1
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Sagiroglugil M, Yasar F. Catalytic Reaction Mechanism of Bacterial GH92 α-1,2-Mannosidase: A QM/MM Metadynamics Study. Chemphyschem 2023; 24:e202300628. [PMID: 37782219 DOI: 10.1002/cphc.202300628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/23/2023] [Accepted: 10/01/2023] [Indexed: 10/03/2023]
Abstract
The catalytic mechanism of aC a + 2 ${C{a}^{+2}}$ -dependent family 92 α ${{\rm \alpha }}$ -mannosidase, which is abundantly present in human gut flora and malfunctions leading to the lysosomal storage disease α-mannosidosis, has been investigated using quantum mechanics/molecular mechanics and metadynamics methods. Computational efforts show that the enzyme follows a conformational itinerary of and theC a + 2 ${C{a}^{+2}}$ ion serves a dual purpose, as it not only distorts the sugar ring but also plays a crucial role in orchestrating the arrangement of catalytic residues. This orchestration, in turn, contributes to the facilitation of O S 2 ${{{\rm \ }}^{{\rm O}}{{\rm S}}_{2}}$ conformers for the ensuing reaction. This mechanistic insight is well-aligned with the experimental predictions of the catalytic pathway, and the computed energies are of the same order of magnitude as the experimental estimations. Hence, our results extend the mechanistic understanding of glycosidases.
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Affiliation(s)
- Mert Sagiroglugil
- Department of Physics Engineering, Hacettepe University, Üniversiteler Mahallesi Beytepe Kampüsü, 06800, Ankara, Turkey
- Current Address: Departament de Química Inorgànica i Orgànica (Seccióde Química Orgànica), Institut de Química Teòrica i Computacional (IQTCUB) Universitat de Barcelona, Carrer de Martí i Franquès, 1, 08028, Barcelona, Spain
| | - Fatih Yasar
- Department of Physics Engineering, Hacettepe University, Üniversiteler Mahallesi Beytepe Kampüsü, 06800, Ankara, Turkey
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2
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Males A, Kok K, Nin-Hill A, de Koster N, van den Beukel S, Beenakker TJM, van der Marel GA, Codée JDC, Aerts JMFG, Overkleeft HS, Rovira C, Davies GJ, Artola M. Trans-cyclosulfamidate mannose-configured cyclitol allows isoform-dependent inhibition of GH47 α-d-mannosidases through a bump-hole strategy. Chem Sci 2023; 14:13581-13586. [PMID: 38033892 PMCID: PMC10685318 DOI: 10.1039/d3sc05016e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 10/29/2023] [Indexed: 12/02/2023] Open
Abstract
Class I inverting exo-acting α-1,2-mannosidases (CAZY family GH47) display an unusual catalytic itinerary featuring ring-flipped mannosides, 3S1 → 3H4‡ → 1C4. Conformationally locked 1C4 compounds, such as kifunensine, display nanomolar inhibition but large multigene GH47 mannosidase families render specific "isoform-dependent" inhibition impossible. Here we develop a bump-and-hole strategy in which a new mannose-configured 1,6-trans-cyclic sulfamidate inhibits α-d-mannosidases by virtue of its 1C4 conformation. This compound does not inhibit the wild-type GH47 model enzyme by virtue of a steric clash, a "bump", in the active site. An L310S (a conserved residue amongst human GH47 enzymes) mutant of the model Caulobacter GH47 awoke 574 nM inhibition of the previously dormant inhibitor, confirmed by structural analysis of a 0.97 Å structure. Considering that L310 is a conserved residue amongst human GH47 enzymes, this work provides a unique framework for future biotechnological studies on N-glycan maturation and ER associated degradation by isoform-specific GH47 α-d-mannosidase inhibition through a bump-and-hole approach.
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Affiliation(s)
- Alexandra Males
- York Structural Biology Laboratory, Department of Chemistry, The University of York York YO10 5DD UK
| | - Ken Kok
- Department of Medical Biochemistry, Leiden Institute of Chemistry (LIC), Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
| | - Alba Nin-Hill
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica), 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
| | - Nicky de Koster
- Department of Medical Biochemistry, Leiden Institute of Chemistry (LIC), Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
| | - Sija van den Beukel
- Department of Medical Biochemistry, Leiden Institute of Chemistry (LIC), Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
| | - Thomas J M Beenakker
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry (LIC), Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Gijsbert A van der Marel
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry (LIC), Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Jeroen D C Codée
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry (LIC), Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Johannes M F G Aerts
- Department of Medical Biochemistry, Leiden Institute of Chemistry (LIC), Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
| | - Herman S Overkleeft
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry (LIC), Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica), 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
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York York YO10 5DD UK
| | - Marta Artola
- Department of Medical Biochemistry, Leiden Institute of Chemistry (LIC), Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
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3
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Bhosale S, Deen MC, Proceviat C, Hettle A, Winter DK, Brockerman J, Levene M, Bennet AJ, Spino C, Boraston AB, Vocadlo DJ. A Fluorogenic Disaccharide Substrate for α-Mannosidases Enables High-Throughput Screening and Identification of an Inhibitor of the GH92 Virulence Factor from Streptococcus pneumoniae. ACS Chem Biol 2023; 18:1730-1737. [PMID: 37531094 DOI: 10.1021/acschembio.3c00053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Trimming of host glycans is a mechanism that is broadly employed by both commensal and pathogenic microflora to enable colonization. Host glycan trimming by the opportunistic Gram-positive bacterium Streptococcus pneumoniae has been demonstrated to be an important mechanism of virulence. While S. pneumoniae employs a multitude of glycan processing enzymes, the exo-mannosidase SpGH92 has been shown to be an important virulence factor. Accordingly, SpGH92 is hypothesized to be a target for much-needed new treatments of S. pneumoniae infection. Here we report the synthesis of 4-methylumbelliferyl α-d-mannopyranosyl-(1→2)-β-d-mannopyranoside (Manα1,2Manβ-4MU) as a fluorogenic disaccharide substrate and development of an assay for SpGH92 that overcomes its requirement for +1 binding site occupancy. We miniaturize our in vitro assay and apply it to a high-throughput screen of >65 000 compounds, identifying a single inhibitory chemotype, LIPS-343. We further show that Manα1,2Manβ-4MU is also a substrate of the human Golgi-localized α-mannosidase MAN1A1, suggesting that this substrate should be useful for assessing the activity of this and other mammalian α-mannosidases.
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Affiliation(s)
- Sandeep Bhosale
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Matthew C Deen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Cameron Proceviat
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Andrew Hettle
- Department of Biochemistry & Microbiology, University of Victoria, P.O. Box 3055 STN CSC, Victoria, British Columbia V8W 3P6, Canada
| | - Dana K Winter
- Département de Chimie, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - Jacob Brockerman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Marina Levene
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Andrew J Bennet
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Claude Spino
- Département de Chimie, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - Alisdair B Boraston
- Department of Biochemistry & Microbiology, University of Victoria, P.O. Box 3055 STN CSC, Victoria, British Columbia V8W 3P6, Canada
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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4
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Pengthaisong S, Piniello B, Davies GJ, Rovira C, Ketudat Cairns JR. Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation. ACS Catal 2023; 13:5850-5863. [PMID: 37180965 PMCID: PMC10167657 DOI: 10.1021/acscatal.3c00620] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/15/2023] [Indexed: 05/16/2023]
Abstract
Retaining glycoside hydrolases use acid/base catalysis with an enzymatic acid/base protonating the glycosidic bond oxygen to facilitate leaving-group departure alongside attack by a catalytic nucleophile to form a covalent intermediate. Generally, this acid/base protonates the oxygen laterally with respect to the sugar ring, which places the catalytic acid/base and nucleophile carboxylates within about 4.5-6.5 Å of each other. However, in glycoside hydrolase (GH) family 116, including disease-related human acid β-glucosidase 2 (GBA2), the distance between the catalytic acid/base and the nucleophile is around 8 Å (PDB: 5BVU) and the catalytic acid/base appears to be above the plane of the pyranose ring, rather than being lateral to that plane, which could have catalytic consequences. However, no structure of an enzyme-substrate complex is available for this GH family. Here, we report the structures of Thermoanaerobacterium xylanolyticum β-glucosidase (TxGH116) D593N acid/base mutant in complexes with cellobiose and laminaribiose and its catalytic mechanism. We confirm that the amide hydrogen bonding to the glycosidic oxygen is in a perpendicular rather than lateral orientation. Quantum mechanics/molecular mechanics (QM/MM) simulations of the glycosylation half-reaction in wild-type TxGH116 indicate that the substrate binds with the nonreducing glucose residue in an unusual relaxed 4C1 chair at the -1 subsite. Nevertheless, the reaction can still proceed through a 4H3 half-chair transition state, as in classical retaining β-glucosidases, as the catalytic acid D593 protonates the perpendicular electron pair. The glucose C6OH is locked in a gauche, trans orientation with respect to the C5-O5 and C4-C5 bonds to facilitate perpendicular protonation. These data imply a unique protonation trajectory in Clan-O glycoside hydrolases, which has strong implications for the design of inhibitors specific to either lateral protonators, such as human GBA1, or perpendicular protonators, such as human GBA2.
