51
|
Artola M, Wu L, Ferraz MJ, Kuo CL, Raich L, Breen IZ, Offen WA, Codée JDC, van der Marel GA, Rovira C, Aerts JMF, Davies GJ, Overkleeft HS. 1,6-Cyclophellitol Cyclosulfates: A New Class of Irreversible Glycosidase Inhibitor. ACS CENTRAL SCIENCE 2017; 3:784-793. [PMID: 28776021 PMCID: PMC5532717 DOI: 10.1021/acscentsci.7b00214] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Indexed: 05/28/2023]
Abstract
The essential biological roles played by glycosidases, coupled to the diverse therapeutic benefits of pharmacologically targeting these enzymes, provide considerable motivation for the development of new inhibitor classes. Cyclophellitol epoxides and aziridines are recently established covalent glycosidase inactivators. Inspired by the application of cyclic sulfates as electrophilic equivalents of epoxides in organic synthesis, we sought to test whether cyclophellitol cyclosulfates would similarly act as irreversible glycosidase inhibitors. Here we present the synthesis, conformational analysis, and application of novel 1,6-cyclophellitol cyclosulfates. We show that 1,6-epi-cyclophellitol cyclosulfate (α-cyclosulfate) is a rapidly reacting α-glucosidase inhibitor whose 4C1 chair conformation matches that adopted by α-glucosidase Michaelis complexes. The 1,6-cyclophellitol cyclosulfate (β-cyclosulfate) reacts more slowly, likely reflecting its conformational restrictions. Selective glycosidase inhibitors are invaluable as mechanistic probes and therapeutic agents, and we propose cyclophellitol cyclosulfates as a valuable new class of carbohydrate mimetics for application in these directions.
Collapse
Affiliation(s)
- Marta Artola
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Liang Wu
- Department
of Chemistry, University of York, Heslington, York, YO10
5DD, U.K.
| | - Maria J. Ferraz
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Chi-Lin Kuo
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Lluís Raich
- Departament
de Química Inorgànica i Orgànica (Secció
de Química Orgànica) and Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Imogen Z. Breen
- Department
of Chemistry, University of York, Heslington, York, YO10
5DD, U.K.
| | - Wendy A. Offen
- Department
of Chemistry, University of York, Heslington, York, YO10
5DD, U.K.
| | - Jeroen D. C. Codée
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Gijsbert A. van der Marel
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Carme Rovira
- Departament
de Química Inorgànica i Orgànica (Secció
de Química Orgànica) and Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Fundació
Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Johannes M. F.
G. Aerts
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Gideon J. Davies
- Department
of Chemistry, University of York, Heslington, York, YO10
5DD, U.K.
| | - Herman S. Overkleeft
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| |
Collapse
|
52
|
Abdul Manas NH, Md Illias R, Mahadi NM. Strategy in manipulating transglycosylation activity of glycosyl hydrolase for oligosaccharide production. Crit Rev Biotechnol 2017; 38:272-293. [PMID: 28683572 DOI: 10.1080/07388551.2017.1339664] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND The increasing market demand for oligosaccharides has intensified the need for efficient biocatalysts. Glycosyl hydrolases (GHs) are still gaining popularity as biocatalyst for oligosaccharides synthesis owing to its simple reaction and high selectivity. PURPOSE Over the years, research has advanced mainly directing to one goal; to reduce hydrolysis activity of GHs for increased transglycosylation activity in achieving high production of oligosaccharides. DESIGN AND METHODS This review concisely presents the strategies to increase transglycosylation activity of GHs for oligosaccharides synthesis, focusing on controlling the reaction equilibrium, and protein engineering. Various modifications of the subsites of GHs have been demonstrated to significantly modulate the hydrolysis and transglycosylation activity of the enzymes. The clear insight of the roles of each amino acid in these sites provides a platform for designing an enzyme that could synthesize a specific oligosaccharide product. CONCLUSIONS The key strategies presented here are important for future improvement of GHs as a biocatalyst for oligosaccharide synthesis.
Collapse
Affiliation(s)
- Nor Hasmaliana Abdul Manas
- a Department of Chemical Engineering and Energy Sustainability, Faculty of Engineering , Universiti Malaysia Sarawak , Kota Samarahan , Malaysia.,b BioMolecular and Microbial Process Research Group , Health and Wellness Research Alliance, Universiti Teknologi Malaysia , Johor , Malaysia
| | - Rosli Md Illias
- b BioMolecular and Microbial Process Research Group , Health and Wellness Research Alliance, Universiti Teknologi Malaysia , Johor , Malaysia.,c Department of Bioprocess Engineering, Faculty of Chemical and Energy Engineering , Universiti Teknologi Malaysia , Skudai , Malaysia
| | - Nor Muhammad Mahadi
- d Comparative Genomics and Genetics Research Centre , Malaysia Genome Institute , Kajang , Malaysia
| |
Collapse
|
53
|
Rashid MHO, Sadik G, Alam AK, Tanaka T. Chemical and structural characterization of α-N-acetylgalactosaminidase I and II from starfish, asterina amurensis. BMC BIOCHEMISTRY 2017; 18:9. [PMID: 28545388 PMCID: PMC5445309 DOI: 10.1186/s12858-017-0085-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/16/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND The marine invertebrate starfish was found to contain a novel α-N-acetylgalactosaminidase, α-GalNAcase II, which catalyzes removal of terminal α-N-acetylgalactosamine (α-GalNAc), in addition to a typical α-N-acetylgalactosaminidase, α-GalNAcase I, which catalyzes removal of terminal α-N-acetylgalactosamine (α-GalNAc) and, to a lesser extent, galactose. The interrelationship between α-GalNAcase I and α-GalNAcase II and the molecular basis of their differences in substrate specificity remain unknown. RESULTS Chemical and structural comparisons between α-GalNAcase I and II using immunostaining, N-terminal amino acid sequencing and peptide analysis showed high homology to each other and also to other glycoside hydrolase family (GHF) 27 members. The amino acid sequence of peptides showed conserved residues at the active site as seen in typical α-GalNAcase. Some substitutions of conserved amino acid residues were found in α-GalNAcase II that were located near catalytic site. Among them G171 and A173, in place of C171 and W173, respectively in α-GalNAcase were identified to be responsible for lacking intrinsic α-galactosidase activity of α-GalNAcase II. Chemical modifications supported the presence of serine, aspartate and tryptophan as active site residues. Two tryptophan residues (W16 and W173) were involved in α-galactosidase activity, and one (W16) of them was involved in α-GalNAcase activity. CONCLUSIONS The results suggested that α-GalNAcase I and II are closely related with respect to primary and higher order structure and that their structural differences are responsible for difference in substrate specificities.
Collapse
Affiliation(s)
- Md Harun-Or Rashid
- Institute of Biological Science, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Golam Sadik
- Department of Pharmacy, University of Rajshahi, Rajshahi, 6205, Bangladesh.
| | - Ahm Khurshid Alam
- Department of Pharmacy, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Toshihisa Tanaka
- Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
| |
Collapse
|
54
|
Veleti SK, Petit C, Lindenberger JJ, Ronning DR, Sucheck SJ. Zwitterionic pyrrolidene-phosphonates: inhibitors of the glycoside hydrolase-like phosphorylase Streptomyces coelicolor GlgEI-V279S. Org Biomol Chem 2017; 15:3884-3891. [PMID: 28422240 DOI: 10.1039/c7ob00388a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We synthesized and evaluated new zwitterionic inhibitors against glycoside hydrolase-like phosphorylase Streptomyces coelicolor (Sco) GlgEI-V279S which plays a role in α-glucan biosynthesis. Sco GlgEI-V279S serves as a model enzyme for validated anti-tuberculosis (TB) target Mycobacterium tuberculosis (Mtb) GlgE. Pyrrolidine inhibitors 5 and 6 were designed based on transition state considerations and incorporate a phosphonate on the pyrrolidine moiety to expand the interaction network between the inhibitor and the enzyme active site. Compounds 5 and 6 inhibited Sco GlgEI-V279S with Ki = 45 ± 4 μM and 95 ± 16 μM, respectively, and crystal structures of Sco GlgE-V279S-5 and Sco GlgE-V279S-6 were obtained at a 3.2 Å and 2.5 Å resolution, respectively.
