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Alimohamadi H, Luo EWC, Gupta S, de Anda J, Yang R, Mandal T, Wong GCL. Comparing Multifunctional Viral and Eukaryotic Proteins for Generating Scission Necks in Membranes. ACS NANO 2024; 18:15545-15556. [PMID: 38838261 DOI: 10.1021/acsnano.4c00277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Deterministic formation of membrane scission necks by protein machinery with multiplexed functions is critical in biology. A microbial example is M2 viroporin, a proton pump from the influenza A virus that is multiplexed with membrane remodeling activity to induce budding and scission in the host membrane during viral maturation. In comparison, the dynamin family constitutes a class of eukaryotic proteins implicated in mitochondrial fission, as well as various budding and endocytosis pathways. In the case of Dnm1, the mitochondrial fission protein in yeast, the membrane remodeling activity is multiplexed with mechanoenzyme activity to create fission necks. It is not clear why these functions are combined in these scission processes, which occur in drastically different compositions and solution conditions. In general, direct experimental access to changing neck sizes induced by individual proteins or peptide fragments is challenging due to the nanoscale dimensions and influence of thermal fluctuations. Here, we use a mechanical model to estimate the size of scission necks by leveraging small-angle X-ray scattering structural data of protein-lipid systems under different conditions. The influence of interfacial tension, lipid composition, and membrane budding morphology on the size of the induced scission necks is systematically investigated using our data and molecular dynamic simulations. We find that the M2 budding protein from the influenza A virus has robust pH-dependent membrane activity that induces nanoscopic necks within the range of spontaneous hemifission for a broad range of lipid compositions. In contrast, the sizes of scission necks generated by mitochondrial fission proteins strongly depend on lipid composition, which suggests a role for mechanical constriction.
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Affiliation(s)
- Haleh Alimohamadi
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Elizabeth Wei-Chia Luo
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Shivam Gupta
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Jaime de Anda
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Rena Yang
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Taraknath Mandal
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
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2
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Kariya M, Omoto K, Nomura K, Yonezawa K, Kamikubo H, Nishino T, Inoie T, Rapenne G, Yasuhara K. Lipid cubic phase with an organic-inorganic hybrid structure formed by organoalkoxysilane lipid. Chem Commun (Camb) 2024; 60:2168-2171. [PMID: 38205510 DOI: 10.1039/d3cc05167f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
A lipid cubic phase encompassing a cross-linked siloxane structure was formed by the self-assembly of a synthetic organoalkoxysilane lipid in water. The spontaneous sol-gel reaction of the alkoxysilane moiety on the lipid head group produced an organic-inorganic hybrid material with a double gyroid Ia3d cubic structure.
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Affiliation(s)
- Miki Kariya
- Division of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan.
| | - Kenichiro Omoto
- Division of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan.
| | - Kaoru Nomura
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, 619-0284, Japan
| | - Kento Yonezawa
- Division of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan.
- Center for Digital Green-innovation, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan
| | - Hironari Kamikubo
- Division of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan.
- Center for Digital Green-innovation, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan
| | - Toshio Nishino
- Division of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan.
| | - Tomomi Inoie
- Division of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan.
| | - Gwénaël Rapenne
- Division of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan.
- CEMES-CNRS, Université de Toulouse, CNRS, 29 Rue Marvig, F-31055 Toulouse Cedex 4, France
| | - Kazuma Yasuhara
- Division of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan.
- Center for Digital Green-innovation, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan
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3
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Carter T, Iqbal M. The Influenza A Virus Replication Cycle: A Comprehensive Review. Viruses 2024; 16:316. [PMID: 38400091 PMCID: PMC10892522 DOI: 10.3390/v16020316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
Influenza A virus (IAV) is the primary causative agent of influenza, colloquially called the flu. Each year, it infects up to a billion people, resulting in hundreds of thousands of human deaths, and causes devastating avian outbreaks with worldwide losses worth billions of dollars. Always present is the possibility that a highly pathogenic novel subtype capable of direct human-to-human transmission will spill over into humans, causing a pandemic as devastating if not more so than the 1918 influenza pandemic. While antiviral drugs for influenza do exist, they target very few aspects of IAV replication and risk becoming obsolete due to antiviral resistance. Antivirals targeting other areas of IAV replication are needed to overcome this resistance and combat the yearly epidemics, which exact a serious toll worldwide. This review aims to summarise the key steps in the IAV replication cycle, along with highlighting areas of research that need more focus.
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Affiliation(s)
- Toby Carter
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK;
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4
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Alimohamadi H, Luo EWC, Gupta S, de Anda J, Yang R, Mandal T, Wong GCL. Comparing multifunctional viral and eukaryotic proteins for generating scission necks in membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574447. [PMID: 38260291 PMCID: PMC10802413 DOI: 10.1101/2024.01.05.574447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Deterministic formation of membrane scission necks by protein machinery with multiplexed functions is critical in biology. A microbial example is the M2 viroporin, a proton pump from the influenza A virus which is multiplexed with membrane remodeling activity to induce budding and scission in the host membrane during viral maturation. In comparison, the dynamin family constitutes a class of eukaryotic proteins implicated in mitochondrial fission, as well as various budding and endocytosis pathways. In the case of Dnm1, the mitochondrial fission protein in yeast, the membrane remodeling activity is multiplexed with mechanoenzyme activity to create fission necks. It is not clear why these functions are combined in these scission processes, which occur in drastically different compositions and solution conditions. In general, direct experimental access to changing neck sizes induced by individual proteins or peptide fragments is challenging due to the nanoscale dimensions and influence of thermal fluctuations. Here, we use a mechanical model to estimate the size of scission necks by leveraging Small-Angle X-ray Scattering (SAXS) structural data of protein-lipid systems under different conditions. The influence of interfacial tension, lipid composition, and membrane budding morphology on the size of the induced scission necks is systematically investigated using our data and molecular dynamic simulations. We find that the M2 budding protein from the influenza A virus has robust pH-dependent membrane activity that induces nanoscopic necks within the range of spontaneous hemi-fission for a broad range of lipid compositions. In contrast, the sizes of scission necks generated by mitochondrial fission proteins strongly depend on lipid composition, which suggests a role for mechanical constriction.
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5
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Alimohamadi H, de Anda J, Lee MW, Schmidt NW, Mandal T, Wong GCL. How Cell-Penetrating Peptides Behave Differently from Pore-Forming Peptides: Structure and Stability of Induced Transmembrane Pores. J Am Chem Soc 2023; 145:26095-26105. [PMID: 37989570 DOI: 10.1021/jacs.3c08014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Peptide-induced transmembrane pore formation is commonplace in biology. Examples of transmembrane pores include pores formed by antimicrobial peptides (AMPs) and cell-penetrating peptides (CPPs) in bacterial membranes and eukaryotic membranes, respectively. In general, however, transmembrane pore formation depends on peptide sequences, lipid compositions, and intensive thermodynamic variables and is difficult to observe directly under realistic solution conditions, with structures that are challenging to measure directly. In contrast, the structure and phase behavior of peptide-lipid systems are relatively straightforward to map out experimentally for a broad range of conditions. Cubic phases are often observed in systems involving pore-forming peptides; however, it is not clear how the structural tendency to induce negative Gaussian curvature (NGC) in such phases is quantitatively related to the geometry of biological pores. Here, we leverage the theory of anisotropic inclusions and devise a facile method to estimate transmembrane pore sizes from geometric parameters of cubic phases measured from small-angle X-ray scattering (SAXS) and show that such estimates compare well with known pore sizes. Moreover, our model suggests that although AMPs can induce stable transmembrane pores for membranes with a broad range of conditions, pores formed by CPPs are highly labile, consistent with atomistic simulations.
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Affiliation(s)
- Haleh Alimohamadi
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Jaime de Anda
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Michelle W Lee
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
| | - Nathan W Schmidt
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
| | - Taraknath Mandal
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
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6
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Tewari DN, Biswas A, Chakrabarti AK, Dutta S. AMFR promotes innate immunity activation and proteasomal degradation of HMGCR in response to influenza virus infection in A549 cells. Virology 2023; 587:109875. [PMID: 37703797 DOI: 10.1016/j.virol.2023.109875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 08/18/2023] [Accepted: 08/29/2023] [Indexed: 09/15/2023]
Abstract
Differential regulation of the 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR), which is considered the rate-limiting enzyme of the cholesterol biosynthesis pathway, has been reported in case of infection with many viruses. In our study, we have found that influenza virus infection decreases total cellular cholesterol level which is directly related to the downregulation of HMGCR protein. We found that HMGCR is degraded through ubiquitination and proteasomal-mediated pathway upon viral infection. Upregulation of Autocrine Motility Factor Receptor (AMFR), which is an E3-ubiquitin ligase of HMGCR, was also observed. Furthermore, knockdown of AMFR inhibits ubiquitination of HMGCR and also leads to inactivation of the innate immunity components TANK-binding kinase 1 (TBK1) and Interferon regulatory factor 3 (IRF3). Our study is the first to show the role of HMGCR and AMFR in influenza virus infection and reveals that AMFR plays a crucial role in the downregulation of HMGCR and the activation of innate immunity following influenza virus infection.
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Affiliation(s)
- Devendra Nath Tewari
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, 700010, India
| | - Asim Biswas
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, 700010, India
| | - Alok Kumar Chakrabarti
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, 700010, India.
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, 700010, India
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7
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Martins da Silva AY, Arouche TDS, Siqueira MRS, Ramalho TC, de Faria LJG, Gester RDM, Carvalho Junior RND, Santana de Oliveira M, Neto AMDJC. SARS-CoV-2 external structures interacting with nanospheres using docking and molecular dynamics. J Biomol Struct Dyn 2023:1-16. [PMID: 37712854 DOI: 10.1080/07391102.2023.2252930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 08/22/2023] [Indexed: 09/16/2023]
Abstract
Coronavirus is caused by the SARS-CoV-2 virus has shown rapid proliferation and scarcity of treatments with proven effectiveness. In this way, we simulated the hospitalization of carbon nanospheres, with external active sites of the SARS-CoV-2 virus (M-Pro, S-Gly and E-Pro), which can be adsorbed or inactivated when interacting with the nanospheres. The computational procedures performed in this work were developed with the SwissDock server for molecular docking and the GROMACS software for molecular dynamics, making it possible to extract relevant data on affinity energy, distance between molecules, free Gibbs energy and mean square deviation of atomic positions, surface area accessible to solvents. Molecular docking indicates that all ligands have an affinity for the receptor's active sites. The nanospheres interact favorably with all proteins, showing promising results, especially C60, which presented the best affinity energy and RMSD values for all protein macromolecules investigated. The C60 with E-Pro exhibited the highest affinity energy of -9.361 kcal/mol, demonstrating stability in both molecular docking and molecular dynamics simulations. Our RMSD calculations indicated that the nanospheres remained predominantly stable, fluctuating within a range of 2 to 3 Å. Additionally, the analysis of other structures yielded promising results that hold potential for application in other proteases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anderson Yuri Martins da Silva
- Laboratory for the Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, Belem, Brazil
- Graduated in Chemical Engineering, ITEC, Federal University of Pará, Belém, Brazil
- Postgraduate Program in Chemical Engineering, ITEC, Federal University of Pará, Belém, Brazil
| | - Tiago da Silva Arouche
- Laboratory for the Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, Belem, Brazil
- Graduated in Chemical Engineering, ITEC, Federal University of Pará, Belém, Brazil
| | | | - Teodorico Castro Ramalho
- Postgraduate Program in Engineering of Natural Resources of the Amazon, ITEC, Federal University of Pará, Belém, Brazil
| | | | - Rodrigo do Monte Gester
- Institute of Exact Sciences (ICE), Federal University of the South and Southeast of Pará, Maraba, Brazil
| | - Raul Nunes de Carvalho Junior
- Postgraduate Program in Chemical Engineering, ITEC, Federal University of Pará, Belém, Brazil
- Postgraduate Program in Engineering of Natural Resources of the Amazon, ITEC, Federal University of Pará, Belém, Brazil
- Faculty of Food Engineering ITEC, Federal University of Pará, Belém, Brazil
| | | | - Antonio Maia de Jesus Chaves Neto
- Laboratory for the Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, Belem, Brazil
- Graduated in Chemical Engineering, ITEC, Federal University of Pará, Belém, Brazil
- Postgraduate Program in Chemical Engineering, ITEC, Federal University of Pará, Belém, Brazil
- National Professional Master's in Physics Teaching, Federal University of Pará, Belém, Brazil
- Museu Paraense Emílio Goeldi, Diretoria, Coordenação de Botânica, Rua Augusto Corrêa, Belém, Brazil
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8
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Alimohamadi H, de Anda J, Lee MW, Schmidt NW, Mandal T, Wong GCL. How cell penetrating peptides behave differently from pore forming peptides: structure and stability of induced transmembrane pores. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.26.550729. [PMID: 37546874 PMCID: PMC10402029 DOI: 10.1101/2023.07.26.550729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Peptide induced trans-membrane pore formation is commonplace in biology. Examples of transmembrane pores include pores formed by antimicrobial peptides (AMPs) and cell penetrating peptides (CPPs) in bacterial membranes and eukaryotic membranes, respectively. In general, however, transmembrane pore formation depends on peptide sequences, lipid compositions and intensive thermodynamic variables and is difficult to observe directly under realistic solution conditions, with structures that are challenging to measure directly. In contrast, the structure and phase behavior of peptide-lipid systems are relatively straightforward to map out experimentally for a broad range of conditions. Cubic phases are often observed in systems involving pore forming peptides; however, it is not clear how the structural tendency to induce negative Gaussian curvature (NGC) in such phases is quantitatively related to the geometry of biological pores. Here, we leverage the theory of anisotropic inclusions and devise a facile method to estimate transmembrane pore sizes from geometric parameters of cubic phases measured from small angle X-ray scattering (SAXS) and show that such estimates compare well with known pore sizes. Moreover, our model suggests that whereas AMPs can induce stable transmembrane pores for membranes with a broad range of conditions, pores formed by CPPs are highly labile, consistent with atomistic simulations.