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Affiliation(s)
- Salila Pengthaisong
- School
of Chemistry, Institute of Science, Suranaree
University of Technology, Nakhon
Ratchasima 30000, Thailand
- Center
for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Beatriz Piniello
- Departament
de Quımica Inorgánica i Orgànica (Secció
de Química Orgànica) and Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Gideon J. Davies
- Department
of Chemistry, University of York, Heslington, York YO10
5DD, U.K.
| | - Carme Rovira
- Departament
de Quımica Inorgánica i Orgànica (Secció
de Química Orgànica) and Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avancats (ICREA), 08010 Barcelona, Spain
| | - James R. Ketudat Cairns
- School
of Chemistry, Institute of Science, Suranaree
University of Technology, Nakhon
Ratchasima 30000, Thailand
- Center
for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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5
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Morais MAB, Nin-Hill A, Rovira C. Glycosidase mechanisms: Sugar conformations and reactivity in endo- and exo-acting enzymes. Curr Opin Chem Biol 2023; 74:102282. [PMID: 36931022 DOI: 10.1016/j.cbpa.2023.102282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/19/2023] [Accepted: 02/09/2023] [Indexed: 03/17/2023]
Abstract
The enzymatic breakdown of carbohydrates plays a critical role in several biological events and enables the development of sustainable processes to obtain bioproducts and biofuels. In this scenario, the design of efficient inhibitors for glycosidases that can act as drug targets and the engineering of carbohydrate-active enzymes with tailored catalytic properties is of remarkable importance. To guide rational approaches, it is necessary to elucidate enzyme molecular mechanisms, in particular understanding how the microenvironment modulates the conformational space explored by the substrate. Computer simulations, especially those based on ab initio methods, have provided a suitable atomic description of carbohydrate conformations and catalytic reactions in several glycosidase families. In this review, we will focus on how the active-site topology (pocket or cleft) and mode of cleavage (endo or exo) can affect the catalytic mechanisms adopted by glycosidases, in particular the substrate conformations along the reaction coordinate.
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Affiliation(s)
- Mariana Abrahão Bueno Morais
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, Brazil
| | - Alba Nin-Hill
- Departament de Química Inorgànica i Orgànica & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain.
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6
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J N C, Mallajosyula SS. Impact of Polarization on the Ring Puckering Dynamics of Hexose Monosaccharides. J Chem Inf Model 2023; 63:208-223. [PMID: 36475659 DOI: 10.1021/acs.jcim.2c01286] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Analysis of crystal structures of hexose monosaccharides α-d-mannose (α-MAN), β-d-mannose (β-MAN), α-d-glucose (α-GLC), β-d-glucose (β-GLC), α-d-galactose (α-GAL), β-d-galactose (β-GAL), α-d-altrose (α-ALT), β-d-altrose (β-ALT), α-d-idose (α-IDO), and β-d-idose (β-IDO) reveals that the monosaccharide ring adopts multiple ring conformations. These ring conformations can be broadly classified as chair, half-chair, envelope, boat, and skew-boat conformations. The ability of the monosaccharide ring to adopt multiple conformations has been closely tied with their bioactivity. However, it has been difficult to capture the dynamic information of these conformations from experimental studies. Even from simulations, capturing these different conformations is challenging because of the energy barriers involved in the transitions between the stable 4C1 and 1C4 chair forms. In this study, we analyze the influence of the polarizable force field on the ring dynamics of five major types of unsubstituted aldohexoses─glucose, mannose, galactose, altrose, and idose─and their anomers. We simulate microsecond trajectories to capture the influence of the CHARMM36 additive and polarizable carbohydrate force fields on the ring dynamics. The microsecond trajectories allow us to comment on the issues associated with equilibrium molecular dynamics simulations. Further, we use the extended system adaptive biasing force (eABF) method to compare the conformational sampling efficiencies of the additive and polarizable force fields. Our studies reveal that inclusion of polarization enhances the sampling of ring conformations and lowers the energy barriers between the 4C1 and 1C4 conformations. Overall, the CHARMM36 additive force field is observed to be rigid and favor the 4C1 conformations. Although the inclusion of polarizability results in enhancing ring flexibility, we observe sampling that does not agree with experimental results, warranting a revision of the polarizable Drude parameters.
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Affiliation(s)
- Chythra J N
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat382355, India
| | - Sairam S Mallajosyula
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat382355, India
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7
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Abstract
Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.
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Affiliation(s)
- Serge Perez
- Centre de Recherche sur les Macromolecules Vegetales, University of Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble F-38041, France
| | - Olga Makshakova
- FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, Kazan 420111, Russia
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8
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Fadda E. Molecular simulations of complex carbohydrates and glycoconjugates. Curr Opin Chem Biol 2022; 69:102175. [PMID: 35728307 DOI: 10.1016/j.cbpa.2022.102175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/17/2022]
Abstract
Complex carbohydrates (glycans) are the most abundant and versatile biopolymers in nature. The broad diversity of biochemical functions that carbohydrates cover is a direct consequence of the variety of 3D architectures they can adopt, displaying branched or linear arrangements, widely ranging in sizes, and with the highest diversity of building blocks of any other natural biopolymer. Despite this unparalleled complexity, a common denominator can be found in the glycans' inherent flexibility, which hinders experimental characterization, but that can be addressed by high-performance computing (HPC)-based molecular simulations. In this short review, I present and discuss the state-of-the-art of molecular simulations of complex carbohydrates and glycoconjugates, highlighting methodological strengths and weaknesses, important insights through emblematic case studies, and suggesting perspectives for future developments.
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Affiliation(s)
- Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Ireland.
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9
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Li P, Shi M, Wang X, Xu D. QM/MM investigation of the catalytic mechanism of processive endoglucanase Cel9G from Clostridium cellulovorans. Phys Chem Chem Phys 2022; 24:11919-11930. [PMID: 35514276 DOI: 10.1039/d2cp00593j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Carbohydrate degradation catalyzed by glucoside hydrolases (GHs) is a major mechanism in biomass conversion. GH family 9 endoglucanase (Cel9G) from Clostridium cellulovorans, a typical multimodular enzyme, contains a catalytic domain closely linked to a family 3c carbohydrate-binding module (CBM3c). Unlike the conventional behavior proposed for other carbohydrate-binding modules, CBM3c has a direct impact on catalytic activity. In this work, extensive molecular dynamics (MD) simulations were employed to clarify the functional role of CBM3c. Furthermore, the detailed catalytic mechanism of Cel9G was investigated at the atomistic level using the combined quantum mechanical and molecular mechanical (QM/MM) method. Based on these simulations, owing to the rigidity of the peptide linker, CBM3c may affect the enzymatic activity via direct interactions with alpha helix 4 of GH9, especially with the K123 and H125 residues. In addition, using cellohexaose as a substrate, the QM/MM MD simulations confirmed that this enzyme can cleave the β-1,4-glycosidic linkage via an inverting mechanism. An oxocarbenium ion-like transition state was located with a barrier height of 19.6 kcal mol-1. Furthermore, the G(-1) pyranose unit preferentially adopted a distorted 1S5/4H5 conformer in the enzyme-substrate complex. For the cleavage of the glycosidic bond, we were able to identify a plausible route (1S5/4H5 → [4H5/4E]# → 4C1) from the reactant to the product at the G(-1) site.
