151
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Cino EA, Borbuliak M, Hu S, Tieleman DP. Lipid distributions and transleaflet cholesterol migration near heterogeneous surfaces in asymmetric bilayers. Faraday Discuss 2021; 232:103-113. [PMID: 34549760 DOI: 10.1039/d1fd00003a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Specific and nonspecific protein-lipid interactions in cell membranes have important roles in an abundance of biological functions. We have used coarse-grained (CG) molecular dynamics (MD) simulations to assess lipid distributions and cholesterol flipping dynamics around surfaces in a model asymmetric plasma membrane containing one of six structurally distinct entities: aquaporin-1 (AQP1), the bacterial β-barrel outer membrane proteins OmpF and OmpX, the KcsA potassium channel, the WALP23 peptide and a carbon nanotube (CNT). Our findings revealed varied lipid partitioning and cholesterol flipping times around the different solutes and putative cholesterol binding sites in AQP1 and KcsA. The results suggest that protein-lipid interactions can be highly variable, and that surface-dependent lipid profiles are effectively manifested in CG simulations with the Martini force field.
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Affiliation(s)
- Elio A Cino
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada. .,Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Mariia Borbuliak
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada.
| | - Shangnong Hu
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada.
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada.
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152
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Shi J, Hyman AJ, De Vecchis D, Chong J, Lichtenstein L, Futers TS, Rouahi M, Salvayre AN, Auge N, Kalli AC, Beech DJ. Sphingomyelinase Disables Inactivation in Endogenous PIEZO1 Channels. Cell Rep 2021; 33:108225. [PMID: 33027663 PMCID: PMC7539531 DOI: 10.1016/j.celrep.2020.108225] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/30/2020] [Accepted: 09/11/2020] [Indexed: 11/29/2022] Open
Abstract
Endogenous PIEZO1 channels of native endothelium lack the hallmark inactivation often seen when these channels are overexpressed in cell lines. Because prior work showed that the force of shear stress activates sphingomyelinase in endothelium, we considered if sphingomyelinase is relevant to endogenous PIEZO1. Patch clamping was used to quantify PIEZO1-mediated signals in freshly isolated murine endothelium exposed to the mechanical forces caused by shear stress and membrane stretch. Neutral sphingomyelinase inhibitors and genetic disruption of sphingomyelin phosphodiesterase 3 (SMPD3) cause PIEZO1 to switch to profoundly inactivating behavior. Ceramide (a key product of SMPD3) rescues non-inactivating channel behavior. Its co-product, phosphoryl choline, has no effect. In contrast to ceramide, sphingomyelin (the SMPD3 substrate) does not affect inactivation but alters channel force sensitivity. The data suggest that sphingomyelinase activity, ceramide, and sphingomyelin are determinants of native PIEZO gating that enable sustained activity. SMPD3 sphingomyelinase enables long-lasting PIEZO1 activity in response to force Ceramide, a key lipid product of SMPD3, promotes long-lasting activity Sphingomyelin, the SMPD3 substrate, does not affect the duration of activity Sphingomyelin alters PIEZO1 force sensitivity
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Affiliation(s)
- Jian Shi
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds LS2 9JT, UK.
| | - Adam J Hyman
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Dario De Vecchis
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Jiehan Chong
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Laeticia Lichtenstein
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - T Simon Futers
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Myriam Rouahi
- INSERM U-1048 and Université Paul Sabatier, 31432 Cedex 4 Toulouse, France
| | | | - Nathalie Auge
- INSERM U-1048 and Université Paul Sabatier, 31432 Cedex 4 Toulouse, France
| | - Antreas C Kalli
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - David J Beech
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds LS2 9JT, UK.
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153
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Hancock AM, Son M, Nairat M, Wei T, Jeuken LJC, Duffy CDP, Schlau-Cohen GS, Adams PG. Ultrafast energy transfer between lipid-linked chromophores and plant light-harvesting complex II. Phys Chem Chem Phys 2021; 23:19511-19524. [PMID: 34524278 PMCID: PMC8442836 DOI: 10.1039/d1cp01628h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Light-Harvesting Complex II (LHCII) is a membrane protein found in plant chloroplasts that has the crucial role of absorbing solar energy and subsequently performing excitation energy transfer to the reaction centre subunits of Photosystem II. LHCII provides strong absorption of blue and red light, however, it has minimal absorption in the green spectral region where solar irradiance is maximal. In a recent proof-of-principle study, we enhanced the absorption in this spectral range by developing a biohybrid system where LHCII proteins together with lipid-linked Texas Red (TR) chromophores were assembled into lipid membrane vesicles. The utility of these systems was limited by significant LHCII quenching due to protein-protein interactions and heterogeneous lipid structures. Here, we organise TR and LHCII into a lipid nanodisc, which provides a homogeneous, well-controlled platform to study the interactions between TR molecules and single LHCII complexes. Fluorescence spectroscopy determined that TR-to-LHCII energy transfer has an efficiency of at least 60%, resulting in a 262% enhancement of LHCII fluorescence in the 525-625 nm range, two-fold greater than in the previous system. Ultrafast transient absorption spectroscopy revealed two time constants of 3.7 and 128 ps for TR-to-LHCII energy transfer. Structural modelling and theoretical calculations indicate that these timescales correspond to TR-lipids that are loosely- or tightly-associated with the protein, respectively, with estimated TR-to-LHCII separations of ∼3.5 nm and ∼1 nm. Overall, we demonstrate that a nanodisc-based biohybrid system provides an idealised platform to explore the photophysical interactions between extrinsic chromophores and membrane proteins with potential applications in understanding more complex natural or artificial photosynthetic systems.
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Affiliation(s)
- Ashley M Hancock
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Minjung Son
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA.
| | - Muath Nairat
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA.
| | - Tiejun Wei
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Lars J C Jeuken
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.,Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Leiden Institute of Chemistry, Leiden University, 2300 RA Leiden, The Netherlands
| | - Christopher D P Duffy
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Gabriela S Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA.
| | - Peter G Adams
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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154
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Smirnov MA, Tolmachev DA, Glova AD, Sokolova MP, Geydt PV, Lukasheva NV, Lyulin SV. Combined Use of Atomic Force Microscopy and Molecular Dynamics in the Study of Biopolymer Systems. POLYMER SCIENCE SERIES C 2021. [DOI: 10.1134/s1811238221020089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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155
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Brzezinski P, Moe A, Ädelroth P. Structure and Mechanism of Respiratory III-IV Supercomplexes in Bioenergetic Membranes. Chem Rev 2021; 121:9644-9673. [PMID: 34184881 PMCID: PMC8361435 DOI: 10.1021/acs.chemrev.1c00140] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Indexed: 12/12/2022]
Abstract
In the final steps of energy conservation in aerobic organisms, free energy from electron transfer through the respiratory chain is transduced into a proton electrochemical gradient across a membrane. In mitochondria and many bacteria, reduction of the dioxygen electron acceptor is catalyzed by cytochrome c oxidase (complex IV), which receives electrons from cytochrome bc1 (complex III), via membrane-bound or water-soluble cytochrome c. These complexes function independently, but in many organisms they associate to form supercomplexes. Here, we review the structural features and the functional significance of the nonobligate III2IV1/2 Saccharomyces cerevisiae mitochondrial supercomplex as well as the obligate III2IV2 supercomplex from actinobacteria. The analysis is centered around the Q-cycle of complex III, proton uptake by CytcO, as well as mechanistic and structural solutions to the electronic link between complexes III and IV.
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Affiliation(s)
- Peter Brzezinski
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Agnes Moe
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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156
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Ernst M, Robertson JL. The Role of the Membrane in Transporter Folding and Activity. J Mol Biol 2021; 433:167103. [PMID: 34139219 PMCID: PMC8756397 DOI: 10.1016/j.jmb.2021.167103] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/23/2022]
Abstract
The synthesis, folding, and function of membrane transport proteins are critical factors for defining cellular physiology. Since the stability of these proteins evolved amidst the lipid bilayer, it is no surprise that we are finding that many of these membrane proteins demonstrate coupling of their structure or activity in some way to the membrane. More and more transporter structures are being determined with some information about the surrounding membrane, and computational modeling is providing further molecular details about these solvation structures. Thus, the field is moving towards identifying which molecular mechanisms - lipid interactions, membrane perturbations, differential solvation, and bulk membrane effects - are involved in linking membrane energetics to transporter stability and function. In this review, we present an overview of these mechanisms and the growing evidence that the lipid bilayer is a major determinant of the fold, form, and function of membrane transport proteins in membranes.
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Affiliation(s)
- Melanie Ernst
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Janice L Robertson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
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157
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Weigle AT, Carr M, Shukla D. Impact of Increased Membrane Realism on Conformational Sampling of Proteins. J Chem Theory Comput 2021; 17:5342-5357. [PMID: 34339605 DOI: 10.1021/acs.jctc.1c00276] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The realism and accuracy of lipid bilayer simulations through molecular dynamics (MD) are heavily dependent on the lipid composition. While the field is pushing toward implementing more heterogeneous and realistic membrane compositions, a lack of high-resolution lipidomic data prevents some membrane protein systems from being modeled with the highest level of realism. Given the additional diversity of real-world cellular membranes and protein-lipid interactions, it is still not fully understood how altering membrane complexity affects modeled membrane protein functions or if it matters over long-timescale simulations. This is especially true for organisms whose membrane environments have little to no computational study, such as the plant plasma membrane. Tackling these issues in tandem, a generalized, realistic, and asymmetric plant plasma membrane with more than 10 different lipid species is constructed herein. Classical MD simulations of pure membrane constructs were performed to evaluate how altering the compositional complexity of the membrane impacted the plant membrane properties. The apo form of a plant sugar transporter, OsSWEET2b, was inserted into membrane models where lipid diversity was calculated in either a size-dependent or size-independent manner. An adaptive sampling simulation regime validated by Markov-state models was performed to capture the gating dynamics of OsSWEET2b in each of these membrane constructs. In comparison to previous OsSWEET2b simulations performed in a pure POPC bilayer, we confirm that simulations performed within a native-like membrane composition alter the stabilization of apo OsSWEET2b conformational states by ∼1 kcal/mol. The free-energy barriers of intermediate conformational states decrease when realistic membrane complexity is simplified, albeit roughly within sampling error, suggesting that protein-specific responses to membranes differ due to altered packing caused by compositional fluctuations. This work serves as a case study where a more realistic bilayer composition makes unbiased conformational sampling easier to achieve than with simplified bilayers.