Collapse
Affiliation(s)
- Sri Kumar Veleti
- Department of Chemistry and Biochemistry and School of Green Chemistry and Engineering, The University of Toledo, 2801 W. Bancroft Street, Toledo, Ohio 43606, USA.
| | | | | | | | | |
Collapse
|
55
|
Montgomery AP, Xiao K, Wang X, Skropeta D, Yu H. Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design. STRUCTURAL AND MECHANISTIC ENZYMOLOGY 2017; 109:25-76. [DOI: 10.1016/bs.apcsb.2017.04.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
56
|
Colomer JP, Fernández de Toro B, Cañada FJ, Corzana F, Jiménez Barbero J, Canales Á, Varela O. Diastereomeric Glycosyl Sulfoxides Display Different Recognition Features versusE. coliβ-Galactosidase. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600835] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Juan P. Colomer
- CIHIDECAR-CONICET-UBA; Department of Organic Chemistry; Exact and Natural Sciences Faculty; University of Buenos Aires; Ciudad Universitaria, Pab. II 1428 Buenos Aires Argentina
| | - Beatriz Fernández de Toro
- Department of Chemical and Physical Biology; Biological Research Center; Spanish National Research Council (CIB-CSIC); Ramiro de Maeztu 9 28040 Madrid Spain
| | - F. Javier Cañada
- Department of Chemical and Physical Biology; Biological Research Center; Spanish National Research Council (CIB-CSIC); Ramiro de Maeztu 9 28040 Madrid Spain
| | - Francisco Corzana
- Department of Chemistry; Research Center of Chemistry Synthesis; University of La Rioja; Madre de Dios 53 26006 Logroño Spain
| | - Jesús Jiménez Barbero
- CIC bioGUNE; Bizkaia Science and Technology Park; Building 801A 48160 Derio Spain
- IKERBASQUE; Basque Foundation for Science; 48009 Bilbao Spain
- Departament of Organic Chemistry II; Faculty of Science & Technology; University of the Basque Country; 48940 Leioa Spain
| | - Ángeles Canales
- Department of Organic Chemistry I; Chemical Sciences Faculty; Complutense University; 28040 Madrid Spain
| | - Oscar Varela
- CIHIDECAR-CONICET-UBA; Department of Organic Chemistry; Exact and Natural Sciences Faculty; University of Buenos Aires; Ciudad Universitaria, Pab. II 1428 Buenos Aires Argentina
| |
Collapse
|
57
|
Mayes HB, Knott BC, Crowley MF, Broadbelt LJ, Ståhlberg J, Beckham GT. Who's on base? Revealing the catalytic mechanism of inverting family 6 glycoside hydrolases. Chem Sci 2016; 7:5955-5968. [PMID: 30155195 PMCID: PMC6091422 DOI: 10.1039/c6sc00571c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/29/2016] [Indexed: 12/16/2022] Open
Abstract
In several important classes of inverting carbohydrate-active enzymes, the identity of the catalytic base remains elusive, including in family 6 Glycoside Hydrolase (GH6) enzymes, which are key components of cellulase cocktails for cellulose depolymerization. Despite many structural and kinetic studies with both wild-type and mutant enzymes, especially on the Trichoderma reesei (Hypocrea jecorina) GH6 cellulase (TrCel6A), the catalytic base in the single displacement inverting mechanism has not been definitively identified in the GH6 family. Here, we employ transition path sampling to gain insight into the catalytic mechanism, which provides unbiased atomic-level understanding of key order parameters involved in cleaving the strong glycosidic bond. Our hybrid quantum mechanics and molecular mechanics (QM/MM) simulations reveal a network of hydrogen bonding that aligns two active site water molecules that play key roles in hydrolysis: one water molecule drives the reaction by nucleophilic attack on the substrate and a second shuttles a proton to the putative base (D175) via a short water wire. We also investigated the case where the putative base is mutated to an alanine, an enzyme that is experimentally still partially active. The simulations predict that proton hopping along a water wire via a Grotthuss mechanism provides a mechanism of catalytic rescue. Further simulations reveal that substrate processive motion is 'driven' by strong electrostatic interactions with the protein at the product sites and that the -1 sugar adopts a 2SO ring configuration as it reaches its binding site. This work thus elucidates previously elusive steps in the processive catalytic mechanism of this important class of enzymes.
Collapse
Affiliation(s)
- Heather B Mayes
- Department of Chemical and Biological Engineering , Northwestern University , Evanston , IL 60208 , USA
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA .
| | - Brandon C Knott
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA .
| | - Michael F Crowley
- Biosciences Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA
| | - Linda J Broadbelt
- Department of Chemical and Biological Engineering , Northwestern University , Evanston , IL 60208 , USA
| | - Jerry Ståhlberg
- Department of Chemistry and Biotechnology , Swedish University of Agricultural Sciences , SE-75007 , Uppsala , Sweden .
| | - Gregg T Beckham
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA .
| |
Collapse
|
58
|
The Details of Glycolipid Glycan Hydrolysis by the Structural Analysis of a Family 123 Glycoside Hydrolase from Clostridium perfringens. J Mol Biol 2016; 428:3253-3265. [DOI: 10.1016/j.jmb.2016.03.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/17/2016] [Accepted: 03/21/2016] [Indexed: 01/02/2023]
|
59
|
Oliveira Udry GA, Repetto E, Vega DR, Varela O. Synthesis of Enantiomeric Polyhydroxyalkylpyrrolidines from 1,3-Dipolar Cycloadducts. Evaluation as Inhibitors of a β-Galactofuranosidase. J Org Chem 2016; 81:4179-89. [PMID: 27116655 DOI: 10.1021/acs.joc.6b00514] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Enantiomeric 2,3,4-tris(hydroxyalkyl)-5-phenylpyrrolidines have been synthesized from the major cycloadducts obtained by the 1,3-dipolar cycloaddition of sugar enones with azomethine ylides derived from natural amino acids. Reduction of the ketone carbonyl group of the cycloadducts, which possess a basic structure of bicyclic 6-(menthyloxy)hexahydropyrano[4,3-c]pyrrol-7(6H)one, afforded a number of pyrrolidine-based bicyclic systems. A sequence of reactions, which involved hydrolysis of the menthyloxy substituent, reduction, N-protection, and degradative oxidation, afforded varied pyrrolidine structures having diverse configurations and patterns of substitution; in particular, polyhydroxylated derivatives have been obtained. The unprotected products were isolated as pyrrolidinium trifluoroacetates. Because of the furanose-like nature of the target trihydroxyalkyl pyrrolidines, these molecules have been evaluated as inhibitors of the β-galactofuranosidase from Penicillium fellutanum. The compounds showed practically no inhibitory activity for concentration of pyrrolidines in the range of 0.1-1.6 mM.
Collapse
Affiliation(s)
- Guillermo A Oliveira Udry
- CIHIDECAR-CONICET-UBA, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , Pabellón 2, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - Evangelina Repetto
- CIHIDECAR-CONICET-UBA, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , Pabellón 2, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - Daniel R Vega
- Departamento Física de la Materia Condensada, GAIyANN-CAC-CNEA y ECyT-UNSAM , Av. Gral. Paz 1499, San Martín, 1650 Buenos Aires, Argentina
| | - Oscar Varela
- CIHIDECAR-CONICET-UBA, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , Pabellón 2, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| |
Collapse
|
60
|
Nakajima M, Yoshida R, Miyanaga A, Abe K, Takahashi Y, Sugimoto N, Toyoizumi H, Nakai H, Kitaoka M, Taguchi H. Functional and Structural Analysis of a β-Glucosidase Involved in β-1,2-Glucan Metabolism in Listeria innocua. PLoS One 2016; 11:e0148870. [PMID: 26886583 PMCID: PMC4757417 DOI: 10.1371/journal.pone.0148870] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 01/25/2016] [Indexed: 11/18/2022] Open
Abstract
Despite the presence of β-1,2-glucan in nature, few β-1,2-glucan degrading enzymes have been reported to date. Recently, the Lin1839 protein from Listeria innocua was identified as a 1,2-β-oligoglucan phosphorylase. Since the adjacent lin1840 gene in the gene cluster encodes a putative glycoside hydrolase family 3 β-glucosidase, we hypothesized that Lin1840 is also involved in β-1,2-glucan dissimilation. Here we report the functional and structural analysis of Lin1840. A recombinant Lin1840 protein (Lin1840r) showed the highest hydrolytic activity toward sophorose (Glc-β-1,2-Glc) among β-1,2-glucooligosaccharides, suggesting that Lin1840 is a β-glucosidase involved in sophorose degradation. The enzyme also rapidly hydrolyzed laminaribiose (β-1,3), but not cellobiose (β-1,4) or gentiobiose (β-1,6) among β-linked gluco-disaccharides. We determined the crystal structures of Lin1840r in complexes with sophorose and laminaribiose as productive binding forms. In these structures, Arg572 forms many hydrogen bonds with sophorose and laminaribiose at subsite +1, which seems to be a key factor for substrate selectivity. The opposite side of subsite +1 from Arg572 is connected to a large empty space appearing to be subsite +2 for the binding of sophorotriose (Glc-β-1,2-Glc-β-1,2-Glc) in spite of the higher Km value for sophorotriose than that for sophorose. The conformations of sophorose and laminaribiose are almost the same on the Arg572 side but differ on the subsite +2 side that provides no interaction with a substrate. Therefore, Lin1840r is unable to distinguish between sophorose and laminaribiose as substrates. These results provide the first mechanistic insights into β-1,2-glucooligosaccharide recognition by β-glucosidase.