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Affiliation(s)
- Penghui Li
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, Sichuan, 610064, P. R. China.
| | - Mingsong Shi
- State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Xin Wang
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, Sichuan, 610064, P. R. China.
| | - Dingguo Xu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, Sichuan, 610064, P. R. China.
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10
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Takihara H, Miura N, Aoki-Kinoshita KF, Okuda S. Functional glyco-metagenomics elucidates the role of glycan-related genes in environments. BMC Bioinformatics 2021; 22:505. [PMID: 34663219 PMCID: PMC8522060 DOI: 10.1186/s12859-021-04425-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/04/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Glycan-related genes play a fundamental role in various processes for energy acquisition and homeostasis maintenance while adapting to the environment in which the organism exists; however, their role in the microbiome in the environment is unclear. METHODS Sequence alignment was performed between known glycan-related genes and complete genomes of microorganisms, and optimal parameters for identifying glycan-related genes were determined based on the alignments. Using the constructed scheme (> 90% of identity and > 25 aa of alignment length), glycan-related genes in various environments were identified from 198 different metagenome data. RESULTS As a result, we identified 86.73 million glycan-related genes from the metagenome data. Among the 12 environments classified in this study, the percentage of glycan-related genes was high in the human-associated environment, suggesting that these environments utilize glycan metabolism better than other environments. On the other hand, the relative abundances of both glycoside hydrolases and glycosyltransferases surprisingly had a coverage of over 80% in all the environments. These glycoside hydrolases and glycosyltransferases were classified into two groups of (1) general enzyme families identified in various environments and (2) specific enzymes found only in certain environments. The general enzyme families were mostly from genes involved in monosaccharide metabolism, and most of the specific enzymes were polysaccharide degrading enzymes. CONCLUSION These findings suggest that environmental microorganisms could change the composition of their glycan-related genes to adapt the processes involved in acquiring energy from glycans in their environments. Our functional glyco-metagenomics approach has made it possible to clarify the relationship between the environment and genes from the perspective of carbohydrates, and the existence of glycan-related genes that exist specifically in the environment.
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Affiliation(s)
- Hayato Takihara
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan
| | - Nobuaki Miura
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan
| | - Kiyoko F Aoki-Kinoshita
- Glycan and Life Systems Integration Center, Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo, 192-8577, Japan
| | - Shujiro Okuda
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan.
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11
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Quirke JCK, Crich D. GH47 and Other Glycoside Hydrolases Catalyze Glycosidic Bond Cleavage with the Assistance of Substrate Super-arming at the Transition State. ACS Catal 2021; 11:10308-10315. [PMID: 34777906 PMCID: PMC8579916 DOI: 10.1021/acscatal.1c02750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Super-armed glycosyl donors, whose substituents are predominantly held in pseudoaxial positions, exhibit strongly increased reactivity in glycosylation through significant stabilization of oxocarbenium-like transition states. Examination of X-ray crystal structures reveals that the GH47 family of glycoside hydrolases have evolved so as to distort their substrates away from the ground state conformation in such a manner as to present multiple C-O bonds in pseudoaxial positions and so benefit from conformational super-arming of their substrates, thereby enhancing catalysis. Through analysis of literature mutagenic studies, we show that a suitably placed aromatic residue in GHs 6 and 47 sterically enforces super-armed conformations on their substrates. GH families 45, 81, and 134 on the other hand impose conformational super-arming on their substrates, by maintaining the more active ring conformation through hydrogen bonding rather than steric interactions. The recognition of substrate super-arming by select GH families provides a further parallel with synthetic carbohydrate chemistry and nature and opens further avenues for the design of improved glycosidase inhibitors.
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Affiliation(s)
- Jonathan C K Quirke
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, GA 30602, USA
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, GA 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - David Crich
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, GA 30602, USA
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, GA 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
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12
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Uhrig ML, Mora Flores EW, Postigo A. Approaches to the Synthesis of Perfluoroalkyl-Modified Carbohydrates and Derivatives: Thiosugars, Iminosugars, and Tetrahydro(thio)pyrans. Chemistry 2021; 27:7813-7825. [PMID: 33462910 DOI: 10.1002/chem.202005229] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/06/2021] [Indexed: 12/11/2022]
Abstract
Fluoroalkyl-substituted carbohydrates play relevant roles in diverse areas such as supramolecular chemistry, glycoconjugation, liquid crystals, and surfactants, with direct applications as wetting, antifreeze, and coating agents. In light of these promising applications, new methodologies for the late-stage incorporation of fluoroalkyl RF groups into carbohydrates and derivatives are herein presented as they are relevant to the synthetic carbohydrate community. Previously reviewed protocols for the installation of RF groups onto carbohydrates and derivatives will be succinctly summarized in the light of the new achievements. Fluoroalkyl-substituted iminosugars, on the other hand, are also interesting glycomimetic derivatives with prominent roles as glycosidases and glycosyltransferases inhibitors, as has recently been demonstrated. Also, they positively contribute to the study of sugar-protein interactions and enzyme mechanisms. New advances in the syntheses of fluoroalkyl-substituted iminosugars will also be presented here.
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Affiliation(s)
- María Laura Uhrig
- Departamento de Química Orgánica, Universidad de Buenos Aires, Facultad de Ciencias ExactasyNaturales, Pabellón 2, Ciudad Universitaria, C1428EG, Buenos Aires, Argentina.,Centro de Investigaciones en Hidratos de Carbono (CIHIDECAR), CONICET- Universidad de Buenos Aires, CP1428, Buenos Aires, Argentina
| | - Erwin W Mora Flores
- Departamento de Química Orgánica, Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Junín 954, CP1113-, Buenos Aires, Argentina
| | - Al Postigo
- Departamento de Química Orgánica, Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Junín 954, CP1113-, Buenos Aires, Argentina
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13
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Morais MAB, Coines J, Domingues MN, Pirolla RAS, Tonoli CCC, Santos CR, Correa JBL, Gozzo FC, Rovira C, Murakami MT. Two distinct catalytic pathways for GH43 xylanolytic enzymes unveiled by X-ray and QM/MM simulations. Nat Commun 2021; 12:367. [PMID: 33446650 PMCID: PMC7809346 DOI: 10.1038/s41467-020-20620-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023] Open
Abstract
Xylanolytic enzymes from glycoside hydrolase family 43 (GH43) are involved in the breakdown of hemicellulose, the second most abundant carbohydrate in plants. Here, we kinetically and mechanistically describe the non-reducing-end xylose-releasing exo-oligoxylanase activity and report the crystal structure of a native GH43 Michaelis complex with its substrate prior to hydrolysis. Two distinct calcium-stabilized conformations of the active site xylosyl unit are found, suggesting two alternative catalytic routes. These results are confirmed by QM/MM simulations that unveil the complete hydrolysis mechanism and identify two possible reaction pathways, involving different transition state conformations for the cleavage of xylooligosaccharides. Such catalytic conformational promiscuity in glycosidases is related to the open architecture of the active site and thus might be extended to other exo-acting enzymes. These findings expand the current general model of catalytic mechanism of glycosidases, a main reaction in nature, and impact on our understanding about their interaction with substrates and inhibitors.
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Affiliation(s)
- Mariana A B Morais
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
- Departament de Química Inorgànica i Orgànica & Institut de Química Teórica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, 08028, Spain
| | - Joan Coines
- Departament de Química Inorgànica i Orgànica & Institut de Química Teórica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, 08028, Spain
| | - Mariane N Domingues
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Renan A S Pirolla
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Celisa C C Tonoli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Camila R Santos
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Jessica B L Correa
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Fabio C Gozzo
- Dalton Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, Campinas, 13083-970, Brazil
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & Institut de Química Teórica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, 08028, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010, Spain.
| | - Mario T Murakami
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil.
