1
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Sheikh MO, Thieker D, Chalmers G, Schafer CM, Ishihara M, Azadi P, Woods RJ, Glushka JN, Bendiak B, Prestegard JH, West CM. O 2 sensing-associated glycosylation exposes the F-box-combining site of the Dictyostelium Skp1 subunit in E3 ubiquitin ligases. J Biol Chem 2017; 292:18897-18915. [PMID: 28928219 PMCID: PMC5704474 DOI: 10.1074/jbc.m117.809160] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/12/2017] [Indexed: 11/06/2022] Open
Abstract
Skp1 is a conserved protein linking cullin-1 to F-box proteins in SCF (Skp1/Cullin-1/F-box protein) E3 ubiquitin ligases, which modify protein substrates with polyubiquitin chains that typically target them for 26S proteasome-mediated degradation. In Dictyostelium (a social amoeba), Toxoplasma gondii (the agent for human toxoplasmosis), and other protists, Skp1 is regulated by a unique pentasaccharide attached to hydroxylated Pro-143 within its C-terminal F-box-binding domain. Prolyl hydroxylation of Skp1 contributes to O2-dependent Dictyostelium development, but full glycosylation at that position is required for optimal O2 sensing. Previous studies have shown that the glycan promotes organization of the F-box-binding region in Skp1 and aids in Skp1's association with F-box proteins. Here, NMR and MS approaches were used to determine the glycan structure, and then a combination of NMR and molecular dynamics simulations were employed to characterize the impact of the glycan on the conformation and motions of the intrinsically flexible F-box-binding domain of Skp1. Molecular dynamics trajectories of glycosylated Skp1 whose calculated monosaccharide relaxation kinetics and rotational correlation times agreed with the NMR data indicated that the glycan interacts with the loop connecting two α-helices of the F-box-combining site. In these trajectories, the helices separated from one another to create a more accessible and dynamic F-box interface. These results offer an unprecedented view of how a glycan modification influences a disordered region of a full-length protein. The increased sampling of an open Skp1 conformation can explain how glycosylation enhances interactions with F-box proteins in cells.
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Affiliation(s)
- M Osman Sheikh
- From the Department of Biochemistry and Molecular Biology
- the Complex Carbohydrate Research Center, and
- the Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, and
| | | | - Gordon Chalmers
- the Complex Carbohydrate Research Center, and
- the Department of Computer Science, University of Georgia, Athens, Georgia 30602
| | - Christopher M Schafer
- the Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, and
| | | | | | - Robert J Woods
- From the Department of Biochemistry and Molecular Biology
- the Complex Carbohydrate Research Center, and
| | | | - Brad Bendiak
- the Department of Cell and Developmental Biology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - James H Prestegard
- From the Department of Biochemistry and Molecular Biology
- the Complex Carbohydrate Research Center, and
| | - Christopher M West
- From the Department of Biochemistry and Molecular Biology,
- the Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, and
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2
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García I, Sánchez-Iglesias A, Henriksen-Lacey M, Grzelczak M, Penadés S, Liz-Marzán LM. Glycans as Biofunctional Ligands for Gold Nanorods: Stability and Targeting in Protein-Rich Media. J Am Chem Soc 2015; 137:3686-92. [DOI: 10.1021/jacs.5b01001] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Isabel García
- CIC biomaGUNE, Paseo de Miramón 182, 20009 Donostia-San Sebastián, Spain
- Biomedical Research Networking Center in Bioengineering Biomaterials and Nanomedicine (CIBER-BBN), 50018 Aragon, Spain
| | | | | | - Marek Grzelczak
- CIC biomaGUNE, Paseo de Miramón 182, 20009 Donostia-San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Soledad Penadés
- CIC biomaGUNE, Paseo de Miramón 182, 20009 Donostia-San Sebastián, Spain
- Biomedical Research Networking Center in Bioengineering Biomaterials and Nanomedicine (CIBER-BBN), 50018 Aragon, Spain
| | - Luis M. Liz-Marzán
- CIC biomaGUNE, Paseo de Miramón 182, 20009 Donostia-San Sebastián, Spain
- Biomedical Research Networking Center in Bioengineering Biomaterials and Nanomedicine (CIBER-BBN), 50018 Aragon, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