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Affiliation(s)
- Austin T Weigle
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Matthew Carr
- Independent Software Development Provider310 East Marlette Avenue, Phoenix, Arizona 85012, United States
| | - Diwakar Shukla
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Center for Digital Agriculture, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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158
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Paré P, Reales G, Paixão-Côrtes VR, Vargas-Pinilla P, Viscardi LH, Fam B, Pissinatti A, Santos FR, Bortolini MC. Molecular evolutionary insights from PRLR in mammals. Gen Comp Endocrinol 2021; 309:113791. [PMID: 33872604 DOI: 10.1016/j.ygcen.2021.113791] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/02/2021] [Accepted: 04/13/2021] [Indexed: 12/12/2022]
Abstract
Prolactin (PRL) is a pleiotropic neurohormone secreted by the mammalian pituitary gland into the blood, thus reaching many tissues and organs beyond the brain. PRL binds to its receptor, PRLR, eliciting a molecular signaling cascade. This system modulates essential mammalian behaviors and promotes notable modifications in the reproductive female tissues and organs. Here, we explore how the intracellular domain of PRLR (PRLR-ICD) modulates the expression of the PRLR gene. Despite differences in the reproductive strategies between eutherian and metatherian mammals, there is no clear distinction between PRLR-ICD functional motifs. However, we found selection signatures that showed differences between groups, with many conserved functional elements strongly maintained through purifying selection across the class Mammalia. We observed a few residues under relaxed selection, the levels of which were more pronounced in Eutheria and particularly striking in primates (Simiiformes), which could represent a pre-adaptive genetic element protected from purifying selection. Alternative, new motifs, such as YLDP (318-321) and others with residues Y283 and Y290, may already be functional. These motifs would have been co-opted in primates as part of a complex genetic repertoire related to some derived adaptive phenotypes, but these changes would have no impact on the primordial functions that characterize the mammals as a whole and that are related to the PRL-PRLR system.
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Affiliation(s)
- Pamela Paré
- Laboratório de Evolução Humana e Molecular, Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Guillermo Reales
- Laboratório de Evolução Humana e Molecular, Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Vanessa R Paixão-Côrtes
- Laboratório de Biologia Evolutiva e Genômica (LABEG), Programa de Pós-Graduação em Biodiversidade e Evolução, Instituto de Biologia, Universidade Federal da Bahia (UFBA), Salvador, BA, Brazil
| | - Pedro Vargas-Pinilla
- Laboratório de Evolução Humana e Molecular, Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Faculdade de Medicina de Ribeirão Preto, Departamento de Bioquímica e Imunologia, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Lucas Henriques Viscardi
- Laboratório de Evolução Humana e Molecular, Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Bibiana Fam
- Laboratório de Evolução Humana e Molecular, Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | | | - Fabrício R Santos
- Laboratório de Biodiversidade e Evolução Molecular, Departamento de Genética, Ecologia e Evolução da Universidade Federal de Minas Gerais (UFMG), Belo-Horizonte, MG, Brazil.
| | - Maria Cátira Bortolini
- Laboratório de Evolução Humana e Molecular, Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
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159
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Corey RA, Song W, Duncan AL, Ansell TB, Sansom MSP, Stansfeld PJ. Identification and assessment of cardiolipin interactions with E. coli inner membrane proteins. SCIENCE ADVANCES 2021; 7:eabh2217. [PMID: 34417182 PMCID: PMC8378812 DOI: 10.1126/sciadv.abh2217] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/30/2021] [Indexed: 05/03/2023]
Abstract
Integral membrane proteins are localized and/or regulated by lipids present in the surrounding bilayer. While bacteria have relatively simple membranes, there is ample evidence that many bacterial proteins bind to specific lipids, especially the anionic lipid cardiolipin. Here, we apply molecular dynamics simulations to assess lipid binding to 42 different Escherichia coli inner membrane proteins. Our data reveal an asymmetry between the membrane leaflets, with increased anionic lipid binding to the inner leaflet regions of the proteins, particularly for cardiolipin. From our simulations, we identify >700 independent cardiolipin binding sites, allowing us to identify the molecular basis of a prototypical cardiolipin binding site, which we validate against structures of bacterial proteins bound to cardiolipin. This allows us to construct a set of metrics for defining a high-affinity cardiolipin binding site on bacterial membrane proteins, paving the way for a heuristic approach to defining other protein-lipid interactions.
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Affiliation(s)
- Robin A Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Wanling Song
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - T Bertie Ansell
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
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160
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Urbančič I, Schiffelers L, Jenkins E, Gong W, Santos AM, Schneider F, O'Brien-Ball C, Vuong MT, Ashman N, Sezgin E, Eggeling C. Aggregation and mobility of membrane proteins interplay with local lipid order in the plasma membrane of T cells. FEBS Lett 2021; 595:2127-2146. [PMID: 34160065 DOI: 10.1002/1873-3468.14153] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/07/2021] [Accepted: 06/18/2021] [Indexed: 01/17/2023]
Abstract
To disentangle the elusive lipid-protein interactions in T-cell activation, we investigate how externally imposed variations in mobility of key membrane proteins (T-cell receptor [TCR], kinase Lck, and phosphatase CD45) affect the local lipid order and protein colocalisation. Using spectral imaging with polarity-sensitive membrane probes in model membranes and live Jurkat T cells, we find that partial immobilisation of proteins (including TCR) by aggregation or ligand binding changes their preference towards a more ordered lipid environment, which can recruit Lck. Our data suggest that the cellular membrane is poised to modulate the frequency of protein encounters upon alterations of their mobility, for example in ligand binding, which offers new mechanistic insight into the involvement of lipid-mediated interactions in membrane-hosted signalling events.
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Affiliation(s)
- Iztok Urbančič
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
- Jožef Stefan Institute, Ljubljana, Slovenia
| | - Lisa Schiffelers
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Edward Jenkins
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Weijian Gong
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Ana Mafalda Santos
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Falk Schneider
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | | | - Mai Tuyet Vuong
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Nicole Ashman
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Erdinc Sezgin
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
- Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Christian Eggeling
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Jena, Germany
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161
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Teo RD, Tieleman DP. Modulation of Phospholipid Bilayer Properties by Simvastatin. J Phys Chem B 2021; 125:8406-8418. [PMID: 34296883 DOI: 10.1021/acs.jpcb.1c03359] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Simvastatin (Zocor) is one of the most prescribed drugs for reducing high cholesterol. Although simvastatin is ingested in its inactive lactone form, it is converted to its active dihydroxyheptanoate form by carboxylesterases in the liver. The dihydroxyheptanoate form can also be converted back to its original lactone form. Unfortunately, some of the side effects associated with the intake of simvastatin and other lipophilic statins at higher doses include statin-associated myopathy (SAM) and, in more severe cases, kidney failure. While the cause of SAM is unknown, it is hypothesized that these side effects are dependent on the localization of statins in lipid bilayers and their impact on bilayer properties. In this work, we carry out all-atom molecular dynamics simulations on both the lactone and dihydroxyheptanoate forms of simvastatin (termed "SN" and "SA", respectively) with a pure 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer and a POPC/cholesterol (30 mol %) binary mixture as membrane models. Additional simulations were carried out with multiple simvastatin molecules to mimic in vitro conditions that produced pleiotropic effects. Both SN and SA spontaneously diffused into the lipid bilayer, and a longer simulation time of 4 μs was needed for the complete incorporation of multiple SAs into the bilayer. By constructing potential mean force and electron density profiles, we find that SN localizes deeper within the hydrophobic interior of the bilayer and that SA has a greater tendency to form hydrogen-bonding interactions with neighboring water molecules and lipid headgroups. For the pure POPC bilayer, both SN and SA increase membrane order, while membrane fluidity increases for the POPC/cholesterol bilayer.
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Affiliation(s)
- Ruijie D Teo
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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162
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Capelli R, Gardin A, Empereur-mot C, Doni G, Pavan GM. A Data-Driven Dimensionality Reduction Approach to Compare and Classify Lipid Force Fields. J Phys Chem B 2021; 125:7785-7796. [PMID: 34254518 PMCID: PMC8311647 DOI: 10.1021/acs.jpcb.1c02503] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/30/2021] [Indexed: 01/05/2023]
Abstract
Molecular dynamics simulations of all-atom and coarse-grained lipid bilayer models are increasingly used to obtain useful insights for understanding the structural dynamics of these assemblies. In this context, one crucial point concerns the comparison of the performance and accuracy of classical force fields (FFs), which sometimes remains elusive. To date, the assessments performed on different classical potentials are mostly based on the comparison with experimental observables, which typically regard average properties. However, local differences of the structure and dynamics, which are poorly captured by average measurements, can make a difference, but these are nontrivial to catch. Here, we propose an agnostic way to compare different FFs at different resolutions (atomistic, united-atom, and coarse-grained), by means of a high-dimensional similarity metrics built on the framework of Smooth Overlap of Atomic Position (SOAP). We compare and classify a set of 13 FFs, modeling 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers. Our SOAP kernel-based metrics allows us to compare, discriminate, and correlate different FFs at different model resolutions in an unbiased, high-dimensional way. This also captures differences between FFs in modeling nonaverage events (originating from local transitions), for example, the liquid-to-gel phase transition in dipalmitoylphosphatidylcholine (DPPC) bilayers, for which our metrics allows us to identify nucleation centers for the phase transition, highlighting some intrinsic resolution limitations in implicit versus explicit solvent FFs.
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Affiliation(s)
- Riccardo Capelli
- Department
of Applied Science and Technology, Politecnico
di Torino, Corso Duca Degli Abruzzi 24, I-10129 Torino, Italy
| | - Andrea Gardin
- Department
of Applied Science and Technology, Politecnico
di Torino, Corso Duca Degli Abruzzi 24, I-10129 Torino, Italy
| | - Charly Empereur-mot
- Department
of Innovative Technologies, University of
Applied Sciences and Arts of Southern Switzerland, Polo Universitario
Lugano, Campus Est, Via
la Santa 1, CH-6962 Lugano-Viganello, Switzerland
| | - Giovanni Doni
- Department
of Innovative Technologies, University of
Applied Sciences and Arts of Southern Switzerland, Polo Universitario
Lugano, Campus Est, Via
la Santa 1, CH-6962 Lugano-Viganello, Switzerland
| | - Giovanni M. Pavan
- Department
of Applied Science and Technology, Politecnico
di Torino, Corso Duca Degli Abruzzi 24, I-10129 Torino, Italy
- Department
of Innovative Technologies, University of
Applied Sciences and Arts of Southern Switzerland, Polo Universitario
Lugano, Campus Est, Via
la Santa 1, CH-6962 Lugano-Viganello, Switzerland
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163
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Islam S, Mukhopadhyay C. Aggregation of Lysozyme in the Presence of a Mixed Bilayer of POPC and POPG. ACS OMEGA 2021; 6:17861-17869. [PMID: 34308021 PMCID: PMC8295997 DOI: 10.1021/acsomega.1c01145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/30/2021] [Indexed: 05/04/2023]
Abstract
Understanding the molecular mechanisms by which amyloidogenic proteins interact with membranes is a challenging task. Amyloid accumulates from many human diseases have been observed to contain membrane lipids. In this work, coarse-grained molecular dynamics simulations have been used to inspect hen egg white lysozyme (HEWL) aggregation and membrane association in the presence of a pure POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) bilayer and a POPC and POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol) mixed bilayer. It was observed that, in both cases, two HEWLs formed aggregates. In the presence of a mixed bilayer, after aggregation, the aggregated system started to interact with the membrane. It has been found that one of the lysozymes which came closer to the mixed bilayer unfolded more. The process of the initial insertion of an aggregated system in the mixed bilayer has been analyzed. The structural rearrangements of the protein and lipids were analyzed as well along the course of the simulation. Although with a pure POPC bilayer, aggregation was observed, the aggregated system moved away from the membrane. We believe that our study will provide considerable insights into lysozyme aggregation in the presence of a membrane environment.