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9
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Hudait A, Hurley JH, Voth GA. Dynamics of upstream ESCRT organization at the HIV-1 budding site. Biophys J 2023; 122:2655-2674. [PMID: 37218128 PMCID: PMC10397573 DOI: 10.1016/j.bpj.2023.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/27/2023] [Accepted: 05/11/2023] [Indexed: 05/24/2023] Open
Abstract
In the late stages of the HIV-1 life cycle, membrane localization and self-assembly of Gag polyproteins induce membrane deformation and budding. Release of the virion requires direct interaction between immature Gag lattice and upstream ESCRT machinery at the viral budding site, followed by assembly of downstream ESCRT-III factors, culminating in membrane scission. However, molecular details of upstream ESCRT assembly dynamics at the viral budding site remain unclear. In this work, using coarse-grained (CG) molecular dynamics (MD) simulations, we investigated the interactions between Gag, ESCRT-I, ESCRT-II, and membrane to delineate the dynamical mechanisms by which upstream ESCRTs assemble templated by late-stage immature Gag lattice. We first systematically derived "bottom-up" CG molecular models and interactions of upstream ESCRT proteins from experimental structural data and extensive all-atom MD simulations. Using these molecular models, we performed CG MD simulations of ESCRT-I oligomerization and ESCRT-I/II supercomplex formation at the neck of the budding virion. Our simulations demonstrate that ESCRT-I can effectively oligomerize to higher-order complexes templated by the immature Gag lattice both in the absence of ESCRT-II and when multiple copies of ESCRT-II are localized at the bud neck. The ESCRT-I/II supercomplexes formed in our simulations exhibit predominantly columnar structures, which has important implications for the nucleation pathway of downstream ESCRT-III polymers. Importantly, ESCRT-I/II supercomplexes bound to Gag initiate membrane neck constriction by pulling the inner edge of the bud neck closer to the ESCRT-I headpiece ring. Our findings serve to elucidate a network of interactions between upstream ESCRT machinery, immature Gag lattice, and membrane neck that regulate protein assembly dynamics at the HIV-1 budding site.
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Affiliation(s)
- Arpa Hudait
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois
| | - James H Hurley
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois.
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10
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Dregni AJ, McKay MJ, Surya W, Queralt-Martin M, Medeiros-Silva J, Wang HK, Aguilella V, Torres J, Hong M. The Cytoplasmic Domain of the SARS-CoV-2 Envelope Protein Assembles into a β-Sheet Bundle in Lipid Bilayers. J Mol Biol 2023; 435:167966. [PMID: 36682677 PMCID: PMC9851921 DOI: 10.1016/j.jmb.2023.167966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/23/2022] [Accepted: 01/11/2023] [Indexed: 01/21/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope (E) protein forms a pentameric ion channel in the lipid membrane of the endoplasmic reticulum Golgi intermediate compartment (ERGIC) of the infected cell. The cytoplasmic domain of E interacts with host proteins to cause virus pathogenicity and may also mediate virus assembly and budding. To understand the structural basis of these functions, here we investigate the conformation and dynamics of an E protein construct (residues 8-65) that encompasses the transmembrane domain and the majority of the cytoplasmic domain using solid-state NMR. 13C and 15N chemical shifts indicate that the cytoplasmic domain adopts a β-sheet-rich conformation that contains three β-strands separated by turns. The five subunits associate into an umbrella-shaped bundle that is attached to the transmembrane helices by a disordered loop. Water-edited NMR spectra indicate that the third β-strand at the C terminus of the protein is well hydrated, indicating that it is at the surface of the β-bundle. The structure of the cytoplasmic domain cannot be uniquely determined from the inter-residue correlations obtained here due to ambiguities in distinguishing intermolecular and intramolecular contacts for a compact pentameric assembly of this small domain. Instead, we present four structural topologies that are consistent with the measured inter-residue contacts. These data indicate that the cytoplasmic domain of the SARS-CoV-2 E protein has a strong propensity to adopt β-sheet conformations when the protein is present at high concentrations in lipid bilayers. The equilibrium between the β-strand conformation and the previously reported α-helical conformation may underlie the multiple functions of E in the host cell and in the virion.
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Affiliation(s)
- Aurelio J Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Matthew J McKay
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Wahyu Surya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Maria Queralt-Martin
- Laboratory of Molecular Biophysics. Department of Physics. Universitat Jaume I. 12080 Castellón, Spain
| | - João Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Harrison K Wang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Vicente Aguilella
- Laboratory of Molecular Biophysics. Department of Physics. Universitat Jaume I. 12080 Castellón, Spain
| | - Jaume Torres
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.
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11
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Close, but not too close: a mesoscopic description of (a)symmetry and membrane shaping mechanisms. Emerg Top Life Sci 2023; 7:81-93. [PMID: 36645200 DOI: 10.1042/etls20220078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 01/17/2023]
Abstract
Biomembranes are fundamental to our understanding of the cell, the basic building block of all life. An intriguing aspect of membranes is their ability to assume a variety of shapes, which is crucial for cell function. Here, we review various membrane shaping mechanisms with special focus on the current understanding of how local curvature and local rigidity induced by membrane proteins leads to emerging forces and consequently large-scale membrane deformations. We also argue that describing the interaction of rigid proteins with membranes purely in terms of local membrane curvature is incomplete and that changes in the membrane rigidity moduli must also be considered.
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12
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Madsen JJ, Rossman JS. Cholesterol and M2 Rendezvous in Budding and Scission of Influenza A Virus. Subcell Biochem 2023; 106:441-459. [PMID: 38159237 DOI: 10.1007/978-3-031-40086-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
The cholesterol of the host cell plasma membrane and viral M2 protein plays a crucial role in multiple stages of infection and replication of the influenza A virus. Cholesterol is required for the formation of heterogeneous membrane microdomains (or rafts) in the budozone of the host cell that serves as assembly sites for the viral components. The raft microstructures act as scaffolds for several proteins. Cholesterol may further contribute to the mechanical forces necessary for membrane scission in the last stage of budding and help to maintain the stability of the virus envelope. The M2 protein has been shown to cause membrane scission in model systems by promoting the formation of curved lipid bilayer structures that, in turn, can lead to membrane vesicles budding off or scission intermediates. Membrane remodeling by M2 is intimately linked with cholesterol as it affects local lipid composition, fluidity, and stability of the membrane. Thus, both cholesterol and M2 protein contribute to the efficient and proper release of newly formed influenza viruses from the virus-infected cells.
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Affiliation(s)
- Jesper J Madsen
- Global and Planetary Health, Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, FL, USA.
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Jeremy S Rossman
- School of Biosciences, University of Kent, Canterbury, Kent, UK
- Research-Aid Networks, Chicago, IL, USA
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13
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Heterogeneity and deformation behavior of lipid vesicles. Curr Opin Colloid Interface Sci 2022. [DOI: 10.1016/j.cocis.2022.101646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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14
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Sutherland M, Tran N, Hong M. Clustering of tetrameric influenza M2 peptides in lipid bilayers investigated by 19F solid-state NMR. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183909. [PMID: 35276226 DOI: 10.1016/j.bbamem.2022.183909] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/08/2022] [Accepted: 03/05/2022] [Indexed: 11/19/2022]
Abstract
The influenza M2 protein forms a drug-targeted tetrameric proton channel to mediate virus uncoating, and carries out membrane scission to enable virus release. While the proton channel function of M2 has been extensively studied, the mechanism by which M2 catalyzes membrane scission is still not well understood. Previous fluorescence and electron microscopy studies indicated that M2 tetramers concentrate at the neck of the budding virus in the host plasma membrane. However, molecular evidence for this clustering is scarce. Here, we use 19F solid-state NMR to investigate M2 clustering in phospholipid bilayers. By mixing equimolar amounts of 4F-Phe47 labeled M2 peptide and CF3-Phe47 labeled M2 peptide and measuring F-CF3 cross peaks in 2D 19F19F correlation spectra, we show that M2 tetramers form nanometer-scale clusters in lipid bilayers. This clustering is stronger in cholesterol-containing membranes and phosphatidylethanolamine (PE) membranes than in cholesterol-free phosphatidylcholine and phosphatidylglycerol membranes. The observed correlation peaks indicate that Phe47 sidechains from different tetramers are less than ~2 nm apart. 1H19F correlation peaks between lipid chain protons and fluorinated Phe47 indicate that Phe47 is more deeply inserted into the lipid bilayer in the presence of cholesterol than in its absence, suggesting that Phe47 preferentially interacts with cholesterol. Static 31P NMR spectra indicate that M2 induces negative Gaussian curvature in the PE membrane. These results suggest that M2 tetramers cluster at cholesterol- and PE-rich regions of cell membranes to cause membrane curvature, which in turn can facilitate membrane scission in the last step of virus budding and release.
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Affiliation(s)
- Madeleine Sutherland
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Nhi Tran
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America.
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15
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Xia X, Cheng A, Wang M, Ou X, Sun D, Mao S, Huang J, Yang Q, Wu Y, Chen S, Zhang S, Zhu D, Jia R, Liu M, Zhao XX, Gao Q, Tian B. Functions of Viroporins in the Viral Life Cycle and Their Regulation of Host Cell Responses. Front Immunol 2022; 13:890549. [PMID: 35720341 PMCID: PMC9202500 DOI: 10.3389/fimmu.2022.890549] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
Viroporins are virally encoded transmembrane proteins that are essential for viral pathogenicity and can participate in various stages of the viral life cycle, thereby promoting viral proliferation. Viroporins have multifaceted effects on host cell biological functions, including altering cell membrane permeability, triggering inflammasome formation, inducing apoptosis and autophagy, and evading immune responses, thereby ensuring that the virus completes its life cycle. Viroporins are also virulence factors, and their complete or partial deletion often reduces virion release and reduces viral pathogenicity, highlighting the important role of these proteins in the viral life cycle. Thus, viroporins represent a common drug-protein target for inhibiting drugs and the development of antiviral therapies. This article reviews current studies on the functions of viroporins in the viral life cycle and their regulation of host cell responses, with the aim of improving the understanding of this growing family of viral proteins.
