1
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Gao Y, Widmalm G, Im W. Modeling and Simulation of Bacterial Outer Membranes with Lipopolysaccharides and Capsular Polysaccharides. J Chem Inf Model 2023; 63:1592-1601. [PMID: 36802606 DOI: 10.1021/acs.jcim.3c00072] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Capsule is one of the common virulence factors in Gram-negative bacteria protecting pathogens from host defenses and consists of long-chain capsular polysaccharides (CPS) anchored in the outer membrane (OM). Elucidating structural properties of CPS is important to understand its biological functions as well as the OM properties. However, the outer leaflet of the OM in current simulation studies is represented exclusively by LPS due to the complexity and diversity of CPS. In this work, representative Escherichia coli CPS, KLPS (a lipid A-linked form) and KPG (a phosphatidylglycerol-linked form), are modeled and incorporated into various symmetric bilayers with co-existing LPS in different ratios. All-atom molecular dynamics simulations of these systems have been conducted to characterize various bilayer properties. Incorporation of KLPS makes the acyl chains of LPS more rigid and ordered, while incorporation of KPG makes them less ordered and flexible. These results are consistent with the calculated area per lipid (APL) of LPS, in which the APL of LPS becomes smaller when KLPS is incorporated, whereas it gets larger when KPG is included. Torsional analysis reveals that the influence of the CPS presence on the conformational distributions of the glycosidic linkages of LPS is small, and minor differences are also detected for the inner and outer regions of the CPS. Combined with previously modeled enterobacterial common antigens (ECAs) in the form of mixed bilayers, this work provides more realistic OM models as well as the basis for characterization of interactions between the OM and OM proteins.
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Affiliation(s)
- Ya Gao
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, Shanghai 201620, China.,Department of Biological Sciences, Department of Chemistry, and Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Wonpil Im
- Department of Biological Sciences, Department of Chemistry, and Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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2
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González-Fernández C, Basauri A, Fallanza M, Bringas E, Oostenbrink C, Ortiz I. Fighting Against Bacterial Lipopolysaccharide-Caused Infections through Molecular Dynamics Simulations: A Review. J Chem Inf Model 2021; 61:4839-4851. [PMID: 34559524 PMCID: PMC8549069 DOI: 10.1021/acs.jcim.1c00613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
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Lipopolysaccharide
(LPS) is the primary component of the outer
leaflet of Gram-negative bacterial outer membranes. LPS elicits an
overwhelming immune response during infection, which can lead to life-threatening
sepsis or septic shock for which no suitable treatment is available
so far. As a result of the worldwide expanding multidrug-resistant
bacteria, the occurrence and frequency of sepsis are expected to increase;
thus, there is an urge to develop novel strategies for treating bacterial
infections. In this regard, gaining an in-depth understanding about
the ability of LPS to both stimulate the host immune system and interact
with several molecules is crucial for fighting against LPS-caused
infections and allowing for the rational design of novel antisepsis
drugs, vaccines and LPS sequestration and detection methods. Molecular
dynamics (MD) simulations, which are understood as being a computational
microscope, have proven to be of significant value to understand LPS-related
phenomena, driving and optimizing experimental research studies. In
this work, a comprehensive review on the methods that can be combined
with MD simulations, recently applied in LPS research, is provided.
We focus especially on both enhanced sampling methods, which enable
the exploration of more complex systems and access to larger time
scales, and free energy calculation approaches. Thereby, apart from
outlining several strategies for surmounting LPS-caused infections,
this work reports the current state-of-the-art of the methods applied
with MD simulations for moving a step forward in the development of
such strategies.