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14
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Xiong J, Xu D. Mechanistic Insights into the Hydrolysis of O-GlcNAcylation Catalyzed by Human O-GlcNAcase. J Phys Chem B 2020; 124:9310-9322. [PMID: 32970432 DOI: 10.1021/acs.jpcb.0c05755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
O-GlcNAc glycosylation occurs on specific serine/threonine residues of intracellular proteins, which is widely related to various diseases, including type II diabetes, cancer, and Alzheimer's disease. Human O-GlcNAcase (hOGA) is responsible for the removal of O-GlcNAc modification and thus serves as the main target for inhibitor design. In this work, we systematically investigated the mechanism catalyzed by hOGA using the quantum mechanical/molecular mechanical method. Based on calculated free energy profiles, two essential steps named cyclization (Cyc) step and ring opening step are required to generate the final hemiacetal product. The Cyc of the 2-acetamido group, the rate-limiting step, leads to the generation of the intermediate of a bicyclic oxazolinium ion (EI1). Next, the oxazoline ring could be broken via the nucleophilic attack of a water molecule at the C1 position, which generates the final product. Along with this, our simulations clearly suggest the existence of an oxazoline intermediate (EI2), which is produced via proton transfer (PT) from the 2-acetamido group (EI1) to D174. This PT step features a reversible process with a low energy barrier, which could be attributed to a low barrier hydrogen bond between the donor and acceptor. The stabilizing effect of the low barrier hydrogen bond on EI1 is proposed to be very important for accelerating the overall reaction. In fact, the site-directed mutagenesis simulations of D174A and D175A strongly indicate that the catalytic residues mainly affect the observed reaction rate by affecting the stability of the intermediate.
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Affiliation(s)
- Jing Xiong
- School of Pharmacy, Chengdu Medical College, Chengdu, Sichuan 610500, P. R. China
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry & Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China
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15
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Nin-Hill A, Rovira C. The Catalytic Reaction Mechanism of the β-Galactocerebrosidase Enzyme Deficient in Krabbe Disease. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02609] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Alba Nin-Hill
- Departament de Quı́mica Inorgànica i Orgànica (Secció de Quı́mica Orgànica) & Institut de Quı́mia Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Carme Rovira
- Departament de Quı́mica Inorgànica i Orgànica (Secció de Quı́mica Orgànica) & Institut de Quı́mia Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08020 Barcelona, Spain
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16
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Alonso-Gil S. Mimicking the transition state of reactions of glycoside hydrolases: Updating the conformational space of the oxocarbenium cation. J Carbohydr Chem 2020. [DOI: 10.1080/07328303.2020.1766481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Santiago Alonso-Gil
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Prague 8, Czech Republic
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17
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Bharadwaj VS, Knott BC, Ståhlberg J, Beckham GT, Crowley MF. The hydrolysis mechanism of a GH45 cellulase and its potential relation to lytic transglycosylase and expansin function. J Biol Chem 2020; 295:4477-4487. [PMID: 32054684 DOI: 10.1074/jbc.ra119.011406] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/12/2020] [Indexed: 11/06/2022] Open
Abstract
Family 45 glycoside hydrolases (GH45) are endoglucanases that are integral to cellulolytic secretomes, and their ability to break down cellulose has been successfully exploited in textile and detergent industries. In addition to their industrial relevance, understanding the molecular mechanism of GH45-catalyzed hydrolysis is of fundamental importance because of their structural similarity to cell wall-modifying enzymes such as bacterial lytic transglycosylases (LTs) and expansins present in bacteria, plants, and fungi. Our understanding of the catalytic itinerary of GH45s has been incomplete because a crystal structure with substrate spanning the -1 to +1 subsites is currently lacking. Here we constructed and validated a putative Michaelis complex in silico and used it to elucidate the hydrolytic mechanism in a GH45, Cel45A from the fungus Humicola insolens, via unbiased simulation approaches. These molecular simulations revealed that the solvent-exposed active-site architecture results in lack of coordination for the hydroxymethyl group of the substrate at the -1 subsite. This lack of coordination imparted mobility to the hydroxymethyl group and enabled a crucial hydrogen bond with the catalytic acid during and after the reaction. This suggests the possibility of a nonhydrolytic reaction mechanism when the catalytic base aspartic acid is missing, as is the case in some LTs (murein transglycosylase A) and expansins. We calculated reaction free energies and demonstrate the thermodynamic feasibility of the hydrolytic and nonhydrolytic reaction mechanisms. Our results provide molecular insights into the hydrolysis mechanism in HiCel45A, with possible implications for elucidating the elusive catalytic mechanism in LTs and expansins.
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Affiliation(s)
- Vivek S Bharadwaj
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Brandon C Knott
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P. O. Box 7015, 750 07 Uppsala, Sweden
| | - Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Michael F Crowley
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
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18
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Endo S, Wako H. Normal mode analysis calculation for a full-atom model with a smaller number of degrees of freedom for huge protein molecules. Biophys Physicobiol 2020; 16:205-212. [PMID: 31984173 PMCID: PMC6975923 DOI: 10.2142/biophysico.16.0_205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 06/27/2019] [Indexed: 12/01/2022] Open
Abstract
The number of degrees of freedom (DOF), N, in normal mode analysis (NMA) calculations of proteins is a crucial problem in huge systems because the eigenvalue problem of an N-by-N matrix must be solved. If it were possible to perform the analysis with a smaller number of DOF for the same system with minimal deterioration in accuracy, this would make a significant impact on the computational study of protein dynamics. We examined two models in which the number of DOF was reduced. Both of them adopted a full-atom model with dihedral angles as independent variables. In one model, side-chain dihedral angles, χ's, and a main-chain dihedral angle, ω, were fixed and only the main-chain dihedral angles, ϕ and ψ, were variable. In another model, the dihedral angles around virtual bonds that connect neighboring Cα atoms were tested. The number of DOFs for the two models was two and one per residue, respectively. The residue-by-residue fluctuation profiles for atoms and dihedral angles were well reproduced in both models. The motion of atoms in the individual lowest-frequency normal modes of the two models was also very similar to those of the original model in which all rotatable dihedral angles were variable. Consequently, these models could predict large-amplitude concerted motion. These results also imply that proteins in a full-atom model can undergo only limited large-scale conformational changes around the native conformation, and consequently, NMA results do not strongly depend on the independent variables adopted.
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Affiliation(s)
- Shigeru Endo
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
| | - Hiroshi Wako
- School of Social Sciences, Waseda University, Shinjuku-ku, Tokyo 169-8050, Japan
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19
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Rovira C, Males A, Davies GJ, Williams SJ. Mannosidase mechanism: at the intersection of conformation and catalysis. Curr Opin Struct Biol 2019; 62:79-92. [PMID: 31891872 DOI: 10.1016/j.sbi.2019.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/06/2019] [Accepted: 11/15/2019] [Indexed: 12/17/2022]
Abstract
Mannosidases are a diverse group of enzymes that are important in the biological processing of mannose-containing polysaccharides and complex glycoconjugates. They are found in 12 of the >160 sequence-based glycosidase families. We discuss evidence that nature has evolved a small set of common mechanisms that unite almost all of these mannosidase families. Broadly, mannosidases (and the closely related rhamnosidases) perform catalysis through just two conformations of the oxocarbenium ion-like transition state: a B2,5 (or enantiomeric 2,5B) boat and a 3H4 half-chair. This extends to a new family (GT108) of GDPMan-dependent β-1,2-mannosyltransferases/phosphorylases that perform mannosyl transfer through a boat conformation as well as some mannosidases that are metalloenzymes and require divalent cations for catalysis. Yet, among this commonality lies diversity. New evidence shows that one unique family (GH99) of mannosidases use an unusual mechanism involving anchimeric assistance via a 1,2-anhydro sugar (epoxide) intermediate.
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Affiliation(s)
- Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| | - Alexandra Males
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Gideon J Davies
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
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20
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Coines J, Raich L, Rovira C. Modeling catalytic reaction mechanisms in glycoside hydrolases. Curr Opin Chem Biol 2019; 53:183-191. [PMID: 31731209 DOI: 10.1016/j.cbpa.2019.09.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/22/2019] [Accepted: 09/24/2019] [Indexed: 01/21/2023]
Abstract
Modeling catalysis in carbohydrate-active enzymes is a daunting challenge because of the high flexibility and diversity of both enzymes and carbohydrates. Glycoside hydrolases (GHs) are an illustrative example, where conformational changes and subtle interactions have been shown to be critical for catalysis. GHs have pivotal roles in industry (e.g. biofuel or detergent production) and biomedicine (e.g. targets for cancer and diabetes), and thus, a huge effort is devoted to unveil their molecular mechanisms. Besides experimental techniques, computational methods have served to provide an in-depth understanding of GH mechanisms, capturing complex reaction coordinates and the conformational itineraries that substrates follow during the whole catalytic pathway, providing a framework that ultimately may assist the engineering of these enzymes and the design of new inhibitors.