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Affiliation(s)
- Xiaoyan Xia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Xin-Xin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
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16
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Siegel DP. Bicontinuous inverted cubic phase stabilization as an index of antimicrobial and membrane fusion peptide activity. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183815. [PMID: 34748744 DOI: 10.1016/j.bbamem.2021.183815] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/06/2021] [Accepted: 10/29/2021] [Indexed: 02/07/2023]
Abstract
Some antimicrobial peptides (AMPs) and membrane fusion-catalyzing peptides (FPs) stabilize bicontinuous inverted cubic (QII) phases. Previous authors proposed a topological rationale: since AMP-induced pores, fusion intermediates, and QII phases all have negative Gaussian curvature (NGC), peptides which produce NGC in one structure also do it in another. This assumes that peptides change the curvature energy of the lipid membranes. Here I test this with a Helfrich curvature energy model. First, experimentally, I show that lipid systems often used to study peptide NGC have NGC without peptides at higher temperatures. To determine the net effect of an AMP on NGC, the equilibrium phase behavior of the host lipids must be determined. Second, the model shows that AMPs must make large changes in the curvature energy to stabilize AMP-induced pores. Peptide-induced changes in elastic constants affect pores and QII phase differently. Changes in spontaneous curvature affect them in opposite ways. The observed correlation between QII phase stabilization and AMP activity doesn't show that AMPs act by lowering pore curvature energy. A different rationale is proposed. In theory, AMPs could simultaneously stabilize QII phase and pores by drastically changing two particular elastic constants. This could be tested by measuring AMP effects on the individual constants. I propose experiments to do that. Unlike AMPs, FPs must make only small changes in the curvature energy to catalyze fusion. It they act in this way, their fusion activity should correlate with their ability to stabilize QII phases.
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Affiliation(s)
- D P Siegel
- Givaudan Inc., 1199 Edison Drive, Cincinnati, OH 45216, United States of America.
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17
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Kratochvil HT, Newberry RW, Mensa B, Mravic M, DeGrado WF. Spiers Memorial Lecture: Analysis and de novo design of membrane-interactive peptides. Faraday Discuss 2021; 232:9-48. [PMID: 34693965 PMCID: PMC8979563 DOI: 10.1039/d1fd00061f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Membrane-peptide interactions play critical roles in many cellular and organismic functions, including protection from infection, remodeling of membranes, signaling, and ion transport. Peptides interact with membranes in a variety of ways: some associate with membrane surfaces in either intrinsically disordered conformations or well-defined secondary structures. Peptides with sufficient hydrophobicity can also insert vertically as transmembrane monomers, and many associate further into membrane-spanning helical bundles. Indeed, some peptides progress through each of these stages in the process of forming oligomeric bundles. In each case, the structure of the peptide and the membrane represent a delicate balance between peptide-membrane and peptide-peptide interactions. We will review this literature from the perspective of several biologically important systems, including antimicrobial peptides and their mimics, α-synuclein, receptor tyrosine kinases, and ion channels. We also discuss the use of de novo design to construct models to test our understanding of the underlying principles and to provide useful leads for pharmaceutical intervention of diseases.
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Affiliation(s)
- Huong T Kratochvil
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Robert W Newberry
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Bruk Mensa
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Marco Mravic
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
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18
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Kolokouris D, Kalenderoglou IE, Kolocouris A. Inside and Out of the Pore: Comparing Interactions and Molecular Dynamics of Influenza A M2 Viroporin Complexes in Standard Lipid Bilayers. J Chem Inf Model 2021; 61:5550-5568. [PMID: 34714655 DOI: 10.1021/acs.jcim.1c00264] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ion channels located at viral envelopes (viroporins) have a critical function for the replication of infectious viruses and are important drug targets. Over the last decade, the number and duration of molecular dynamics (MD) simulations of the influenza A M2 ion channel owing to the increased computational efficiency. Here, we aimed to define the system setup and simulation conditions for the correct description of the protein-pore and the protein-lipid interactions for influenza A M2 in comparison with experimental data. We performed numerous MD simulations of the influenza A M2 protein in complex with adamantane blockers in standard lipid bilayers using OPLS2005 and CHARMM36 (C36) force fields. We explored the effect of varying the M2 construct (M2(22-46) and M2(22-62)), the lipid buffer size and type (stiffer DMPC or softer POPC with or without 20% cholesterol), the simulation time, the H37 protonation site (Nδ or Νε), the conformational state of the W41 channel gate, and M2's cholesterol binding sites (BSs). We report that the 200 ns MD with M2(22-62) (having Nε Η37) in the 20 Å lipid buffer with the C36 force field accurately describe: (a) the M2 pore structure and interactions inside the pore, that is, adamantane channel blocker location, water clathrate structure, and water or chloride anion blockage/passage from the M2 pore in the presence of a channel blocker and (b) interactions between M2 and the membrane environment as reflected by the calculation of the M2 bundle tilt, folding of amphipathic helices, and cholesterol BSs. Strikingly, we also observed that the C36 1 μs MD simulations using M2(22-62) embedded in a 20 Å POPC:cholesterol (5:1) scrambled membrane produced frequent interactions with cholesterol, which when combined with computational kinetic analysis, revealed the experimentally observed BSs of cholesterol and suggested three similarly long-interacting positions in the top leaflet that have previously not been observed experimentally. These findings promise to be useful for other viroporin systems.
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Affiliation(s)
- Dimitrios Kolokouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
| | - Iris E Kalenderoglou
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
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19
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Thorsen MK, Lai A, Lee MW, Hoogerheide DP, Wong GCL, Freed JH, Heldwein EE. Highly Basic Clusters in the Herpes Simplex Virus 1 Nuclear Egress Complex Drive Membrane Budding by Inducing Lipid Ordering. mBio 2021; 12:e0154821. [PMID: 34425706 PMCID: PMC8406295 DOI: 10.1128/mbio.01548-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/28/2021] [Indexed: 02/01/2023] Open
Abstract
During replication of herpesviruses, capsids escape from the nucleus into the cytoplasm by budding at the inner nuclear membrane. This unusual process is mediated by the viral nuclear egress complex (NEC) that deforms the membrane around the capsid by oligomerizing into a hexagonal, membrane-bound scaffold. Here, we found that highly basic membrane-proximal regions (MPRs) of the NEC alter lipid order by inserting into the lipid headgroups and promote negative Gaussian curvature. We also find that the electrostatic interactions between the MPRs and the membranes are essential for membrane deformation. One of the MPRs is phosphorylated by a viral kinase during infection, and the corresponding phosphomimicking mutations block capsid nuclear egress. We show that the same phosphomimicking mutations disrupt the NEC-membrane interactions and inhibit NEC-mediated budding in vitro, providing a biophysical explanation for the in vivo phenomenon. Our data suggest that the NEC generates negative membrane curvature by both lipid ordering and protein scaffolding and that phosphorylation acts as an off switch that inhibits the membrane-budding activity of the NEC to prevent capsid-less budding. IMPORTANCE Herpesviruses are large viruses that infect nearly all vertebrates and some invertebrates and cause lifelong infections in most of the world's population. During replication, herpesviruses export their capsids from the nucleus into the cytoplasm by an unusual mechanism in which the viral nuclear egress complex (NEC) deforms the nuclear membrane around the capsid. However, how membrane deformation is achieved is unclear. Here, we show that the NEC from herpes simplex virus 1, a prototypical herpesvirus, uses clusters of positive charges to bind membranes and order membrane lipids. Reducing the positive charge or introducing negative charges weakens the membrane deforming ability of the NEC. We propose that the virus employs electrostatics to deform nuclear membrane around the capsid and can control this process by changing the NEC charge through phosphorylation. Blocking NEC-membrane interactions could be exploited as a therapeutic strategy.
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Affiliation(s)
- Michael K. Thorsen
- Department of Molecular Biology and Microbiology, Graduate Program in Cellular, Molecular and Developmental Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Alex Lai
- Department of Chemistry and Chemical Biology and National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, New York, USA
| | - Michelle W. Lee
- Department of Bioengineering, Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - David P. Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Gerard C. L. Wong
- Department of Bioengineering, Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - Jack H. Freed
- Department of Chemistry and Chemical Biology and National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, New York, USA
| | - Ekaterina E. Heldwein
- Department of Molecular Biology and Microbiology, Graduate Program in Cellular, Molecular and Developmental Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
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20
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Sutherland M, Kwon B, Hong M. Interactions of HIV gp41's membrane-proximal external region and transmembrane domain with phospholipid membranes from 31P NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183723. [PMID: 34352242 DOI: 10.1016/j.bbamem.2021.183723] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/22/2021] [Accepted: 07/30/2021] [Indexed: 11/30/2022]
Abstract
HIV-1 entry into cells requires coordinated changes of the conformation and dynamics of both the fusion protein, gp41, and the lipids in the cell membrane and virus envelope. Commonly proposed features of membrane deformation during fusion include high membrane curvature, lipid disorder, and membrane surface dehydration. The virus envelope and target cell membrane contain a diverse set of phospholipids and cholesterol. To dissect how different lipids interact with gp41 to contribute to membrane fusion, here we use 31P solid-state NMR spectroscopy to investigate the curvature, dynamics, and hydration of POPE, POPC and POPS membranes, with and without cholesterol, in the presence of a peptide comprising the membrane proximal external region (MPER) and transmembrane domain (TMD) of gp41. Static 31P NMR spectra indicate that the MPER-TMD induces strong negative Gaussian curvature (NGC) to the POPE membrane but little curvature to POPC and POPC:POPS membranes. The NGC manifests as an isotropic peak in the static NMR spectra, whose intensity increases with the peptide concentration. Cholesterol inhibits the NGC formation and stabilizes the lamellar phase. Relative intensities of magic-angle spinning 31P cross-polarization and direct-polarization spectra indicate that all three phospholipids become more mobile upon peptide binding. Finally, 2D 1H-31P correlation spectra show that the MPER-TMD enhances water 1H polarization transfer to the lipids, indicating that the membrane surfaces become more hydrated. These results suggest that POPE is an essential component of the high-curvature fusion site, and lipid dynamic disorder is a general feature of membrane restructuring during fusion.
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Affiliation(s)
- Madeleine Sutherland
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Byungsu Kwon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
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21
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Liu X, Xu F, Ren L, Zhao F, Huang Y, Wei L, Wang Y, Wang C, Fan Z, Mei S, Song J, Zhao Z, Cen S, Liang C, Wang J, Guo F. MARCH8 inhibits influenza A virus infection by targeting viral M2 protein for ubiquitination-dependent degradation in lysosomes. Nat Commun 2021; 12:4427. [PMID: 34285233 PMCID: PMC8292393 DOI: 10.1038/s41467-021-24724-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 06/30/2021] [Indexed: 01/05/2023] Open
Abstract
The membrane-associated RING-CH (MARCH) proteins are E3 ligases that regulate the stability of various cellular membrane proteins. MARCH8 has been reported to inhibit the infection of HIV-1 and a few other viruses, thus plays an important role in host antiviral defense. However, the antiviral spectrum and the underlying mechanisms of MARCH8 are incompletely defined. Here, we demonstrate that MARCH8 profoundly inhibits influenza A virus (IAV) replication both in vitro and in mice. Mechanistically, MARCH8 suppresses IAV release through redirecting viral M2 protein from the plasma membrane to lysosomes for degradation. Specifically, MARCH8 catalyzes the K63-linked polyubiquitination of M2 at lysine residue 78 (K78). A recombinant A/Puerto Rico/8/34 virus carrying the K78R M2 protein shows greater replication and more severe pathogenicity in cells and mice. More importantly, we found that the M2 protein of the H1N1 IAV has evolved to acquire non-lysine amino acids at positions 78/79 to resist MARCH8-mediated ubiquitination and degradation. Together, our data support the important role of MARCH8 in host anti-IAV intrinsic immune defense by targeting M2, and suggest the inhibitory pressure of MARCH8 on H1N1 IAV transmission in the human population.