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Affiliation(s)
- Cristina González-Fernández
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
| | - Arantza Basauri
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
| | - Marcos Fallanza
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
| | - Eugenio Bringas
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Inmaculada Ortiz
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
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3
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Luna E, Kim S, Gao Y, Widmalm G, Im W. Influences of Vibrio cholerae Lipid A Types on LPS Bilayer Properties. J Phys Chem B 2021; 125:2105-2112. [PMID: 33600188 DOI: 10.1021/acs.jpcb.0c09144] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Lipopolysaccharides (LPS) present in the outer leaflet of Gram-negative bacterial outer membranes protect the bacteria from external threats and influence antibiotic permeability as well as immune system recognition. The structure of lipid A, the anchor of an LPS molecule to the outer membrane, can make direct influences on membrane properties. Particularly, in Vibrio cholerae, a Gram-negative bacterium responsible for cholera, a severe diarrheal disease, modifications of lipid A structures grant antibiotic resistance and are a primary factor that led to the current cholera pandemic. However, the difference in structural properties incurred by such modifications has not been fully explored. In this work, five symmetric bilayer systems comprised of distinct lipid A structures of Vibrio cholerae LPS with O1 O-antigen were modeled and simulated to explore influences of different lipid A types on membrane properties. All-atom molecular dynamics simulations reveal that membrane properties such as hydrophobic thickness, acyl chain order parameter, and area per lipid are largely impacted by lipid A modifications due to differences in composition and acyl chain distortions. The modified lipid A is also less negatively charged, which possibly reveals a resistance mechanism to cationic antimicrobial peptide evasion. These findings present a possible explanation for Vibrio cholerae's immune system evasion properties and establish the differences between the lipid A types, which should be of use for any future study of the Gram-negative bacteria.
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Affiliation(s)
- Emanuel Luna
- Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Seonghoon Kim
- Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States.,School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Ya Gao
- School of Mathematics, Physics, and Statistics, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Wonpil Im
- Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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4
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Gao Y, Lee J, Widmalm G, Im W. Modeling and Simulation of Bacterial Outer Membranes with Lipopolysaccharides and Enterobacterial Common Antigen. J Phys Chem B 2020; 124:5948-5956. [DOI: 10.1021/acs.jpcb.0c03353] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ya Gao
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, Shanghai 201620, China
- Department of Biological Sciences, Department of Chemistry, and Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Jumin Lee
- Department of Biological Sciences, Department of Chemistry, and Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Wonpil Im
- Department of Biological Sciences, Department of Chemistry, and Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
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5
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Whitfield C, Williams DM, Kelly SD. Lipopolysaccharide O-antigens-bacterial glycans made to measure. J Biol Chem 2020; 295:10593-10609. [PMID: 32424042 DOI: 10.1074/jbc.rev120.009402] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/17/2020] [Indexed: 01/05/2023] Open
Abstract
Lipopolysaccharides are critical components of bacterial outer membranes. The more conserved lipid A part of the lipopolysaccharide molecule is a major element in the permeability barrier imposed by the outer membrane and offers a pathogen-associated molecular pattern recognized by innate immune systems. In contrast, the long-chain O-antigen polysaccharide (O-PS) shows remarkable structural diversity and fulfills a range of functions, depending on bacterial lifestyles. O-PS production is vital for the success of clinically important Gram-negative pathogens. The biological properties and functions of O-PSs are mostly independent of specific structures, but the size distribution of O-PS chains is particularly important in many contexts. Despite the vast O-PS chemical diversity, most are produced in bacterial cells by two assembly strategies, and the different mechanisms employed in these pathways to regulate chain-length distribution are emerging. Here, we review our current understanding of the mechanisms involved in regulating O-PS chain-length distribution and discuss their impact on microbial cell biology.
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Affiliation(s)
- Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Danielle M Williams
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Steven D Kelly
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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6
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Patel DS, Blasco P, Widmalm G, Im W. Escherichia coli O176 LPS structure and dynamics: A NMR spectroscopy and MD simulation study. Curr Res Struct Biol 2020; 2:79-88. [PMID: 34235471 PMCID: PMC8244359 DOI: 10.1016/j.crstbi.2020.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/06/2020] [Accepted: 04/08/2020] [Indexed: 01/30/2023] Open
Abstract
A lipopolysaccharide (LPS) molecule is a key component of the bacterial outer membrane used to protect the bacterium and to interact with the environment. To gain insight into its function, the study of the LPS conformation and dynamics at the molecular and cellular levels is necessary, but these highly diverse and dynamic membrane-LPS systems are difficult to study. In this work, by using NMR spectroscopy and molecular dynamics (MD) simulations, we determined the conformational preferences of an E. coli O176 O-antigen polysaccharide at the atomic level. Moreover, we analyzed the use of non-uniform sampling (NUS) for the acquisition of high dynamic range spectra, like 1H,1H-NOESY NMR experiments. A comparison of the effective transglycosidic distances derived from conventional uniformly sampled and NUS 1H,1H-NOESY data showed high similarity under equal measuring time conditions. Furthermore, the experimentally derived internuclear distances of the O-antigen polysaccharide with ten repeating units (RUs) showed very good agreement to those calculated from the MD simulations of the same O-antigen polysaccharide in solution. Analysis of the LPS bilayer simulations with five and with ten RUs revealed that, although similar with respect to populated states in solution, the O-antigen in LPS bilayers had more extended chains as a result of spatial limitations due to close packing. Additional MD simulations of O-antigen polysaccharides from E. coli O6 (branched repeating unit) and O91 (negatively charged linear repeating unit) in solution and LPS bilayers were performed and compared to those of O176 (linear polymer). For all three O-antigens, the ensemble of structures present for the polysaccharides in solution were consistent with the results from their 1H,1H-NOESY experiments. In addition, the similarities between the O-antigen on its own and as a constituent of the full LPS in bilayer environment makes it possible to realistically describe the LPS conformation and dynamics from the MD simulations. Uniform and non-uniform sampled NOESY NMR data yield similar internuclear distances. O-antigen internuclear distances from NMR and MD show excellent agreement. O-antigen ensemble structures from MD are consistent with NMR observations. O-antigen structures are more extended in LPS bilayers than in solution. MD simulations can describe realistic LPS conformation and dynamics.