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Affiliation(s)
- Joan Coines
- 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
| | - 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
| | - 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; Institució Catalana de Recerca I Estudis Avançats (ICREA) Passeig Lluís Companys 23, 08010 Barcelona, Spain.
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21
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Males A, Speciale G, Williams SJ, Davies GJ. Distortion of mannoimidazole supports a B2,5 boat transition state for the family GH125 α-1,6-mannosidase from Clostridium perfringens. Org Biomol Chem 2019; 17:7863-7869. [DOI: 10.1039/c9ob01161g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Enzyme transition-state mimics can act as powerful inhibitors and allow structural studies that report on the conformation of the transition-state.
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Affiliation(s)
- Alexandra Males
- York Structural Biology Laboratory
- Department of Chemistry
- The University of York
- YO10 5DD York
- UK
| | - Gaetano Speciale
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute
- University of Melbourne
- Melbourne
- Australia
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute
- University of Melbourne
- Melbourne
- Australia
| | - Gideon J. Davies
- York Structural Biology Laboratory
- Department of Chemistry
- The University of York
- YO10 5DD York
- UK
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22
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Artola M, Hedberg C, Rowland RJ, Raich L, Kytidou K, Wu L, Schaaf A, Ferraz MJ, van der Marel GA, Codée JDC, Rovira C, Aerts JMFG, Davies GJ, Overkleeft HS. α-d-Gal-cyclophellitol cyclosulfamidate is a Michaelis complex analog that stabilizes therapeutic lysosomal α-galactosidase A in Fabry disease. Chem Sci 2019. [DOI: 10.1039/c9sc03342d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
α-d-Gal-cyclophellitol cyclosulfamidate is a new class of neutral, conformationally-constrained competitive glycosidase inhibitor that stabilizes α-gal A and prevents its degradation both in vitro and in cellulo by mimicry of the Michaelis complex conformation.
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23
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Fernandes PZ, Petricevic M, Sobala L, Davies GJ, Williams SJ. Exploration of Strategies for Mechanism-Based Inhibitor Design for Family GH99 endo-α-1,2-Mannanases. Chemistry 2018; 24:7464-7473. [PMID: 29508463 PMCID: PMC6001782 DOI: 10.1002/chem.201800435] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Indexed: 11/06/2022]
Abstract
endo-α-1,2-Mannosidases and -mannanases, members of glycoside hydrolase family 99 (GH99), cleave α-Glc/Man-1,3-α-Man-OR structures within mammalian N-linked glycans and fungal α-mannan, respectively. They are proposed to act through a two-step mechanism involving a 1,2-anhydrosugar "epoxide" intermediate incorporating two conserved catalytic carboxylates. In the first step, one carboxylate acts as a general base to deprotonate the 2-hydroxy group adjacent to the fissile glycosidic bond, and the other provides general acid assistance to the departure of the aglycon. We report herein the synthesis of two inhibitors designed to interact with either the general base (α-mannosyl-1,3-(2-aminodeoxymannojirimycin), Man2NH2 DMJ) or the general acid (α-mannosyl-1,3-mannoimidazole, ManManIm). Modest affinities were observed for an endo-α-1,2-mannanase from Bacteroides thetaiotaomicron. Structural studies revealed that Man2NH2 DMJ binds like other iminosugar inhibitors, which suggests that the poor inhibition shown by this compound is not a result of a failure to achieve the expected interaction with the general base, but rather the reduction in basicity of the endocyclic nitrogen caused by introduction of a vicinal, protonated amine at C2. ManManIm binds with the imidazole headgroup distorted downwards, a result of an unfavourable interaction with a conserved active site tyrosine. This study has identified important limitations associated with mechanism-inspired inhibitor design for GH99 enzymes.
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Affiliation(s)
- Pearl Z. Fernandes
- School of ChemistryBio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVic3010Australia
| | - Marija Petricevic
- School of ChemistryBio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVic3010Australia
| | - Lukasz Sobala
- York Structural Biology LaboratoryDepartment of ChemistryUniversity of YorkHeslingtonYO10 5DDUK
| | - Gideon J. Davies
- York Structural Biology LaboratoryDepartment of ChemistryUniversity of YorkHeslingtonYO10 5DDUK
| | - Spencer J. Williams
- School of ChemistryBio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVic3010Australia
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24
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Thompson AJ, Spears RJ, Zhu Y, Suits MDL, Williams SJ, Gilbert HJ, Davies GJ. Bacteroides thetaiotaomicron generates diverse α-mannosidase activities through subtle evolution of a distal substrate-binding motif. Acta Crystallogr D Struct Biol 2018; 74:394-404. [PMID: 29717710 PMCID: PMC5930347 DOI: 10.1107/s2059798318002942] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/19/2018] [Indexed: 11/17/2022] Open
Abstract
A dominant human gut microbe, the well studied symbiont Bacteroides thetaiotaomicron (Bt), is a glyco-specialist that harbors a large repertoire of genes devoted to carbohydrate processing. Despite strong similarities among them, many of the encoded enzymes have evolved distinct substrate specificities, and through the clustering of cognate genes within operons termed polysaccharide-utilization loci (PULs) enable the fulfilment of complex biological roles. Structural analyses of two glycoside hydrolase family 92 α-mannosidases, BT3130 and BT3965, together with mechanistically relevant complexes at 1.8-2.5 Å resolution reveal conservation of the global enzyme fold and core catalytic apparatus despite different linkage specificities. Structure comparison shows that Bt differentiates the activity of these enzymes through evolution of a highly variable substrate-binding region immediately adjacent to the active site. These observations unveil a genetic/biochemical mechanism through which polysaccharide-processing bacteria can evolve new and specific biochemical activities from otherwise highly similar gene products.
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Affiliation(s)
- Andrew J. Thompson
- Department of Chemistry, University of York, Heslington, York YO10 5DD, England
| | - Richard J. Spears
- Department of Chemistry, University of York, Heslington, York YO10 5DD, England
| | - Yanping Zhu
- Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, England
| | - Michael D. L. Suits
- Department of Chemistry, University of York, Heslington, York YO10 5DD, England
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Harry J. Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, England
| | - Gideon J. Davies
- Department of Chemistry, University of York, Heslington, York YO10 5DD, England
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25
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Rother C, Gutmann A, Gudiminchi R, Weber H, Lepak A, Nidetzky B. Biochemical Characterization and Mechanistic Analysis of the Levoglucosan Kinase from Lipomyces starkeyi. Chembiochem 2018; 19:596-603. [DOI: 10.1002/cbic.201700587] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Christina Rother
- Institute of Biotechnology and Biochemical Engineering; Graz University of Technology, NAWI Graz; Petersgasse 12 8010 Graz Austria
| | - Alexander Gutmann
- Institute of Biotechnology and Biochemical Engineering; Graz University of Technology, NAWI Graz; Petersgasse 12 8010 Graz Austria
| | - Ramakrishna Gudiminchi
- Institute of Biotechnology and Biochemical Engineering; Graz University of Technology, NAWI Graz; Petersgasse 12 8010 Graz Austria
- Austrian Centre of Industrial Biotechnology; Petersgasse 14 8010 Graz Austria
| | - Hansjörg Weber
- Graz University of Technology, NAWI Graz; Stremayrgasse 9 8010 Graz Austria
| | - Alexander Lepak
- Institute of Biotechnology and Biochemical Engineering; Graz University of Technology, NAWI Graz; Petersgasse 12 8010 Graz Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering; Graz University of Technology, NAWI Graz; Petersgasse 12 8010 Graz Austria
- Austrian Centre of Industrial Biotechnology; Petersgasse 14 8010 Graz Austria
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26
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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.