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Affiliation(s)
- Xiaoman Liu
- NHC Key Laboratory of Systems Biology of Pathogens and Center for AIDS Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Fengwen Xu
- NHC Key Laboratory of Systems Biology of Pathogens and Center for AIDS Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lili Ren
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Fei Zhao
- NHC Key Laboratory of Systems Biology of Pathogens and Center for AIDS Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yu Huang
- NHC Key Laboratory of Systems Biology of Pathogens and Center for AIDS Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Liang Wei
- NHC Key Laboratory of Systems Biology of Pathogens and Center for AIDS Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yingying Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Conghui Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhangling Fan
- NHC Key Laboratory of Systems Biology of Pathogens and Center for AIDS Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shan Mei
- NHC Key Laboratory of Systems Biology of Pathogens and Center for AIDS Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jingdong Song
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhendong Zhao
- NHC Key Laboratory of Systems Biology of Pathogens and Center for AIDS Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chen Liang
- McGill University AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, Canada
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China. .,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Fei Guo
- NHC Key Laboratory of Systems Biology of Pathogens and Center for AIDS Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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22
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Elkins MR, Bandara A, Pantelopulos GA, Straub JE, Hong M. Direct Observation of Cholesterol Dimers and Tetramers in Lipid Bilayers. J Phys Chem B 2021; 125:1825-1837. [DOI: 10.1021/acs.jpcb.0c10631] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Matthew R. Elkins
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Asanga Bandara
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - George A. Pantelopulos
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - John E. Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
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23
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Kihara S, Köper I, Mata JP, McGillivray DJ. Reviewing nanoplastic toxicology: It's an interface problem. Adv Colloid Interface Sci 2021; 288:102337. [PMID: 33385776 DOI: 10.1016/j.cis.2020.102337] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/06/2020] [Accepted: 12/07/2020] [Indexed: 01/19/2023]
Abstract
Multiple international agencies have recently raised environmental and health concerns regarding plastics in nanoforms (nanoplastics), but there is insufficient knowledge of their properties to allow for an accurate risk assessment to be conducted and any risks managed. For this reason, research into the toxicity of nanoplastics has focused strongly on documenting their impacts on biological organisms. One scope of this review is to summarise the recent findings on the adverse effects on biological organisms and strategies which can be adopted to advance our understanding of nanoplastic properties and their toxicity. Specifically, a mechanistic approach has already been employed in nanotoxicology, which focuses on the cause-and-effect relationships to establish a tool that predicts the biological impacts based on nanoparticle characteristics. Identifying the chemical and biological bases behind the observed biological effects (such as in vitro cellular response) is a major challenge, due to the intricate nature of nanoparticle-biological molecule complexes and an unawareness of their interaction with other biological targets, particularly at interfacial level. An exemplary case includes protein corona formation and ecological molecule corona (eco-corona) for nanoplastics. Therefore, the second scope of this review is to discuss recent findings and importance of (for both non-plastic and plastic nanoparticles) coronae formation and structure. Finally, we discuss the opportunities provided by model system approaches (model protein corona and lipid bilayer) to deepen the understanding of the above-mentioned perspectives, and corroborate the findings from in vitro experiments.
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Affiliation(s)
- Shinji Kihara
- School of Chemical Sciences, The University of Auckland, Auckland 1010, New Zealand; The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6140, New Zealand
| | - Ingo Köper
- Institute for Nanoscale Science and Technology, College for Science and Engineering, Flinders University, Adelaide, SA 5042, Australia
| | - Jitendra P Mata
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights, NSW 2234, Australia.
| | - Duncan J McGillivray
- School of Chemical Sciences, The University of Auckland, Auckland 1010, New Zealand; The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6140, New Zealand
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24
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Zhou YC, Argudo D, Marcoline F, Grabe M. A Computational Model of Protein Induced Membrane Morphology with Geodesic Curvature Driven Protein-Membrane Interface. JOURNAL OF COMPUTATIONAL PHYSICS 2020; 422:109755. [PMID: 32921806 PMCID: PMC7480790 DOI: 10.1016/j.jcp.2020.109755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Continuum or hybrid modeling of bilayer membrane morphological dynamics induced by embedded proteins necessitates the identification of protein-membrane interfaces and coupling of deformations of two surfaces. In this article we developed (i) a minimal total geodesic curvature model to describe these interfaces, and (ii) a numerical one-one mapping between two surface through a conformal mapping of each surface to the common middle annulus. Our work provides the first computational tractable approach for determining the interfaces between bilayer and embedded proteins. The one-one mapping allows a convenient coupling of the morphology of two surfaces. We integrated these two new developments into the energetic model of protein-membrane interactions, and developed the full set of numerical methods for the coupled system. Numerical examples are presented to demonstrate (1) the efficiency and robustness of our methods in locating the curves with minimal total geodesic curvature on highly complicated protein surfaces, (2) the usefulness of these interfaces as interior boundaries for membrane deformation, and (3) the rich morphology of bilayer surfaces for different protein-membrane interfaces.
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Affiliation(s)
- Y. C. Zhou
- Department of Mathematics, Colorado State University, Fort Collins, CO 80523
| | - David Argudo
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, CA 94143
| | - Frank Marcoline
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, CA 94143
| | - Michael Grabe
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, CA 94143
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25
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Lombardo D, Calandra P, Kiselev MA. Structural Characterization of Biomaterials by Means of Small Angle X-rays and Neutron Scattering (SAXS and SANS), and Light Scattering Experiments. Molecules 2020; 25:E5624. [PMID: 33260426 PMCID: PMC7730346 DOI: 10.3390/molecules25235624] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Scattering techniques represent non-invasive experimental approaches and powerful tools for the investigation of structure and conformation of biomaterial systems in a wide range of distances, ranging from the nanometric to micrometric scale. More specifically, small-angle X-rays and neutron scattering and light scattering techniques represent well-established experimental techniques for the investigation of the structural properties of biomaterials and, through the use of suitable models, they allow to study and mimic various biological systems under physiologically relevant conditions. They provide the ensemble averaged (and then statistically relevant) information under in situ and operando conditions, and represent useful tools complementary to the various traditional imaging techniques that, on the contrary, reveal more local structural information. Together with the classical structure characterization approaches, we introduce the basic concepts that make it possible to examine inter-particles interactions, and to study the growth processes and conformational changes in nanostructures, which have become increasingly relevant for an accurate understanding and prediction of various mechanisms in the fields of biotechnology and nanotechnology. The upgrade of the various scattering techniques, such as the contrast variation or time resolved experiments, offers unique opportunities to study the nano- and mesoscopic structure and their evolution with time in a way not accessible by other techniques. For this reason, highly performant instruments are installed at most of the facility research centers worldwide. These new insights allow to largely ameliorate the control of (chemico-physical and biologic) processes of complex (bio-)materials at the molecular length scales, and open a full potential for the development and engineering of a variety of nano-scale biomaterials for advanced applications.
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Affiliation(s)
- Domenico Lombardo
- CNR-IPCF, Consiglio Nazionale delle Ricerche, Istituto per i Processi Chimico-Fisici, 98158 Messina, Italy
| | - Pietro Calandra
- CNR-ISMN, Consiglio Nazionale delle Ricerche, Istituto Studio Materiali Nanostrutturati, 00015 Roma, Italy;
| | - Mikhail A. Kiselev
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, 141980 Moscow, Russia;
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26
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Stylianakis I, Shalev A, Scheiner S, Sigalas MP, Arkin IT, Glykos N, Kolocouris A. The balance between side-chain and backbone-driven association in folding of the α-helical influenza A transmembrane peptide. J Comput Chem 2020; 41:2177-2188. [PMID: 32735736 DOI: 10.1002/jcc.26381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 11/07/2022]
Abstract
The correct balance between attractive, repulsive and peptide hydrogen bonding interactions must be attained for proteins to fold correctly. To investigate these important contributors, we sought a comparison of the folding between two 25-residues peptides, the influenza A M2 protein transmembrane domain (M2TM) and the 25-Ala (Ala25 ). M2TM forms a stable α-helix as is shown by circular dichroism (CD) experiments. Molecular dynamics (MD) simulations with adaptive tempering show that M2TM monomer is more dynamic in nature and quickly interconverts between an ensemble of various α-helical structures, and less frequently turns and coils, compared to one α-helix for Ala25 . DFT calculations suggest that folding from the extended structure to the α-helical structure is favored for M2TM compared with Ala25 . This is due to CH⋯O attractive interactions which favor folding to the M2TM α-helix, and cannot be described accurately with a force field. Using natural bond orbital (NBO) analysis and quantum theory atoms in molecules (QTAIM) calculations, 26 CH⋯O interactions and 22 NH⋯O hydrogen bonds are calculated for M2TM. The calculations show that CH⋯O hydrogen bonds, although individually weaker, have a cumulative effect that cannot be ignored and may contribute as much as half of the total hydrogen bonding energy, when compared to NH⋯O, to the stabilization of the α-helix in M2TM. Further, a strengthening of NH⋯O hydrogen bonding interactions is calculated for M2TM compared to Ala25 . Additionally, these weak CH⋯O interactions can dissociate and associate easily leading to the ensemble of folded structures for M2TM observed in folding MD simulations.
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Affiliation(s)
- Ioannis Stylianakis
- Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Ariella Shalev
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, Israel
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, USA
| | - Michael P Sigalas
- Department of Chemistry, Laboratory of Applied Quantum Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Isaiah T Arkin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, Israel
| | - Nikolas Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Antonios Kolocouris
- Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
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27
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Martyna A, Bahsoun B, Madsen JJ, Jackson FSJS, Badham MD, Voth GA, Rossman JS. Cholesterol Alters the Orientation and Activity of the Influenza Virus M2 Amphipathic Helix in the Membrane. J Phys Chem B 2020; 124:6738-6747. [PMID: 32644803 PMCID: PMC7515559 DOI: 10.1021/acs.jpcb.0c03331] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
The
influenza virus M2 amphipathic helix (M2AH) alters membrane
curvature in a cholesterol-dependent manner, mediating viral membrane
scission during influenza virus budding. Here, we have investigated
the biophysical effects of cholesterol on the ability of an M2AH peptide
to manipulate membrane properties. We see that the ability of the
M2AH to interact with membranes and form an α-helix is independent
of membrane cholesterol concentration; however, cholesterol affects
the angle of the M2AH peptide within the membrane. This change in
membrane orientation affects the ability of the M2AH to alter lipid
order. In low-cholesterol membranes, the M2AH is inserted near the
level of the lipid head groups, increasing lipid order, which may
contribute to generation of the membrane curvature. As the cholesterol
content increases, the M2AH insertion becomes flatter and slightly
deeper in the membrane below the lipid headgroups, where the polar
face can continue to interact with the headgroups while the hydrophobic
face binds cholesterol. This changed orientation minimizes lipid packing
defects and lipid order changes, likely reducing the generation of
membrane curvature. Thus, cholesterol regulates M2 membrane scission
by precisely modulating M2AH positioning within the membrane. This
has implications for the understanding of many of amphipathic-helix-driven
cellular budding processes that occur in specific lipid environments.
