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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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Hamark C, Berntsson RPA, Masuyer G, Henriksson LM, Gustafsson R, Stenmark P, Widmalm G. Glycans Confer Specificity to the Recognition of Ganglioside Receptors by Botulinum Neurotoxin A. J Am Chem Soc 2016; 139:218-230. [PMID: 27958736 DOI: 10.1021/jacs.6b09534] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The highly poisonous botulinum neurotoxins, produced by the bacterium Clostridium botulinum, act on their hosts by a high-affinity association to two receptors on neuronal cell surfaces as the first step of invasion. The glycan motifs of gangliosides serve as initial coreceptors for these protein complexes, whereby a membrane protein receptor is bound. Herein we set out to characterize the carbohydrate minimal binding epitope of the botulinum neurotoxin serotype A. By means of ligand-based NMR spectroscopy, X-ray crystallography, computer simulations, and isothermal titration calorimetry, a screening of ganglioside analogues together with a detailed characterization of various carbohydrate ligand complexes with the toxin were accomplished. We show that the representation of the glycan epitope to the protein affects the details of binding. Notably, both branches of the oligosaccharide GD1a can associate to botulinum neurotoxin serotype A when expressed as individual trisaccharides. It is, however, the terminal branch of GD1a as well as this trisaccharide motif alone, corresponding to the sialyl-Thomsen-Friedenreich antigen, that represents the active ligand epitope, and these compounds bind to the neurotoxin with a high degree of predisposition but with low affinities. This finding does not correlate with the oligosaccharide moieties having a strong contribution to the total affinity, which was expected to be the case. We here propose that the glycan part of the ganglioside receptors mainly provides abundance and specificity, whereas the interaction with the membrane itself and protein receptor brings about the strong total binding of the toxin to the neuronal membrane.
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Affiliation(s)
- Christoffer Hamark
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , S-106 91 Stockholm, Sweden
| | - Ronnie P-A Berntsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University , S-106 91 Stockholm, Sweden
| | - Geoffrey Masuyer
- Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University , S-106 91 Stockholm, Sweden
| | - Linda M Henriksson
- Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University , S-106 91 Stockholm, Sweden
| | - Robert Gustafsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University , S-106 91 Stockholm, Sweden
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University , S-106 91 Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , S-106 91 Stockholm, Sweden
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Soltesova M, Kowalewski J, Widmalm G. Dynamics of exocyclic groups in the Escherichia coli O91 O-antigen polysaccharide in solution studied by carbon-13 NMR relaxation. JOURNAL OF BIOMOLECULAR NMR 2013; 57:37-45. [PMID: 23897032 DOI: 10.1007/s10858-013-9763-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 07/17/2013] [Indexed: 06/02/2023]
Abstract
Carbon-13 relaxation data are reported for exocyclic groups of hexopyranosyl sugar residues in the repeating unit within the Escherichia coli O91 O-antigen polysaccharide in a dilute D2O solution. The measurements of T 1, T 2 and heteronuclear nuclear Overhauser enhancements were carried out at 310 K at two magnetic fields (16.4 T, 21.1 T). The data were analyzed using the standard and extended Lipari-Szabo models, as well as a conformational jump model. The extended version of the Lipari-Szabo and the two-site jump models were most successful for the hydroxymethyl groups of Gal and GlcNAc sugar residues. Different dynamics was found for the hydroxymethyl groups associated with different configurations (D-gluco, D-galacto) of the sugar residues, the latter being faster than the former.
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Affiliation(s)
- Maria Soltesova
- Arrhenius Laboratory, Department of Materials and Environmental Chemistry, Stockholm University, 106 91, Stockholm, Sweden
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Mertz B, Lu M, Brown MF, Feller SE. Steric and electronic influences on the torsional energy landscape of retinal. Biophys J 2011; 101:L17-9. [PMID: 21806916 DOI: 10.1016/j.bpj.2011.06.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Revised: 06/08/2011] [Accepted: 06/13/2011] [Indexed: 10/17/2022] Open
Abstract
We have performed quantum mechanical calculations for retinal model compounds to establish the rotational energy barriers for the C5-, C9-, and C13-methyl groups known to play an essential role in rhodopsin activation. Intraretinal steric interactions as well as electronic effects lower the rotational barriers of both the C9- and C13-methyl groups, consistent with experimental (2)H NMR data. Each retinal methyl group has a unique rotational behavior which must be treated individually. These results are highly relevant for the parameterization of molecular mechanics force fields which form the basis of molecular dynamics simulations of retinal proteins such as rhodopsin.