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3
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Parasuraman P, Murugan V, Selvin JFA, Gromiha MM, Fukui K, Veluraja K. Insights into the binding specificity of wild type and mutated wheat germ agglutinin towards Neu5Acα(2-3)Gal: a study by in silico mutations and molecular dynamics simulations. J Mol Recognit 2015; 27:482-92. [PMID: 24984865 DOI: 10.1002/jmr.2369] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 02/02/2014] [Accepted: 02/02/2014] [Indexed: 02/06/2023]
Abstract
Wheat germ agglutinin (WGA) is a plant lectin, which specifically recognizes the sugars NeuNAc and GlcNAc. Mutated WGA with enhanced binding specificity can be used as biomarkers for cancer. In silico mutations are performed at the active site of WGA to enhance the binding specificity towards sialylglycans, and molecular dynamics simulations of 20 ns are carried out for wild type and mutated WGAs (WGA1, WGA2, and WGA3) in complex with sialylgalactose to examine the change in binding specificity. MD simulations reveal the change in binding specificity of wild type and mutated WGAs towards sialylgalactose and bound conformational flexibility of sialylgalactose. The mutated polar amino acid residues Asn114 (S114N), Lys118 (G118K), and Arg118 (G118R) make direct and water mediated hydrogen bonds and hydrophobic interactions with sialylgalactose. An analysis of possible hydrogen bonds, hydrophobic interactions, total pair wise interaction energy between active site residues and sialylgalactose and MM-PBSA free energy calculation reveals the plausible binding modes and the role of water in stabilizing different binding modes. An interesting observation is that the binding specificity of mutated WGAs (cyborg lectin) towards sialylgalactose is found to be higher in double point mutation (WGA3). One of the substituted residues Arg118 plays a crucial role in sugar binding. Based on the interactions and energy calculations, it is concluded that the order of binding specificity of WGAs towards sialylgalactose is WGA3 > WGA1 > WGA2 > WGA. On comparing with the wild type, double point mutated WGA (WGA3) exhibits increased specificity towards sialylgalactose, and thus, it can be effectively used in targeted drug delivery and as biological cell marker in cancer therapeutics.
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Affiliation(s)
- Ponnusamy Parasuraman
- Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, 627 012, India
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4
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Jiménez-Barbero J, Javier Cañada F, Asensio JL, Aboitiz N, Vidal P, Canales A, Groves P, Gabius HJ, Siebert HC. Hevein Domains: An Attractive Model to Study Carbohydrate–Protein Interactions at Atomic Resolution. Adv Carbohydr Chem Biochem 2006; 60:303-54. [PMID: 16750446 DOI: 10.1016/s0065-2318(06)60007-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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5
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Gupta D, Surolia A. Synthesis of Specifically Deuteriated Derivatives of D-Galactose and D-Galactosamine. J Carbohydr Chem 1992. [DOI: 10.1080/07328309208017798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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Szilágyi L, Forgó P. Enzyme-inhibitor complexes of lysozyme with glucosamine inhibitors A molecular dynamics study through 2H-NMR. Biophys Chem 1991; 40:89-96. [PMID: 17014774 DOI: 10.1016/0301-4622(91)85033-m] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/1990] [Revised: 10/19/1990] [Accepted: 11/07/1990] [Indexed: 11/18/2022]
Abstract
2H relaxation measurements coupled with multiple specific 2H labeling have provided insight into the molecular dynamics of N-acetyl-D-glucosamine (GlcNAc) inhibitors bound to lysozyme. Deuteron T1 and T2 data for the bound state of methyl alpha- and -beta-GlcNAc 2H-labeled in the glycosidic methyl and C2 positions have been derived from measurements at different enzyme/inhibitor ratios. Rotational correlation times calculated therefrom for the labeled sites indicate, in both cases, tight binding for the sugar ring (tau(b) = 3.0 x 10(-9) s) accompanied by fast internal rotation, about one axis, of the glycosidic methyl groups (tau(r) = 5.5-7.6 x 10(-11) s). The small but consistent difference in the rates of internal rotation for the alpha- and beta-anomeric inhibitors may be indicative of different solution structures of the enzyme-inhibitor complexes.
