1
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Richardson NI, Kuttel MM, Ravenscroft N. Modeling of pneumococcal serogroup 10 capsular polysaccharide molecular conformations provides insight into epitopes and observed cross-reactivity. Front Mol Biosci 2022; 9:961532. [PMID: 36003080 PMCID: PMC9393222 DOI: 10.3389/fmolb.2022.961532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 07/04/2022] [Indexed: 11/21/2022] Open
Abstract
Streptococcus pneumoniae is an encapsulated gram-negative bacterium and a significant human pathogen. The capsular polysaccharide (CPS) is essential for virulence and a target antigen for vaccines. Although widespread introduction of pneumococcal conjugate vaccines (PCVs) has significantly reduced disease, the prevalence of non-vaccine serotypes has increased. On the basis of the CPS, S. pneumoniae serogroup 10 comprises four main serotypes 10A, 10B, 10C, and 10F; as well as the recently identified 10D. As it is the most prevalent, serotype 10A CPS has been included as a vaccine antigen in the next generation PCVs. Here we use molecular modeling to provide conformational rationales for the complex cross-reactivity reported between serotypes 10A, 10B, 10C, and 10F anti-sera. Although the highly mobile phosphodiester linkages produce very flexible CPS, shorter segments are conformationally defined, with exposed β-D-galactofuranose (β DGalf) side chains that are potential antibody binding sites. We identify four distinct conformational epitopes for the immunodominant β DGalf that assist in rationalizing the complex asymmetric cross-reactivity relationships. In particular, we find that strongly cross-reactive serotypes share common epitopes. Further, we show that human intelectin-1 has the potential to bind the exposed exocyclic 1,2-diol of the terminal β DGalf in each serotype; the relative accessibility of three- or six-linked β DGalf may play a role in the strength of the innate immune response and hence serotype disease prevalence. In conclusion, our modeling study and relevant serological studies support the inclusion of serotype 10A in a vaccine to best protect against serogroup 10 disease.
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Affiliation(s)
| | - Michelle M. Kuttel
- Department of Computer Science, University of Cape Town, Cape Town, South Africa
| | - Neil Ravenscroft
- Department of Chemistry, University of Cape Town, Cape Town, South Africa
- *Correspondence: Neil Ravenscroft,
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2
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Lazar RD, Akher FB, Ravenscroft N, Kuttel MM. Carbohydrate Force Fields: The Role of Small Partial Atomic Charges in Preventing Conformational Collapse. J Chem Theory Comput 2022; 18:1156-1172. [PMID: 35015958 DOI: 10.1021/acs.jctc.1c00534] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although the quality of current additive all-atom force fields for carbohydrates has been demonstrated in many applications, occasional significant differences reported for the hydrodynamic behavior of specific polysaccharides modeled with different force fields is a cause for concern. In particular, irreversible conformational collapse has been noted for some polysaccharide simulations with the GLYCAM06j force field. Here, we investigate the cause of this phenomenon through comparative simulations of a range of saccharides with both the GLYCAM06j and the CHARMM36 carbohydrate force fields. We find that conformational collapse in GLYCAM06j occurs for saccharide chains containing the deoxy sugar α-l-rhamnose after relatively long simulation intervals. Further, we explore the mechanism of conformational collapse and show that this phenomenon arises because of the anomalous low energy in GLYCAM06j (as compared to quantum mechanical calculations) of a specific orientation of α-l-Rha to α-l-Rha glycosidic linkages, which are subsequently sustained by intramolecular interactions in the saccharide chain. We identify the lack of partial charges on aliphatic hydrogens in GLYCAM as the source of this anomaly, demonstrating that addition of small partial atomic charges on the aliphatic protons in rhamnose removes the conformational collapse phenomenon. This work reveals the large cumulative impact that small partial charges may have on the dynamic behavior of polysaccharides and indicates that future reparameterization of the GLYCAM06j force field should investigate the addition of partial charges on all aliphatic hydrogens.