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Affiliation(s)
- Dhilon S Patel
- Departments of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, PA, 18015, USA
| | - Pilar Blasco
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Wonpil Im
- Departments of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, PA, 18015, USA
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7
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Abstract
Gram-negative bacteria are protected by a multicompartmental molecular architecture known as the cell envelope that contains two membranes and a thin cell wall. As the cell envelope controls influx and efflux of molecular species, in recent years both experimental and computational studies of such architectures have seen a resurgence due to the implications for antibiotic development. In this article we review recent progress in molecular simulations of bacterial membranes. We show that enormous progress has been made in terms of the lipidic and protein compositions of bacterial systems. The simulations have moved away from the traditional setup of one protein surrounded by a large patch of the same lipid type toward a more bio-logically representative viewpoint. Simulations with multiple cell envelope components are also emerging. We review some of the key method developments that have facilitated recent progress, discuss some current limitations, and offer a perspective on future directions.
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Affiliation(s)
- Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton S017 1BJ, United Kingdom
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8
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Domínguez-Medina CC, Pérez-Toledo M, Schager AE, Marshall JL, Cook CN, Bobat S, Hwang H, Chun BJ, Logan E, Bryant JA, Channell WM, Morris FC, Jossi SE, Alshayea A, Rossiter AE, Barrow PA, Horsnell WG, MacLennan CA, Henderson IR, Lakey JH, Gumbart JC, López-Macías C, Bavro VN, Cunningham AF. Outer membrane protein size and LPS O-antigen define protective antibody targeting to the Salmonella surface. Nat Commun 2020; 11:851. [PMID: 32051408 PMCID: PMC7015928 DOI: 10.1038/s41467-020-14655-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 01/23/2020] [Indexed: 11/28/2022] Open
Abstract
Lipopolysaccharide (LPS) O-antigen (O-Ag) is known to limit antibody binding to surface antigens, although the relationship between antibody, O-Ag and other outer-membrane antigens is poorly understood. Here we report, immunization with the trimeric porin OmpD from Salmonella Typhimurium (STmOmpD) protects against infection. Atomistic molecular dynamics simulations indicate this is because OmpD trimers generate footprints within the O-Ag layer sufficiently sized for a single IgG Fab to access. While STmOmpD differs from its orthologue in S. Enteritidis (SEn) by a single amino-acid residue, immunization with STmOmpD confers minimal protection to SEn. This is due to the OmpD-O-Ag interplay restricting IgG binding, with the pairing of OmpD with its native O-Ag being essential for optimal protection after immunization. Thus, both the chemical and physical structure of O-Ag are key for the presentation of specific epitopes within proteinaceous surface-antigens. This enhances combinatorial antigenic diversity in Gram-negative bacteria, while reducing associated fitness costs. The O-antigen of LPS is known to limit the binding of antibody to bacterial surface antigens. Here the AUs show that the chemical and physical structure of the O-antigen are central factors in limiting the exposure of surface antigens to antibodies during Salmonella infection, thus defining their protective qualities.