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Affiliation(s)
- Shahee Islam
- Department of Chemistry, University
of Calcutta, 92, A. P. C. Road, Kolkata 700009, India
| | - Chaitali Mukhopadhyay
- Department of Chemistry, University
of Calcutta, 92, A. P. C. Road, Kolkata 700009, India
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164
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Unravelling the structural complexity of protein-lipid interactions with neutron reflectometry. Biochem Soc Trans 2021; 49:1537-1546. [PMID: 34240735 DOI: 10.1042/bst20201071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/02/2021] [Accepted: 06/14/2021] [Indexed: 11/17/2022]
Abstract
Neutron reflectometry (NR) is a large-facility technique used to examine structure at interfaces. In this brief review an introduction to the utilisation of NR in the study of protein-lipid interactions is given. Cold neutron beams penetrate matter deeply, have low energies, wavelengths in the Ångstrom regime and are sensitive to light elements. High differential hydrogen sensitivity (between protium and deuterium) enables solution and sample isotopic labelling to be utilised to enhance or diminish the scattering signal of individual components within complex biological structures. The combination of these effects means NR can probe buried structures such as those at the solid-liquid interface and encode molecular level structural information on interfacial protein-lipid complexes revealing the relative distribution of components as well as the overall structure. Model biological membrane sample systems can be structurally probed to examine phenomena such as antimicrobial mode of activity, as well as structural and mechanistic properties peripheral/integral proteins within membrane complexes. Here, the example of the antimicrobial protein α1-purothionin binding to a model Gram negative bacterial outer membrane is used to highlight the utilisation of this technique, detailing how changes in the protein/lipid distributions across the membrane before and after the protein interaction can be easily encoded using hydrogen isotope labelling.
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165
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Jodaitis L, van Oene T, Martens C. Assessing the Role of Lipids in the Molecular Mechanism of Membrane Proteins. Int J Mol Sci 2021; 22:7267. [PMID: 34298884 PMCID: PMC8306737 DOI: 10.3390/ijms22147267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023] Open
Abstract
Membrane proteins have evolved to work optimally within the complex environment of the biological membrane. Consequently, interactions with surrounding lipids are part of their molecular mechanism. Yet, the identification of lipid-protein interactions and the assessment of their molecular role is an experimental challenge. Recently, biophysical approaches have emerged that are compatible with the study of membrane proteins in an environment closer to the biological membrane. These novel approaches revealed specific mechanisms of regulation of membrane protein function. Lipids have been shown to play a role in oligomerization, conformational transitions or allosteric coupling. In this review, we summarize the recent biophysical approaches, or combination thereof, that allow to decipher the role of lipid-protein interactions in the mechanism of membrane proteins.
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Affiliation(s)
| | | | - Chloé Martens
- Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (L.J.); (T.v.O.)
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166
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Sejdiu BI, Tieleman DP. ProLint: a web-based framework for the automated data analysis and visualization of lipid-protein interactions. Nucleic Acids Res 2021; 49:W544-W550. [PMID: 34038536 PMCID: PMC8262751 DOI: 10.1093/nar/gkab409] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/25/2021] [Accepted: 05/24/2021] [Indexed: 12/18/2022] Open
Abstract
The functional activity of membrane proteins is carried out in a complex lipid environment. Increasingly, it is becoming clear that lipids are an important player in regulating or generally modulating their activity. A routinely used method to gain insight into this interplay between lipids and proteins are Molecular Dynamics (MD) simulations, since they allow us to study interactions at atomic or near-atomic detail as a function of time. A major bottleneck, however, is analyzing and visualizing lipid-protein interactions, which, in practice, is a time-demanding task. Here, we present ProLint (www.prolint.ca), a webserver that completely automates analysis of MD generated files and visualization of lipid-protein interactions. Analysis is modular allowing users to select their preferred method, and visualization is entirely interactive through custom built applications that enable a detailed qualitative and quantitative exploration of lipid-protein interactions. ProLint also includes a database of published MD results that have been processed through the ProLint workflow and can be visualized by anyone regardless of their level of experience with MD. The automated analysis, feature-rich visualization, database integration, and open-source distribution with an easy to install process, will allow ProLint to become a routine workflow in lipid-protein interaction studies.
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Affiliation(s)
- Besian I Sejdiu
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Alberta T2N 1N4, Canada
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Alberta T2N 1N4, Canada
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167
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Prakaash D, Cook GP, Acuto O, Kalli AC. Multi-scale simulations of the T cell receptor reveal its lipid interactions, dynamics and the arrangement of its cytoplasmic region. PLoS Comput Biol 2021; 17:e1009232. [PMID: 34280187 PMCID: PMC8321403 DOI: 10.1371/journal.pcbi.1009232] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/29/2021] [Accepted: 07/01/2021] [Indexed: 12/27/2022] Open
Abstract
The T cell receptor (TCR-CD3) initiates T cell activation by binding to peptides of Major Histocompatibility Complexes (pMHC). The TCR-CD3 topology is well understood but the arrangement and dynamics of its cytoplasmic tails remains unknown, limiting our grasp of the signalling mechanism. Here, we use molecular dynamics simulations and modelling to investigate the entire TCR-CD3 embedded in a model membrane. Our study demonstrates conformational changes in the extracellular and transmembrane domains, and the arrangement of the TCR-CD3 cytoplasmic tails. The cytoplasmic tails formed highly interlaced structures while some tyrosines within the immunoreceptor tyrosine-based activation motifs (ITAMs) penetrated the hydrophobic core of the membrane. Interactions between the cytoplasmic tails and phosphatidylinositol phosphate lipids in the inner membrane leaflet led to the formation of a distinct anionic lipid fingerprint around the TCR-CD3. These results increase our understanding of the TCR-CD3 dynamics and the importance of membrane lipids in regulating T cell activation.
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Affiliation(s)
- Dheeraj Prakaash
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, United Kingdom
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Graham P. Cook
- Leeds Institute of Medical Research at St James’s, School of Medicine, University of Leeds, Leeds, United Kingdom
| | - Oreste Acuto
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Antreas C. Kalli
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, United Kingdom
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- * E-mail:
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168
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Impact of Membrane Lipids on UapA and AzgA Transporter Subcellular Localization and Activity in Aspergillus nidulans. J Fungi (Basel) 2021; 7:jof7070514. [PMID: 34203131 PMCID: PMC8304608 DOI: 10.3390/jof7070514] [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: 06/01/2021] [Revised: 06/24/2021] [Accepted: 06/24/2021] [Indexed: 12/21/2022] Open
Abstract
Recent biochemical and biophysical evidence have established that membrane lipids, namely phospholipids, sphingolipids and sterols, are critical for the function of eukaryotic plasma membrane transporters. Here, we study the effect of selected membrane lipid biosynthesis mutations and of the ergosterol-related antifungal itraconazole on the subcellular localization, stability and transport kinetics of two well-studied purine transporters, UapA and AzgA, in Aspergillus nidulans. We show that genetic reduction in biosynthesis of ergosterol, sphingolipids or phosphoinositides arrest A. nidulans growth after germling formation, but solely blocks in early steps of ergosterol (Erg11) or sphingolipid (BasA) synthesis have a negative effect on plasma membrane (PM) localization and stability of transporters before growth arrest. Surprisingly, the fraction of UapA or AzgA that reaches the PM in lipid biosynthesis mutants is shown to conserve normal apparent transport kinetics. We further show that turnover of UapA, which is the transporter mostly sensitive to membrane lipid content modification, occurs during its trafficking and by enhanced endocytosis, and is partly dependent on autophagy and Hect-type HulARsp5 ubiquitination. Our results point out that the role of specific membrane lipids on transporter biogenesis and function in vivo is complex, combinatorial and transporter-dependent.
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169
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Borisov VB. Effect of Membrane Environment on the Ligand-Binding Properties of the Terminal Oxidase Cytochrome bd-I from Escherichia coli. BIOCHEMISTRY (MOSCOW) 2021; 85:1603-1612. [PMID: 33705298 DOI: 10.1134/s0006297920120123] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cytochrome bd-I is a terminal oxidase of the Escherichia coli respiratory chain. This integral membrane protein contains three redox-active prosthetic groups (hemes b558, b595, and d) and couples the electron transfer from quinol to molecular oxygen to the generation of proton motive force, as one of its important physiological functions. The study was aimed at examining the effect of the membrane environment on the ligand-binding properties of cytochrome bd-I by absorption spectroscopy. The membrane environment was found to modulate the ligand-binding characteristics of the hemoprotein in both oxidized and reduced states. Absorption changes upon the addition of exogenous ligands, such as cyanide or carbon monoxide (CO), to the detergent-solubilized enzyme were much more significant and heterogeneous than those observed with the membrane-bound enzyme. In the native membranes, both cyanide and CO interacted mainly with heme d. An additional ligand-binding site (heme b558) appeared in the isolated enzyme, as was evidenced by more pronounced changes in the absorption in the Soret band. This additional reactivity could also be detected after treatment of E. coli membranes with a detergent. The observed effect did not result from the enzyme denaturation, since reconstitution of the isolated enzyme into azolectin liposomes restored the ligand-binding pattern close to that observed for the intact membranes.
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Affiliation(s)
- V B Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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170
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Rathod J, Yen HC, Liang B, Tseng YY, Chen CS, Wu WS. YPIBP: A repository for phosphoinositide-binding proteins in yeast. Comput Struct Biotechnol J 2021; 19:3692-3707. [PMID: 34285772 PMCID: PMC8261538 DOI: 10.1016/j.csbj.2021.06.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/08/2021] [Accepted: 06/22/2021] [Indexed: 11/25/2022] Open
Abstract
Phosphoinositides (PIs) are a family of eight lipids consisting of phosphatidylinositol (PtdIns) and its seven phosphorylated forms. PIs have important regulatory functions in the cell including lipid signaling, protein transport, and membrane trafficking. Yeast has been recognized as a eukaryotic model system to study lipid-protein interactions. Hundreds of yeast PI-binding proteins have been identified, but this research knowledge remains scattered. Besides, the complete PI-binding spectrum and potential PI-binding domains have not been interlinked. No comprehensive databases are available to support the lipid-protein interaction research on phosphoinositides. Here we constructed the first knowledgebase of Yeast Phosphoinositide-Binding Proteins (YPIBP), a repository consisting of 679 PI-binding proteins collected from high-throughput proteome-array and lipid-array studies, QuickGO, and a rigorous literature mining. The YPIBP also contains protein domain information in categories of lipid-binding domains, lipid-related domains and other domains. The YPIBP provides search and browse modes along with two enrichment analyses (PI-binding enrichment analysis and domain enrichment analysis). An interactive visualization is given to summarize the PI-domain-protein interactome. Finally, three case studies were given to demonstrate the utility of YPIBP. The YPIBP knowledgebase consolidates the present knowledge and provides new insights of the PI-binding proteins by bringing comprehensive and in-depth interaction network of the PI-binding proteins. YPIBP is available at http://cosbi7.ee.ncku.edu.tw/YPIBP/.