Collapse
Affiliation(s)
- Masahiro Nakajima
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
- * E-mail:
| | - Ryuta Yoshida
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Koichi Abe
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Yuta Takahashi
- Graduate School of Science & Technology, Niigata University, Nishi-ku, Niigata, Japan
| | - Naohisa Sugimoto
- Graduate School of Science & Technology, Niigata University, Nishi-ku, Niigata, Japan
| | - Hiroyuki Toyoizumi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Hiroyuki Nakai
- Graduate School of Science & Technology, Niigata University, Nishi-ku, Niigata, Japan
| | - Motomitsu Kitaoka
- National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Hayao Taguchi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| |
Collapse
|
61
|
Natori Y, Imahori T, Yoshimura Y. Development of Stereoselective Synthesis of Biologically Active Nitrogen-heterocyclic Compounds: Applications for Syntheses of Natural Product and Organocatalyst. J SYN ORG CHEM JPN 2016. [DOI: 10.5059/yukigoseikyokaishi.74.335] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yoshihiro Natori
- Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University
| | | | - Yuichi Yoshimura
- Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University
| |
Collapse
|
62
|
O'Neill H, Shah R, Evans BR, He J, Pingali SV, Chundawat SPS, Jones AD, Langan P, Davison BH, Urban V. Production of bacterial cellulose with controlled deuterium-hydrogen substitution for neutron scattering studies. Methods Enzymol 2015; 565:123-46. [PMID: 26577730 DOI: 10.1016/bs.mie.2015.08.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Isotopic enrichment of biomacromolecules is a widely used technique that enables the investigation of the structural and dynamic properties to provide information not accessible with natural abundance isotopic composition. This study reports an approach for deuterium incorporation into bacterial cellulose. A media formulation for growth of Acetobacter xylinus subsp. sucrofermentans and Gluconacetobacter hansenii was formulated that supports cellulose production in deuterium (D) oxide. The level of D incorporation can be varied by altering the ratio of deuterated and protiated glycerol used during cell growth in the D2O-based growth medium. Spectroscopic analysis and mass spectrometry show that the level of deuterium incorporation is high (>90%) for the perdeuterated form of bacterial cellulose. The small-angle neutron scattering profiles of the cellulose with different amounts of D incorporation are all similar indicating that there are no structural changes in the cellulose due to substitution of deuterium for hydrogen. In addition, by varying the amount of deuterated glycerol in the media it was possible to vary the scattering length density of the deuterated cellulose. The ability to control deuterium content of cellulose extends the range of experiments using techniques such as neutron scattering to reveal information about the structure and dynamics of cellulose, and its interactions with other biomacromolecules as well as synthetic polymers used for development of composite materials.
Collapse
Affiliation(s)
- Hugh O'Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
| | - Riddhi Shah
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA; Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA
| | - Barbara R Evans
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Junhong He
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Sai Venkatesh Pingali
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Shishir P S Chundawat
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, New Jersey, USA
| | - A Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA; Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Paul Langan
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Brian H Davison
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Volker Urban
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| |
Collapse
|
63
|
Tsai LC, Amiraslanov I, Chen HR, Chen YW, Lee HL, Liang PH, Liaw YC. Structures of exoglucanase from Clostridium cellulovorans: cellotetraose binding and cleavage. Acta Crystallogr F Struct Biol Commun 2015; 71:1264-72. [PMID: 26457517 PMCID: PMC4601590 DOI: 10.1107/s2053230x15015915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/25/2015] [Indexed: 11/10/2022] Open
Abstract
Exoglucanase/cellobiohydrolase (EC 3.2.1.176) hydrolyzes a β-1,4-glycosidic bond from the reducing end of cellulose and releases cellobiose as the major product. Three complex crystal structures of the glycosyl hydrolase 48 (GH48) cellobiohydrolase S (ExgS) from Clostridium cellulovorans with cellobiose, cellotetraose and triethylene glycol molecules were solved. The product cellobiose occupies subsites +1 and +2 in the open active-site cleft of the enzyme-cellotetraose complex structure, indicating an enzymatic hydrolysis function. Moreover, three triethylene glycol molecules and one pentaethylene glycol molecule are located at active-site subsites -2 to -6 in the structure of the ExgS-triethylene glycol complex shown here. Modelling of glucose into subsite -1 in the active site of the ExgS-cellobiose structure revealed that Glu50 acts as a proton donor and Asp222 plays a nucleophilic role.
Collapse
Affiliation(s)
- Li-Chu Tsai
- Molecular Science and Engineering, National Taipei University of Technology, 1, Section 3, Chung-Hsiao E. Road, Taipei 10608, Taiwan
| | - Imamaddin Amiraslanov
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Taipei 11529, Taiwan
| | - Hung-Ren Chen
- Molecular Science and Engineering, National Taipei University of Technology, 1, Section 3, Chung-Hsiao E. Road, Taipei 10608, Taiwan
| | - Yun-Wen Chen
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Taipei 11529, Taiwan
| | - Hsiao-Lin Lee
- Institute of Molecular Biology, Academia Sinica, 128 Academia Road, Section 2, Taipei 11529, Taiwan
| | - Po-Huang Liang
- Institute of Molecular Biology, Academia Sinica, 128 Academia Road, Section 2, Taipei 11529, Taiwan
| | - Yen-Chywan Liaw
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Taipei 11529, Taiwan
| |
Collapse
|
64
|
Tankrathok A, Iglesias-Fernández J, Williams RJ, Pengthaisong S, Baiya S, Hakki Z, Robinson RC, Hrmova M, Rovira C, Williams SJ, Ketudat Cairns JR. A Single Glycosidase Harnesses Different Pyranoside Ring Transition State Conformations for Hydrolysis of Mannosides and Glucosides. ACS Catal 2015. [DOI: 10.1021/acscatal.5b01547] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Anupong Tankrathok
- School of Biochemistry, Institute of Science, and Center
for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
- Department of Biotechnology, Faculty of Agro-Industrial
Technology, Rajamangala University of Technology, Isan, Kalasin Campus, Kalasin 46000, Thailand
| | - Javier Iglesias-Fernández
- Departament de Quı́mica
Orgànica/Institut de Quı́mica Teòrica i
Computacional (IQTCUB), Universitat de Barcelona, Martı́ i Franquès
1, 08028 Barcelona, Spain
| | - Rohan J. Williams
- School of Chemistry and Bio21 Molecular
Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Salila Pengthaisong
- School of Biochemistry, Institute of Science, and Center
for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Supaporn Baiya
- School of Biochemistry, Institute of Science, and Center
for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Zalihe Hakki
- School of Chemistry and Bio21 Molecular
Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robert C. Robinson
- Institute of Molecular
and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673
- Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore 117597
| | - Maria Hrmova
- School of Agriculture, Food and Wine, Australian
Centre for Plant Functional Genomics, University of Adelaide, Waite Campus, Glenn
Osmond, Australia
| | - Carme Rovira
- Departament de Quı́mica
Orgànica/Institut de Quı́mica Teòrica i
Computacional (IQTCUB), Universitat de Barcelona, Martı́ i Franquès
1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluı́s Companys, 23, 08018 Barcelona, Spain
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular
Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - James R. Ketudat Cairns
- School of Biochemistry, Institute of Science, and Center
for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
- Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok 10210, Thailand
| |
Collapse
|
65
|
Kallemeijn WW, Witte MD, Wennekes T, Aerts JMFG. Mechanism-based inhibitors of glycosidases: design and applications. Adv Carbohydr Chem Biochem 2015; 71:297-338. [PMID: 25480507 DOI: 10.1016/b978-0-12-800128-8.00004-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This article covers recent developments in the design and application of activity-based probes (ABPs) for glycosidases, with emphasis on the different enzymes involved in metabolism of glucosylceramide in humans. Described are the various catalytic reaction mechanisms employed by inverting and retaining glycosidases. An understanding of catalysis at the molecular level has stimulated the design of different types of ABPs for glycosidases. Such compounds range from (1) transition-state mimics tagged with reactive moieties, which associate with the target active site—forming covalent bonds in a relatively nonspecific manner in or near the catalytic pocket—to (2) enzyme substrates that exploit the catalytic mechanism of retaining glycosidase targets to release a highly reactive species within the active site of the enzyme, to (3) probes based on mechanism-based, covalent, and irreversible glycosidase inhibitors. Some applications in biochemical and biological research of the activity-based glycosidase probes are discussed, including specific quantitative visualization of active enzyme molecules in vitro and in vivo, and as strategies for unambiguously identifying catalytic residues in glycosidases in vitro.