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Affiliation(s)
- C Coral Domínguez-Medina
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Marisol Pérez-Toledo
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK.,Medical Research Unit on Immunochemistry, Specialties Hospital, National Medical Centre "Siglo XXI" Mexican Institute for Social Security, Mexico City, Mexico
| | - Anna E Schager
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jennifer L Marshall
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Charlotte N Cook
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Saeeda Bobat
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Hyea Hwang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta GA, 30332, USA
| | - Byeong Jae Chun
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta GA, 30332, USA
| | - Erin Logan
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town, Western Cape, 7925, South Africa
| | - Jack A Bryant
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Will M Channell
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Faye C Morris
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Sian E Jossi
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Areej Alshayea
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Amanda E Rossiter
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Paul A Barrow
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - William G Horsnell
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town, Western Cape, 7925, South Africa
| | - Calman A MacLennan
- Jenner Institute, Nuffield Department of Medicine, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford, OX3 7DQ, UK
| | - Ian R Henderson
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jeremy H Lakey
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Constantino López-Macías
- Medical Research Unit on Immunochemistry, Specialties Hospital, National Medical Centre "Siglo XXI" Mexican Institute for Social Security, Mexico City, Mexico
| | - Vassiliy N Bavro
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
| | - Adam F Cunningham
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK. .,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK.
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9
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Copoiu L, Malhotra S. The current structural glycome landscape and emerging technologies. Curr Opin Struct Biol 2020; 62:132-139. [PMID: 32006784 DOI: 10.1016/j.sbi.2019.12.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 11/19/2022]
Abstract
Carbohydrates represent one of the building blocks of life, along with nucleic acids, proteins and lipids. Although glycans are involved in a wide range of processes from embryogenesis to protein trafficking and pathogen infection, we are still a long way from deciphering the glycocode. In this review, we aim to present a few of the challenges that researchers working in the area of glycobiology can encounter and what strategies can be utilised to overcome them. Our goal is to paint a comprehensive picture of the current saccharide landscape available in the Protein Data Bank (PDB). We also review recently updated repositories relevant to the topic proposed, the impact of software development on strategies to structurally solve carbohydrate moieties, and state-of-the-art molecular and cellular biology methods that can shed some light on the function and structure of glycans.
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Affiliation(s)
- Liviu Copoiu
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Sony Malhotra
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom.
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10
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Jefferies D, Shearer J, Khalid S. Role of O-Antigen in Response to Mechanical Stress of the E. coli Outer Membrane: Insights from Coarse-Grained MD Simulations. J Phys Chem B 2019; 123:3567-3575. [DOI: 10.1021/acs.jpcb.8b12168] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Damien Jefferies
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Jonathan Shearer
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
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11
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Leonard AN, Wang E, Monje-Galvan V, Klauda JB. Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes. Chem Rev 2019; 119:6227-6269. [DOI: 10.1021/acs.chemrev.8b00384] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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12
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Hughes AV, Patel DS, Widmalm G, Klauda JB, Clifton LA, Im W. Physical Properties of Bacterial Outer Membrane Models: Neutron Reflectometry & Molecular Simulation. Biophys J 2019; 116:1095-1104. [PMID: 30850116 DOI: 10.1016/j.bpj.2019.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 01/25/2019] [Accepted: 02/05/2019] [Indexed: 12/13/2022] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria is an asymmetric bilayer having phospholipids in the inner leaflet and lipopolysaccharides in the outer leaflet. This unique asymmetry and the complex carbohydrates in lipopolysaccharides make it a daunting task to study the asymmetrical OM structure and dynamics, its interactions with OM proteins, and its roles in translocation of substrates, including antibiotics. In this study, we combine neutron reflectometry and molecular simulation to explore the physical properties of OM mimetics. There is excellent agreement between experiment and simulation, allowing experimental testing of the conclusions from simulations studies and also atomistic interpretation of the behavior of experimental model systems, such as the degree of lipid asymmetry, the lipid component (tail, head, and sugar) profiles along the bilayer normal, and lateral packing (i.e., average surface area per lipid). Therefore, the combination of both approaches provides a powerful new means to explore the biological and biophysical behavior of the bacterial OM.
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Affiliation(s)
- Arwel V Hughes
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Oxford Campus, Didcot, Oxfordshire, United Kingdom.
| | - Dhilon S Patel
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, Pennsylvania
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockhozlm, Sweden
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, Biophysics Program, University of Maryland, College Park, Maryland
| | - Luke A Clifton
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Oxford Campus, Didcot, Oxfordshire, United Kingdom
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, Pennsylvania.
