of these protein receptors to lipid domains known as 'lipid rafts', suggests a new approach to tackle the puzzling phenomenon. In this work, by performing molecular dynamic simulations (MDS) to explore the lipid role, we provide relevant molecular details about the membrane-alcohol interaction at the cut-off point regime. Since the high variability of the cut-off points found on protein receptors in neurons may be a consequence of differences in the lipid composition surrounding such proteins, our results could have a clear-cut importance.
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Affiliation(s)
- Patricio A Zapata-Morin
- Facultad de Ciencias Biológicas, Laboratorio de Micología y Fitopatología, Universidad Autónoma de Nuevo León, San Nicolás de Los Garza, Nuevo León, 66455, Mexico
| | - F J Sierra-Valdez
- Centro de Investigación Biomédica, Hospital Zambrano Hellion, TecSalud, Ave. Batallón de San Patricio 112, San Pedro Garza García, 66278, Nuevo León, Mexico; Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. Eugenio Garza Sada 2501 Sur, Monterrey, Nuevo León, 64849, Mexico
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46
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Gutmann T, Schäfer IB, Poojari C, Brankatschk B, Vattulainen I, Strauss M, Coskun Ü. Cryo-EM structure of the complete and ligand-saturated insulin receptor ectodomain. J Cell Biol 2020; 219:jcb.201907210. [PMID: 31727777 PMCID: PMC7039211 DOI: 10.1083/jcb.201907210] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/19/2019] [Accepted: 10/20/2019] [Indexed: 12/20/2022] Open
Abstract
Glucose homeostasis and growth essentially depend on the hormone insulin engaging its receptor. Despite biochemical and structural advances, a fundamental contradiction has persisted in the current understanding of insulin ligand-receptor interactions. While biochemistry predicts two distinct insulin binding sites, 1 and 2, recent structural analyses have resolved only site 1. Using a combined approach of cryo-EM and atomistic molecular dynamics simulation, we present the structure of the entire dimeric insulin receptor ectodomain saturated with four insulin molecules. Complementing the previously described insulin-site 1 interaction, we present the first view of insulin bound to the discrete insulin receptor site 2. Insulin binding stabilizes the receptor ectodomain in a T-shaped conformation wherein the membrane-proximal domains converge and contact each other. These findings expand the current models of insulin binding to its receptor and of its regulation. In summary, we provide the structural basis for a comprehensive description of ligand-receptor interactions that ultimately will inform new approaches to structure-based drug design.
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Affiliation(s)
- Theresia Gutmann
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum Munich at the University Hospital and Faculty of Medicine Carl Gustav Carus of Technische Universität Dresden, Dresden, Germany.,German Center for Diabetes Research, Neuherberg, Germany
| | - Ingmar B Schäfer
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany
| | - Chetan Poojari
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Beate Brankatschk
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum Munich at the University Hospital and Faculty of Medicine Carl Gustav Carus of Technische Universität Dresden, Dresden, Germany.,German Center for Diabetes Research, Neuherberg, Germany
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, Helsinki, Finland.,Computational Physics Laboratory, Tampere University, Tampere, Finland
| | - Mike Strauss
- Department of Anatomy & Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Ünal Coskun
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum Munich at the University Hospital and Faculty of Medicine Carl Gustav Carus of Technische Universität Dresden, Dresden, Germany.,German Center for Diabetes Research, Neuherberg, Germany
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47
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Paredes SD, Kim S, Rooney MT, Greenwood AI, Hristova K, Cotten ML. Enhancing the membrane activity of Piscidin 1 through peptide metallation and the presence of oxidized lipid species: Implications for the unification of host defense mechanisms at lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183236. [DOI: 10.1016/j.bbamem.2020.183236] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/14/2020] [Accepted: 02/25/2020] [Indexed: 12/12/2022]
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Sämfors S, Fletcher JS. Lipid Diversity in Cells and Tissue Using Imaging SIMS. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:249-271. [PMID: 32212820 DOI: 10.1146/annurev-anchem-091619-103512] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Lipids are an important class of biomolecules with many roles within cells and tissue. As targets for study, they present several challenges. They are difficult to label, as many labels lack the specificity to the many different lipid species or the labels maybe larger than the lipids themselves, thus severely perturbing the natural chemical environment. Mass spectrometry provides exceptional specificity and is often used to examine lipid extracts from different samples. However, spatial information is lost during extraction. Of the different imaging mass spectrometry methods available, secondary ion mass spectrometry (SIMS) is unique in its ability to analyze very small features, with probe sizes <50 nm available. It also offers high surface sensitivity and 3D imaging capability on a subcellular scale. This article reviews the current capabilities and some remaining challenges associated with imaging the diverse lipids present in cell and tissue samples. We show how the technique has moved beyond show-and-tell, proof-of-principle analysis and is now being used to address real biological challenges. These include imaging the microenvironment of cancer tumors, probing the pathophysiology of traumatic brain injury, or tracking the lipid composition through bacterial membranes.