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Affiliation(s)
- Ryan D Lazar
- Department of Computer Science, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Farideh B Akher
- Department of Computer Science, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Neil Ravenscroft
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Michelle M Kuttel
- Department of Computer Science, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
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3
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Hlozek J, Owen S, Ravenscroft N, Kuttel MM. Molecular Modeling of the Shigella flexneri Serogroup 3 and 5 O-Antigens and Conformational Relationships for a Vaccine Containing Serotypes 2a and 3a. Vaccines (Basel) 2020; 8:vaccines8040643. [PMID: 33147882 PMCID: PMC7712985 DOI: 10.3390/vaccines8040643] [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] [Received: 09/16/2020] [Revised: 10/09/2020] [Accepted: 10/29/2020] [Indexed: 12/12/2022] Open
Abstract
The pathogenic bacterium Shigella flexneri is a leading global cause of diarrheal disease. The O-antigen is the primary vaccine target and distinguishes the 30 serotypes reported. Except for serotype 6, all S. flexneri serotypes have a common backbone repeating unit (serotype Y), with variations in substitution creating the various serotypes. A quadrivalent vaccine containing serotypes 2a and 3a (as well as 6 and Shigella sonnei) is proposed to provide broad protection against non-vaccine S. flexneri serotypes through shared epitopes and conformations. Here we model the O-antigen (O-Ag) conformations of serogroups 3 and 5: a continuation of our ongoing systematic study of the S. flexneri O-antigens that began with serogroup 2. Our simulations show that S. flexneri serogroups 2, 3, and 5 all have flexible O-Ags, with substitutions of the backbone altering the chain conformations in different ways. Our analysis suggests three general heuristics for the effects of substitution on the Shigella O-Ag conformations: (1) substitution on rhamnose C reduces the extension of the O-Ag chain; (2) substitution at O-3 of rhamnose A restricts the O-Ags to predominantly helical conformations, (3) substitution at O-3 of rhamnose B has only a slight effect on conformation. The common O-Ag conformations across serotypes identified in this work support the assumption that a quadrivalent vaccine containing serotypes 2a and 3a could provide coverage against S. flexneri serotype 3b and serogroup 5.
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Affiliation(s)
- Jason Hlozek
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa; (J.H.); (N.R.)
| | - Sara Owen
- Department of Computer Science, University of Cape Town, Rondebosch 7701, South Africa;
| | - Neil Ravenscroft
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa; (J.H.); (N.R.)
| | - Michelle M. Kuttel
- Department of Computer Science, University of Cape Town, Rondebosch 7701, South Africa;
- Correspondence:
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4
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Kunstmann S, Engström O, Wehle M, Widmalm G, Santer M, Barbirz S. Increasing the Affinity of an O-Antigen Polysaccharide Binding Site in Shigella flexneri Bacteriophage Sf6 Tailspike Protein. Chemistry 2020; 26:7263-7273. [PMID: 32189378 PMCID: PMC7463171 DOI: 10.1002/chem.202000495] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/09/2020] [Indexed: 12/30/2022]
Abstract
Broad and unspecific use of antibiotics accelerates spread of resistances. Sensitive and robust pathogen detection is thus important for a more targeted application. Bacteriophages contain a large repertoire of pathogen-binding proteins. These tailspike proteins (TSP) often bind surface glycans and represent a promising design platform for specific pathogen sensors. We analysed bacteriophage Sf6 TSP that recognizes the O-polysaccharide of dysentery-causing Shigella flexneri to develop variants with increased sensitivity for sensor applications. Ligand polyrhamnose backbone conformations were obtained from 2D 1 H,1 H-trNOESY NMR utilizing methine-methine and methine-methyl correlations. They agreed well with conformations obtained from molecular dynamics (MD), validating the method for further predictions. In a set of mutants, MD predicted ligand flexibilities that were in good correlation with binding strength as confirmed on immobilized S. flexneri O-polysaccharide (PS) with surface plasmon resonance. In silico approaches combined with rapid screening on PS surfaces hence provide valuable strategies for TSP-based pathogen sensor design.