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Key Words
- ANTH, AP180 N-terminal Homology
- BAR, Bin-Amphiphysin-Rvs
- CAFA, Critical Assessment of Functional Annotation
- CRAL-TRIO, cellular retinaldehyde-binding protein (CRALBP) and TRIO guanine exchange factor
- Cvt, Cytoplasm-to-vacuole targeting
- ENTH, Epsin N-terminal Homology
- FDR, False Discovery Rate
- FYVE, Fab 1 (yeast orthologue of PIKfyve), YOTB, Vac 1 (vesicle transport protein), and EEA1
- GO, Gene Ontology
- ITC, Isothermal Titration Calorimetry
- LBD, Lipid-Binding Domain
- LMPD, LIPID MAPS Proteome Database
- LMSD, LIPID MAPS Structure Database
- LRD, Lipid-Related Domain
- Lipid-binding domain
- OMIM, Online Mendelian Inheritance in Man
- OSBP, Oxysterol-Binding Protein
- PH, Pleckstrin Homology
- PI(3,4)P2, phosphatidylinositol-3,4-bisphosphate
- PI(3,4,5)P3, phosphatidylinositol-3,4,5-trisphosphate
- PI(3,5)P2, phosphatidylinositol-3,5-bisphosphate
- PI(4,5)P2, phosphatidylinositol-4,5-bisphosphate
- PI-binding protein
- PI3P, phosphatidylinositol-3-phosphate
- PI4P, phosphatidylinositol-4-phosphate
- PI5P, phosphatidylinositol-5-phosphate
- PIs, Phosphoinositides
- PMID, PubMed ID
- PX, Phox Homology
- Phosphatidylinositol (PtdIns)
- Phosphoinositides (PIs)
- PtdIns, Phosphatidylinositol
- QCM, Quartz Crystal Microbalance
- S. cerevisiae
- SNX, Sorting Nexin
- SPR, Surface Plasmon Resonance
- YPIBP, Yeast Phosphoinositide-Binding Proteins
- Yeast
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Affiliation(s)
- Jagat Rathod
- Department of Earth Sciences, College of Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Han-Chen Yen
- Department of Electrical Engineering, College of Electrical Engineering and Computer Science, National Cheng Kung University, Tainan 701, Taiwan
| | - Biqing Liang
- Department of Earth Sciences, College of Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Yan-Yuan Tseng
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, MI 48201, USA
| | - Chien-Sheng Chen
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Wei-Sheng Wu
- Department of Electrical Engineering, College of Electrical Engineering and Computer Science, National Cheng Kung University, Tainan 701, Taiwan
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171
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Kim S, Voth GA. Physical Characterization of Triolein and Implications for Its Role in Lipid Droplet Biogenesis. J Phys Chem B 2021; 125:6874-6888. [PMID: 34139844 DOI: 10.1021/acs.jpcb.1c03559] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lipid droplets (LDs) are neutral lipid-storing organelles surrounded by a phospholipid (PL) monolayer. At present, how LDs are formed in the endoplasmic reticulum (ER) bilayer is poorly understood. In this study, we present a revised all-atom (AA) triolein (TG) model, the main constituent of the LD core, and characterize its properties in a bilayer membrane to demonstrate the implications of its behavior in LD biogenesis. In bilayer simulations, TG resides at the surface, adopting PL-like conformations (denoted in this work as SURF-TG). Free energy sampling simulation results estimate the barrier for TG relocating from the bilayer surface to the bilayer center to be ∼2 kcal/mol in the absence of an oil lens. SURF-TG is able to modulate membrane properties by increasing PL ordering, decreasing bending modulus, and creating local negative curvature. The other neutral lipid, dioleoyl-glycerol (DAG), also reduces the membrane bending modulus and populates negative curvature regions. A phenomenological coarse-grained (CG) model is also developed to observe larger-scale SURF-TG-mediated membrane deformation. CG simulations confirm that TG nucleates between the bilayer leaflets at a critical concentration when SURF-TG is evenly distributed. However, when one monolayer contains more SURF-TG, the membrane bends toward the other leaflet, followed by TG nucleation if a concentration is higher than the critical threshold. The central conclusion of this study is that SURF-TG is a negative curvature inducer, as well as a membrane modulator. To this end, a model is proposed in which the accumulation of SURF-TG in the luminal leaflet bends the ER bilayer toward the cytosolic side, followed by TG nucleation.
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Affiliation(s)
- Siyoung Kim
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
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172
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Larsen AH, Sansom MSP. Binding of Ca 2+-independent C2 domains to lipid membranes: A multi-scale molecular dynamics study. Structure 2021; 29:1200-1213.e2. [PMID: 34081910 PMCID: PMC8507603 DOI: 10.1016/j.str.2021.05.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/26/2021] [Accepted: 05/14/2021] [Indexed: 01/17/2023]
Abstract
C2 domains facilitate protein interactions with lipid bilayers in either a Ca2+-dependent or -independent manner. We used molecular dynamics (MD) simulations to explore six Ca2+-independent C2 domains, from KIBRA, PI3KC2α, RIM2, PTEN, SHIP2, and Smurf2. In coarse-grained MD simulations these C2 domains formed transient interactions with zwitterionic bilayers, compared with longer-lived interactions with anionic bilayers containing phosphatidylinositol bisphosphate (PIP2). Type I C2 domains bound non-canonically via the front, back, or side of the β sandwich, whereas type II C2 domains bound canonically, via the top loops. C2 domains interacted strongly with membranes containing PIP2, causing bound anionic lipids to cluster around the protein. Binding modes were refined via atomistic simulations. For PTEN and SHIP2, CG simulations of their phosphatase plus C2 domains with PIP2-containing bilayers were also performed, and the roles of the two domains in membrane localization compared. These studies establish a simulation protocol for membrane-recognition proteins. Binding of Ca2+-independent C2 domains to membranes was explored by MD simulation C2 domains from KIBRA, PI3KC2α, RIM2, PTEN, SHIP2, and Smurf2 were compared C2 domains formed longer-lived interactions with lipid bilayers containing PIP2 For PTEN and SHIP2, simulations of their phosphatase plus C2 domains were performed
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Affiliation(s)
- Andreas Haahr Larsen
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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173
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Lee AG. Interfacial binding sites for cholesterol on GABA A receptors and competition with neurosteroids. Biophys J 2021; 120:2710-2722. [PMID: 34022235 DOI: 10.1016/j.bpj.2021.05.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/06/2021] [Accepted: 05/13/2021] [Indexed: 01/17/2023] Open
Abstract
γ-Aminobutyric acid type A (GABAA) receptors in the brain are located in the outer membranes of brain cells where the concentration of cholesterol is high. Of the 25 available high-resolution structures available for GABAA receptors, none were determined in the presence of cholesterol, but four include resolved molecules of cholesterol hemisuccinate (CHS). Here, a molecular docking procedure is used to sweep the transmembrane (TM) surfaces of the receptors for cholesterol binding sites. Cholesterol docking poses determined in this way match 89% of the resolved CHS when CHS molecules deemed unlikely to represent typical bound cholesterols are excluded. The receptors are pentameric, and their TM surfaces consist of a set of five facets, each including pairs of TM helices from two adjacent subunits. Each facet contains hydrophobic hollows running from one side of the membrane to the other, within which are six potential binding sites for cholesterol, three on each side of the membrane. High-resolution structures of GABAA receptors with bound neurosteroids show that neurosteroids bind in these cholesterol binding sites, so the binding of neurosteroids and cholesterol will be competitive.
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Affiliation(s)
- Anthony G Lee
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom.
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174
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Cherniavskyi YK, Fathizadeh A, Elber R, Tieleman DP. Computer simulations of a heterogeneous membrane with enhanced sampling techniques. J Chem Phys 2021; 153:144110. [PMID: 33086798 PMCID: PMC7556882 DOI: 10.1063/5.0014176] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Computational determination of the equilibrium state of heterogeneous phospholipid membranes is a significant challenge. We wish to explore the rich phase diagram of these multi-component systems. However, the diffusion and mixing times in membranes are long compared to typical time scales of computer simulations. Here, we evaluate the combination of the enhanced sampling techniques molecular dynamics with alchemical steps and Monte Carlo with molecular dynamics with a coarse-grained model of membranes (Martini) to reduce the number of steps and force evaluations that are needed to reach equilibrium. We illustrate a significant gain compared to straightforward molecular dynamics of the Martini model by factors between 3 and 10. The combination is a useful tool to enhance the study of phase separation and the formation of domains in biological membranes.
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Affiliation(s)
- Yevhen K Cherniavskyi
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Arman Fathizadeh
- The Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Ron Elber
- The Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - D Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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175
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Kostritskii AY, Machtens JP. Molecular mechanisms of ion conduction and ion selectivity in TMEM16 lipid scramblases. Nat Commun 2021; 12:2826. [PMID: 33990555 PMCID: PMC8121942 DOI: 10.1038/s41467-021-22724-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 03/23/2021] [Indexed: 02/03/2023] Open
Abstract
TMEM16 lipid scramblases transport lipids and also operate as ion channels with highly variable ion selectivities and various physiological functions. However, their molecular mechanisms of ion conduction and selectivity remain largely unknown. Using computational electrophysiology simulations at atomistic resolution, we identified the main ion-conductive state of TMEM16 lipid scramblases, in which an ion permeation pathway is lined by lipid headgroups that directly interact with permeating ions in a voltage polarity-dependent manner. We found that lipid headgroups modulate the ion-permeability state and regulate ion selectivity to varying degrees in different scramblase isoforms, depending on the amino-acid composition of the pores. Our work has defined the structural basis of ion conduction and selectivity in TMEM16 lipid scramblases and uncovered the mechanisms responsible for the direct effects of membrane lipids on the conduction properties of ion channels.