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Affiliation(s)
- L Szilágyi
- Department of Organic Chemistry, L. Kossuth University, Pf. 20, H-4010 Debrecen, Hungary
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7
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Bundle DR, Gerken M, Peters T. Synthesis of antigenic determinants of the Brucella A antigen, utilizing methyl 4-azido-4,6-dideoxy-alpha-D-mannopyranoside efficiently derived from D-mannose. Carbohydr Res 1988; 174:239-51. [PMID: 2454158 DOI: 10.1016/0008-6215(88)85094-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A strategy for the synthesis of Brucella O-antigenic determinants containing 2-linked 4,6-dideoxy-4-formamido-alpha-D-mannopyranosyl residues is described. The approach adopted also permits the N-acyl moiety to be varied. A high-yield synthesis of methyl 4-azido-4,6-dideoxy-alpha-D-mannopyranoside from D-mannose on the 10-20-g scale provided the key intermediate. Regioselective acetylation of 7 gave the 2-acetate 8, which, on treatment with benzyl trichloroacetimidate, provided methyl 2-O-acetyl-4-azido-3-O-benzyl-4,6-dideoxy-alpha-D-mannopyranoside. This compound served as a common precursor to the glycosyl donor 12 and acceptor 10 molecules. Silver trifluoromethanesulphonate-promoted glycosylation of 10 by 12 gave a disaccharide derivative, hydrogenolysis of which gave methyl 4-amino-2-O-(4-amino-4,6-dideoxy-alpha-D-mannopyranosyl)-4,6-dideoxy- alpha-D-mannopyranoside from which the N-formyl and N-acetyl derivatives were obtained. Deacetylation of 13 followed by glycosylation with 12 gave a trisaccharide derivative. The N-formylated disaccharide 17 inhibited the binding of Brucella O-polysaccharide to Brucella-specific monoclonal antibodies.
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Affiliation(s)
- D R Bundle
- Division of Biological Sciences, National Research Council of Canada, Ottawa, Ontario
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8
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Berman E, Lis H, James TL. Binding of [1-13C]galactose-enriched hen ovalbumin to Erythrina cristagalli agglutinin as studied by 13C-NMR spectroscopy. EUROPEAN JOURNAL OF BIOCHEMISTRY 1986; 161:589-94. [PMID: 3792309 DOI: 10.1111/j.1432-1033.1986.tb10482.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A study of the equilibrium binding of glycoproteins to lectins was undertaken using the titled compounds as a model system for such interactions. The binding of hen ovalbumin, enriched in galactose specifically 13C-labelled at C1, to Erythrina cristagalli agglutinin was studied by 13C-NMR spectroscopy. The lectin was shown to be bivalent for ovalbumin with an apparent estimated association constant, at infinite dilution, of about 10(4) M-1. The observed association is similar to that found for the corresponding disaccharide, Gal(beta 1-4)GlcNAc. The results strongly suggest that only the N-acetyllactosamine moiety in the carbohydrate side chain of galactose-enriched ovalbumin participates in the binding to the lectin with little, if any, interactions from other parts of either the side chain or the polypeptide backbone of ovalbumin.
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9
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Preston C, Preston JM. Proton nuclear magnetic resonance studies of soybean lectin-monosaccharide interactions: computer analysis of complex binding behavior. Arch Biochem Biophys 1986; 247:190-200. [PMID: 3010876 DOI: 10.1016/0003-9861(86)90548-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
1H NMR was used to quantify soybean lectin binding to monosaccharides, using presaturation of HOD plus a spin-echo sequence to observe sugar -NHCOCH3 and -OCH3 to below 0.01 mM. Binding is in the very-slow-exchange limit; there is no broadening or shifting and only unbound sugar is observed for pH 5 to 8 and 25 to 75 degrees C. Preliminary results were consistent with those previously reported for methyl 2-acetamido-2-deoxy-alpha-D-galactopyranoside (Me alpha-D-GalNAcp) (K = 3 X 10(4) liters mol-1 with four sites per tetramer). More detailed studies, however, gave concave Scatchard plots for methyl 2-acetamido-2-deoxy-alpha- and beta-D-galactopyranoside, (Me alpha- and Me beta-D-GalNAcp), best fitted using K1 values of (6-12) X 10(4) liters mol-1, K2 values less than or equal to 0.5 X 10(4) liters mol-1, and four sites of each type in D2O or 80% H2O at 25 degrees C and pH 7.2. Data for methyl alpha-D-galactopyranoside were fitted with K = 0.5 X 10(4) liters mol-1 and eight sites of the same K. Monosaccharides may be binding in the recently reported "hydrophobic sites" of soybean lectin. Both methyl 2-acetamido-2-deoxy-beta-D-galactofuranoside (Me beta-D-GalNAcf) and methyl 2-acetamido-2-deoxy-alpha-D-glucopyranoside (Me alpha-D-GlcNAcP) showed some binding by 1H NMR; K's were similar to those for the high-affinity sugars, but the occupancy was much lower. The soybean lectin in this study was saturated in Ca2+ (greater than or equal to 4 mol/tetramer), but low in Mn2+, with Mn2+ plus Mg2+ less than 4. We report new melting points for D-N-acetylgalactosamine, Me alpha-D-GlcNAcp, Me beta-D-GalNAcp, and Me beta-D-GalNAcf, and a fully listed program for fitting curved Scatchard plots using Apple IIc and IIe computers.