Collapse
Affiliation(s)
- Wouter W Kallemeijn
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| | - Martin D Witte
- Department of Bio-Organic Chemistry, Stratingh Institute for Chemistry, University of Groningen, Groningen, The Netherlands.
| | - Tom Wennekes
- Department of Synthetic Organic Chemistry, Wageningen University, Wageningen, The Netherlands.
| | - Johannes M F G Aerts
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
66
|
Abstract
The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.
Collapse
Affiliation(s)
- Serge Pérez
- Department of Molecular Pharmacochemistry, CNRS, University Grenoble-Alpes, Grenoble, France.
| | - Igor Tvaroška
- Department of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic; Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University, Nitra, Slovak Republic.
| |
Collapse
|
67
|
Glycosynthesis in a waterworld: new insight into the molecular basis of transglycosylation in retaining glycoside hydrolases. Biochem J 2015; 467:17-35. [PMID: 25793417 DOI: 10.1042/bj20141412] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Carbohydrates are ubiquitous in Nature and play vital roles in many biological systems. Therefore the synthesis of carbohydrate-based compounds is of considerable interest for both research and commercial purposes. However, carbohydrates are challenging, due to the large number of sugar subunits and the multiple ways in which these can be linked together. Therefore, to tackle the challenge of glycosynthesis, chemists are increasingly turning their attention towards enzymes, which are exquisitely adapted to the intricacy of these biomolecules. In Nature, glycosidic linkages are mainly synthesized by Leloir glycosyltransferases, but can result from the action of non-Leloir transglycosylases or phosphorylases. Advantageously for chemists, non-Leloir transglycosylases are glycoside hydrolases, enzymes that are readily available and exhibit a wide range of substrate specificities. Nevertheless, non-Leloir transglycosylases are unusual glycoside hydrolases in as much that they efficiently catalyse the formation of glycosidic bonds, whereas most glycoside hydrolases favour the mechanistically related hydrolysis reaction. Unfortunately, because non-Leloir transglycosylases are almost indistinguishable from their hydrolytic counterparts, it is unclear how these enzymes overcome the ubiquity of water, thus avoiding the hydrolytic reaction. Without this knowledge, it is impossible to rationally design non-Leloir transglycosylases using the vast diversity of glycoside hydrolases as protein templates. In this critical review, a careful analysis of literature data describing non-Leloir transglycosylases and their relationship to glycoside hydrolase counterparts is used to clarify the state of the art knowledge and to establish a new rational basis for the engineering of glycoside hydrolases.
Collapse
|
68
|
Veyron A, Reddy PV, Koos P, Bayle A, Greene AE, Delair P. Stereocontrolled synthesis of glycosidase inhibitors (+)-hyacinthacines A1 and A2. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.tetasy.2014.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
69
|
Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| |
Collapse
|
70
|
Moorthy BS, Xie B, Moussa EM, Iyer LK, Chandrasekhar S, Panchal JP, Topp EM. Effect of Hydrolytic Degradation on the In Vivo Properties of Monoclonal Antibodies. BIOBETTERS 2015. [DOI: 10.1007/978-1-4939-2543-8_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
71
|
Langille MGI, Meehan CJ, Koenig JE, Dhanani AS, Rose RA, Howlett SE, Beiko RG. Microbial shifts in the aging mouse gut. MICROBIOME 2014; 2:50. [PMID: 25520805 PMCID: PMC4269096 DOI: 10.1186/s40168-014-0050-9] [Citation(s) in RCA: 291] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 11/13/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND The changes that occur in the microbiome of aging individuals are unclear, especially in light of the imperfect correlation of frailty with age. Studies in older human subjects have reported subtle effects, but these results may be confounded by other variables that often change with age such as diet and place of residence. To test these associations in a more controlled model system, we examined the relationship between age, frailty, and the gut microbiome of female C57BL/6 J mice. RESULTS The frailty index, which is based on the evaluation of 31 clinical signs of deterioration in mice, showed a near-perfect correlation with age. We observed a statistically significant relationship between age and the taxonomic composition of the corresponding microbiome. Consistent with previous human studies, the Rikenellaceae family, which includes the Alistipes genus, was the most significantly overrepresented taxon within middle-aged and older mice. The functional profile of the mouse gut microbiome also varied with host age and frailty. Bacterial-encoded functions that were underrepresented in older mice included cobalamin (B12) and biotin (B7) biosynthesis, and bacterial SOS genes associated with DNA repair. Conversely, creatine degradation, associated with muscle wasting, was overrepresented within the gut microbiomes of the older mice, as were bacterial-encoded β-glucuronidases, which can influence drug-induced epithelial cell toxicity. Older mice also showed an overabundance of monosaccharide utilization genes relative to di-, oligo-, and polysaccharide utilization genes, which may have a substantial impact on gut homeostasis. CONCLUSION We have identified taxonomic and functional patterns that correlate with age and frailty in the mouse microbiome. Differences in functions related to host nutrition and drug pharmacology vary in an age-dependent manner, suggesting that the availability and timing of essential functions may differ significantly with age and frailty. Future work with larger cohorts of mice will aim to separate the effects of age and frailty, and other factors.
Collapse
Affiliation(s)
- Morgan GI Langille
- />Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia Canada
- />Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia Canada
| | - Conor J Meehan
- />Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia Canada
- />Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jeremy E Koenig
- />Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia Canada
| | - Akhilesh S Dhanani
- />Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia Canada
| | - Robert A Rose
- />Department of Physiology and Biophysics, Dalhousie University, Halifax, Nova Scotia Canada
| | - Susan E Howlett
- />Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia Canada
- />Department of Medicine (Geriatric Medicine), Dalhousie University, Halifax, Nova Scotia Canada
| | - Robert G Beiko
- />Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia Canada
| |
Collapse
|
72
|
Neumann P, Tittmann K. Marvels of enzyme catalysis at true atomic resolution: distortions, bond elongations, hidden flips, protonation states and atom identities. Curr Opin Struct Biol 2014; 29:122-33. [PMID: 25460275 DOI: 10.1016/j.sbi.2014.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 10/31/2014] [Accepted: 11/03/2014] [Indexed: 10/24/2022]
Abstract
Although general principles of enzyme catalysis are fairly well understood nowadays, many important details of how exactly the substrate is bound and processed in an enzyme remain often invisible and as such elusive. In fortunate cases, structural analysis of enzymes can be accomplished at true atomic resolution thus making possible to shed light on otherwise concealed fine-structural traits of bound substrates, intermediates, cofactors and protein groups. We highlight recent structural studies of enzymes using ultrahigh-resolution X-ray protein crystallography showcasing its enormous potential as a tool in the elucidation of enzymatic mechanisms and in unveiling fundamental principles of enzyme catalysis. We discuss the observation of seemingly hyper-reactive, physically distorted cofactors and intermediates with elongated scissile substrate bonds, the detection of 'hidden' conformational and chemical equilibria and the analysis of protonation states with surprising findings. In delicate cases, atomic resolution is required to unambiguously disclose the identity of atoms as demonstrated for the metal cluster in nitrogenase. In addition to the pivotal structural findings and the implications for our understanding of enzyme catalysis, we further provide a practical framework for resolution enhancement through optimized data acquisition and processing.