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Affiliation(s)
- Sonja Kunstmann
- Physikalische BiochemieUniversität PotsdamKarl-Liebknecht-Str. 24–2514476PotsdamGermany
- Theory and BiosystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Current address: Department of Biotechnology and BiomedicineTechnical University of DenmarkSøltofts Plads2800 Kgs.LyngbyDenmark
| | - Olof Engström
- Department of Organic ChemistryArrhenius LaboratoryStockholm University10691StockholmSweden
| | - Marko Wehle
- Theory and BiosystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Göran Widmalm
- Department of Organic ChemistryArrhenius LaboratoryStockholm University10691StockholmSweden
| | - Mark Santer
- Theory and BiosystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Stefanie Barbirz
- Physikalische BiochemieUniversität PotsdamKarl-Liebknecht-Str. 24–2514476PotsdamGermany
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5
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Hlozek J, Ravenscroft N, Kuttel MM. Effects of Glucosylation and O-Acetylation on the Conformation of Shigella flexneri Serogroup 2 O-Antigen Vaccine Targets. J Phys Chem B 2020; 124:2806-2814. [PMID: 32204588 DOI: 10.1021/acs.jpcb.0c01595] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Shigellosis is an enteric disease with high morbidity and mortality, particularly in developing countries. There is currently no licensed vaccine available. Most infection is caused by Shigella flexneri, of which 30 serotypes have been recognized based on O-antigen polysaccharide structure. Almost all S. flexneri serotypes share the same repeating unit backbone (serotype Y), with varying glucosylation, O-acetylation and phosphorylation. The O-antigen is the primary vaccine target; the vaccine valency (and hence cost) can be reduced by cross-protection. Our planned systematic conformational study of S. flexneri starts here with 2a, the dominant cause of infection globally. We employ microsecond molecular dynamics simulations to compare the conformation of the unsubstituted serotype Y backbone with the serogroup 2 O-antigens, to investigate the effect of glucosylation and O-acetylation (O-factor 9) on conformation. We find that serotype Y is highly flexible, whereas glucosylation in 2a restricts flexibility and induces C-curve conformations. Further, the glucose side-chains adopt two distinct conformations, corroborated by the antibody-bound crystal structure data. Additional substitution on O-3 of rhamnose A (whether O-acetylation in 2a or glucosylation in 2b) induces helical conformations. Our results suggest that the O-3-acetylated 2a antigen will elicit cross-protection against 2b, as well as other serotypes containing O-factor 9.
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Affiliation(s)
- Jason Hlozek
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Neil Ravenscroft
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Michelle M Kuttel
- Department of Computer Science, University of Cape Town, Rondebosch 7701, South Africa
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6
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Li A, Schertzer JW, Yong X. Molecular dynamics modeling of Pseudomonas aeruginosa outer membranes. Phys Chem Chem Phys 2018; 20:23635-23648. [PMID: 30191217 DOI: 10.1039/c8cp04278k] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Pseudomonas aeruginosa is a common Gram-negative bacterium and opportunistic human pathogen. The distinctive structure of its outer membrane (OM) and outer membrane vesicles (OMVs) plays a fundamental role in bacterial virulence, colonization ability, and antibiotic resistance. To provide critical insights into OM and OMV functionality, we conducted an all-atom molecular dynamics study of asymmetric membranes that are biologically relevant to P. aeruginosa. We hybridized a GLYCAM06-based lipopolysaccharides force field with the Stockholm lipids force field (Slipids) to model bilayer membranes with Lipid A molecules in one leaflet and physiologically relevant phospholipid molecules in the other, including 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE), 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), 1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol (DPPG), and 1,2-dioleoyl-sn-glycero-3-phosphoglycerol (DOPG). In particular, a membrane with phospholipid composition representing the P. aeruginosa OM was constructed and modeled by mixing the physiologically dominant components. The detailed structure of membranes was characterized by area per lipid, transmembrane mass and charge densities, radial distribution function (RDF), deuterium order parameter (SCD) of acyl chains, and inclination angles of phosphates and disaccharide in Lipid A. The membrane fluidity in equilibrium and the hydration of functional groups were probed and characterized quantitatively. The consistent properties of the Lipid A leaflets in different membranes demonstrate its compatibility with various phospholipids present in the P. aeruginosa OM. The more ordered acyl chains of Lipid A compared to the cytoplasmic cell membrane contribute to the low permeability of bacterial outer membrane. The findings of this computational investigation of P. aeruginosa OM will further the understanding of microbial pathogenesis and enable future study of OMV biogenesis.