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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
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27
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Males A, Raich L, Williams SJ, Rovira C, Davies GJ. Conformational Analysis of the Mannosidase Inhibitor Kifunensine: A Quantum Mechanical and Structural Approach. Chembiochem 2017; 18:1496-1501. [DOI: 10.1002/cbic.201700166] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Alexandra Males
- York Structural Biology Laboratory Department of Chemistry The University of York York YO10 5DD UK
| | - 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
| | - Spencer J. Williams
- School of Chemistry Bio21 Molecular Science and Biotechnology Institute University of Melbourne Parkville VIC 3010 Australia
| | - 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
- Institució Catalana de Recerca i Estudis Avançats (ICREA) Passeig Lluís Companys 23 08010 Barcelona Spain
| | - Gideon J. Davies
- York Structural Biology Laboratory Department of Chemistry The University of York York YO10 5DD UK
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28
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Beenakker TM, Wander DPA, Offen WA, Artola M, Raich L, Ferraz MJ, Li KY, Houben JHPM, van Rijssel ER, Hansen T, van der Marel GA, Codée JDC, Aerts JMF, Rovira C, Davies GJ, Overkleeft HS. Carba-cyclophellitols Are Neutral Retaining-Glucosidase Inhibitors. J Am Chem Soc 2017; 139:6534-6537. [PMID: 28463498 PMCID: PMC5437670 DOI: 10.1021/jacs.7b01773] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Indexed: 01/15/2023]
Abstract
The conformational analysis of glycosidases affords a route to their specific inhibition through transition-state mimicry. Inspired by the rapid reaction rates of cyclophellitol and cyclophellitol aziridine-both covalent retaining β-glucosidase inhibitors-we postulated that the corresponding carba "cyclopropyl" analogue would be a potent retaining β-glucosidase inhibitor for those enzymes reacting through the 4H3 transition-state conformation. Ab initio metadynamics simulations of the conformational free energy landscape for the cyclopropyl inhibitors show a strong bias for the 4H3 conformation, and carba-cyclophellitol, with an N-(4-azidobutyl)carboxamide moiety, proved to be a potent inhibitor (Ki = 8.2 nM) of the Thermotoga maritima TmGH1 β-glucosidase. 3-D structural analysis and comparison with unreacted epoxides show that this compound indeed binds in the 4H3 conformation, suggesting that conformational strain induced through a cyclopropyl unit may add to the armory of tight-binding inhibitor designs.
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Affiliation(s)
- Thomas
J. M. Beenakker
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Dennis P. A. Wander
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Wendy A. Offen
- Department
of Chemistry, University of York, Heslington, York, YO10
5DD, U.K.
| | - Marta Artola
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Lluís Raich
- Departament
de Química Inorgànica i Orgànica (Secció
de Química Orgànica) & Institut de Quimica Teòrica
i Computacional (IQTCUB), Universitat de
Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
| | - Maria J. Ferraz
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Kah-Yee Li
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Judith H. P. M. Houben
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Erwin R. van Rijssel
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Thomas Hansen
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 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, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Jeroen D. C. Codée
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Johannes M. F.
G. Aerts
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Carme Rovira
- Departament
de Química Inorgànica i Orgànica (Secció
de Química Orgànica) & Institut de Quimica Teòrica
i Computacional (IQTCUB), Universitat de
Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), 08020 Barcelona, Spain
| | - 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, Einsteinweg 55, 2300 RA Leiden, The Netherlands
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29
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van Rijssel ER, Janssen APA, Males A, Davies GJ, van der Marel GA, Overkleeft HS, Codée JDC. Conformational Behaviour of Azasugars Based on Mannuronic Acid. Chembiochem 2017; 18:1297-1304. [DOI: 10.1002/cbic.201700080] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Erwin R. van Rijssel
- Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Antonius P. A. Janssen
- Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Alexandra Males
- York Structural Biology Laboratory; Department of Chemistry; The University of York; York YO10 5DD UK
| | - Gideon J. Davies
- York Structural Biology Laboratory; Department of Chemistry; The University of York; York YO10 5DD UK
| | | | - Herman S. Overkleeft
- Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Jeroen D. C. Codée
- Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
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30
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Wang J. Systematic analysis of residual density suggests that a major limitation in well-refined X-ray structures of proteins is the omission of ordered solvent. Protein Sci 2017; 26:1012-1023. [PMID: 28244185 DOI: 10.1002/pro.3145] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 02/21/2017] [Accepted: 02/23/2017] [Indexed: 12/23/2022]
Abstract
In the residual electron density map of a fully refined X-ray protein model, there should be no peaks arising from modeling errors or missing atoms. Any residual peaks that do occur should be contributed by random residual intensity differences between the model and the data. If the model is incomplete (i.e., some atoms are missing), there will be more positive peaks than negative ones. On the other hand, if the model includes inappropriately located atoms, there will be an excess of negative peaks. In this study, random residual peaks are quantified using the probability density function P(x), which is defined as the probability for a peak having peak height between x and x + dx. It is found that P(x) is single-exponential and symmetric for both positive and negative peaks. Thus, P(x) can be used to discriminate residual peaks contributed by random noise in complete models from residual peaks being attributable to modeling errors in incomplete models. For a number of representative structures in the PDB it is found that P(x) has far more large (greater than 5 sigma) positive peaks than large negative peaks. This excess of large positive peaks suggests that the main defect in these refined structures is the omission of ordered water molecules.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520
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31
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Alonso-Gil S, Males A, Fernandes PZ, Williams SJ, Davies GJ, Rovira C. Computational Design of Experiment Unveils the Conformational Reaction Coordinate of GH125 α-Mannosidases. J Am Chem Soc 2017; 139:1085-1088. [DOI: 10.1021/jacs.6b11247] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Santiago Alonso-Gil
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Alexandra Males
- York
Structural Biology Laboratory, Department of Chemistry, The University of York, YO10 5DD York, United Kingdom
| | - Pearl Z. Fernandes
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Spencer J. Williams
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Gideon J. Davies
- York
Structural Biology Laboratory, Department of Chemistry, The University of York, YO10 5DD York, United Kingdom
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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32
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Sladek V, Kóňa J, Tokiwa H. In silico analysis of interaction pattern switching in ligand⋯receptor binding in Golgi α-mannosidase II induced by the protonated states of inhibitors. Phys Chem Chem Phys 2017; 19:12527-12537. [DOI: 10.1039/c7cp01200d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Different binding modes for charge-neutral and protonated inhibitor forms in Golgi α-mannosidase II active sites may influence their biological activities.
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Affiliation(s)
- V. Sladek
- Institute of Chemistry – Centre for Glycomics
- Slovak Academy of Sciences
- 845 38 Bratislava
- Slovakia
- Dept. of Chemistry
| | - J. Kóňa
- Institute of Chemistry – Centre for Glycomics
- Slovak Academy of Sciences
- 845 38 Bratislava
- Slovakia
| | - H. Tokiwa
- Dept. of Chemistry
- Rikkyo University
- Toshima
- Japan
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33
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Colombo C, Bennet AJ. Probing Transition State Analogy in Glycoside Hydrolase Catalysis. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2017. [DOI: 10.1016/bs.apoc.2017.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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34
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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]
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35
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Jin Y, Petricevic M, John A, Raich L, Jenkins H, Portela
De Souza L, Cuskin F, Gilbert H, Rovira C, Goddard-Borger ED, Williams SJ, Davies GJ. A β-Mannanase with a Lysozyme-like Fold and a Novel Molecular Catalytic Mechanism. ACS CENTRAL SCIENCE 2016; 2:896-903. [PMID: 28058278 PMCID: PMC5200933 DOI: 10.1021/acscentsci.6b00232] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Indexed: 06/06/2023]
Abstract
The enzymatic cleavage of β-1,4-mannans is achieved by endo-β-1,4-mannanases, enzymes involved in germination of seeds and microbial hemicellulose degradation, and which have increasing industrial and consumer product applications. β-Mannanases occur in a range of families of the CAZy sequence-based glycoside hydrolase (GH) classification scheme including families 5, 26, and 113. In this work we reveal that β-mannanases of the newly described GH family 134 differ from other mannanase families in both their mechanism and tertiary structure. A representative GH family 134 endo-β-1,4-mannanase from a Streptomyces sp. displays a fold closely related to that of hen egg white lysozyme but acts with inversion of stereochemistry. A Michaelis complex with mannopentaose, and a product complex with mannotriose, reveal ligands with pyranose rings distorted in an unusual inverted chair conformation. Ab initio quantum mechanics/molecular mechanics metadynamics quantified the energetically accessible ring conformations and provided evidence in support of a 1C4 → 3H4‡ → 3S1 conformational itinerary along the reaction coordinate. This work, in concert with that on GH family 124 cellulases, reveals how the lysozyme fold can be co-opted to catalyze the hydrolysis of different polysaccharides in a mechanistically distinct manner.