Collapse
Affiliation(s)
- Piotr Neumann
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Justus-von-Liebig-Weg 11, Georg-August-Universität Göttingen, Göttingen D-37077, Germany.
| | - Kai Tittmann
- Abteilung Molekulare Enzymologie, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Justus-von-Liebig-Weg 11, Georg-August-Universität Göttingen, Göttingen D-37077, Germany.
| |
Collapse
|
73
|
Taghzouti H, Goumain S, Harakat D, Portella C, Behr JB, Plantier-Royon R. Synthesis of 2-carboxymethyl polyhydroxyazepanes and their evaluation as glycosidase inhibitors. Bioorg Chem 2014; 58:11-7. [PMID: 25462622 DOI: 10.1016/j.bioorg.2014.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/30/2014] [Accepted: 11/04/2014] [Indexed: 01/06/2023]
Abstract
A series of diastereomeric tetrahydroxylated azepanes featuring a carboxymethyl group at the pseudo-anomeric position have been synthesized from a common unsaturated intermediate. Syn- and anti-dihydroxylation reactions were achieved to yield the target compounds after efficient one-step deprotection of carbamate, ester and acetonide groups simultaneously. Screening of these polyhydroxylated azepanes toward a range of commercially available glycosidases was performed and one of the stereoisomers showed potent and selective inhibition toward β-galactosidase (IC50=21 μM).
Collapse
Affiliation(s)
- Hanaa Taghzouti
- Université de Reims Champagne-Ardenne, Institut de Chimie Moléculaire de Reims (ICMR), CNRS UMR 7312, UFR Sciences Exactes et Naturelles, BP 1039, F-51687 Reims Cedex 2, France
| | - Sophie Goumain
- Université de Reims Champagne-Ardenne, Institut de Chimie Moléculaire de Reims (ICMR), CNRS UMR 7312, UFR Sciences Exactes et Naturelles, BP 1039, F-51687 Reims Cedex 2, France
| | - Dominique Harakat
- Université de Reims Champagne-Ardenne, Institut de Chimie Moléculaire de Reims (ICMR), CNRS UMR 7312, UFR Sciences Exactes et Naturelles, BP 1039, F-51687 Reims Cedex 2, France
| | - Charles Portella
- Université de Reims Champagne-Ardenne, Institut de Chimie Moléculaire de Reims (ICMR), CNRS UMR 7312, UFR Sciences Exactes et Naturelles, BP 1039, F-51687 Reims Cedex 2, France
| | - Jean-Bernard Behr
- Université de Reims Champagne-Ardenne, Institut de Chimie Moléculaire de Reims (ICMR), CNRS UMR 7312, UFR Sciences Exactes et Naturelles, BP 1039, F-51687 Reims Cedex 2, France.
| | - Richard Plantier-Royon
- Université de Reims Champagne-Ardenne, Institut de Chimie Moléculaire de Reims (ICMR), CNRS UMR 7312, UFR Sciences Exactes et Naturelles, BP 1039, F-51687 Reims Cedex 2, France.
| |
Collapse
|
74
|
Govender KK, Naidoo KJ. Evaluating AM1/d-CB1 for Chemical Glycobiology QM/MM Simulations. J Chem Theory Comput 2014; 10:4708-17. [DOI: 10.1021/ct500373p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Krishna K. Govender
- Scientific Computing
Research Unit and Department
of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kevin J. Naidoo
- Scientific Computing
Research Unit and Department
of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| |
Collapse
|
75
|
Govender K, Gao J, Naidoo KJ. AM1/d-CB1: A Semiempirical Model for QM/MM Simulations of Chemical Glycobiology Systems. J Chem Theory Comput 2014; 10:4694-4707. [PMID: 26120288 DOI: 10.1021/ct500372s] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A semiempirical method based on the AM1/d Hamiltonian is introduced to model chemical glycobiological systems. We included in the parameter training set glycans and the chemical environment often found about them in glycoenzymes. Starting with RM1 and AM1/d-PhoT models we optimized H, C, N, O, and P atomic parameters targeting the best performing molecular properties that contribute to enzyme catalyzed glycan reaction mechanisms. The training set comprising glycans, amino acids, phosphates and small organic model systems was used to derive parameters that reproduce experimental data or high-level density functional results for carbohydrate, phosphate and amino acid heats of formation, amino acid proton affinities, amino acid and monosaccharide dipole moments, amino acid ionization potentials, water-phosphate interaction energies, and carbohydrate ring pucker relaxation times. The result is the AM1/d-Chemical Biology 1 or AM1/d-CB1 model that is considerably more accurate than existing NDDO methods modeling carbohydrates and the amino acids often present in the catalytic domains of glycoenzymes as well as the binding sites of lectins. Moreover, AM1/d-CB1 computed proton affinities, dipole moments, ionization potentials and heats of formation for transition state puckered carbohydrate ring conformations, observed along glycoenzyme catalyzed reaction paths, are close to values computed using DFT M06-2X. AM1/d-CB1 provides a platform from which to accurately model reactions important in chemical glycobiology.
Collapse
Affiliation(s)
- Krishna Govender
- Scientific Computing Research Unit, University of Cape Town, Rondebosch 7701, South Africa ; Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Jiali Gao
- State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun, Jilin Province 130012, China ; Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Kevin J Naidoo
- Scientific Computing Research Unit, University of Cape Town, Rondebosch 7701, South Africa ; Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| |
Collapse
|
76
|
Fustero S, Simón-Fuentes A, Barrio P, Haufe G. Olefin Metathesis Reactions with Fluorinated Substrates, Catalysts, and Solvents. Chem Rev 2014; 115:871-930. [DOI: 10.1021/cr500182a] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Santos Fustero
- Departamento
de Química Orgánica, Universidad de Valencia, E-46100 Burjassot, Spain
- Laboratorio
de Moléculas Orgánicas, Centro de Investigación Príncipe Felipe, E-46012 Valencia, Spain
| | | | - Pablo Barrio
- Departamento
de Química Orgánica, Universidad de Valencia, E-46100 Burjassot, Spain
| | - Günter Haufe
- Organisch-Chemisches
Institut, Westfälische Wilhelms-Universität, Corrensstrasse 40, D-48149 Münster, Germany
| |
Collapse
|
77
|
Synthesis and α-glucosidase inhibitory activity of chrysin, diosmetin, apigenin, and luteolin derivatives. CHINESE CHEM LETT 2014. [DOI: 10.1016/j.cclet.2014.05.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
78
|
Brás NF, Cerqueira NMFSA, Ramos MJ, Fernandes PA. Glycosidase inhibitors: a patent review (2008 – 2013). Expert Opin Ther Pat 2014; 24:857-74. [DOI: 10.1517/13543776.2014.916280] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
79
|
Correa A, Pacheco S, Mechaly AE, Obal G, Béhar G, Mouratou B, Oppezzo P, Alzari PM, Pecorari F. Potent and specific inhibition of glycosidases by small artificial binding proteins (affitins). PLoS One 2014; 9:e97438. [PMID: 24823716 PMCID: PMC4019568 DOI: 10.1371/journal.pone.0097438] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Accepted: 04/17/2014] [Indexed: 01/05/2023] Open
Abstract
Glycosidases are associated with various human diseases. The development of efficient and specific inhibitors may provide powerful tools to modulate their activity. However, achieving high selectivity is a major challenge given that glycosidases with different functions can have similar enzymatic mechanisms and active-site architectures. As an alternative approach to small-chemical compounds, proteinaceous inhibitors might provide a better specificity by involving a larger surface area of interaction. We report here the design and characterization of proteinaceous inhibitors that specifically target endoglycosidases representative of the two major mechanistic classes; retaining and inverting glycosidases. These inhibitors consist of artificial affinity proteins, Affitins, selected against the thermophilic CelD from Clostridium thermocellum and lysozyme from hen egg. They were obtained from libraries of Sac7d variants, which involve either the randomization of a surface or the randomization of a surface and an artificially-extended loop. Glycosidase binders exhibited affinities in the nanomolar range with no cross-recognition, with efficient inhibition of lysozyme (Ki = 45 nM) and CelD (Ki = 95 and 111 nM), high expression yields in Escherichia coli, solubility, and thermal stabilities up to 81.1°C. The crystal structures of glycosidase-Affitin complexes validate our library designs. We observed that Affitins prevented substrate access by two modes of binding; covering or penetrating the catalytic site via the extended loop. In addition, Affitins formed salt-bridges with residues essential for enzymatic activity. These results lead us to propose the use of Affitins as versatile selective glycosidase inhibitors and, potentially, as enzymatic inhibitors in general.