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Affiliation(s)
- Andrei Y. Kostritskii
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, Jülich, Germany ,grid.1957.a0000 0001 0728 696XInstitute of Clinical Pharmacology, RWTH Aachen University, Aachen, Germany ,grid.1957.a0000 0001 0728 696XDepartment of Physics, RWTH Aachen University, Aachen, Germany
| | - Jan-Philipp Machtens
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, Jülich, Germany ,grid.1957.a0000 0001 0728 696XInstitute of Clinical Pharmacology, RWTH Aachen University, Aachen, Germany
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176
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Novel Roles of SH2 and SH3 Domains in Lipid Binding. Cells 2021; 10:cells10051191. [PMID: 34068055 PMCID: PMC8152464 DOI: 10.3390/cells10051191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 01/07/2023] Open
Abstract
Signal transduction, the ability of cells to perceive information from the surroundings and alter behavior in response, is an essential property of life. Studies on tyrosine kinase action fundamentally changed our concept of cellular regulation. The induced assembly of subcellular hubs via the recognition of local protein or lipid modifications by modular protein interactions is now a central paradigm in signaling. Such molecular interactions are mediated by specific protein interaction domains. The first such domain identified was the SH2 domain, which was postulated to be a reader capable of finding and binding protein partners displaying phosphorylated tyrosine side chains. The SH3 domain was found to be involved in the formation of stable protein sub-complexes by constitutively attaching to proline-rich surfaces on its binding partners. The SH2 and SH3 domains have thus served as the prototypes for a diverse collection of interaction domains that recognize not only proteins but also lipids, nucleic acids, and small molecules. It has also been found that particular SH2 and SH3 domains themselves might also bind to and rely on lipids to modulate complex assembly. Some lipid-binding properties of SH2 and SH3 domains are reviewed here.
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177
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Itaya H, Kasahara K, Xie Q, Yano Y, Matsuzaki K, Takahashi T. All-Atom Molecular Dynamics Elucidating Molecular Mechanisms of Single-Transmembrane Model Peptide Dimerization in a Lipid Bilayer. ACS OMEGA 2021; 6:11458-11465. [PMID: 34056301 PMCID: PMC8153988 DOI: 10.1021/acsomega.1c00482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Protein-protein interactions between transmembrane helices are essential elements for membrane protein structures and functions. To understand the effects of peptide sequences and lipid compositions on these interactions, single-molecule experiments using model systems comprising artificial peptides and membranes have been extensively performed. However, their dynamic behavior at the atomic level remains largely unclear. In this study, we applied the all-atom molecular dynamics (MD) method to simulate the interactions of single-transmembrane helical peptide dimers in membrane environments, which has previously been analyzed by single-molecule experiments. The simulations were performed with two peptides (Ala- and Leu-based artificially designed peptides, termed "host peptide", and the host peptide added with the GXXXG motif, termed "GXXXG peptide"), two membranes (pure-POPC and POPC mixed with 30% cholesterols), and two dimer directions (parallel and antiparallel), consistent with those in the previous experiment. As a result, the MD simulations with parallel dimers reproduced the experimentally observed tendency that introducing cholesterols weakened the interactions in the GXXXG dimer and facilitated those in the host dimer. Our simulation suggested that the host dimer formed hydrogen bonds but the GXXXG dimer did not. However, some discrepancies were also observed between the experiments and simulations. Limitations in the space and time scales of simulations restrict the large-scale undulation and peristaltic motions of the membranes, resulting in differences in lateral pressure profiles. This effect could cause a discrepancy in the rotation angles of helices against the membrane normal.
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Affiliation(s)
- Hayato Itaya
- Graduate
School of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577, Japan
| | - Kota Kasahara
- College
of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577, Japan
| | - Qilin Xie
- College
of Pharmaceutical Sciences, Ritsumeikan
University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577, Japan
| | - Yoshiaki Yano
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, 46-29 Yoshida-Shimo-Adachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Katsumi Matsuzaki
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, 46-29 Yoshida-Shimo-Adachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takuya Takahashi
- College
of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577, Japan
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178
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Identification of multiple substrate binding sites in SLC4 transporters in the outward-facing conformation: Insights into the transport mechanism. J Biol Chem 2021; 296:100724. [PMID: 33932403 PMCID: PMC8191340 DOI: 10.1016/j.jbc.2021.100724] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/21/2021] [Accepted: 04/27/2021] [Indexed: 01/17/2023] Open
Abstract
Solute carrier family 4 (SLC4) transporters mediate the transmembrane transport of HCO3-, CO32-, and Cl- necessary for pH regulation, transepithelial H+/base transport, and ion homeostasis. Substrate transport with varying stoichiometry and specificity is achieved through an exchange mechanism and/or through coupling of the uptake of anionic substrates to typically co-transported Na+. Recently solved outward-facing structures of two SLC4 members (human anion exchanger 1 [hAE1] and human electrogenic sodium bicarbonate cotransporter 1 [hNBCe1]) with different transport modes (Cl-/HCO3- exchange versus Na+-CO32- symport) revealed highly conserved three-dimensional organization of their transmembrane domains. However, the exact location of the ion binding sites and their protein-ion coordination motifs are still unclear. In the present work, we combined site identification by ligand competitive saturation mapping and extensive molecular dynamics sampling with functional mutagenesis studies which led to the identification of two substrate binding sites (entry and central) in the outward-facing states of hAE1 and hNBCe1. Mutation of residues in the identified binding sites led to impaired transport in both proteins. We also showed that R730 in hAE1 is crucial for anion binding in both entry and central sites, whereas in hNBCe1, a Na+ acts as an anchor for CO32- binding to the central site. Additionally, protonation of the central acidic residues (E681 in hAE1 and D754 in hNBCe1) alters the ion dynamics in the permeation cavity and may contribute to the transport mode differences in SLC4 proteins. These results provide a basis for understanding the functional differences between hAE1 and hNBCe1 and may facilitate potential drug development for diseases such as proximal and distal renal tubular acidosis.
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179
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Lamprakis C, Andreadelis I, Manchester J, Velez-Vega C, Duca JS, Cournia Z. Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments. J Chem Theory Comput 2021; 17:3088-3102. [PMID: 33913726 DOI: 10.1021/acs.jctc.0c00507] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein-protein complex assembly is one of the major drivers of biological response. Understanding the mechanisms of protein oligomerization/dimerization would allow one to elucidate how these complexes participate in biological activities and could ultimately lead to new approaches in designing novel therapeutic agents. However, determining the exact association pathways and structures of such complexes remains a challenge. Here, we use parallel tempering metadynamics simulations in the well-tempered ensemble to evaluate the performance of Martini 2.2P and Martini open-beta 3 (Martini 3) force fields in reproducing the structure and energetics of the dimerization process of membrane proteins and proteins in an aqueous solution in reasonable accuracy and throughput. We find that Martini 2.2P systematically overestimates the free energy of association by estimating large barriers in distinct areas, which likely leads to overaggregation when multiple monomers are present. In comparison, the less viscous Martini 3 results in a systematic underestimation of the free energy of association for proteins in solution, while it performs well in describing the association of membrane proteins. In all cases, the near-native dimer complexes are identified as minima in the free energy surface albeit not always as the lowest minima. In the case of Martini 3, we find that the spurious supramolecular protein aggregation present in Martini 2.2P multimer simulations is alleviated and thus this force field may be more suitable for the study of protein oligomerization. We propose that the use of enhanced sampling simulations with a refined coarse-grained force field and appropriately defined collective variables is a robust approach for studying the protein dimerization process, although one should be cautious of the ranking of energy minima.
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Affiliation(s)
- Christos Lamprakis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Ioannis Andreadelis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - John Manchester
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Camilo Velez-Vega
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - José S Duca
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
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180
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Monje-Galvan V, Voth GA. Molecular interactions of the M and E integral membrane proteins of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33948595 DOI: 10.1101/2021.04.29.442018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Specific lipid-protein interactions are key for cellular processes, and even more so for the replication of pathogens. The COVID-19 pandemic has drastically changed our lives and cause the death of nearly three million people worldwide, as of this writing. SARS-CoV-2 is the virus that causes the disease and has been at the center of scientific research over the past year. Most of the research on the virus is focused on key players during its initial attack and entry into the cellular host; namely the S protein, its glycan shield, and its interactions with the ACE2 receptors of human cells. As cases continue to raise around the globe, and new mutants are identified, there is an urgent need to understand the mechanisms of this virus during different stages of its life cycle. Here, we consider two integral membrane proteins of SARS-CoV-2 known to be important for viral assembly and infectivity. We have used microsecond-long all-atom molecular dynamics to examine the lipid-protein and protein-protein interactions of the membrane (M) and envelope (E) structural proteins of SARS-CoV-2 in a complex membrane model. We contrast the two proposed protein complexes for each of these proteins, and quantify their effect on their local lipid environment. This ongoing work also aims to provide molecular-level understanding of the mechanisms of action of this virus to possibly aid in the design of novel treatments.
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181
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Crul T, Maléth J. Endoplasmic Reticulum-Plasma Membrane Contact Sites as an Organizing Principle for Compartmentalized Calcium and cAMP Signaling. Int J Mol Sci 2021; 22:4703. [PMID: 33946838 PMCID: PMC8124356 DOI: 10.3390/ijms22094703] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 01/14/2023] Open
Abstract
In eukaryotic cells, ultimate specificity in activation and action-for example, by means of second messengers-of the myriad of signaling cascades is primordial. In fact, versatile and ubiquitous second messengers, such as calcium (Ca2+) and cyclic adenosine monophosphate (cAMP), regulate multiple-sometimes opposite-cellular functions in a specific spatiotemporal manner. Cells achieve this through segregation of the initiators and modulators to specific plasma membrane (PM) subdomains, such as lipid rafts and caveolae, as well as by dynamic close contacts between the endoplasmic reticulum (ER) membrane and other intracellular organelles, including the PM. Especially, these membrane contact sites (MCSs) are currently receiving a lot of attention as their large influence on cell signaling regulation and cell physiology is increasingly appreciated. Depletion of ER Ca2+ stores activates ER membrane STIM proteins, which activate PM-residing Orai and TRPC Ca2+ channels at ER-PM contact sites. Within the MCS, Ca2+ fluxes relay to cAMP signaling through highly interconnected networks. However, the precise mechanisms of MCS formation and the influence of their dynamic lipid environment on their functional maintenance are not completely understood. The current review aims to provide an overview of our current understanding and to identify open questions of the field.