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Affiliation(s)
- Sanna Sämfors
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41296 Gothenburg, Sweden;
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - John S Fletcher
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41296 Gothenburg, Sweden;
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49
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Llorente García I, Marsh M. A biophysical perspective on receptor-mediated virus entry with a focus on HIV. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2020; 1862:183158. [PMID: 31863725 PMCID: PMC7156917 DOI: 10.1016/j.bbamem.2019.183158] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 12/14/2022]
Abstract
As part of their entry and infection strategy, viruses interact with specific receptor molecules expressed on the surface of target cells. The efficiency and kinetics of the virus-receptor interactions required for a virus to productively infect a cell is determined by the biophysical properties of the receptors, which are in turn influenced by the receptors' plasma membrane (PM) environments. Currently, little is known about the biophysical properties of these receptor molecules or their engagement during virus binding and entry. Here we review virus-receptor interactions focusing on the human immunodeficiency virus type 1 (HIV), the etiological agent of acquired immunodeficiency syndrome (AIDS), as a model system. HIV is one of the best characterised enveloped viruses, with the identity, roles and structure of the key molecules required for infection well established. We review current knowledge of receptor-mediated HIV entry, addressing the properties of the HIV cell-surface receptors, the techniques used to measure these properties, and the macromolecular interactions and events required for virus entry. We discuss some of the key biophysical principles underlying receptor-mediated virus entry and attempt to interpret the available data in the context of biophysical mechanisms. We also highlight crucial outstanding questions and consider how new tools might be applied to advance understanding of the biophysical properties of viral receptors and the dynamic events leading to virus entry.
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Affiliation(s)
| | - Mark Marsh
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
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50
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Seena S, Sobral O, Cano A. Metabolomic, functional, and ecologic responses of the common freshwater fungus Neonectria lugdunensis to mine drainage stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 718:137359. [PMID: 32092520 DOI: 10.1016/j.scitotenv.2020.137359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 06/10/2023]
Abstract
Metal contamination of watersheds is a global problem. Here, we conducted litter decomposition studies with Neonectria lugdunensis, a cosmopolitan aquatic fungus. Fungal isolates from four reference (non-impacted) and six metal-contaminated streams (due to mine drainage) were exposed to mine drainage and reference stream waters in Central Portugal. Impact of mine drainage waters on N. lugdunensis hyphae was investigated by performing metabolomic profiling of 200 lipids and 25 amino acids (AA) with ultra-high performance liquid chromatography-mass spectrometry. In parallel, functional response of N. lugdunensis isolates was assessed through expression profiles of a functional gene, cellobiohydrolase I (CbhI). Ecological performance via leaf mass loss was also determined. Exposure to mine drainage waters altered the concentration of numerous AA and lipids. Most strikingly, a gradual increase in the concentration of the triacylglycerols (TAG) with shorter acyl chains and lesser unsaturation was observed after the exposure to mine drainage waters. In addition, the changes in the concentration of numerous TAG, lysophosphatidylcholines, and AA were more significant in the isolates from the metal-contaminated streams after exposure to mine drainage water. CbhI gene of the isolates from reference streams was down-regulated by metal stress, while those from metal-contaminated streams remained unaffected. Finally, leaf mass loss was influenced by both exposure to mine drainage waters and the origin of isolates. Overall, our study demonstrates unique functional signatures displayed by fungi under metal stress and the relevant role that fungal AA and lipids play to cope with metal toxicity.
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Affiliation(s)
- Sahadevan Seena
- MARE - Marine and Environmental Sciences Centre, University of Coimbra, PT-3004-517 Coimbra, Portugal; CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Olímpia Sobral
- MARE - Marine and Environmental Sciences Centre, University of Coimbra, PT-3004-517 Coimbra, Portugal; CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Ainara Cano
- ONE WAY LIVER, S.L., Parque Tecnológico de Bizkaia, edif.502- plta 0, 48160 Derio, Bizkaia, Spain
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