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Affiliation(s)
- Ao Li
- Department of Mechanical Engineering, Binghamton University, The State University of New York, Binghamton, New York 13902, USA.
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7
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Combining scattering and computer simulation for the study of biomolecular soft interfaces. Curr Opin Colloid Interface Sci 2018. [DOI: 10.1016/j.cocis.2018.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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8
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Kunstmann S, Scheidt T, Buchwald S, Helm A, Mulard LA, Fruth A, Barbirz S. Bacteriophage Sf6 Tailspike Protein for Detection of Shigella flexneri Pathogens. Viruses 2018; 10:E431. [PMID: 30111705 PMCID: PMC6116271 DOI: 10.3390/v10080431] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/26/2018] [Accepted: 08/09/2018] [Indexed: 12/30/2022] Open
Abstract
Bacteriophage research is gaining more importance due to increasing antibiotic resistance. However, for treatment with bacteriophages, diagnostics have to be improved. Bacteriophages carry adhesion proteins, which bind to the bacterial cell surface, for example tailspike proteins (TSP) for specific recognition of bacterial O-antigen polysaccharide. TSP are highly stable proteins and thus might be suitable components for the integration into diagnostic tools. We used the TSP of bacteriophage Sf6 to establish two applications for detecting Shigella flexneri (S. flexneri), a highly contagious pathogen causing dysentery. We found that Sf6TSP not only bound O-antigen of S. flexneri serotype Y, but also the glucosylated O-antigen of serotype 2a. Moreover, mass spectrometry glycan analyses showed that Sf6TSP tolerated various O-acetyl modifications on these O-antigens. We established a microtiter plate-based ELISA like tailspike adsorption assay (ELITA) using a Strep-tag®II modified Sf6TSP. As sensitive screening alternative we produced a fluorescently labeled Sf6TSP via coupling to an environment sensitive dye. Binding of this probe to the S. flexneri O-antigen Y elicited a fluorescence intensity increase of 80% with an emission maximum in the visible light range. The Sf6TSP probes thus offer a promising route to a highly specific and sensitive bacteriophage TSP-based Shigella detection system.
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Affiliation(s)
- Sonja Kunstmann
- Physical Biochemistry, University of Potsdam, 14476 Potsdam, Germany.
| | - Tom Scheidt
- Physical Biochemistry, University of Potsdam, 14476 Potsdam, Germany.
| | - Saskia Buchwald
- Physical Biochemistry, University of Potsdam, 14476 Potsdam, Germany.
| | - Alexandra Helm
- Physical Biochemistry, University of Potsdam, 14476 Potsdam, Germany.
| | - Laurence A Mulard
- Institut Pasteur, Unité de Chimie des Biomolécules, 28 rue du Roux, 75015 Paris, France.
- CNRS UMR 3523, Institut Pasteur, 75015 Paris, France.
| | - Angelika Fruth
- National Reference Centre for Salmonella and other Bacterial Enterics, Robert Koch Institute, 38855 Wernigerode, Germany.
| | - Stefanie Barbirz
- Physical Biochemistry, University of Potsdam, 14476 Potsdam, Germany.