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Affiliation(s)
- Agnieszka Martyna
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Basma Bahsoun
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Jesper J Madsen
- Department of Chemistry and Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States.,James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.,Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida 33612, United States
| | | | - Matthew D Badham
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Gregory A Voth
- Department of Chemistry and Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States.,James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Jeremy S Rossman
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
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28
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Bozelli JC, Epand RM. Membrane Shape and the Regulation of Biological Processes. J Mol Biol 2020; 432:5124-5136. [DOI: 10.1016/j.jmb.2020.03.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 01/06/2023]
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29
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Chemokine CCL28 Is a Potent Therapeutic Agent for Oropharyngeal Candidiasis. Antimicrob Agents Chemother 2020; 64:AAC.00210-20. [PMID: 32423961 DOI: 10.1128/aac.00210-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/15/2020] [Indexed: 12/28/2022] Open
Abstract
Candida albicans is a commensal organism that causes life-threatening or life-altering opportunistic infections. Treatment of Candida infections is limited by the paucity of antifungal drug classes. Naturally occurring antimicrobial peptides are promising agents for drug development. CCL28 is a CC chemokine that is abundant in saliva and has in vitro antimicrobial activity. In this study, we examine the in vivo Candida killing capacity of CCL28 in oropharyngeal candidiasis as well as the spectrum and mechanism of anti-Candida activity. In the mouse model of oropharyngeal candidiasis, application of wild-type CCL28 reduces oral fungal burden in severely immunodeficient mice without causing excessive inflammation or altering tissue neutrophil recruitment. CCL28 is effective against multiple clinical strains of C. albicans Polyamine protein transporters are not required for CCL28 anti-Candida activity. Both structured and unstructured CCL28 proteins show rapid and sustained fungicidal activity that is superior to that of clinical antifungal agents. Application of wild-type CCL28 to C. albicans results in membrane disruption as measured by solute movement, enzyme leakage, and induction of negative Gaussian curvature on model membranes. Membrane disruption is reduced in CCL28 lacking the functional C-terminal tail. Our results strongly suggest that CCL28 can exert antifungal activity in part via membrane permeation and has potential for development as an anti-Candida therapeutic agent without inflammatory side effects.
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30
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Chakraborty A, Deligey F, Quach J, Mentink-Vigier F, Wang P, Wang T. Biomolecular complex viewed by dynamic nuclear polarization solid-state NMR spectroscopy. Biochem Soc Trans 2020; 48:1089-1099. [PMID: 32379300 PMCID: PMC7565284 DOI: 10.1042/bst20191084] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/17/2020] [Accepted: 04/20/2020] [Indexed: 01/07/2023]
Abstract
Solid-state nuclear magnetic resonance (ssNMR) is an indispensable tool for elucidating the structure and dynamics of insoluble and non-crystalline biomolecules. The recent advances in the sensitivity-enhancing technique magic-angle spinning dynamic nuclear polarization (MAS-DNP) have substantially expanded the territory of ssNMR investigations and enabled the detection of polymer interfaces in a cellular environment. This article highlights the emerging MAS-DNP approaches and their applications to the analysis of biomolecular composites and intact cells to determine the folding pathway and ligand binding of proteins, the structural polymorphism of low-populated biopolymers, as well as the physical interactions between carbohydrates, proteins, and lignin. These structural features provide an atomic-level understanding of many cellular processes, promoting the development of better biomaterials and inhibitors. It is anticipated that the capabilities of MAS-DNP in biomolecular and biomaterial research will be further enlarged by the rapid development of instrumentation and methodology.
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Affiliation(s)
- Arnab Chakraborty
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Fabien Deligey
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jenny Quach
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | | | - Ping Wang
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
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31
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Dishman AF, Lee MW, de Anda J, Lee EY, He J, Huppler AR, Wong GCL, Volkman BF. Switchable Membrane Remodeling and Antifungal Defense by Metamorphic Chemokine XCL1. ACS Infect Dis 2020; 6:1204-1213. [PMID: 32243126 PMCID: PMC7258946 DOI: 10.1021/acsinfecdis.0c00011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Antimicrobial peptides (AMPs) are
a class of molecules which generally
kill pathogens via preferential cell membrane disruption. Chemokines
are a family of signaling proteins that direct immune cell migration
and share a conserved α–β tertiary structure. Recently,
it was found that a subset of chemokines can also function as AMPs,
including CCL20, CXCL4, and XCL1. It is therefore surprising that
machine learning based analysis predicts that CCL20 and CXCL4’s
α-helices are membrane disruptive, while XCL1’s helix
is not. XCL1, however, is the only chemokine known to be a metamorphic
protein which can interconvert reversibly between two distinct native
structures (a β-sheet dimer and the α–β chemokine
structure). Here, we investigate XCL1’s antimicrobial mechanism
of action with a focus on the role of metamorphic folding. We demonstrate
that XCL1 is a molecular “Swiss army knife” that can
refold into different structures for distinct context-dependent functions:
whereas the α–β chemokine structure controls cell
migration by binding to G-Protein Coupled Receptors (GPCRs), we find
using small angle X-ray scattering (SAXS) that only the β-sheet
and unfolded XCL1 structures can induce negative Gaussian curvature
(NGC) in membranes, the type of curvature topologically required for
membrane permeation. Moreover, the membrane remodeling activity of
XCL1’s β-sheet structure is strongly dependent on membrane
composition: XCL1 selectively remodels bacterial model membranes but
not mammalian model membranes. Interestingly, XCL1 also permeates
fungal model membranes and exhibits anti-Candida activity in vitro, in contrast to the usual mode of antifungal defense
which requires Th17 mediated cell-based responses. These observations
suggest that metamorphic XCL1 is capable of a versatile multimodal
form of antimicrobial defense.
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Affiliation(s)
- Acacia F. Dishman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226 United States
| | - Michelle W. Lee
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Jaime de Anda
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Ernest Y. Lee
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90095, United States
- UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Jie He
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin 53226 United States
| | - Anna R. Huppler
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin 53226 United States
| | - Gerard C. L. Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Brian F. Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226 United States
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32
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Lee MW, de Anda J, Kroll C, Bieniossek C, Bradley K, Amrein KE, Wong GCL. How do cyclic antibiotics with activity against Gram-negative bacteria permeate membranes? A machine learning informed experimental study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183302. [PMID: 32311341 DOI: 10.1016/j.bbamem.2020.183302] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 12/30/2022]
Abstract
All antibiotics have to engage bacterial amphiphilic barriers such as the lipopolysaccharide-rich outer membrane or the phospholipid-based inner membrane in some manner, either by disrupting them outright and/or permeating them and thereby allow the antibiotic to get into bacteria. There is a growing class of cyclic antibiotics, many of which are of bacterial origin, that exhibit activity against Gram-negative bacteria, which constitute an urgent problem in human health. We examine a diverse collection of these cyclic antibiotics, both natural and synthetic, which include bactenecin, polymyxin B, octapeptin, capreomycin, and Kirshenbaum peptoids, in order to identify what they have in common when they interact with bacterial lipid membranes. We find that they virtually all have the ability to induce negative Gaussian curvature (NGC) in bacterial membranes, the type of curvature geometrically required for permeation mechanisms such as pore formation, blebbing, and budding. This is interesting since permeation of membranes is a function usually ascribed to antimicrobial peptides (AMPs) from innate immunity. As prototypical test cases of cyclic antibiotics, we analyzed amino acid sequences of bactenecin, polymyxin B, and capreomycin using our recently developed machine-learning classifier trained on α-helical AMP sequences. Although the original classifier was not trained on cyclic antibiotics, a modified classifier approach correctly predicted that bactenecin and polymyxin B have the ability to induce NGC in membranes, while capreomycin does not. Moreover, the classifier was able to recapitulate empirical structure-activity relationships from alanine scans in polymyxin B surprisingly well. These results suggest that there exists some common ground in the sequence design of hybrid cyclic antibiotics and linear AMPs.
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Affiliation(s)
- Michelle W Lee
- Department of Bioengineering, Department of Chemistry, California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Jaime de Anda
- Department of Bioengineering, Department of Chemistry, California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Carsten Kroll
- Roche Pharma Research and Early Development Pharmaceutical Science, Roche, Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Christoph Bieniossek
- Roche Pharma Research and Early Development Pharmaceutical Science, Roche, Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Kenneth Bradley
- Roche Pharma Research and Early Development Pharmaceutical Science, Roche, Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Kurt E Amrein
- Roche Pharma Research and Early Development Pharmaceutical Science, Roche, Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Gerard C L Wong
- Department of Bioengineering, Department of Chemistry, California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States.
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33
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Thomaston JL, Konstantinidi A, Liu L, Lambrinidis G, Tan J, Caffrey M, Wang J, DeGrado WF, Kolocouris A. X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. Biochemistry 2020; 59:627-634. [PMID: 31894969 PMCID: PMC7224692 DOI: 10.1021/acs.biochem.9b00971] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The V27A mutation confers adamantane resistance on the influenza A matrix 2 (M2) proton channel and is becoming more prevalent in circulating populations of influenza A virus. We have used X-ray crystallography to determine structures of a spiro-adamantyl amine inhibitor bound to M2(22-46) V27A and also to M2(21-61) V27A in the Inwardclosed conformation. The spiro-adamantyl amine binding site is nearly identical for the two crystal structures. Compared to the M2 "wild type" (WT) with valine at position 27, we observe that the channel pore is wider at its N-terminus as a result of the V27A mutation and that this removes V27 side chain hydrophobic interactions that are important for binding of amantadine and rimantadine. The spiro-adamantyl amine inhibitor blocks proton conductance in the WT and V27A mutant channels by shifting its binding site in the pore depending on which residue is present at position 27. Additionally, in the structure of the M2(21-61) V27A construct, the C-terminus of the channel is tightly packed relative to that of the M2(22-46) construct. We observe that residues Asp44, Arg45, and Phe48 face the center of the channel pore and would be well-positioned to interact with protons exiting the M2 channel after passing through the His37 gate. A 300 ns molecular dynamics simulation of the M2(22-46) V27A-spiro-adamantyl amine complex predicts with accuracy the position of the ligands and waters inside the pore in the X-ray crystal structure of the M2(22-46) V27A complex.
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Affiliation(s)
- Jessica L. Thomaston
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
- Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Athina Konstantinidi
- Department of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Lijun Liu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- DLX Scientific, Lawrence, KS 66049, USA
| | - George Lambrinidis
- Department of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Jingquan Tan
- Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Martin Caffrey
- Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, USA
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Antonios Kolocouris
- Department of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece
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34
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Konstantinidi A, Chountoulesi M, Naziris N, Sartori B, Amenitsch H, Mali G, Čendak T, Plakantonaki M, Triantafyllakou I, Tselios T, Demetzos C, Busath DD, Mavromoustakos T, Kolocouris A. The boundary lipid around DMPC-spanning influenza A M2 transmembrane domain channels: Its structure and potential for drug accommodation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183156. [PMID: 31846647 DOI: 10.1016/j.bbamem.2019.183156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/11/2019] [Accepted: 12/12/2019] [Indexed: 10/25/2022]
Abstract
We have investigated the perturbation of influenza A M2TM in DMPC bilayers. We have shown that (a) DSC and SAXS detect changes in membrane organization caused by small changes (micromolar) in M2TM or aminoadamantane concentration and aminoadamantane structure, by comparison of amantadine and spiro[pyrrolidine-2,2'-adamantane] (AK13), (b) that WAXS and MD can suggest details of ligand topology. DSC and SAXS show that at a low M2TM micromolar concentration in DPMC bilayers, two lipid domains are observed, which likely correspond to M2TM boundary lipids and bulk-like lipids. At higher M2TM concentrations, one domain only is identified, which constitutes essentially all of the lipid molecules behaving as boundary lipids. According to SAXS, WAXS, and DSC in the absence of M2TM, both aminoadamantane drugs exert a similar perturbing effect on the bilayer at low concentrations. At the same concentrations of the drug when M2TM is present, amantadine and, to a lesser extent, AK13 cause, according to WAXS, a significant disordering of chain-stacking, which also leads to the formation of two lipid domains. This effect is likely due, according to MD simulations, to the preference of the more lipophilic AK13 to locate closer to the lateral surfaces of M2TM when compared to amantadine, which forms stronger ionic interactions with phosphate groups. The preference of AK13 to concentrate inside the lipid bilayer close to the exterior of the hydrophobic M2TM helices may contribute to its higher binding affinity compared to amantadine.