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Affiliation(s)
- Yi Jin
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, U.K.
| | - Marija Petricevic
- School of Chemistry and Bio21 Molecular Science
and Biotechnology
Institute and Department of Medical Biology, University
of Melbourne, Parkville, Victoria 3010, Australia
| | - Alan John
- School of Chemistry and Bio21 Molecular Science
and Biotechnology
Institute and Department of Medical Biology, University
of Melbourne, Parkville, Victoria 3010, Australia
- ACRF
Chemical Biology Division, The Walter and
Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
| | - Lluís Raich
- Departament
de Química Inorgànica i Orgànica (Secció
de Química Orgànica) & IQTCUB, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Huw Jenkins
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, U.K.
| | - Leticia Portela
De Souza
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, U.K.
| | - Fiona Cuskin
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Harry
J. Gilbert
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Carme Rovira
- Departament
de Química Inorgànica i Orgànica (Secció
de Química Orgànica) & IQTCUB, Universitat de Barcelona, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), 08020 Barcelona, Spain
| | - Ethan D. Goddard-Borger
- School of Chemistry and Bio21 Molecular Science
and Biotechnology
Institute and Department of Medical Biology, University
of Melbourne, Parkville, Victoria 3010, Australia
- ACRF
Chemical Biology Division, The Walter and
Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular Science
and Biotechnology
Institute and Department of Medical Biology, University
of Melbourne, Parkville, Victoria 3010, Australia
| | - Gideon J. Davies
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, U.K.
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36
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Ladevèze S, Laville E, Despres J, Mosoni P, Potocki-Véronèse G. Mannoside recognition and degradation by bacteria. Biol Rev Camb Philos Soc 2016; 92:1969-1990. [PMID: 27995767 DOI: 10.1111/brv.12316] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 11/01/2016] [Accepted: 11/11/2016] [Indexed: 11/29/2022]
Abstract
Mannosides constitute a vast group of glycans widely distributed in nature. Produced by almost all organisms, these carbohydrates are involved in numerous cellular processes, such as cell structuration, protein maturation and signalling, mediation of protein-protein interactions and cell recognition. The ubiquitous presence of mannosides in the environment means they are a reliable source of carbon and energy for bacteria, which have developed complex strategies to harvest them. This review focuses on the various mannosides that can be found in nature and details their structure. It underlines their involvement in cellular interactions and finally describes the latest discoveries regarding the catalytic machinery and metabolic pathways that bacteria have developed to metabolize them.
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Affiliation(s)
- Simon Ladevèze
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, France
| | - Elisabeth Laville
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, France
| | - Jordane Despres
- INRA, UR454 Microbiologie, F-63122, Saint-Genès Champanelle, France
| | - Pascale Mosoni
- INRA, UR454 Microbiologie, F-63122, Saint-Genès Champanelle, France
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37
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Substrate recognition and catalysis by GH47 α-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway. Proc Natl Acad Sci U S A 2016; 113:E7890-E7899. [PMID: 27856750 DOI: 10.1073/pnas.1611213113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Maturation of Asn-linked oligosaccharides in the eukaryotic secretory pathway requires the trimming of nascent glycan chains to remove all glucose and several mannose residues before extension into complex-type structures on the cell surface and secreted glycoproteins. Multiple glycoside hydrolase family 47 (GH47) α-mannosidases, including endoplasmic reticulum (ER) α-mannosidase I (ERManI) and Golgi α-mannosidase IA (GMIA), are responsible for cleavage of terminal α1,2-linked mannose residues to produce uniquely trimmed oligomannose isomers that are necessary for ER glycoprotein quality control and glycan maturation. ERManI and GMIA have similar catalytic domain structures, but each enzyme cleaves distinct residues from tribranched oligomannose glycan substrates. The structural basis for branch-specific cleavage by ERManI and GMIA was explored by replacing an essential enzyme-bound Ca2+ ion with a lanthanum (La3+) ion. This ion swap led to enzyme inactivation while retaining high-affinity substrate interactions. Cocrystallization of La3+-bound enzymes with Man9GlcNAc2 substrate analogs revealed enzyme-substrate complexes with distinct modes of glycan branch insertion into the respective enzyme active-site clefts. Both enzymes had glycan interactions that extended across the entire glycan structure, but each enzyme engaged a different glycan branch and used different sets of glycan interactions. Additional mutagenesis and time-course studies of glycan cleavage probed the structural basis of enzyme specificity. The results provide insights into the enzyme catalytic mechanisms and reveal structural snapshots of the sequential glycan cleavage events. The data also indicate that full steric access to glycan substrates determines the efficiency of mannose-trimming reactions that control the conversion to complex-type structures in mammalian cells.
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38
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Raich L, Nin-Hill A, Ardèvol A, Rovira C. Enzymatic Cleavage of Glycosidic Bonds: Strategies on How to Set Up and Control a QM/MM Metadynamics Simulation. Methods Enzymol 2016; 577:159-83. [PMID: 27498638 DOI: 10.1016/bs.mie.2016.05.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Carbohydrates play crucial roles in many biological processes, from cell-cell adhesion to chemical signaling. Their complexity and diversity, related to α/β anomeric configuration, ring substituents, and conformational variations, require a diverse set of enzymes for their processing. Among them, glycoside hydrolases (GHs) are responsible for the hydrolysis of one of the strongest bonds in nature: the glycosidic bond. These highly specialized biological catalysts select particular conformations their carbohydrate substrates to enhance catalysis. The evolution of this conformation during the reaction of glycosidic bond cleavage, known as the conformational catalytic itinerary, is of fundamental interest in glycobiology, with impact on inhibitor and drug design. Here we review some of the aspects and the main strategies one needs to take into account when simulating a reaction in a GH enzyme using QM/MM metadynamics. Several specific aspects are highlighted, from the importance of the distortion of the substrate at the Michaelis complex to the variable control during the metadynamics simulation or the analysis of the reaction mechanism and conformational itinerary. The increasing speed of computer power and methodological advances have added a vital tool to the study of GH mechanisms, as shown here and recent reviews. It is hoped that this chapter will serve as a first guide for those attempting to perform a metadynamics simulation of these relevant and fascinating enzymes.
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Affiliation(s)
- L Raich
- Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, Spain
| | - A Nin-Hill
- Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, Spain
| | - A Ardèvol
- Max-Planck Institut für Biophysik, Frankfurt am Main, Germany
| | - C Rovira
- Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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39
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A building block approach to the synthesis of a family of S-linked α-1,6-oligomannosides. Carbohydr Res 2016; 429:38-47. [DOI: 10.1016/j.carres.2016.04.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/11/2016] [Accepted: 04/11/2016] [Indexed: 11/19/2022]
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40
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Abstract
The enzyme-catalysed degradation of oligo and polysaccharides is of considerable interest in many fields ranging from the fundamental–understanding the intrinsic chemical beauty–through to the applied, including diverse practical applications in medicine and biotechnology. Carbohydrates are the most stereochemically-complex biopolymer, and myriad different natural polysaccharides have led to evolution of multifaceted enzyme consortia for their degradation. The glycosidic bonds that link sugar monomers are among the most chemically-stable, yet enzymatically-labile, bonds in the biosphere. That glycoside hydrolases can achieve a rate enhancement (kcat/kuncat) >1017-fold provides testament to their remarkable proficiency and the sophistication of their catalysis reaction mechanisms. The last two decades have seen significant advances in the discovery of new glycosidase sequences, sequence-based classification into families and clans, 3D structures and reaction mechanisms, providing new insights into enzymatic catalysis. New impetus to these studies has been provided by the challenges inherent in plant and microbial polysaccharide degradation, both in the context of environmentally-sustainable routes to foods and biofuels, and increasingly in human nutrition. Study of the reaction mechanism of glycoside hydrolases has also inspired the development of enzyme inhibitors, both as mechanistic probes and increasingly as therapeutic agents. We are on the cusp of a new era where we are learning how to dovetail powerful computational techniques with structural and kinetic data to provide an unprecedented view of conformational details of enzyme action.
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41
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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
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42
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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.
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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.