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Affiliation(s)
- Tim Crul
- First Department of Medicine, University of Szeged, H6720 Szeged, Hungary
- HAS-USZ Momentum Epithelial Cell Signaling and Secretion Research Group, University of Szeged, H6720 Szeged, Hungary
- HCEMM-SZTE Molecular Gastroenterology Research Group, University of Szeged, H6720 Szeged, Hungary
| | - József Maléth
- First Department of Medicine, University of Szeged, H6720 Szeged, Hungary
- HAS-USZ Momentum Epithelial Cell Signaling and Secretion Research Group, University of Szeged, H6720 Szeged, Hungary
- HCEMM-SZTE Molecular Gastroenterology Research Group, University of Szeged, H6720 Szeged, Hungary
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182
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Kostelic MM, Zak CK, Jayasekera HS, Marty MT. Assembly of Model Membrane Nanodiscs for Native Mass Spectrometry. Anal Chem 2021; 93:5972-5979. [PMID: 33797873 DOI: 10.1021/acs.analchem.1c00735] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Native mass spectrometry (MS) with nanodiscs is a promising technique for characterizing membrane protein and peptide interactions in lipid bilayers. However, prior studies have used nanodiscs made of only one or two lipids, which lack the complexity of a natural lipid bilayer. To better model specific biological membranes, we developed model mammalian, bacterial, and mitochondrial nanodiscs with up to four different phospholipids. Careful selection of lipids with similar masses that balance the fluidity and curvature enabled these complex nanodiscs to be assembled and resolved with native MS. We then applied this approach to characterize the specificity and incorporation of LL-37, a human antimicrobial peptide, in single-lipid nanodiscs versus model bacterial nanodiscs. Overall, development of these model membrane nanodiscs reveals new insights into the assembly of complex nanodiscs and provides a useful toolkit for studying membrane protein, peptide, and lipid interactions in model biological membranes.
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Affiliation(s)
- Marius M Kostelic
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Ciara K Zak
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Hiruni S Jayasekera
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States.,Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
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183
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Zakany F, Szabo M, Batta G, Kárpáti L, Mándity IM, Fülöp P, Varga Z, Panyi G, Nagy P, Kovacs T. An ω-3, but Not an ω-6 Polyunsaturated Fatty Acid Decreases Membrane Dipole Potential and Stimulates Endo-Lysosomal Escape of Penetratin. Front Cell Dev Biol 2021; 9:647300. [PMID: 33912562 PMCID: PMC8074792 DOI: 10.3389/fcell.2021.647300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/22/2021] [Indexed: 12/21/2022] Open
Abstract
Although the largely positive intramembrane dipole potential (DP) may substantially influence the function of transmembrane proteins, its investigation is deeply hampered by the lack of measurement techniques suitable for high-throughput examination of living cells. Here, we describe a novel emission ratiometric flow cytometry method based on F66, a 3-hydroxiflavon derivative, and demonstrate that 6-ketocholestanol, cholesterol and 7-dehydrocholesterol, saturated stearic acid (SA) and ω-6 γ-linolenic acid (GLA) increase, while ω-3 α-linolenic acid (ALA) decreases the DP. These changes do not correlate with alterations in cell viability or membrane fluidity. Pretreatment with ALA counteracts, while SA or GLA enhances cholesterol-induced DP elevations. Furthermore, ALA (but not SA or GLA) increases endo-lysosomal escape of penetratin, a cell-penetrating peptide. In summary, we have developed a novel method to measure DP in large quantities of individual living cells and propose ALA as a physiological DP lowering agent facilitating cytoplasmic entry of penetratin.
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Affiliation(s)
- Florina Zakany
- Division of Biophysics, Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Mate Szabo
- Division of Biophysics, Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gyula Batta
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Levente Kárpáti
- Department of Organic Chemistry, Faculty of Pharmacy, Semmelweis University, Budapest, Hungary
| | - István M. Mándity
- Department of Organic Chemistry, Faculty of Pharmacy, Semmelweis University, Budapest, Hungary
- Lendület-Artificial Chloride Ion Transporter Group, Institute of Materials and Environmental Chemistry, Research Center for Natural Sciences, Budapest, Hungary
| | - Péter Fülöp
- Division of Metabolism, Department of Internal Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zoltan Varga
- Division of Biophysics, Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gyorgy Panyi
- Division of Biophysics, Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Peter Nagy
- Division of Biophysics, Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Tamas Kovacs
- Division of Biophysics, Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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184
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Souza PCT, Limongelli V, Wu S, Marrink SJ, Monticelli L. Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations. Front Mol Biosci 2021; 8:657222. [PMID: 33855050 PMCID: PMC8039319 DOI: 10.3389/fmolb.2021.657222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/05/2021] [Indexed: 01/12/2023] Open
Abstract
Molecular docking is central to rational drug design. Current docking techniques suffer, however, from limitations in protein flexibility and solvation models and by the use of simplified scoring functions. All-atom molecular dynamics simulations, on the other hand, feature a realistic representation of protein flexibility and solvent, but require knowledge of the binding site. Recently we showed that coarse-grained molecular dynamics simulations, based on the most recent version of the Martini force field, can be used to predict protein/ligand binding sites and pathways, without requiring any a priori information, and offer a level of accuracy approaching all-atom simulations. Given the excellent computational efficiency of Martini, this opens the way to high-throughput drug screening based on dynamic docking pipelines. In this opinion article, we sketch the roadmap to achieve this goal.
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Affiliation(s)
- Paulo C. T. Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
- PharmCADD, Busan, South Korea
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, Lyon, France
| | - Vittorio Limongelli
- Faculty of Biomedical Sciences, Institute of Computational Science, Università della Svizzera Italiana (USI), Lugano, Switzerland
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
| | - Sangwook Wu
- PharmCADD, Busan, South Korea
- Department of Physics, Pukyong National University, Busan, South Korea
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, Lyon, France
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185
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Miranda WE, Guo J, Mesa-Galloso H, Corradi V, Lees-Miller JP, Tieleman DP, Duff HJ, Noskov SY. Lipid regulation of hERG1 channel function. Nat Commun 2021; 12:1409. [PMID: 33658490 PMCID: PMC7930123 DOI: 10.1038/s41467-021-21681-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 01/29/2021] [Indexed: 01/31/2023] Open
Abstract
The lipid regulation of mammalian ion channel function has emerged as a fundamental mechanism in the control of electrical signalling and transport specificity in various cell types. In this work, we combine molecular dynamics simulations, mutagenesis, and electrophysiology to provide mechanistic insights into how lipophilic molecules (ceramide-sphingolipid probe) alter gating kinetics and K+ currents of hERG1. We show that the sphingolipid probe induced a significant left shift of activation voltage, faster deactivation rates, and current blockade comparable to traditional hERG1 blockers. Microseconds-long MD simulations followed by experimental mutagenesis elucidated ceramide specific binding locations at the interface between the pore and voltage sensing domains. This region constitutes a unique crevice present in mammalian channels with a non-swapped topology. The combined experimental and simulation data provide evidence for ceramide-induced allosteric modulation of the channel by a conformational selection mechanism.
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Affiliation(s)
- Williams E Miranda
- Centre for Molecular Simulation and Department of Biological Sciences, 507 Campus Drive, University of Calgary, Calgary, AB, Canada
| | - Jiqing Guo
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, 3280 Hospital Dr., University of Calgary, Calgary, AB, Canada
| | - Haydee Mesa-Galloso
- Centre for Molecular Simulation and Department of Biological Sciences, 507 Campus Drive, University of Calgary, Calgary, AB, Canada
| | - Valentina Corradi
- Centre for Molecular Simulation and Department of Biological Sciences, 507 Campus Drive, University of Calgary, Calgary, AB, Canada
| | - James P Lees-Miller
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, 3280 Hospital Dr., University of Calgary, Calgary, AB, Canada
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, 507 Campus Drive, University of Calgary, Calgary, AB, Canada.
| | - Henry J Duff
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, 3280 Hospital Dr., University of Calgary, Calgary, AB, Canada.
| | - Sergei Yu Noskov
- Centre for Molecular Simulation and Department of Biological Sciences, 507 Campus Drive, University of Calgary, Calgary, AB, Canada.
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186
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Kandy SK, Janmey PA, Radhakrishnan R. Membrane signalosome: where biophysics meets systems biology. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 25:34-41. [PMID: 33997528 PMCID: PMC8117111 DOI: 10.1016/j.coisb.2021.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We opine on the recent advances in experiments and modeling of modular signaling complexes assembled on mammalian cell membranes (membrane signalosomes) in the context of several applications including intracellular trafficking, cell migration, and immune response. Characterizing the individual components of the membrane assemblies at the nanoscale, ranging from protein-lipid and protein-protein interactions, to membrane morphology, and the energetics of emergent assemblies at the subcellular to cellular scales pose significant challenges. Overcoming these challenges through the iterative coupling of multiscale modeling and experiment can be transformative in terms of addressing the gaps between structural biology and super-resolution microscopy, as it holds the key to the discovery of fundamental mechanisms behind the emergence of function in the membrane signalosome.
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Affiliation(s)
- Sreeja K Kandy
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA
| | - Paul A Janmey
- Department of Physiology, University of Pennsylvania, Philadelphia, PA
- Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA
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187
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Saponaro A, Sharifzadeh AS, Moroni A. Detection of ligand binding to purified HCN channels using fluorescence-based size exclusion chromatography. Methods Enzymol 2021; 652:105-123. [PMID: 34059279 DOI: 10.1016/bs.mie.2021.01.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Biochemical measurements of ligand binding to eukaryotic membrane proteins are challenging because they can require large amounts of purified protein. For this reason, ligand binding is preferentially evaluated on soluble domains rather than on the full length proteins. In this chapter, we describe the use of fluorescence size exclusion chromatography-based thermostability (FSEC-TS) as an assay to monitor ligand binding to the full length mammalian ion channel HCN4. FSEC-TS monitors the effect of the ligand on the thermal denaturation curve of the protein by following the fluorescence of a fused GFP protein. Changes in the melting temperature (Tm) provide a quantitative value for measuring ligand-protein interaction. As a proof of concept, we describe here the protocol for monitoring the binding of the second messenger cAMP and of the known HCN drug Ivabradine to the purified GFP-HCN4 channel. cTMP, a known non-binder of HCN channels, is used as a control. Due to the small amount of protein required, the assay represents a high-throughput screening system for evaluating binding of small molecules to full length proteins.
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Affiliation(s)
- Andrea Saponaro
- Department of Biosciences, University of Milan, Milan, Italy
| | | | - Anna Moroni
- Department of Biosciences, University of Milan, Milan, Italy.
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188
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Wu H, Yao S, Wang T, Wang J, Ren K, Yang H, Ma W, Ji P, Lu Y, Ma H, He C, Wei W, Zhang L, Liu G. Effects of Melatonin on Dairy Herd Improvement (DHI) of Holstein Cow with High SCS. Molecules 2021; 26:molecules26040834. [PMID: 33562613 PMCID: PMC7915447 DOI: 10.3390/molecules26040834] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/30/2021] [Accepted: 02/01/2021] [Indexed: 11/16/2022] Open
Abstract
Mastitis is a common disease in cows breeding. The milk quality will be significantly reduced with increased milk somatic cells, which often occurs in cows with mastitis. In this study, the influence of seasonal changes, age and lactation stages in the Dairy Herd Improvement (DHI) of cows was investigated. Then, the Dairy Herd Improvement (DHI) of cows with high somatic cell score (SCS) after melatonin treatment was systemically investigated. The results showed that melatonin significantly suppressed the milk somatic cell score under all of the tested conditions. The melatonin treatment also improved the milk nutritional value by reducing its fat but increasing its lactose and protein contents. The application of melatonin significantly improved the DHI. The beneficial effects of melatonin on DHI are likely attributed to the antioxidant and anti-inflammatory activities of melatonin.