Collapse
Affiliation(s)
- Agustín Correa
- Institut Pasteur de Montevideo, Recombinant Protein Unit, Montevideo, Uruguay
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528, Paris, France
| | - Sabino Pacheco
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528, Paris, France
- INSERM UMR 892 - CRCNA, Nantes, France
- CNRS UMR 6299, Nantes, France
- University of Nantes, Nantes, France
| | - Ariel E. Mechaly
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528, Paris, France
| | - Gonzalo Obal
- Institut Pasteur de Montevideo, Protein Biophysics Unit, Montevideo, Uruguay
| | - Ghislaine Béhar
- INSERM UMR 892 - CRCNA, Nantes, France
- CNRS UMR 6299, Nantes, France
- University of Nantes, Nantes, France
| | - Barbara Mouratou
- INSERM UMR 892 - CRCNA, Nantes, France
- CNRS UMR 6299, Nantes, France
- University of Nantes, Nantes, France
| | - Pablo Oppezzo
- Institut Pasteur de Montevideo, Recombinant Protein Unit, Montevideo, Uruguay
| | - Pedro M. Alzari
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528, Paris, France
| | - Frédéric Pecorari
- INSERM UMR 892 - CRCNA, Nantes, France
- CNRS UMR 6299, Nantes, France
- University of Nantes, Nantes, France
| |
Collapse
|
80
|
Compain P, Bodlenner A. The Multivalent Effect in Glycosidase Inhibition: A New, Rapidly Emerging Topic in Glycoscience. Chembiochem 2014; 15:1239-51. [DOI: 10.1002/cbic.201402026] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Indexed: 11/07/2022]
|
81
|
Lu D, Shang G, Zhang H, Yu Q, Cong X, Yuan J, He F, Zhu C, Zhao Y, Yin K, Chen Y, Hu J, Zhang X, Yuan Z, Xu S, Hu W, Cang H, Gu L. Structural insights into the T6SS effector protein Tse3 and the Tse3-Tsi3 complex fromPseudomonas aeruginosareveal a calcium-dependent membrane-binding mechanism. Mol Microbiol 2014; 92:1092-112. [DOI: 10.1111/mmi.12616] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Defen Lu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
- The Liver Centre of Fujian Province; MengChao Hepatobiliary Hospital of Fujian Medical University; Fuzhou 350025 Fujian China
| | - Guijun Shang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Heqiao Zhang
- Institute of Biophysics; Chinese Academy of Sciences; Beijing 100101 China
- School of Life Sciences; Tsinghua University; Beijing 100084 China
| | - Qian Yu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Xiaoyan Cong
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Jupeng Yuan
- Institute of Medical Genetics; Shandong University School of Medicine; Jinan 250012 Shandong China
| | - Fengjuan He
- Institute of Medical Genetics; Shandong University School of Medicine; Jinan 250012 Shandong China
| | - Chunyuan Zhu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Yanyu Zhao
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Kun Yin
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Yuanyuan Chen
- Institute of Biophysics; Chinese Academy of Sciences; Beijing 100101 China
| | - Junqiang Hu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Xiaodan Zhang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Zenglin Yuan
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Sujuan Xu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Wei Hu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Huaixing Cang
- Institute of Biophysics; Chinese Academy of Sciences; Beijing 100101 China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| |
Collapse
|
82
|
Stubbs KA. Activity-based proteomics probes for carbohydrate-processing enzymes: current trends and future outlook. Carbohydr Res 2014; 390:9-19. [DOI: 10.1016/j.carres.2014.02.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 02/21/2014] [Accepted: 02/22/2014] [Indexed: 11/27/2022]
|
83
|
Syson K, Stevenson CEM, Rashid AM, Saalbach G, Tang M, Tuukkanen A, Svergun DI, Withers SG, Lawson DM, Bornemann S. Structural insight into how Streptomyces coelicolor maltosyl transferase GlgE binds α-maltose 1-phosphate and forms a maltosyl-enzyme intermediate. Biochemistry 2014; 53:2494-504. [PMID: 24689960 PMCID: PMC4048318 DOI: 10.1021/bi500183c] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
GlgE (EC 2.4.99.16) is an α-maltose
1-phosphate:(1→4)-α-d-glucan 4-α-d-maltosyltransferase of the CAZy
glycoside hydrolase 13_3 family. It is the defining enzyme of a bacterial
α-glucan biosynthetic pathway and is a genetically validated
anti-tuberculosis target. It catalyzes the α-retaining transfer
of maltosyl units from α-maltose 1-phosphate to maltooligosaccharides
and is predicted to use a double-displacement mechanism. Evidence
of this mechanism was obtained using a combination of site-directed
mutagenesis of Streptomyces coelicolor GlgE isoform
I, substrate analogues, protein crystallography, and mass spectrometry.
The X-ray structures of α-maltose 1-phosphate bound to a D394A
mutein and a β-2-deoxy-2-fluoromaltosyl-enzyme intermediate
with a E423A mutein were determined. There are few examples of CAZy
glycoside hydrolase family 13 members that have had their glycosyl-enzyme
intermediate structures determined, and none before now have been
obtained with a 2-deoxy-2-fluoro substrate analogue. The covalent
modification of Asp394 was confirmed using mass spectrometry. A similar
modification of wild-type GlgE proteins from S. coelicolor and Mycobacterium tuberculosis was also observed.
Small-angle X-ray scattering of the M. tuberculosis enzyme revealed a homodimeric assembly similar to that of the S. coelicolor enzyme but with slightly differently oriented
monomers. The deeper understanding of the structure–function
relationships of S. coelicolor GlgE will aid the
development of inhibitors of the M. tuberculosis enzyme.
Collapse
Affiliation(s)
- Karl Syson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park , Norwich NR4 7UH, United Kingdom
| | | | | | | | | | | | | | | | | | | |
Collapse
|
84
|
Biochemical properties and atomic resolution structure of a proteolytically processed β-mannanase from cellulolytic Streptomyces sp. SirexAA-E. PLoS One 2014; 9:e94166. [PMID: 24710170 PMCID: PMC3978015 DOI: 10.1371/journal.pone.0094166] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/11/2014] [Indexed: 01/07/2023] Open
Abstract
β-Mannanase SACTE_2347 from cellulolytic Streptomyces sp. SirexAA-E is abundantly secreted into the culture medium during growth on cellulosic materials. The enzyme is composed of domains from the glycoside hydrolase family 5 (GH5), fibronectin type-III (Fn3), and carbohydrate binding module family 2 (CBM2). After secretion, the enzyme is proteolyzed into three different, catalytically active variants with masses of 53, 42 and 34 kDa corresponding to the intact protein, loss of the CBM2 domain, or loss of both the Fn3 and CBM2 domains. The three variants had identical N-termini starting with Ala51, and the positions of specific proteolytic reactions in the linker sequences separating the three domains were identified. To conduct biochemical and structural characterizations, the natural proteolytic variants were reproduced by cloning and heterologously expressed in Escherichia coli. Each SACTE_2347 variant hydrolyzed only β-1,4 mannosidic linkages, and also reacted with pure mannans containing partial galactosyl- and/or glucosyl substitutions. Examination of the X-ray crystal structure of the GH5 domain of SACTE_2347 suggests that two loops adjacent to the active site channel, which have differences in position and length relative to other closely related mannanases, play a role in producing the observed substrate selectivity.
Collapse
|
85
|
Srinivas G, Cheng X, Smith JC. Coarse-Grain Model for Natural Cellulose Fibrils in Explicit Water. J Phys Chem B 2014; 118:3026-34. [DOI: 10.1021/jp407953p] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Goundla Srinivas
- University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, P.O.