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43
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Reilly PJ, Rovira C. Computational Studies of Glycoside, Carboxylic Ester, and Thioester Hydrolase Mechanisms: A Review. Ind Eng Chem Res 2015. [DOI: 10.1021/acs.iecr.5b01312] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter J. Reilly
- Department
of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011-2230, United States
| | - Carme Rovira
- Departament de Química Orgànica
and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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44
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Ardèvol A, Rovira C. Reaction Mechanisms in Carbohydrate-Active Enzymes: Glycoside Hydrolases and Glycosyltransferases. Insights from ab Initio Quantum Mechanics/Molecular Mechanics Dynamic Simulations. J Am Chem Soc 2015; 137:7528-47. [DOI: 10.1021/jacs.5b01156] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Albert Ardèvol
- Departament
de Química Orgànica and Institut de Química Teòrica
i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
| | - Carme Rovira
- Departament
de Química Orgànica and Institut de Química Teòrica
i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
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45
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Thompson AJ, Speciale G, Iglesias-Fernández J, Hakki Z, Belz T, Cartmell A, Spears RJ, Chandler E, Temple MJ, Stepper J, Gilbert HJ, Rovira C, Williams SJ, Davies GJ. Evidence for a Boat Conformation at the Transition State of GH76 α-1,6-Mannanases-Key Enzymes in Bacterial and Fungal Mannoprotein Metabolism. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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46
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Thompson AJ, Speciale G, Iglesias-Fernández J, Hakki Z, Belz T, Cartmell A, Spears RJ, Chandler E, Temple MJ, Stepper J, Gilbert HJ, Rovira C, Williams SJ, Davies GJ. Evidence for a boat conformation at the transition state of GH76 α-1,6-mannanases--key enzymes in bacterial and fungal mannoprotein metabolism. Angew Chem Int Ed Engl 2015; 54:5378-82. [PMID: 25772148 DOI: 10.1002/anie.201410502] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/29/2015] [Indexed: 01/21/2023]
Abstract
α-Mannosidases and α-mannanases have attracted attention for the insight they provide into nucleophilic substitution at the hindered anomeric center of α-mannosides, and the potential of mannosidase inhibitors as cellular probes and therapeutic agents. We report the conformational itinerary of the family GH76 α-mannanases studied through structural analysis of the Michaelis complex and synthesis and evaluation of novel aza/imino sugar inhibitors. A Michaelis complex in an (O) S2 conformation, coupled with distortion of an azasugar in an inhibitor complex to a high energy B2,5 conformation are rationalized through ab initio QM/MM metadynamics that show how the enzyme surface restricts the conformational landscape of the substrate, rendering the B2,5 conformation the most energetically stable on-enzyme. We conclude that GH76 enzymes perform catalysis using an itinerary that passes through (O) S2 and B2,5 (≠) conformations, information that should inspire the development of new antifungal agents.
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Affiliation(s)
- Andrew J Thompson
- Department of Chemistry, University of York, Heslington, York, YO10 5DD (UK)
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47
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Wang J. Estimation of the quality of refined protein crystal structures. Protein Sci 2015; 24:661-9. [PMID: 25581292 DOI: 10.1002/pro.2639] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/30/2014] [Accepted: 01/05/2015] [Indexed: 01/13/2023]
Abstract
Crystallographic R work and R free values, which are measures of the ability of the models of macromolecular structures to explain the crystallographic data on which they are based, are often used to assess structure quality. It is widely known, and confirmed here that both are sensitive to the methods used to compute them, and can be manipulated to improve the apparent quality of the model. As an alternative it is proposed here that the quality of crystallographic models should be assessed using a global goodness-of-fit metric RO2A /R work where RO2A is the number of reflections used for refinement divided by the number of nonhydrogen atoms in the structure, and R work is the working R-factor of the refined structure. Also, analysis of structures in the Protein Data Bank suggests that many data sets have been truncated at high resolution, thereby improving the R-factor statistics. To discourage this practice, it is proposed that the resolution of a dataset be defined as the resolution of the shell of data where <I/σI > falls to 1. The proposed goodness-of-fit metric encourages investigators to use all the data available rather than a truncated subset.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520
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48
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Iglesias-Fernández J, Raich L, Ardèvol A, Rovira C. The complete conformational free energy landscape of β-xylose reveals a two-fold catalytic itinerary for β-xylanases. Chem Sci 2015; 6:1167-1177. [PMID: 29560204 PMCID: PMC5811086 DOI: 10.1039/c4sc02240h] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 10/27/2014] [Indexed: 01/28/2023] Open
Abstract
Unraveling the conformational catalytic itinerary of glycoside hydrolases (GHs) is a growing topic of interest in glycobiology, with major impact in the design of GH inhibitors. β-xylanases are responsible for the hydrolysis of glycosidic bonds in β-xylans, a group of hemicelluloses of high biotechnological interest that are found in plant cell walls. The precise conformations followed by the substrate during catalysis in β-xylanases have not been unambiguously resolved, with three different pathways being proposed from structural analyses. In this work, we compute the conformational free energy landscape (FEL) of β-xylose to predict the most likely catalytic itineraries followed by β-xylanases. The calculations are performed by means of ab initio metadynamics, using the Cremer-Pople puckering coordinates as collective variables. The computed FEL supports only two of the previously proposed itineraries, 2SO → [2,5B]ǂ → 5S1 and 1S3 → [4H3]ǂ → 4C1, which clearly appear in low energy regions of the FEL. Consistently, 2SO and 1S3 are conformations preactivated for catalysis in terms of free energy/anomeric charge and bond distances. The results however exclude the OE → [OS2]ǂ → B2,5 itinerary that has been recently proposed for a family 11 xylanase. Classical and ab initio QM/MM molecular dynamics simulations reveal that, in this case, the observed OE conformation has been enforced by enzyme mutation. These results add a word of caution on using modified enzymes to inform on catalytic conformational itineraries of glycoside hydrolases.
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Affiliation(s)
- Javier Iglesias-Fernández
- Departament de Química Orgànica and Institut de Química Teòrica i Computacional (IQTCUB) , Universitat de Barcelona , Martí i Franquès 1 , 08028 Barcelona , Spain .
| | - Lluís Raich
- Departament de Química Orgànica and Institut de Química Teòrica i Computacional (IQTCUB) , Universitat de Barcelona , Martí i Franquès 1 , 08028 Barcelona , Spain .
| | - Albert Ardèvol
- Department of Chemistry and Applied Biosciences , ETH Zürich , USI Campus , 6900 Lugano , Switzerland
| | - Carme Rovira
- Departament de Química Orgànica and Institut de Química Teòrica i Computacional (IQTCUB) , Universitat de Barcelona , Martí i Franquès 1 , 08028 Barcelona , Spain .
- Institució Catalana de Recerca i Estudis Avançats (ICREA) , Passeig Lluís Companys , 23 , 08018 Barcelona , Spain
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49
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Speciale G, Thompson AJ, Davies GJ, Williams SJ. Dissecting conformational contributions to glycosidase catalysis and inhibition. Curr Opin Struct Biol 2014; 28:1-13. [PMID: 25016573 PMCID: PMC4220041 DOI: 10.1016/j.sbi.2014.06.003] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 06/02/2014] [Accepted: 06/10/2014] [Indexed: 01/15/2023]
Abstract
The conformational itinerary describes the changes in sugar shape during catalysis. Stereoelectronic requirements for glycoside hydrolysis are discussed. Major and emerging approaches to define conformational itineraries are reviewed. New assignments of glycosidase conformational itineraries are summarized.
Glycoside hydrolases (GHs) are classified into >100 sequence-based families. These enzymes process a wide variety of complex carbohydrates with varying stereochemistry at the anomeric and other ring positions. The shapes that these sugars adopt upon binding to their cognate GHs, and the conformational changes that occur along the catalysis reaction coordinate is termed the conformational itinerary. Efforts to define the conformational itineraries of GHs have focussed upon the critical points of the reaction: substrate-bound (Michaelis), transition state, intermediate (if relevant) and product-bound. Recent approaches to defining conformational itineraries that marry X-ray crystallography of enzymes bound to ligands that mimic the critical points, along with advanced computational methods and kinetic isotope effects are discussed.
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Affiliation(s)
- Gaetano Speciale
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andrew J Thompson
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Gideon J Davies
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
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50
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Zheng S, Pfaendtner J. Enhanced sampling of chemical and biochemical reactions with metadynamics. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.923574] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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