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Affiliation(s)
- Blake Mertz
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
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Venable RM, Hatcher E, Guvench O, MacKerell AD, Pastor RW. Comparing simulated and experimental translation and rotation constants: range of validity for viscosity scaling. J Phys Chem B 2010; 114:12501-7. [PMID: 20831149 PMCID: PMC3040444 DOI: 10.1021/jp105549s] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proper simulation of dynamic properties, including molecular diffusion, is an important goal of empirical force fields. However, the widely used TIP3P water model does not reproduce the experimental viscosity of water. Consequently, scaling of simulated diffusion constants of solutes in aqueous solutions is required to effectively compare them with experiment. It is proposed that scaling by the ratio of viscosities of model and real water is appropriate in the regime where the concentration dependence of simulated and experimental solution viscosities is parallel. With this ansatz, viscosity scaling can be carried out for glucose and trehalose up to 20 wt % for simulations carried out with the CHARMM additive carbohydrate force field C35 and TIP3P water; above this value, the concentration dependence of simulated viscosities lags that of experiment, and scaling is not advised. Scaled translational diffusion constants for glucose and the disaccharides trehalose, maltose, and melibiose at low concentration agree nearly quantitatively with experiment, as do NMR (13)C T(1)'s for glucose, trehalose, and maltose; these results support the use of C35 for simulations of sugar transport properties at low concentration. At high concentrations the scaled diffusion constants for glucose and trehalose underestimate and overestimate experiment, respectively. Hydrodynamic bead model calculations indicate a hydration level of approximately 1 water/hydroxyl for glucose. Patterns for the disaccharides are more complicated, though trehalose binds 0.5 to 1 more water than does maltose depending on the analysis.
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Affiliation(s)
- Richard M. Venable
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Elizabeth Hatcher
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, MD 21201
| | - Olgun Guvench
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, MD 21201
- Department of Pharmaceutical Sciences, University of New England College of Pharmacy, 716 Stevens Ave, Portland, ME 04103
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, MD 21201
| | - Richard W. Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
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Brown MF, Salgado GFJ, Struts AV. Retinal dynamics during light activation of rhodopsin revealed by solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1798:177-93. [PMID: 19716801 DOI: 10.1016/j.bbamem.2009.08.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 07/25/2009] [Accepted: 08/12/2009] [Indexed: 11/28/2022]
Abstract
Rhodopsin is a canonical member of class A of the G protein-coupled receptors (GPCRs) that are implicated in many of the drug interventions in humans and are of great pharmaceutical interest. The molecular mechanism of rhodopsin activation remains unknown as atomistic structural information for the active metarhodopsin II state is currently lacking. Solid-state (2)H NMR constitutes a powerful approach to study atomic-level dynamics of membrane proteins. In the present application, we describe how information is obtained about interactions of the retinal cofactor with rhodopsin that change with light activation of the photoreceptor. The retinal methyl groups play an important role in rhodopsin function by directing conformational changes upon transition into the active state. Site-specific (2)H labels have been introduced into the methyl groups of retinal and solid-state (2)H NMR methods applied to obtain order parameters and correlation times that quantify the mobility of the cofactor in the inactive dark state, as well as the cryotrapped metarhodopsin I and metarhodopsin II states. Analysis of the angular-dependent (2)H NMR line shapes for selectively deuterated methyl groups of rhodopsin in aligned membranes enables determination of the average ligand conformation within the binding pocket. The relaxation data suggest that the beta-ionone ring is not expelled from its hydrophobic pocket in the transition from the pre-activated metarhodopsin I to the active metarhodopsin II state. Rather, the major structural changes of the retinal cofactor occur already at the metarhodopsin I state in the activation process. The metarhodopsin I to metarhodopsin II transition involves mainly conformational changes of the protein within the membrane lipid bilayer rather than the ligand. The dynamics of the retinylidene methyl groups upon isomerization are explained by an activation mechanism involving cooperative rearrangements of extracellular loop E2 together with transmembrane helices H5 and H6. These activating movements are triggered by steric clashes of the isomerized all-trans retinal with the beta4 strand of the E2 loop and the side chains of Glu(122) and Trp(265) within the binding pocket. The solid-state (2)H NMR data are discussed with regard to the pathway of the energy flow in the receptor activation mechanism.
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Affiliation(s)
- Michael F Brown
- Department of Chemistry, University of Arizona, Tucson, AZ 85721, USA; Department of Physics, University of Arizona, Tucson, AZ 85721, USA.
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The form of an internal reorientational correlation function. Chem Phys 2001. [DOI: 10.1016/s0301-0104(00)00380-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Zhang Y, Bull TE. Nonlinearly coupled generalized Fokker-Planck equation for rotational relaxation. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1994; 49:4886-4902. [PMID: 9961808 DOI: 10.1103/physreve.49.4886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Zhang Y. Path-integral formalism for classical Brownian motion in a general environment. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1993; 47:3745-3748. [PMID: 9960434 DOI: 10.1103/physreve.47.3745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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