Box 2008, Oak Ridge, Tennessee 37831-6164, United States
- Joint School of Nanoscience and Nanoengineering, North Carolina A&T State University, 2907 East Lee Street, Greensboro, North Carolina 27401, United States
| | - Xiaolin Cheng
- University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, P.O.
Box 2008, Oak Ridge, Tennessee 37831-6164, United States
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Science, Knoxville, Tennessee 37996-0840, United States
| | - Jeremy C. Smith
- University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, P.O.
Box 2008, Oak Ridge, Tennessee 37831-6164, United States
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Science, Knoxville, Tennessee 37996-0840, United States
| |
Collapse
|
86
|
Mhlongo NN, Skelton AA, Kruger G, Soliman ME, Williams IH. A critical survey of average distances between catalytic carboxyl groups in glycoside hydrolases. Proteins 2014; 82:1747-55. [DOI: 10.1002/prot.24528] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 12/20/2013] [Accepted: 01/28/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Ndumiso N. Mhlongo
- Discipline of Pharmaceutical Sciences; School of Health Sciences; University of KwaZulu-Natal; Durban 4001 South Africa
| | - Adam A. Skelton
- Discipline of Pharmaceutical Sciences; School of Health Sciences; University of KwaZulu-Natal; Durban 4001 South Africa
| | - Gert Kruger
- Catalysis and Peptide Research Unit; School of Health Sciences; University of KwaZulu-Natal; Durban 4001 South Africa
| | - Mahmoud E.S. Soliman
- Discipline of Pharmaceutical Sciences; School of Health Sciences; University of KwaZulu-Natal; Durban 4001 South Africa
| | - Ian H. Williams
- Department of Chemistry; University of Bath; Bath BA2 7AY United Kingdom
| |
Collapse
|
87
|
Laborda P, Sayago FJ, Cativiela C, Parella T, Joglar J, Clapés P. Aldolase-Catalyzed Synthesis of Conformationally Constrained Iminocyclitols: Preparation of Polyhydroxylated Benzopyrrolizidines and Cyclohexapyrrolizidines. Org Lett 2014; 16:1422-5. [DOI: 10.1021/ol5002158] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pedro Laborda
- Departamento
de Química Orgánica, Instituto de Síntesis Química
y Catálisis Homogénea, Universidad de Zaragoza-CSIC, 50009 Zaragoza, Spain
| | - Francisco J. Sayago
- Departamento
de Química Orgánica, Instituto de Síntesis Química
y Catálisis Homogénea, Universidad de Zaragoza-CSIC, 50009 Zaragoza, Spain
| | - Carlos Cativiela
- Departamento
de Química Orgánica, Instituto de Síntesis Química
y Catálisis Homogénea, Universidad de Zaragoza-CSIC, 50009 Zaragoza, Spain
| | - Teodor Parella
- Servei
de RMN and Dept. Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Jesús Joglar
- Biotransformation
and Bioactive Molecules Group, Instituto de Química Avanzada de Cataluña, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Pere Clapés
- Biotransformation
and Bioactive Molecules Group, Instituto de Química Avanzada de Cataluña, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| |
Collapse
|
88
|
Abstract
Over the sixty years since Koshland initially formulated the classical mechanisms for retaining and inverting glycosidases, researchers have assembled a large body of supporting evidence and have documented variations of these mechanisms. Recently, however, researchers have uncovered a number of completely distinct mechanisms for enzymatic cleavage of glycosides involving elimination and/or hydration steps. In family GH4 and GH109 glycosidases, the reaction proceeds via transient NAD(+)-mediated oxidation at C3, thereby acidifying the proton at C2 and allowing for elimination across the C1-C2 bond. Subsequent Michael-type addition of water followed by reduction at C3 generates the hydrolyzed product. Enzymes employing this mechanism can hydrolyze thioglycosides as well as both anomers of activated substrates. Sialidases employ a conventional retaining mechanism in which a tyrosine functions as the nucleophile, but in some cases researchers have observed off-path elimination end products. These reactions occur via the normal covalent intermediate, but instead of an attack by water on the anomeric center, the catalytic acid/base residue abstracts an adjacent proton. These enzymes can also catalyze hydration of the enol ether via the reverse pathway. Reactions of α-(1,4)-glucan lyases also proceed through a covalent intermediate with subsequent abstraction of an adjacent proton to give elimination. However, in this case, the departing carboxylate "nucleophile" serves as the base in a concerted but asynchronous syn-elimination process. These enzymes perform only elimination reactions. Polysaccharide lyases, which act on uronic acid-containing substrates, also catalyze only elimination reactions. Substrate binding neutralizes the charge on the carboxylate, which allows for abstraction of the proton on C5 and leads to an elimination reaction via an E1cb mechanism. These enzymes can also cleave thioglycosides, albeit slowly. The unsaturated product of polysaccharide lyases can then serve as a substrate for a hydration reaction carried out by unsaturated glucuronyl hydrolases. This hydration is initiated by protonation at C4 and proceeds in a Markovnikov fashion rather than undergoing a Michael-type addition, giving a hemiketal at C5. This hemiketal then undergoes a rearrangement that results in cleavage of the anomeric bond. These enzymes can also hydrolyze thioglycosides efficiently and slowly turn over substrates with inverted anomeric configuration. The mechanisms discussed in this Account proceed through transition states that involve either positive or negative charges, unlike the exclusively cationic transition states of the classical Koshland retaining and inverting glycosidases. In addition, the distribution of this charge throughout the substrate can vary substantially. The nature of these mechanisms and their transition states means that any inhibitors or inactivators of these unusual enzymes probably differ from those presently used for Koshland retaining or inverting glycosidases.
Collapse
Affiliation(s)
- Seino A. K. Jongkees
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - Stephen G. Withers
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| |
Collapse
|
89
|
Bissaro B, Saurel O, Arab-Jaziri F, Saulnier L, Milon A, Tenkanen M, Monsan P, O'Donohue MJ, Fauré R. Mutation of a pH-modulating residue in a GH51 α-l-arabinofuranosidase leads to a severe reduction of the secondary hydrolysis of transfuranosylation products. Biochim Biophys Acta Gen Subj 2014; 1840:626-36. [DOI: 10.1016/j.bbagen.2013.10.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 09/23/2013] [Accepted: 10/04/2013] [Indexed: 12/18/2022]
|
90
|
Wan Q, Zhang Q, Hamilton-Brehm S, Weiss K, Mustyakimov M, Coates L, Langan P, Graham D, Kovalevsky A. X-ray crystallographic studies of family 11 xylanase Michaelis and product complexes: implications for the catalytic mechanism. ACTA ACUST UNITED AC 2013; 70:11-23. [PMID: 24419374 DOI: 10.1107/s1399004713023626] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 08/22/2013] [Indexed: 11/10/2022]
Abstract
Xylanases catalyze the hydrolysis of plant hemicellulose xylan into oligosaccharides by cleaving the main-chain glycosidic linkages connecting xylose subunits. To study ligand binding and to understand how the pH constrains the activity of the enzyme, variants of the Trichoderma reesei xylanase were designed to either abolish its activity (E177Q) or to change its pH optimum (N44H). An E177Q-xylohexaose complex structure was obtained at 1.15 Å resolution which represents a pseudo-Michaelis complex and confirmed the conformational movement of the thumb region owing to ligand binding. Co-crystallization of N44H with xylohexaose resulted in a hydrolyzed xylotriose bound in the active site. Co-crystallization of the wild-type enzyme with xylopentaose trapped an aglycone xylotriose and a transglycosylated glycone product. Replacing amino acids near Glu177 decreased the xylanase activity but increased the relative activity at alkaline pH. The substrate distortion in the E177Q-xylohexaose structure expands the possible conformational itinerary of this xylose ring during the enzyme-catalyzed xylan-hydrolysis reaction.