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Affiliation(s)
- Athina Konstantinidi
- Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Maria Chountoulesi
- Section of Pharmaceutical Technology, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Nikolaos Naziris
- Section of Pharmaceutical Technology, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Barbara Sartori
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, A-8010 Graz, Austria
| | - Heinz Amenitsch
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, A-8010 Graz, Austria
| | - Gregor Mali
- Department of Inorganic Chemistry and Technology, National Institute of Chemistry, Ljubljana SI-1001, Slovenia
| | - Tomaž Čendak
- Department of Inorganic Chemistry and Technology, National Institute of Chemistry, Ljubljana SI-1001, Slovenia
| | - Maria Plakantonaki
- Department of Chemistry, School of Natural Sciences, University of Patras, Rion, Patras 26500, Greece
| | - Iro Triantafyllakou
- Department of Chemistry, School of Natural Sciences, University of Patras, Rion, Patras 26500, Greece
| | - Theodore Tselios
- Department of Chemistry, School of Natural Sciences, University of Patras, Rion, Patras 26500, Greece
| | - Costas Demetzos
- Section of Pharmaceutical Technology, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - David D Busath
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602, USA
| | - Thomas Mavromoustakos
- Section of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens 15771, Greece.
| | - Antonios Kolocouris
- Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens 15771, Greece.
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35
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Elkins MR, Hong M. Elucidating ligand-bound structures of membrane proteins using solid-state NMR spectroscopy. Curr Opin Struct Biol 2019; 57:103-109. [PMID: 30903830 PMCID: PMC6697555 DOI: 10.1016/j.sbi.2019.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 02/05/2019] [Accepted: 02/08/2019] [Indexed: 01/08/2023]
Abstract
Magic-angle-spinning (MAS) solid-state NMR spectroscopy is a versatile technique to elucidate functionally important protein-ligand interactions in lipid membranes. Here, we review recent solid-state NMR studies of membrane protein interactions with cholesterol, lipids, transported substrates, and peptide ligands. These studies are conducted in synthetic or native lipid bilayers to provide an accurate environment for ligand binding. The solid-state NMR approaches include multinuclear detection to gain comprehensive structural information, distance measurements to locate ligand-binding sites, and dynamic nuclear polarization and 1H detection to enhance spectral sensitivity. These studies provide novel insights into the mechanisms of virus budding, virus entry into cells, transmembrane signaling, substrate transport, antibacterial action, and many other biological processes.
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Affiliation(s)
- Matthew R Elkins
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States.
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36
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Kim G, Raymond HE, Herneisen AL, Wong-Rolle A, Howard KP. The distal cytoplasmic tail of the influenza A M2 protein dynamically extends from the membrane. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2019; 1861:1421-1427. [PMID: 31153909 PMCID: PMC6625909 DOI: 10.1016/j.bbamem.2019.05.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 12/19/2022]
Abstract
The influenza A M2 protein is a multifunctional membrane-associated homotetramer that orchestrates several essential events in the viral infection cycle. The monomeric subunits of the M2 homotetramer consist of an N-terminal ectodomain, a transmembrane domain, and a C-terminal cytoplasmic domain. The transmembrane domain forms a four-helix proton channel that promotes uncoating of virions upon host cell entry. The membrane-proximal region of the C-terminal domain forms a surface-associated amphipathic helix necessary for viral budding. The structure of the remaining ~34 residues of the distal cytoplasmic tail has yet to be fully characterized despite the functional significance of this region for influenza infectivity. Here, we extend structural and dynamic studies of the poorly characterized M2 cytoplasmic tail. We used SDSL-EPR to collect site-specific information on the mobility, solvent accessibility, and conformational properties of residues 61-70 of the full-length, cell-expressed M2 protein reconstituted into liposomes. Our analysis is consistent with the predominant population of the C-terminal tail dynamically extending away from the membranes surface into the aqueous medium. These findings provide insight into the hypothesis that the C-terminal domain serves as a sensor that regulates how M2 protein participates in critical events in the viral infection cycle.
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Affiliation(s)
- Grace Kim
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, United States of America
| | - Hayley E Raymond
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, United States of America
| | - Alice L Herneisen
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, United States of America
| | - Abigail Wong-Rolle
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, United States of America
| | - Kathleen P Howard
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, United States of America.
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37
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Belessiotis-Richards A, Higgins SG, Butterworth B, Stevens MM, Alexander-Katz A. Single-Nanometer Changes in Nanopore Geometry Influence Curvature, Local Properties, and Protein Localization in Membrane Simulations. NANO LETTERS 2019; 19:4770-4778. [PMID: 31241342 DOI: 10.1021/acs.nanolett.9b01990] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nanoporous surfaces are used in many applications in intracellular sensing and drug delivery. However, the effects of such nanostructures on cell membrane properties are still far from understood. Here, we use coarse-grained molecular dynamics simulations to show that nanoporous substrates can stimulate membrane-curvature effects and that this curvature-sensing effect is much more sensitive than previously thought. We define a series of design parameters for inducing a nanoscale membrane curvature and show that nanopore taper plays a key role in membrane deformation, elucidating a previously unexplored fabrication parameter applicable to many nanostructured biomaterials. We report significant changes in the membrane area per lipid and thickness at regions of curvature. Finally, we demonstrate that regions of the nanopore-induced membrane curvature act as local hotspots for an increased bioactivity. We show spontaneous binding and localization of the epsin N-terminal homology (ENTH) domain to the regions of curvature. Understanding this interplay between the membrane curvature and nanoporosity at the biointerface helps both explain recent biological results and suggests a pathway for developing the next generation of cell-active substrates.
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Affiliation(s)
- Alexis Belessiotis-Richards
- Department of Materials , Imperial College London , Exhibition Road , London SW7 2AZ , United Kingdom
- Department of Bioengineering , Imperial College London , Exhibition Road , London SW7 2AZ , United Kingdom
- Institute of Biomedical Engineering , Imperial College London , Exhibition Road , London SW7 2AZ , United Kingdom
| | - Stuart G Higgins
- Department of Materials , Imperial College London , Exhibition Road , London SW7 2AZ , United Kingdom
- Department of Bioengineering , Imperial College London , Exhibition Road , London SW7 2AZ , United Kingdom
- Institute of Biomedical Engineering , Imperial College London , Exhibition Road , London SW7 2AZ , United Kingdom
| | - Ben Butterworth
- Department of Materials , Imperial College London , Exhibition Road , London SW7 2AZ , United Kingdom
| | - Molly M Stevens
- Department of Materials , Imperial College London , Exhibition Road , London SW7 2AZ , United Kingdom
- Department of Bioengineering , Imperial College London , Exhibition Road , London SW7 2AZ , United Kingdom
- Institute of Biomedical Engineering , Imperial College London , Exhibition Road , London SW7 2AZ , United Kingdom
| | - Alfredo Alexander-Katz
- Department of Materials Science & Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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38
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Musharrafieh R, Lagarias PI, Ma C, Tan GS, Kolocouris A, Wang J. The L46P mutant confers a novel allosteric mechanism of resistance toward the influenza A virus M2 S31N proton channel blockers. Mol Pharmacol 2019; 96:148-157. [PMID: 31175183 DOI: 10.1124/mol.119.116640] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/30/2019] [Indexed: 12/14/2022] Open
Abstract
The Food and Drug Administration-approved influenza A antiviral amantadine inhibits the wild-type (WT) AM2 channel but not the S31N mutant predominantly found in circulating strains. In this study, serial viral passages were applied to select resistance against a newly developed isoxazole-conjugated adamantane inhibitor that targets the AM2 S31N channel. This led to the identification of the novel drug-resistant mutation L46P located outside the drug-binding site, which suggests an allosteric resistance mechanism. Intriguingly, when the L46P mutant was introduced to AM2 WT, the channel remained sensitive toward amantadine inhibition. To elucidate the molecular mechanism, molecular dynamics simulations and binding free energy molecular mechanics-generalized born surface area (MM-GBSA) calculations were performed on WT and mutant channels. It was found that the L46P mutation caused a conformational change in the N terminus of transmembrane residues 22-31 that ultimately broadened the drug-binding site of AM2 S31N inhibitor 4, which spans residues 26-34, but not of AM2 WT inhibitor amantadine, which spans residues 31-34. The MM-GBSA calculations showed stronger binding stability for 4 in complex with AM2 S31N compared with 4 in complex with AM2 S31N/L46P, and equal binding free energies of amantadine in complex with AM2 WT and AM2 L46P. Overall, these results demonstrate a unique allosteric resistance mechanism toward AM2 S31N channel blockers, and the L46P mutant represents the first experimentally confirmed drug-resistant AM2 mutant that is located outside of the pore where drug binds. SIGNIFICANCE STATEMENT: AM2 S31N is a high-profile antiviral drug target, as more than 95% of currently circulating influenza A viruses carry this mutation. Understanding the mechanism of drug resistance is critical in designing the next generation of AM2 S31N channel blockers. Using a previously developed AM2 S31N channel blocker as a chemical probe, this study was the first to identify a novel resistant mutant, L46P. The L46P mutant is located outside of the drug-binding site. Molecular dynamics simulations showed that L46P causes a dilation of drug-binding site between residues 22 and 31, which affects the binding of AM2 S31N channel blockers, but not the AM2 WT inhibitor amantadine.
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Affiliation(s)
- Rami Musharrafieh
- Department of Pharmacology and Toxicology, College of Pharmacy (R.M., C.M., J.W.) and Department of Chemistry and Biochemistry (R.M.), University of Arizona, Tucson, Arizona; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Greece (P.I.L., A.K.); J. Craig Venter Institute, La Jolla, California (G.S.T.); and Department of Medicine, University of California, San Diego, La Jolla, California (G.S.T.)
| | - Panagiotis I Lagarias
- Department of Pharmacology and Toxicology, College of Pharmacy (R.M., C.M., J.W.) and Department of Chemistry and Biochemistry (R.M.), University of Arizona, Tucson, Arizona; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Greece (P.I.L., A.K.); J. Craig Venter Institute, La Jolla, California (G.S.T.); and Department of Medicine, University of California, San Diego, La Jolla, California (G.S.T.)
| | - Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy (R.M., C.M., J.W.) and Department of Chemistry and Biochemistry (R.M.), University of Arizona, Tucson, Arizona; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Greece (P.I.L., A.K.); J. Craig Venter Institute, La Jolla, California (G.S.T.); and Department of Medicine, University of California, San Diego, La Jolla, California (G.S.T.)
| | - Gene S Tan
- Department of Pharmacology and Toxicology, College of Pharmacy (R.M., C.M., J.W.) and Department of Chemistry and Biochemistry (R.M.), University of Arizona, Tucson, Arizona; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Greece (P.I.L., A.K.); J. Craig Venter Institute, La Jolla, California (G.S.T.); and Department of Medicine, University of California, San Diego, La Jolla, California (G.S.T.)
| | - Antonios Kolocouris
- Department of Pharmacology and Toxicology, College of Pharmacy (R.M., C.M., J.W.) and Department of Chemistry and Biochemistry (R.M.), University of Arizona, Tucson, Arizona; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Greece (P.I.L., A.K.); J. Craig Venter Institute, La Jolla, California (G.S.T.); and Department of Medicine, University of California, San Diego, La Jolla, California (G.S.T.)
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy (R.M., C.M., J.W.) and Department of Chemistry and Biochemistry (R.M.), University of Arizona, Tucson, Arizona; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Greece (P.I.L., A.K.); J. Craig Venter Institute, La Jolla, California (G.S.T.); and Department of Medicine, University of California, San Diego, La Jolla, California (G.S.T.)