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10
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Berman E, Brown JH, Lis H, Sharon N. Binding of [1-13C]galactose-labeled N-acetyllactosamine to Erythrina cristagalli agglutinin as studied by 13C-NMR. EUROPEAN JOURNAL OF BIOCHEMISTRY 1985; 152:447-51. [PMID: 4054114 DOI: 10.1111/j.1432-1033.1985.tb09217.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The equilibrium binding kinetics of enzymatically prepared N-acetyllactosamine to the lectin from Erythrina cristagalli have been investigated by 13C-NMR spectroscopy. Under the experimental conditions used, NMR signals in the spectrum, corresponding to both the free and bound disaccharide species, were observed for the first time. This has permitted the simultaneous determinations of the equilibrium binding constant and the number of binding sites per lectin molecule. At the relatively high lectin concentrations used (0.3-0.87 mM), the association constants determined at 31 degrees C (approximately 6 X 10(3) M-1) are typically lower then those obtained by other methods employing much lower lectin concentrations. Extrapolation of the experimentally observed values to infinite dilution gave a better fit of the data (Ka approximately 1.4 X 10(4) M-1) with the binding constant determined by other methods (K approximately 1.1 X 10(4) M-1). The sugar residence time on the lectin (approximately 0.2 s) was determined directly from the signal's line-width using total line-shape analysis. Similar NMR experiments may permit an analysis of the interaction of the lectin with glycoproteins and cells labelled with 13C-enriched galactose residues. Moreover, information on lectin-galactose interactions at the binding site may be obtained by using galactose labeled at various carbons.
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11
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Serianni AS, Barker R. 13C spin-lattice relaxation times of [1−13C]-enriched carbohydrates. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/0022-2364(82)90198-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Neurohr KJ, Young NM, Smith IC, Mantsch HH. Kinetics of binding of methyl alpha- and beta-D-galactopyranoside to peanut agglutinin: a carbon-13 nuclear magnetic resonance study. Biochemistry 1981; 20:3499-504. [PMID: 7260053 DOI: 10.1021/bi00515a030] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The binding kinetics of methyl alpha- and methyl beta-D-galactopyranoside to the anti-T lectin from peanuts were studied by 13C NMR, employing methyl galactopyranosides specifically enriched in 13C at C-1. Association and dissociation rate constants, as well as their activation parameters, are reported. The association rate constants, 4.6 X 10(4) M-1 s-1 for the alpha-galactopyranoside and 3.6 X 10(4) M-1 s-1 for the beta-galactopyranoside, are several orders of magnitude below those expected for a diffusion-controlled process. For both anomers, the association rate constant was temperature independent, implying that the association process occurs without a significant activation enthalpy. However, a considerable association activation entropy was found for both ligands. The dissociation rate constants were in the range of 9-46 s-1 within a temperature range of 5-35 degrees C for the alpha-galactopyranoside, and in the range of 9-39 s-1 within a temperature range of 5-25 degrees C for the beta-galactopyranoside. A considerable dissociation activation enthalpy of ca. 10 kcal mol-1 was found for both anomers. A two-step binding model, consistent with the present NMR data and with previous UV and CD spectroscopic data, is presented.
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