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Affiliation(s)
- Hao Wu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.W.); (S.Y.); (H.Y.); (W.M.); (P.J.); (L.Z.)
| | - Songyang Yao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.W.); (S.Y.); (H.Y.); (W.M.); (P.J.); (L.Z.)
| | - Tiankun Wang
- Beijing Chang Ping District Animal Disease Prevention and Control Center, Beijing 102200, China;
| | - Jun Wang
- Beijing Animal Husbandry and Veterinary General Station, Beijing 100012, China; (J.W.); (K.R.); (Y.L.)
| | - Kang Ren
- Beijing Animal Husbandry and Veterinary General Station, Beijing 100012, China; (J.W.); (K.R.); (Y.L.)
| | - Hai Yang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.W.); (S.Y.); (H.Y.); (W.M.); (P.J.); (L.Z.)
| | - Wenkui Ma
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.W.); (S.Y.); (H.Y.); (W.M.); (P.J.); (L.Z.)
| | - Pengyun Ji
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.W.); (S.Y.); (H.Y.); (W.M.); (P.J.); (L.Z.)
| | - Yongqiang Lu
- Beijing Animal Husbandry and Veterinary General Station, Beijing 100012, China; (J.W.); (K.R.); (Y.L.)
| | - Hui Ma
- Beijing Shou Nong Food Group Co. Ltd., Beijing 100029, China; (H.M.); (C.H.); (W.W.)
| | - Changwang He
- Beijing Shou Nong Food Group Co. Ltd., Beijing 100029, China; (H.M.); (C.H.); (W.W.)
| | - Wenjuan Wei
- Beijing Shou Nong Food Group Co. Ltd., Beijing 100029, China; (H.M.); (C.H.); (W.W.)
| | - Lu Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.W.); (S.Y.); (H.Y.); (W.M.); (P.J.); (L.Z.)
| | - Guoshi Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.W.); (S.Y.); (H.Y.); (W.M.); (P.J.); (L.Z.)
- Correspondence: ; Tel./Fax: +86-10-6273-2735
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189
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Dämgen MA, Biggin PC. State-dependent protein-lipid interactions of a pentameric ligand-gated ion channel in a neuronal membrane. PLoS Comput Biol 2021; 17:e1007856. [PMID: 33571182 PMCID: PMC7904231 DOI: 10.1371/journal.pcbi.1007856] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 02/24/2021] [Accepted: 01/07/2021] [Indexed: 02/06/2023] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) are receptor proteins that are sensitive to their membrane environment, but the mechanism for how lipids modulate function under physiological conditions in a state dependent manner is not known. The glycine receptor is a pLGIC whose structure has been resolved in different functional states. Using a realistic model of a neuronal membrane coupled with coarse-grained molecular dynamics simulations, we demonstrate that some key lipid-protein interactions are dependent on the receptor state, suggesting that lipids may regulate the receptor's conformational dynamics. Comparison with existing structural data confirms known lipid binding sites, but we also predict further protein-lipid interactions including a site at the communication interface between the extracellular and transmembrane domain. Moreover, in the active state, cholesterol can bind to the binding site of the positive allosteric modulator ivermectin. These protein-lipid interaction sites could in future be exploited for the rational design of lipid-like allosteric drugs.
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Affiliation(s)
- Marc A. Dämgen
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Philip C. Biggin
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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190
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Influence of Antiplatelet Agents on the Lipid Composition of Platelet Plasma Membrane: A Lipidomics Approach with Ticagrelor and Its Active Metabolite. Int J Mol Sci 2021; 22:ijms22031432. [PMID: 33572690 PMCID: PMC7866994 DOI: 10.3390/ijms22031432] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/21/2021] [Accepted: 01/23/2021] [Indexed: 12/18/2022] Open
Abstract
Lipids contained in the plasma membrane of platelets play an important role in platelet function. Modifications in the lipid composition can fluidify or rigidify the environment around embedded receptors, in order to facilitate the access of the receptor by the drug. However, data concerning the lipid composition of platelet plasma membrane need to be updated. In addition, data on the impact of drugs on plasma membrane composition, in particular antiplatelet agents, remain sparse. After isolation of platelet plasma membrane, we assessed, using lipidomics, the effect of ticagrelor, a P2Y12 antagonist, and its active metabolite on the lipid composition of these plasma membranes. We describe the exact lipid composition of plasma membrane, including all sub-species. Ticagrelor and its active metabolite significantly increased cholesterol and phosphatidylcholine ether with short saturated acyl chains 16:0/16:0, and decreased phosphatidylcholine, suggesting overall rigidification of the membrane. Furthermore, ticagrelor and its active metabolite decreased some arachidonylated plasmalogens, suggesting a decrease in availability of arachidonic acid from the membrane phospholipids for synthesis of biologically active mediators. To conclude, ticagrelor and its active metabolite seem to influence the lipid environment of receptors embedded in the lipid bilayer and modify the behavior of the plasma membrane.
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191
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Valentine ML, Waterland MK, Fathizadeh A, Elber R, Baiz CR. Interfacial Dynamics in Lipid Membranes: The Effects of Headgroup Structures. J Phys Chem B 2021; 125:1343-1350. [DOI: 10.1021/acs.jpcb.0c08755] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mason L. Valentine
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712-1224, United States
| | - Maya K. Waterland
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712-1224, United States
| | - Arman Fathizadeh
- Oden Institute for Computational Science and Engineering, Austin, Texas 78712, United States
| | - Ron Elber
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712-1224, United States
- Oden Institute for Computational Science and Engineering, Austin, Texas 78712, United States
| | - Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712-1224, United States
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192
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Soñora M, Martínez L, Pantano S, Machado MR. Wrapping Up Viruses at Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for Simulating the Zika Virus. J Chem Inf Model 2021; 61:408-422. [PMID: 33415985 DOI: 10.1021/acs.jcim.0c01205] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Simulating huge biomolecular complexes of million atoms at relevant biological time scales is becoming accessible to the broad scientific community. That proves to be crucial for urgent responses against emergent diseases in real time. Yet, there are still issues to sort regarding the system setup so that molecular dynamics (MD) simulations can be run in a simple and standard way. Here, we introduce an optimized pipeline for building and simulating enveloped virus-like particles (VLP). First, the membrane packing problem is tackled with new features and optimized options in PACKMOL. This allows preparing accurate membrane models of thousands of lipids in the context of a VLP within a few hours using a single CPU. Then, the assembly of the VLP system is done within the multiscale framework of the coarse-grained SIRAH force field. Finally, the equilibration protocol provides a system ready for production MD simulations within a few days on broadly accessible GPU resources. The pipeline is applied to study the Zika virus as a test case for large biomolecular systems. The VLP stabilizes at approximately 0.5 μs of MD simulation, reproducing correlations greater than 0.90 against experimental density maps from cryo-electron microscopy. Detailed structural analysis of the protein envelope also shows very good agreement in root-mean-square deviations and B-factors with the experimental data. The level of details attained shows for the first time a possible role for anionic phospholipids in stabilizing the envelope. Combining an efficient and reliable setup procedure with an accurate coarse-grained force field provides a valuable pipeline for simulating arbitrary viral systems or subcellular compartments, paving the way toward whole-cell simulations.
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Affiliation(s)
- Martín Soñora
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay
| | - Leandro Martínez
- Institute of Chemistry and Center for Computational Engineering & Science, University of Campinas, Rua Josué de Castro s/n, Cidade Universitária "Zeferino Vaz", Barão Geraldo, 13083-861 Campinas, SP, Brazil
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay
| | - Matías R Machado
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay
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193
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Cholesterol content in the membrane promotes key lipid-protein interactions in a pentameric serotonin-gated ion channel. Biointerphases 2021; 15:061018. [PMID: 33397116 DOI: 10.1116/6.0000561] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs), embedded in the lipid membranes of nerve cells, mediate fast synaptic transmission and are major pharmaceutical targets. Because of their complexity and the limited knowledge of their structure, their working mechanisms have still to be fully unraveled at the molecular level. Over the past few years, evidence that the lipid membrane may modulate the function of membrane proteins, including pLGICs, has emerged. Here, we investigate, by means of molecular dynamics simulations, the behavior of the lipid membrane at the interface with the 5-HT3A receptor (5-HT3AR), a representative pLGIC which is the target of nausea-suppressant drugs, in a nonconductive state. Three lipid compositions are studied, spanning different concentrations of the phospholipids, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, and of cholesterol, hence a range of viscosities. A variety of lipid interactions and persistent binding events to different parts of the receptor are revealed in the investigated models, providing snapshots of the dynamical environment at the membrane-receptor interface. Some of these events result in lipid intercalation within the transmembrane domain, and others reach out to protein key sections for signal transmission and receptor activation, such as the Cys-loop and the M2-M3 loop. In particular, phospholipids, with their long hydrophobic tails, play an important role in these interactions, potentially providing a bridge between these two structures. A higher cholesterol content appears to promote lipid persistent binding to the receptor.
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194
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Wilson KA, Wang L, Lin YC, O'Mara ML. Investigating the lipid fingerprint of SLC6 neurotransmitter transporters: a comparison of dDAT, hDAT, hSERT, and GlyT2. BBA ADVANCES 2021; 1:100010. [PMID: 37082011 PMCID: PMC10074915 DOI: 10.1016/j.bbadva.2021.100010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The local lipid annulus, or "fingerprint", of four SLC6 transporters (dDAT, hDAT, hSERT, and GlyT2) embedded in a complex neuronal membrane were compared and characterised using molecular dynamics. Our analysis included the development of new tools to improve membrane leaflet detection and the analysis of leaflet-dependent properties. Overall, the lipid fingerprints of the four transporters are comprised of similar lipids when grouped by headgroup or tail saturation. The enrichment and depletion of specific lipids, including sites of cholesterol contacts, varies between transporters. The subtle differences in lipid fingerprints results in varying membrane biophysical properties near the transporter. Our results highlight that the lipid-fingerprint of SLC6 transporters in complex membranes is highly dependent on membrane composition. Our results further characterize how the presence and identity of membrane proteins affects the complex interplay of lipid-protein interactions, influencing the local lipid environment and membrane biophysical properties.