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13
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Lee J, Patel DS, Ståhle J, Park SJ, Kern NR, Kim S, Lee J, Cheng X, Valvano MA, Holst O, Knirel YA, Qi Y, Jo S, Klauda JB, Widmalm G, Im W. CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans. J Chem Theory Comput 2018; 15:775-786. [PMID: 30525595 DOI: 10.1021/acs.jctc.8b01066] [Citation(s) in RCA: 322] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Glycolipids (such as glycoglycerolipids, glycosphingolipids, and glycosylphosphatidylinositol) and lipoglycans (such as lipopolysaccharides (LPS), lipooligosaccharides (LOS), mycobacterial lipoarabinomannan, and mycoplasma lipoglycans) are typically found on the surface of cell membranes and play crucial roles in various cellular functions. Characterizing their structure and dynamics at the molecular level is essential to understand their biological roles, but systematic generation of glycolipid and lipoglycan structures is challenging because of great variations in lipid structures and glycan sequences (i.e., carbohydrate types and their linkages). To facilitate the generation of all-atom glycolipid/LPS/LOS structures, we have developed Glycolipid Modeler and LPS Modeler in CHARMM-GUI ( http://www.charmm-gui.org ), a web-based interface that simplifies building of complex biological simulation systems. In addition, we have incorporated these modules into Membrane Builder so that users can readily build a complex symmetric or asymmetric biological membrane system with various glycolipids and LPS/LOS. These tools are expected to be useful in innovative and novel glycolipid/LPS/LOS modeling and simulation research by easing tedious and intricate steps in modeling complex biological systems and shall provide insight into structures, dynamics, and underlying mechanisms of complex glycolipid-/LPS-/LOS-containing biological membrane systems.
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Affiliation(s)
- Jumin Lee
- Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
| | - Dhilon S Patel
- Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
| | - Jonas Ståhle
- Department of Organic Chemistry, Arrhenius Laboratory , Stockholm University , SE-106 91 Stockholm , Sweden
| | - Sang-Jun Park
- Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
| | - Nathan R Kern
- Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
| | - Seonghoon Kim
- Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
| | - Joonseong Lee
- Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
| | - Xi Cheng
- State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China
| | - Miguel A Valvano
- Wellcome-Wolfson Institute for Experimental Medicine , Queen's University Belfast BT9 7BL , United Kingdom
| | - Otto Holst
- Division of Structural Biochemistry, Research Center Borstel , Airway Research Center North, Member of the German Center for Lung Research (DZL) , D-23845 Borstel , Germany
| | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry , Russian Academy of Sciences , 119991 Moscow , Russia
| | - Yifei Qi
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , China
| | - Sunhwan Jo
- Leadership Computing Facility , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering and the Biophysics Graduate Program , University of Maryland , College Park , Maryland 20742 , United States
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory , Stockholm University , SE-106 91 Stockholm , Sweden
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
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14
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Lee J, Pothula KR, Kleinekathöfer U, Im W. Simulation Study of Occk5 Functional Properties in Pseudomonas aeruginosa Outer Membranes. J Phys Chem B 2018; 122:8185-8192. [DOI: 10.1021/acs.jpcb.8b07109] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Joonseong Lee
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Karunakar R. Pothula
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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15
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Jo S, Myatt D, Qi Y, Doutch J, Clifton LA, Im W, Widmalm G. Multiple Conformational States Contribute to the 3D Structure of a Glucan Decasaccharide: A Combined SAXS and MD Simulation Study. J Phys Chem B 2018; 122:1169-1175. [DOI: 10.1021/acs.jpcb.7b11085] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sunhwan Jo
- Leadership
Computing Facility, Argonne National Laboratory, 9700 Cass Avenue, Argonne 60439, Illinois, United States
| | - Daniel Myatt
- ISIS
Pulsed Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, Oxfordshire OX11
OQX, U.K
| | - Yifei Qi
- College
of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - James Doutch
- ISIS
Pulsed Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, Oxfordshire OX11
OQX, U.K
| | - Luke A. Clifton
- ISIS
Pulsed Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, Oxfordshire OX11
OQX, U.K
| | - Wonpil Im
- Department
of Biological Sciences and Bioengineering, Lehigh University, Bethlehem 18015, Pennsylvania, United States
| | - Göran Widmalm
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106
91 Stockholm, Sweden
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16
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Colorimetric analysis of lipopolysaccharides based on its self-assembly to inhibit ion transport. Anal Chim Acta 2017; 992:85-93. [DOI: 10.1016/j.aca.2017.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 09/02/2017] [Accepted: 09/03/2017] [Indexed: 11/22/2022]
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