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39
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Silvestre-Roig C, Braster Q, Wichapong K, Lee EY, Teulon JM, Berrebeh N, Winter J, Adrover JM, Santos GS, Froese A, Lemnitzer P, Ortega-Gómez A, Chevre R, Marschner J, Schumski A, Winter C, Perez-Olivares L, Pan C, Paulin N, Schoufour T, Hartwig H, González-Ramos S, Kamp F, Megens RTA, Mowen KA, Gunzer M, Maegdefessel L, Hackeng T, Lutgens E, Daemen M, von Blume J, Anders HJ, Nikolaev VO, Pellequer JL, Weber C, Hidalgo A, Nicolaes GAF, Wong GCL, Soehnlein O. Externalized histone H4 orchestrates chronic inflammation by inducing lytic cell death. Nature 2019; 569:236-240. [PMID: 31043745 PMCID: PMC6716525 DOI: 10.1038/s41586-019-1167-6] [Citation(s) in RCA: 257] [Impact Index Per Article: 51.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/02/2019] [Indexed: 12/22/2022]
Abstract
The perpetuation of inflammation is an important pathophysiological contributor to the global medical burden. Chronic inflammation is promoted by non-programmed cell death1,2; however, how inflammation is instigated, its cellular and molecular mediators, and its therapeutic value are poorly defined. Here we use mouse models of atherosclerosis-a major underlying cause of mortality worldwide-to demonstrate that extracellular histone H4-mediated membrane lysis of smooth muscle cells (SMCs) triggers arterial tissue damage and inflammation. We show that activated lesional SMCs attract neutrophils, triggering the ejection of neutrophil extracellular traps that contain nuclear proteins. Among them, histone H4 binds to and lyses SMCs, leading to the destabilization of plaques; conversely, the neutralization of histone H4 prevents cell death of SMCs and stabilizes atherosclerotic lesions. Our data identify a form of cell death found at the core of chronic vascular disease that is instigated by leukocytes and can be targeted therapeutically.
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Affiliation(s)
- Carlos Silvestre-Roig
- Institute for Cardiovascular Prevention (IPEK), LMU München, Munich, Germany.
- Department of Pathology, AMC, Amsterdam, The Netherlands.
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany.
| | - Quinte Braster
- Institute for Cardiovascular Prevention (IPEK), LMU München, Munich, Germany
- Department of Pathology, AMC, Amsterdam, The Netherlands
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Kanin Wichapong
- Department of Biochemistry, CARIM, University Maastricht, Maastricht, The Netherlands
| | - Ernest Y Lee
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Nihel Berrebeh
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Janine Winter
- Institute for Cardiovascular Prevention (IPEK), LMU München, Munich, Germany
| | - José M Adrover
- Area of Developmental and Cell Biology, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | | | - Alexander Froese
- Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Patricia Lemnitzer
- Institute for Cardiovascular Prevention (IPEK), LMU München, Munich, Germany
| | - Almudena Ortega-Gómez
- Institute for Cardiovascular Prevention (IPEK), LMU München, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Raphael Chevre
- Institute for Cardiovascular Prevention (IPEK), LMU München, Munich, Germany
| | - Julian Marschner
- Medizinische Klinik und Poliklinik IV, LMU München, Munich, Germany
| | - Ariane Schumski
- Institute for Cardiovascular Prevention (IPEK), LMU München, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Carla Winter
- Institute for Cardiovascular Prevention (IPEK), LMU München, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | | | - Chang Pan
- Institute for Cardiovascular Prevention (IPEK), LMU München, Munich, Germany
| | - Nicole Paulin
- Institute for Cardiovascular Prevention (IPEK), LMU München, Munich, Germany
| | - Tom Schoufour
- Department of Pathology, AMC, Amsterdam, The Netherlands
| | - Helene Hartwig
- Institute for Cardiovascular Prevention (IPEK), LMU München, Munich, Germany
- Department of Pathology, AMC, Amsterdam, The Netherlands
| | | | - Frits Kamp
- BMC, Metabolic Biochemistry, LMU München, Munich, Germany
| | - Remco T A Megens
- Institute for Cardiovascular Prevention (IPEK), LMU München, Munich, Germany
- Department of Biomedical Engineering, CARIM, University Maastricht, Maastricht, The Netherlands
| | | | - Matthias Gunzer
- Institute for Experimental Immunology and Imaging, University Hospital Essen, Essen, Germany
| | - Lars Maegdefessel
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- Department of Vascular and Endovascular Surgery, Technical University Munich, Munich, Germany
- Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | - Tilman Hackeng
- Department of Biochemistry, CARIM, University Maastricht, Maastricht, The Netherlands
| | - Esther Lutgens
- Institute for Cardiovascular Prevention (IPEK), LMU München, Munich, Germany
- Department of Medical Biochemistry, AMC, Amsterdam, The Netherlands
| | - Mat Daemen
- Department of Pathology, AMC, Amsterdam, The Netherlands
| | | | | | - Viacheslav O Nikolaev
- Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | | | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), LMU München, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- Department of Biochemistry, CARIM, University Maastricht, Maastricht, The Netherlands
| | - Andrés Hidalgo
- Institute for Cardiovascular Prevention (IPEK), LMU München, Munich, Germany
- Area of Developmental and Cell Biology, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Gerry A F Nicolaes
- Department of Biochemistry, CARIM, University Maastricht, Maastricht, The Netherlands
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Oliver Soehnlein
- Institute for Cardiovascular Prevention (IPEK), LMU München, Munich, Germany.
- Department of Pathology, AMC, Amsterdam, The Netherlands.
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany.
- Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden.
- Department of Physiology and Pharmacology (FyFa), Karolinska Institutet, Stockholm, Sweden.
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40
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Lee EY, Zhang C, Di Domizio J, Jin F, Connell W, Hung M, Malkoff N, Veksler V, Gilliet M, Ren P, Wong GCL. Helical antimicrobial peptides assemble into protofibril scaffolds that present ordered dsDNA to TLR9. Nat Commun 2019; 10:1012. [PMID: 30833557 PMCID: PMC6399285 DOI: 10.1038/s41467-019-08868-w] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 12/27/2018] [Indexed: 01/14/2023] Open
Abstract
Amphiphilicity in ɑ-helical antimicrobial peptides (AMPs) is recognized as a signature of potential membrane activity. Some AMPs are also strongly immunomodulatory: LL37-DNA complexes potently amplify Toll-like receptor 9 (TLR9) activation in immune cells and exacerbate autoimmune diseases. The rules governing this proinflammatory activity of AMPs are unknown. Here we examine the supramolecular structures formed between DNA and three prototypical AMPs using small angle X-ray scattering and molecular modeling. We correlate these structures to their ability to activate TLR9 and show that a key criterion is the AMP's ability to assemble into superhelical protofibril scaffolds. These structures enforce spatially-periodic DNA organization in nanocrystalline immunocomplexes that trigger strong recognition by TLR9, which is conventionally known to bind single DNA ligands. We demonstrate that we can "knock in" this ability for TLR9 amplification in membrane-active AMP mutants, which suggests the existence of tradeoffs between membrane permeating activity and immunomodulatory activity in AMP sequences.
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Affiliation(s)
- Ernest Y Lee
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Changsheng Zhang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, PR China
| | - Jeremy Di Domizio
- Department of Dermatology, Lausanne University Hospital CHUV, 1011, Lausanne, Switzerland
| | - Fan Jin
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei, 230026, PR China
| | - Will Connell
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Mandy Hung
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Nicolas Malkoff
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Veronica Veksler
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Michel Gilliet
- Department of Dermatology, Lausanne University Hospital CHUV, 1011, Lausanne, Switzerland
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA.
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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41
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Elías-Wolff F, Lindén M, Lyubartsev AP, Brandt EG. Curvature sensing by cardiolipin in simulated buckled membranes. SOFT MATTER 2019; 15:792-802. [PMID: 30644502 DOI: 10.1039/c8sm02133c] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cardiolipin is a non-bilayer phospholipid with a unique dimeric structure. It localizes to negative curvature regions in bacteria and is believed to stabilize respiratory chain complexes in the highly curved mitochondrial membrane. Cardiolipin's localization mechanism remains unresolved, because important aspects such as the structural basis and strength for lipid curvature preferences are difficult to determine, partly due to the lack of efficient simulation methods. Here, we report a computational approach to study curvature preferences of cardiolipin by simulated membrane buckling and quantitative modeling. We combine coarse-grained molecular dynamics with simulated buckling to determine the curvature preferences in three-component bilayer membranes with varying concentrations of cardiolipin, and extract curvature-dependent concentrations and lipid acyl chain order parameter profiles. Cardiolipin shows a strong preference for negative curvatures, with a highly asymmetric chain order parameter profile. The concentration profiles are consistent with an elastic model for lipid curvature sensing that relates lipid segregation to local curvature via the material constants of the bilayers. These computations constitute new steps to unravel the molecular mechanism by which cardiolipin senses curvature in lipid membranes, and the method can be generalized to other lipids and membrane components as well.
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Affiliation(s)
- Federico Elías-Wolff
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden and Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
| | - Martin Lindén
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
| | - Erik G Brandt
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
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42
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Lee MW, Lee EY, Ferguson AL, Wong GCL. Machine learning antimicrobial peptide sequences: Some surprising variations on the theme of amphiphilic assembly. Curr Opin Colloid Interface Sci 2018; 38:204-213. [PMID: 31093008 DOI: 10.1016/j.cocis.2018.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Antimicrobial peptides (AMPs) collectively constitute a key component of the host innate immune system. They span a diverse space of sequences and can be α-helical, β-sheet, or unfolded in structure. Despite a wealth of knowledge about them from decades of experiments, it remains difficult to articulate general principles governing such peptides. How are they different from other molecules that are also cationic and amphiphilic? What other functions, in immunity and otherwise, are enabled by these simple sequences? In this short review, we present some recent work that engages these questions using methods not usually applied to AMP studies, such as machine learning. We find that not only do AMP-like sequences confer membrane remodeling activity to an unexpectedly broad range of protein classes, their cationic and amphiphilic signature also allows them to act as meta-antigens and self-assemble with immune ligands into nanocrystalline complexes for multivalent presentation to Toll-like receptors.
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Affiliation(s)
- Michelle W Lee
- Department of Bioengineering, Department of Chemistry, California NanoSystems Institute, University of California, Los Angeles, CA 90095, United States
| | - Ernest Y Lee
- Department of Bioengineering, Department of Chemistry, California NanoSystems Institute, University of California, Los Angeles, CA 90095, United States
| | - Andrew L Ferguson
- Institute for Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, United States
| | - Gerard C L Wong
- Department of Bioengineering, Department of Chemistry, California NanoSystems Institute, University of California, Los Angeles, CA 90095, United States
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43
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Elkins MR, Sergeyev IV, Hong M. Determining Cholesterol Binding to Membrane Proteins by Cholesterol 13C Labeling in Yeast and Dynamic Nuclear Polarization NMR. J Am Chem Soc 2018; 140:15437-15449. [PMID: 30338997 PMCID: PMC6361393 DOI: 10.1021/jacs.8b09658] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a general strategy for determining the cholesterol-binding site of eukaryotic membrane proteins in native-like lipid membranes by NMR spectroscopy. The strategy combines yeast biosynthetic 13C enrichment of cholesterol with detection of protein-cholesterol 13C-13C cross peaks in 2D correlation NMR spectra under the dynamic nuclear polarization (DNP) condition. Low-temperature DNP not only allows high-sensitivity detection of weak protein-cholesterol cross peaks in 2D spectra but also immobilizes cholesterol and protein to enable intermolecular distance measurements. We demonstrate this approach on the influenza M2 protein, which utilizes cholesterol to conduct membrane scission in the last step of virus budding and release from the host cell plasma membrane. A 13C-13C double-quantum filter was employed to significantly simplify the 2D 13C-13C correlation spectra and facilitate the identification of protein-cholesterol cross peaks. A number of cross peaks between the M2 transmembrane residues' side chains and the cholesterol sterol group were detected, which complement recently measured protein contacts to the isooctyl tail of cholesterol to define an extended binding interface. These results provide atomic-level evidence of M2-cholesterol interaction to cause membrane curvature and scission, and the approach is generally applicable to other eukaryotic membrane proteins for understanding the influence of cholesterol on membrane protein function.
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Affiliation(s)
- Matthew R. Elkins
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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Alimohamadi H, Rangamani P. Modeling Membrane Curvature Generation due to Membrane⁻Protein Interactions. Biomolecules 2018; 8:E120. [PMID: 30360496 PMCID: PMC6316661 DOI: 10.3390/biom8040120] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 01/03/2023] Open
Abstract
To alter and adjust the shape of the plasma membrane, cells harness various mechanisms of curvature generation. Many of these curvature generation mechanisms rely on the interactions between peripheral membrane proteins, integral membrane proteins, and lipids in the bilayer membrane. Mathematical and computational modeling of membrane curvature generation has provided great insights into the physics underlying these processes. However, one of the challenges in modeling these processes is identifying the suitable constitutive relationships that describe the membrane free energy including protein distribution and curvature generation capability. Here, we review some of the commonly used continuum elastic membrane models that have been developed for this purpose and discuss their applications. Finally, we address some fundamental challenges that future theoretical methods need to overcome to push the boundaries of current model applications.