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9
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Liu W, Jia X, Wang M, Li P, Wang X, Hu W, Zheng J, Mei Y. Calculations of the absolute binding free energies for Ralstonia solanacearum lectins bound with methyl-α-l-fucoside at molecular mechanical and quantum mechanical/molecular mechanical levels. RSC Adv 2017. [DOI: 10.1039/c7ra06215j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this work, both a molecular mechanical (MM) method and a hybrid quantum mechanical/molecular mechanical (QM/MM) method have been applied in the study of the binding affinities of methyl-α-l-fucoside to Ralstonia solanacearum lectins.
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Xiangyu Jia
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Meiting Wang
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Pengfei Li
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Xiaohui Wang
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Wenxin Hu
- The Computer Center
- School of Computer Science and Software Engineering
- East China Normal University
- Shanghai 200062
- China
| | - Jun Zheng
- The Computer Center
- School of Computer Science and Software Engineering
- East China Normal University
- Shanghai 200062
- China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
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10
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Complex carbohydrate recognition by proteins: Fundamental insights from bacteriophage cell adhesion systems. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.pisc.2016.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Galochkina T, Zlenko D, Nesterenko A, Kovalenko I, Strakhovskaya M, Averyanov A, Rubin A. Conformational Dynamics of the Single Lipopolysaccharide O-Antigen in Solution. Chemphyschem 2016; 17:2839-53. [DOI: 10.1002/cphc.201600524] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Tatiana Galochkina
- Federal Research Clinical Center of Federal Medical & Biological Agency of Russia; Orekhovy boulevard 28 Moscow 115682 Russia
- Department of Biophysics, Faculty of Biology; M. V. Lomonosov Moscow State University; Leninskie gory 1/24 Moscow 119992 Russia
- Institut Camille Jordan; University Lyon 1; 43 bd 11 Novembre 1918 Villeurbanne 69622 France
- INRIA Team Dracula, INRIA Antenne Lyon la Doua; Villeurbanne 69603 France
| | - Dmitry Zlenko
- Department of Biophysics, Faculty of Biology; M. V. Lomonosov Moscow State University; Leninskie gory 1/24 Moscow 119992 Russia
| | - Alexey Nesterenko
- Department of Biophysics, Faculty of Biology; M. V. Lomonosov Moscow State University; Leninskie gory 1/24 Moscow 119992 Russia
- A. N. Belozersky Institute of Physico-Chemical Biology; M. V. Lomonosov Moscow State University; Moscow 119992 Russia
| | - Ilya Kovalenko
- Federal Research Clinical Center of Federal Medical & Biological Agency of Russia; Orekhovy boulevard 28 Moscow 115682 Russia
- Department of Biophysics, Faculty of Biology; M. V. Lomonosov Moscow State University; Leninskie gory 1/24 Moscow 119992 Russia
| | - Marina Strakhovskaya
- Federal Research Clinical Center of Federal Medical & Biological Agency of Russia; Orekhovy boulevard 28 Moscow 115682 Russia
- Department of Biophysics, Faculty of Biology; M. V. Lomonosov Moscow State University; Leninskie gory 1/24 Moscow 119992 Russia
| | - Alexander Averyanov
- Federal Research Clinical Center of Federal Medical & Biological Agency of Russia; Orekhovy boulevard 28 Moscow 115682 Russia
| | - Andrey Rubin
- Department of Biophysics, Faculty of Biology; M. V. Lomonosov Moscow State University; Leninskie gory 1/24 Moscow 119992 Russia
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12
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Kang Y, Gohlke U, Engström O, Hamark C, Scheidt T, Kunstmann S, Heinemann U, Widmalm G, Santer M, Barbirz S. Bacteriophage Tailspikes and Bacterial O-Antigens as a Model System to Study Weak-Affinity Protein–Polysaccharide Interactions. J Am Chem Soc 2016; 138:9109-18. [DOI: 10.1021/jacs.6b00240] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Yu Kang
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Ulrich Gohlke
- Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Olof Engström
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106
91 Stockholm, Sweden
| | - Christoffer Hamark
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106
91 Stockholm, Sweden
| | - Tom Scheidt
- Physikalische
Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Sonja Kunstmann
- Physikalische
Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Udo Heinemann
- Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft, Robert-Rössle-Str. 10, 13125 Berlin, Germany
- Institut
für Chemie und Biochemie, Freie Universität, Takustr. 6, 14195 Berlin, Germany
| | - Göran Widmalm
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106
91 Stockholm, Sweden
| | - Mark Santer
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Stefanie Barbirz
- Physikalische
Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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13
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Plazinski W, Lonardi A, Hünenberger PH. Revision of the GROMOS 56A6(CARBO) force field: Improving the description of ring-conformational equilibria in hexopyranose-based carbohydrates chains. J Comput Chem 2015; 37:354-65. [PMID: 26525424 DOI: 10.1002/jcc.24229] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 10/03/2015] [Accepted: 10/06/2015] [Indexed: 01/19/2023]
Abstract
This article describes a revised version 56A6(CARBO_R) of the GROMOS 56A6(CARBO) force field for hexopyranose-based carbohydrates. The simulated properties of unfunctionalized hexopyranoses are unaltered with respect to 56A6CARBO . In the context of both O1 -alkylated hexopyranoses and oligosaccharides, the revision stabilizes the regular (4) C1 chair for α-anomers, with the opposite effect for β-anomers. As a result, spurious ring inversions observed in α(1→4)-linked chains when using the original 56A6(CARBO) force field are alleviated. The (4) C1 chair is now the most stable conformation for all d-hexopyranose residues, irrespective of the linkage type and anomery, and of the position of the residue along the chain. The methylation of a d-hexopyranose leads to a systematic shift in the ring-inversion free energy ((4) C1 to (1) C4 ) by 7-8 kJ mol(-1), positive for the α-anomers and negative for the β-anomers, which is qualitatively compatible with the expected enhancement of the anomeric effect upon methylation at O1. The ring-inversion free energies for residues within chains are typically smaller in magnitude compared to those of the monomers, and correlate rather poorly with the latter. This suggests that the crowding of ring substituents upon chain formation alters the ring flexibility in a nonsystematic fashion. In general, the description of carbohydrate chains afforded by 56A6(CARBO_R) suggests a significant extent of ring flexibility, i.e., small but often non-negligible equilibrium populations of inverted chairs, and challenges the "textbook" picture of conformationally locked carbohydrate rings.
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Affiliation(s)
- Wojciech Plazinski
- Laboratory of Physical Chemistry, ETH Hönggerberg, HCI, Zürich, CH-8093, Switzerland.,J. Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Ul. Niezapominajek 8, Cracow, 30-239, Poland
| | - Alice Lonardi
- Laboratory of Physical Chemistry, ETH Hönggerberg, HCI, Zürich, CH-8093, Switzerland
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14
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Ma H, Irudayanathan FJ, Jiang W, Nangia S. Simulating Gram-Negative Bacterial Outer Membrane: A Coarse Grain Model. J Phys Chem B 2015; 119:14668-82. [DOI: 10.1021/acs.jpcb.5b07122] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Huilin Ma
- Department of Biomedical
and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | | | - Wenjuan Jiang
- Department of Biomedical
and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Shikha Nangia
- Department of Biomedical
and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
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15
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Brunschweiger A. Report from the Third Annual Symposium of the RIKEN-Max Planck Joint Research Center for Systems Chemical Biology. ACS Chem Biol 2014; 9:1649-52. [PMID: 25123304 DOI: 10.1021/cb500579u] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The third Annual Symposium of the RIKEN-Max Planck Joint Research Center for Systems Chemical Biology was held at Ringberg castle, May 21-24, 2014. At this meeting 45 scientists from Japan and Germany presented the latest results from their research spanning a broad range of topics in chemical biology and glycobiology.
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Affiliation(s)
- Andreas Brunschweiger
- Fakultät
Chemie - Chemische
Biologie, Technische Universität Dortmund, Otto-Hahn-Str.
6, 44227 Dortmund, Germany
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