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195
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Stein N, Subczynski WK. Oxygen Transport Parameter in Plasma Membrane of Eye Lens Fiber Cells by Saturation Recovery EPR. APPLIED MAGNETIC RESONANCE 2021; 52:61-80. [PMID: 33776217 PMCID: PMC7992188 DOI: 10.1007/s00723-020-01237-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/24/2020] [Indexed: 06/02/2023]
Abstract
A probability distribution of rate constants contained within an exponential-like saturation recovery (SR) electron paramagnetic resonance signal can be constructed using stretched exponential function fitting parameters. Previously (Stein et al. Appl. Magn. Reson. 2019.), application of this method was limited to the case where only one relaxation process, namely spin-lattice relaxations due to the rotational diffusion of the spin labels in the intact eye-lens membranes, contributed to an exponential-like SR signal. These conditions were achieved for thoroughly deoxygenated samples. Here, the case is described where the second relaxation process, namely Heisenberg exchange between the spin label and molecular oxygen that occurs during bimolecular collisions, contributes to the decay of SR signals. We have further developed the theory for application of stretched exponential function to analyze SR signals involving these two processes. This new approach allows separation of stretched exponential parameters, namely characteristic stretched rates and heterogeneity parameters for both processes. Knowing these parameters allowed us to separately construct the probability distributions of spin-lattice relaxation rates determined by the rotational diffusion of spin labels and the distribution of relaxations induced strictly by collisions with molecular oxygen. The later distribution is determined by the distribution of oxygen diffusion concentration products within the membrane, which forms a sensitive new way to describe membrane fluidity and heterogeneity. This method was validated in silico and by fitting SR signals from spin-labeled intact nuclear fiber cell plasma membranes extracted from porcine eye lenses equilibrated with different fractions of air.
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Affiliation(s)
- N. Stein
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, USA
| | - W. K. Subczynski
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, USA
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196
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Moqadam M, Tubiana T, Moutoussamy EE, Reuter N. Membrane models for molecular simulations of peripheral membrane proteins. ADVANCES IN PHYSICS: X 2021. [DOI: 10.1080/23746149.2021.1932589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Mahmoud Moqadam
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Thibault Tubiana
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Emmanuel E. Moutoussamy
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Nathalie Reuter
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
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197
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Mao X, Yao S, Yi Q, Xu ZM, Cang X. Function-related asymmetry of the specific cardiolipin binding sites on the mitochondrial ADP/ATP carrier. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183466. [PMID: 32871114 DOI: 10.1016/j.bbamem.2020.183466] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/16/2020] [Accepted: 08/24/2020] [Indexed: 01/04/2023]
Abstract
The ADP/ATP carrier (AAC) transports matrix ATP and cytosolic ADP across the inner mitochondrial membrane (IMM). It is well known that cardiolipin (CL) plays an important role in regulating the function of AAC, yet the underlying mechanism still remains elusive. AAC is composed of three homologous domains, and three specific CL binding sites are located at the domain-domain interfaces near the matrix side. Here we report an in-depth investigation on the dynamic properties of the bound CL within the three specific sites through all-atom molecular dynamics simulations of up to 13 μs in total. Our results highlight the importance of the basic and polar residues in CL binding. The basic residues from the linker helix and/or the [Y/W/F][K/R]G motif enable the bound CL to form an intra-domain binding mode, and the canonical inter-domain binding mode only forms when these basic residues are occupied by an additional phospholipid. Of special significance, differences in the basic and polar residues lead to remarkable asymmetry among the three specific CL binding sites. We found that the bound CL at the interface of domains 2 and 3 predominantly adopts inter-domain binding mode, while CLs at the other two sites have much more intra-domain populations. This is consistent with the asymmetric crystal structure of the matrix state (m-state) AAC which implies an asymmetric transport mechanism. The dynamic equilibrium between the inter-domain and intra-domain binding modes observed in our simulations could be highly important for the bound CLs to adapt to the movements during state transitions.
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Affiliation(s)
- Xiaoting Mao
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China; Institute of Genetics, Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Shihao Yao
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China; Institute of Genetics, Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Qiuzi Yi
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China; Institute of Genetics, Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Zhe-Ming Xu
- Department of Urology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health and National Children's Regional Medical Center, Hangzhou, Zhejiang 310052, China
| | - Xiaohui Cang
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China; Institute of Genetics, Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.
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198
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Kralj-Iglič V, Pocsfalvi G, Mesarec L, Šuštar V, Hägerstrand H, Iglič A. Minimizing isotropic and deviatoric membrane energy - An unifying formation mechanism of different cellular membrane nanovesicle types. PLoS One 2020; 15:e0244796. [PMID: 33382808 PMCID: PMC7775103 DOI: 10.1371/journal.pone.0244796] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/16/2020] [Indexed: 12/25/2022] Open
Abstract
Tiny membrane-enclosed cellular fragments that can mediate interactions between cells and organisms have recently become a subject of increasing attention. In this work the mechanism of formation of cell membrane nanovesicles (CNVs) was studied experimentally and theoretically. CNVs were isolated by centrifugation and washing of blood cells and observed by optical microscopy and scanning electron microscopy. The shape of the biological membrane in the budding process, as observed in phospholipid vesicles, in erythrocytes and in CNVs, was described by an unifying model. Taking the mean curvature h and the curvature deviator d of the membrane surface as the relevant parameters, the shape and the distribution of membrane constituents were determined theoretically by minimization of membrane free energy. Considering these results and previous results on vesiculation of red blood cells it was interpreted that the budding processes may lead to formation of different types of CNVs as regards the compartment (exo/endovesicles), shape (spherical/tubular/torocytic) and composition (enriched/depleted in particular kinds of molecules). It was concluded that the specificity of pinched off nanovesicles derives from the shape of the membrane constituents and not primarily from their chemical identity, which explains evidences on great heterogeneity of isolated extracellular vesicles with respect to composition. One of the amazing properties of a biological membrane is the ability to undergo dramatic changes of its shape. It may exhibit very high curvature and thereby enclose nano-sized compartments that pinch off from the mother membrane and become freely moving cellular nanovesicles (CNVs). CNVs externalize the pieces of the cell and make them available to other cells within the same organism or other organisms. Therefore they have been acknowledged as mediators of communication between microorganisms, plants, animals and human. Furthernore, they dwell on the border between living and non-living things. Recent findings report on heterogeneity of the size and composition of CNVs found in isolates from different biological samples. As communication between cells is involved in many physiological and patophysiological processes, it is of importance to understand the mechanisms of CNVs formation and recognize the natural laws that mainly govern them. We point to an unifying mechanism that explains stability of differently shaped and composed CNVs by taking into account that the biological membrane tends to attain the minimum of its relevant energy. Conveniently, the procedure can be described by a mathematical model which allows for transparent comparison between experimentally induced shapes of membrane-enclosed vesicular structures and numerical calculations.
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Affiliation(s)
- Veronika Kralj-Iglič
- Faculty of Health Sciences, Laboratory of Clinical Biophysics, University of Ljubljana, Ljubljana, Slovenia
- Extracellular Vesicles and Mass Spetrometry Group, Institute of Biosciences and Bioresources, National Research Council of Italy, Napoli, Italy
- * E-mail:
| | - Gabriella Pocsfalvi
- Extracellular Vesicles and Mass Spetrometry Group, Institute of Biosciences and Bioresources, National Research Council of Italy, Napoli, Italy
| | - Luka Mesarec
- Faculty of Electrical Engineering, Laboratory of Physics, University of Ljubljana, Ljubljana, Slovenia
| | - Vid Šuštar
- Faculty of Medicine, Lymphocyte Cytoskeleton Group, University of Turku, Turku, Finland
| | - Henry Hägerstrand
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Åbo/Turku, Finland
- Novia University of Applied Sciences, Ekenäs, Finland
| | - Aleš Iglič
- Extracellular Vesicles and Mass Spetrometry Group, Institute of Biosciences and Bioresources, National Research Council of Italy, Napoli, Italy
- Faculty of Electrical Engineering, Laboratory of Physics, University of Ljubljana, Ljubljana, Slovenia
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199
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Soteriou C, Kalli AC, Connell SD, Tyler AII, Thorne JL. Advances in understanding and in multi-disciplinary methodology used to assess lipid regulation of signalling cascades from the cancer cell plasma membrane. Prog Lipid Res 2020; 81:101080. [PMID: 33359620 DOI: 10.1016/j.plipres.2020.101080] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 12/31/2022]
Abstract
The lipid bilayer is a functional component of cells, forming a stable platform for the initiation of key biological processes, including cell signalling. There are distinct changes in the lipid composition of cell membranes during oncogenic transformation resulting in aberrant activation and inactivation of signalling transduction pathways. Studying the role of the cell membrane in cell signalling is challenging, since techniques are often limited to by timescale, resolution, sensitivity, and averaging. To overcome these limitations, combining 'computational', 'wet-lab' and 'semi-dry' approaches offers the best opportunity to resolving complex biological processes involved in membrane organisation. In this review, we highlight analytical tools that have been applied for the study of cell signalling initiation from the cancer cell membranes through computational microscopy, biological assays, and membrane biophysics. The cancer therapeutic potential of extracellular membrane-modulating agents, such as cholesterol-reducing agents is also discussed, as is the need for future collaborative inter-disciplinary research for studying the role of the cell membrane and its components in cancer therapy.
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Affiliation(s)
- C Soteriou
- School of Food Science and Nutrition, University of Leeds, Leeds LS29JT, UK; Leeds Institute of Cardiovascular and Metabolic Medicine and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK; Molecular and Nanoscale Physics Group, School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - A C Kalli
- Leeds Institute of Cardiovascular and Metabolic Medicine and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - S D Connell
- Molecular and Nanoscale Physics Group, School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - A I I Tyler
- School of Food Science and Nutrition, University of Leeds, Leeds LS29JT, UK
| | - J L Thorne
- School of Food Science and Nutrition, University of Leeds, Leeds LS29JT, UK.
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200
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Pore-forming proteins: From defense factors to endogenous executors of cell death. Chem Phys Lipids 2020; 234:105026. [PMID: 33309552 DOI: 10.1016/j.chemphyslip.2020.105026] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023]
Abstract
Pore-forming proteins (PFPs) and small antimicrobial peptides (AMPs) represent a large family of molecules with the common ability to punch holes in cell membranes to alter their permeability. They play a fundamental role as infectious bacteria's defensive tools against host's immune system and as executors of endogenous machineries of regulated cell death in eukaryotic cells. Despite being highly divergent in primary sequence and 3D structure, specific folds of pore-forming domains have been conserved. In fact, pore formation is considered an ancient mechanism that takes place through a general multistep process involving: membrane partitioning and insertion, oligomerization and pore formation. However, different PFPs and AMPs assemble and form pores following different mechanisms that could end up either in the formation of protein-lined or protein-lipid pores. In this review, we analyze the current findings in the mechanism of action of different PFPs and AMPs that support a wide role of membrane pore formation in nature. We also provide the newest insights into the development of state-of-art techniques that have facilitated the characterization of membrane pores. To understand the physiological role of these peptides/proteins or develop clinical applications, it is essential to uncover the molecular mechanism of how they perforate membranes.
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