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Affiliation(s)
- Haleh Alimohamadi
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, CA 92093, USA.
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, CA 92093, USA.
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45
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Entropic forces drive clustering and spatial localization of influenza A M2 during viral budding. Proc Natl Acad Sci U S A 2018; 115:E8595-E8603. [PMID: 30150411 DOI: 10.1073/pnas.1805443115] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The influenza A matrix 2 (M2) transmembrane protein facilitates virion release from the infected host cell. In particular, M2 plays a role in the induction of membrane curvature and/or in the scission process whereby the envelope is cut upon virion release. Here we show using coarse-grained computer simulations that various M2 assembly geometries emerge due to an entropic driving force, resulting in compact clusters or linearly extended aggregates as a direct consequence of the lateral membrane stresses. Conditions under which these protein assemblies will cause the lipid membrane to curve are explored, and we predict that a critical cluster size is required for this to happen. We go on to demonstrate that under the stress conditions taking place in the cellular membrane as it undergoes large-scale membrane remodeling, the M2 protein will, in principle, be able to both contribute to curvature induction and sense curvature to line up in manifolds where local membrane line tension is high. M2 is found to exhibit linactant behavior in liquid-disordered-liquid-ordered phase-separated lipid mixtures and to be excluded from the liquid-ordered phase, in near-quantitative agreement with experimental observations. Our findings support a role for M2 in membrane remodeling during influenza viral budding both as an inducer and a sensor of membrane curvature, and they suggest a mechanism by which localization of M2 can occur as the virion assembles and releases from the host cell, independent of how the membrane curvature is produced.
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Cholesterol and phosphatidylethanolamine lipids exert opposite effects on membrane modulations caused by the M2 amphipathic helix. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1861:201-209. [PMID: 30071193 DOI: 10.1016/j.bbamem.2018.07.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/12/2018] [Accepted: 07/25/2018] [Indexed: 12/18/2022]
Abstract
Membrane curvature remodeling induced by amphipathic helices (AHs) is essential in many biological processes. Here we studied a model amphipathic peptide, M2AH, derived from influenza A M2. We are interested in how M2AH may promote membrane curvature by altering membrane physical properties. We used atomic force microscopy (AFM) to examine changes in membrane topographic and mechanical properties. We used electron paramagnetic resonance (EPR) spectroscopy to explore changes in lipid chain mobility and chain orientational order. We found that M2AH perturbed lipid bilayers by generating nanoscale pits. The structural data are consistent with lateral expansion of lipid chain packing, resulting in a mechanically weaker bilayer. Our EPR spectroscopy showed that M2AH reduced lipid chain mobility and had a minimal effect on lipid chain orientational order. The EPR data are consistent with the surface-bound state of M2AH that acts as a chain mobility inhibitor. By comparing results from different lipid bilayers, we found that cholesterol enhanced the activity of M2AH in inducing bilayer pits and altering lipid chain mobility. The results were explained by considering specific M2AH-cholesterol recognition and/or cholesterol-induced expansion of interlipid distance. Both AFM and EPR experiments revealed a modest effect of anionic lipids. This highlights that membrane interaction of M2AH is mainly driven by hydrophobic forces. Lastly, we found that phosphatidylethanolamine (PE) lipids inhibited the activity of M2AH. We explained our data by considering interlipid hydrogen-bonding that can stabilize bilayer organization. Our results of lipid-dependent membrane modulations are likely relevant to M2AH-induced membrane restructuring.
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Kwon B, Lee M, Waring AJ, Hong M. Oligomeric Structure and Three-Dimensional Fold of the HIV gp41 Membrane-Proximal External Region and Transmembrane Domain in Phospholipid Bilayers. J Am Chem Soc 2018; 140:8246-8259. [PMID: 29888593 DOI: 10.1021/jacs.8b04010] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The HIV-1 glycoprotein, gp41, mediates fusion of the virus lipid envelope with the target cell membrane during virus entry into cells. Despite extensive studies of this protein, inconsistent and contradictory structural information abounds in the literature about the C-terminal membrane-interacting region of gp41. This C-terminal region contains the membrane-proximal external region (MPER), which harbors the epitopes for four broadly neutralizing antibodies, and the transmembrane domain (TMD), which anchors the protein to the virus lipid envelope. Due to the difficulty of crystallizing and solubilizing the MPER-TMD, most structural studies of this functionally important domain were carried out using truncated peptides either in the absence of membrane-mimetic solvents or bound to detergents and lipid bicelles. To determine the structural architecture of the MPER-TMD in the native environment of lipid membranes, we have now carried out a solid-state NMR study of the full MPER-TMD segment bound to cholesterol-containing phospholipid bilayers. 13C chemical shifts indicate that the majority of the peptide is α-helical, except for the C-terminus of the TMD, which has moderate β-sheet character. Intermolecular 19F-19F distance measurements of singly fluorinated peptides indicate that the MPER-TMD is trimerized in the virus-envelope mimetic lipid membrane. Intramolecular 13C-19F distance measurements indicate the presence of a turn between the MPER helix and the TMD helix. This is supported by lipid-peptide and water-peptide 2D 1H-13C correlation spectra, which indicate that the MPER binds to the membrane surface whereas the TMD spans the bilayer. Together, these data indicate that full-length MPER-TMD assembles into a trimeric helix-turn-helix structure in lipid membranes. We propose that the turn between the MPER and TMD may be important for inducing membrane defects in concert with negative-curvature lipid components such as cholesterol and phosphatidylethanolamine, while the surface-bound MPER helix may interact with N-terminal segments of the protein during late stages of membrane fusion.
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Affiliation(s)
- Byungsu Kwon
- Department of Chemistry , Massachusetts Institute of Technology , 170 Albany Street , Cambridge , Massachusetts 02139 , United States
| | - Myungwoon Lee
- Department of Chemistry , Massachusetts Institute of Technology , 170 Albany Street , Cambridge , Massachusetts 02139 , United States
| | - Alan J Waring
- Department of Medicine , Harbor-UCLA Medical Center , 1000 West Carson Street, Building RB2 , Torrance , California 90502 , United States
| | - Mei Hong
- Department of Chemistry , Massachusetts Institute of Technology , 170 Albany Street , Cambridge , Massachusetts 02139 , United States
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Lee MW, Lee EY, Wong GCL. What Can Pleiotropic Proteins in Innate Immunity Teach Us about Bioconjugation and Molecular Design? Bioconjug Chem 2018; 29:2127-2139. [PMID: 29771496 DOI: 10.1021/acs.bioconjchem.8b00176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A common bioengineering strategy to add function to a given molecule is by conjugation of a new moiety onto that molecule. Adding multiple functions in this way becomes increasingly challenging and leads to composite molecules with larger molecular weights. In this review, we attempt to gain a new perspective by looking at this problem in reverse, by examining nature's strategies of multiplexing different functions into the same pleiotropic molecule using emerging analysis techniques such as machine learning. We concentrate on examples from the innate immune system, which employs a finite repertoire of molecules for a broad range of tasks. An improved understanding of how diverse functions are multiplexed into a single molecule can inspire new approaches for the deterministic design of multifunctional molecules.
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49
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Bhate MP, Lemmin T, Kuenze G, Mensa B, Ganguly S, Peters JM, Schmidt N, Pelton JG, Gross CA, Meiler J, DeGrado WF. Structure and Function of the Transmembrane Domain of NsaS, an Antibiotic Sensing Histidine Kinase in Staphylococcus aureus. J Am Chem Soc 2018; 140:7471-7485. [PMID: 29771498 DOI: 10.1021/jacs.7b09670] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
NsaS is one of four intramembrane histidine kinases (HKs) in Staphylococcus aureus that mediate the pathogen's response to membrane active antimicrobials and human innate immunity. We describe the first integrative structural study of NsaS using a combination of solution state NMR spectroscopy, chemical-cross-linking, molecular modeling and dynamics. Three key structural features emerge: First, NsaS has a short N-terminal amphiphilic helix that anchors its transmembrane (TM) bundle into the inner leaflet of the membrane such that it might sense neighboring proteins or membrane deformations. Second, the transmembrane domain of NsaS is a 4-helix bundle with significant dynamics and structural deformations at the membrane interface. Third, the intracellular linker connecting the TM domain to the cytoplasmic catalytic domains of NsaS is a marginally stable helical dimer, with one state likely to be a coiled-coil. Data from chemical shifts, heteronuclear NOE, H/D exchange measurements and molecular modeling suggest that this linker might adopt different conformations during antibiotic induced signaling.
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Affiliation(s)
- Manasi P Bhate
- Department of Pharmaceutical Chemistry , UC San Francisco , San Francisco , California 94158 , United States
| | - Thomas Lemmin
- Department of Pharmaceutical Chemistry , UC San Francisco , San Francisco , California 94158 , United States
| | - Georg Kuenze
- Department of Chemistry, Center for Structural Biology , Vanderbilt University , 465 21st Avenue South , Nashville , Tennessee 37203 , United States
| | - Bruk Mensa
- Department of Pharmaceutical Chemistry , UC San Francisco , San Francisco , California 94158 , United States
| | - Soumya Ganguly
- Department of Chemistry, Center for Structural Biology , Vanderbilt University , 465 21st Avenue South , Nashville , Tennessee 37203 , United States
| | - Jason M Peters
- Department of Microbiology and Immunology , UC San Francisco , San Francisco , California 94158 , United States
| | - Nathan Schmidt
- Department of Pharmaceutical Chemistry , UC San Francisco , San Francisco , California 94158 , United States
| | - Jeffrey G Pelton
- QB3 Institute , UC Berkeley , Berkeley , California 94720 , United States
| | - Carol A Gross
- Department of Pharmaceutical Chemistry , UC San Francisco , San Francisco , California 94158 , United States
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology , Vanderbilt University , 465 21st Avenue South , Nashville , Tennessee 37203 , United States
| | - William F DeGrado
- Department of Pharmaceutical Chemistry , UC San Francisco , San Francisco , California 94158 , United States
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50
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Snead WT, Stachowiak JC. Structure Versus Stochasticity-The Role of Molecular Crowding and Intrinsic Disorder in Membrane Fission. J Mol Biol 2018; 430:2293-2308. [PMID: 29627460 DOI: 10.1016/j.jmb.2018.03.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/22/2018] [Accepted: 03/26/2018] [Indexed: 01/07/2023]
Abstract
Cellular membranes must undergo remodeling to facilitate critical functions including membrane trafficking, organelle biogenesis, and cell division. An essential step in membrane remodeling is membrane fission, in which an initially continuous membrane surface is divided into multiple, separate compartments. The established view has been that membrane fission requires proteins with conserved structural features such as helical scaffolds, hydrophobic insertions, and polymerized assemblies. In this review, we discuss these structure-based fission mechanisms and highlight recent findings from several groups that support an alternative, structure-independent mechanism of membrane fission. This mechanism relies on lateral collisions among crowded, membrane-bound proteins to generate sufficient steric pressure to drive membrane vesiculation. As a stochastic process, this mechanism contrasts with the paradigm that deterministic protein structures are required to drive fission, raising the prospect that many more proteins may participate in fission than previously thought. Paradoxically, our recent work suggests that intrinsically disordered domains may be among the most potent drivers of membrane fission, owing to their large hydrodynamic radii and substantial chain entropy. This stochastic view of fission also suggests new roles for the structure-based fission proteins. Specifically, we hypothesize that in addition to driving fission directly, the canonical fission machines may facilitate the enrichment and organization of bulky disordered protein domains in order to promote membrane fission by locally amplifying protein crowding.
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Affiliation(s)
- Wilton T Snead
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA.
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