Collapse
Affiliation(s)
- Qun Wan
- Biology and Soft Matter Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - Qiu Zhang
- Biology and Soft Matter Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - Scott Hamilton-Brehm
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - Kevin Weiss
- Biology and Soft Matter Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - Marat Mustyakimov
- Biology and Soft Matter Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - Leighton Coates
- Biology and Soft Matter Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - Paul Langan
- Biology and Soft Matter Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - David Graham
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| |
Collapse
|
91
|
Bianchetti CM, Brumm P, Smith RW, Dyer K, Hura GL, Rutkoski TJ, Phillips GN. Structure, dynamics, and specificity of endoglucanase D from Clostridium cellulovorans. J Mol Biol 2013; 425:4267-85. [PMID: 23751954 PMCID: PMC4039632 DOI: 10.1016/j.jmb.2013.05.030] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 05/22/2013] [Accepted: 05/30/2013] [Indexed: 11/17/2022]
Abstract
The enzymatic degradation of cellulose is a critical step in the biological conversion of plant biomass into an abundant renewable energy source. An understanding of the structural and dynamic features that cellulases utilize to bind a single strand of crystalline cellulose and hydrolyze the β-1,4-glycosidic bonds of cellulose to produce fermentable sugars would greatly facilitate the engineering of improved cellulases for the large-scale conversion of plant biomass. Endoglucanase D (EngD) from Clostridium cellulovorans is a modular enzyme comprising an N-terminal catalytic domain and a C-terminal carbohydrate-binding module, which is attached via a flexible linker. Here, we present the 2.1-Å-resolution crystal structures of full-length EngD with and without cellotriose bound, solution small-angle X-ray scattering (SAXS) studies of the full-length enzyme, the characterization of the active cleft glucose binding subsites, and substrate specificity of EngD on soluble and insoluble polymeric carbohydrates. SAXS data support a model in which the linker is flexible, allowing EngD to adopt an extended conformation in solution. The cellotriose-bound EngD structure revealed an extended active-site cleft that contains seven glucose-binding subsites, but unlike the majority of structurally determined endocellulases, the active-site cleft of EngD is partially enclosed by Trp162 and Tyr232. EngD variants, which lack Trp162, showed a significant reduction in activity and an alteration in the distribution of cellohexaose degradation products, suggesting that Trp162 plays a direct role in substrate binding.
Collapse
Affiliation(s)
- Christopher M. Bianchetti
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706, USA
| | - Phillip Brumm
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706, USA
- Lucigen Corporation and C5-6 Technologies, Madison WI 53562, USA
| | - Robert W. Smith
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706, USA
| | - Kevin Dyer
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Greg L. Hura
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Thomas J. Rutkoski
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706, USA
| | - George N. Phillips
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706, USA
- Department of Biochemistry and Cell Biology Rice University, Houston, TX 77005
| |
Collapse
|
92
|
Zheng M, Xu D. Catalytic Mechanism of Hyaluronate Lyase from Spectrococcus pneumonia: Quantum Mechanical/Molecular Mechanical and Density Functional Theory Studies. J Phys Chem B 2013; 117:10161-72. [DOI: 10.1021/jp406206s] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Min Zheng
- MOE Key Laboratory of Green
Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064, P. R. China
| | - Dingguo Xu
- MOE Key Laboratory of Green
Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064, P. R. China
| |
Collapse
|
93
|
Ghattyvenkatakrishna PK, Alekozai EM, Beckham GT, Schulz R, Crowley MF, Uberbacher EC, Cheng X. Initial recognition of a cellodextrin chain in the cellulose-binding tunnel may affect cellobiohydrolase directional specificity. Biophys J 2013; 104:904-12. [PMID: 23442969 DOI: 10.1016/j.bpj.2012.12.052] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 12/14/2012] [Accepted: 12/27/2012] [Indexed: 10/27/2022] Open
Abstract
Cellobiohydrolases processively hydrolyze glycosidic linkages in individual polymer chains of cellulose microfibrils, and typically exhibit specificity for either the reducing or nonreducing end of cellulose. Here, we conduct molecular dynamics simulations and free energy calculations to examine the initial binding of a cellulose chain into the catalytic tunnel of the reducing-end-specific Family 7 cellobiohydrolase (Cel7A) from Hypocrea jecorina. In unrestrained simulations, the cellulose diffuses into the tunnel from the -7 to the -5 positions, and the associated free energy profiles exhibit no barriers for initial processivity. The comparison of the free energy profiles for different cellulose chain orientations show a thermodynamic preference for the reducing end, suggesting that the preferential initial binding may affect the directional specificity of the enzyme by impeding nonproductive (nonreducing end) binding. Finally, the Trp-40 at the tunnel entrance is shown with free energy calculations to have a significant effect on initial chain complexation in Cel7A.
Collapse
|
94
|
Pluvinage B, Hehemann JH, Boraston AB. Substrate recognition and hydrolysis by a family 50 exo-β-agarase, Aga50D, from the marine bacterium Saccharophagus degradans. J Biol Chem 2013; 288:28078-88. [PMID: 23921382 DOI: 10.1074/jbc.m113.491068] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The bacteria that metabolize agarose use multiple enzymes of complementary specificities to hydrolyze the glycosidic linkages in agarose, a linear polymer comprising the repeating disaccharide subunit of neoagarobiose (3,6-anhydro-l-galactose-α-(1,3)-d-galactose) that are β-(1,4)-linked. Here we present the crystal structure of a glycoside hydrolase family 50 exo-β-agarase, Aga50D, from the marine microbe Saccharophagus degradans. This enzyme catalyzes a critical step in the metabolism of agarose by S. degradans through cleaving agarose oligomers into neoagarobiose products that can be further processed into monomers. The crystal structure of Aga50D to 1.9 Å resolution reveals a (β/α)8-barrel fold that is elaborated with a β-sandwich domain and extensive loops. The structures of catalytically inactivated Aga50D in complex with non-hydrolyzed neoagarotetraose (2.05 Å resolution) and neoagarooctaose (2.30 Å resolution) provide views of Michaelis complexes for a β-agarase. In these structures, the d-galactose residue in the -1 subsite is distorted into a (1)S3 skew boat conformation. The relative positioning of the putative catalytic residues are most consistent with a retaining catalytic mechanism. Additionally, the neoagarooctaose complex showed that this extended substrate made substantial interactions with the β-sandwich domain, which resembles a carbohydrate-binding module, thus creating additional plus (+) subsites and funneling the polymeric substrate through the tunnel-shaped active site. A synthesis of these results in combination with an additional neoagarobiose product complex suggests a potential exo-processive mode of action of Aga50D on the agarose double helix.
Collapse
Affiliation(s)
- Benjamin Pluvinage
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and
| | | | | |
Collapse
|
95
|
Geng Y, Kumar A, Faidallah HM, Albar HA, Mhkalid IA, Schmidt RR. C-(α-d-Glucopyranosyl)-phenyldiazomethanes—irreversible inhibitors of α-glucosidase. Bioorg Med Chem 2013; 21:4793-802. [DOI: 10.1016/j.bmc.2013.05.055] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 04/10/2013] [Accepted: 05/28/2013] [Indexed: 11/25/2022]
|
96
|
Khalili P, Barnett CB, Naidoo KJ. Interpreting medium ring canonical conformers by a triangular plane tessellation of the macrocycle. J Chem Phys 2013; 138:184110. [DOI: 10.1063/1.4803698] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Pegah Khalili
- Scientific Computing Research Unit, University of Cape Town, Cape Town 7701, South Africa
| | | | | |
Collapse
|
97
|
Calle L, Roldós V, Cañada FJ, Uhrig ML, Cagnoni AJ, Manzano VE, Varela O, Jiménez-Barbero J. Escherichia coliβ-Galactosidase Inhibitors through Modifications at the Aglyconic Moiety: Experimental Evidence of Conformational Distortion in the Molecular Recognition Process. Chemistry 2013; 19:4262-70. [DOI: 10.1002/chem.201203673] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Indexed: 11/07/2022]
|
98
|
Fekete CA, Kiss L. A New Approach in the Active Site Investigation of an Inverting β-d-Xylosidase from Thermobifida fusca TM51. Protein J 2013; 32:97-105. [DOI: 10.1007/s10930-013-9463-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
99
|
Wang JT, Lin TC, Chen YH, Lin CH, Fang JM. Polyhydroxylated pyrrolidine and 2-oxapyrrolizidine as glycosidase inhibitors. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00033h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
100
|
Amorim L, Marcelo F, Désiré J, Sollogoub M, Jiménez-Barbero J, Blériot Y. Synthesis and conformational analysis of bicyclic mimics of α- and β-d-glucopyranosides adopting the biologically relevant 2,5B conformation. Carbohydr Res 2012; 361:219-24. [DOI: 10.1016/j.carres.2012.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 07/04/2012] [Accepted: 07/05/2012] [Indexed: 10/28/2022]
|