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  1. Article ; Online: GlycoVHH: optimal sites for introducing N-glycans on the camelid VHH antibody scaffold and use for macrophage delivery.

    van Schie, Loes / Van Breedam, Wander / Roels, Charlotte / Schepens, Bert / Frank, Martin / Mehdipour, Ahmad Reza / Laukens, Bram / Nerinckx, Wim / Santens, Francis / Devos, Simon / Rossey, Iebe / Thooft, Karel / Vanmarcke, Sandrine / Van Hecke, Annelies / Saelens, Xavier / Callewaert, Nico

    mAbs

    2023  Volume 15, Issue 1, Page(s) 2210709

    Abstract: As small and stable high-affinity antigen binders, VHHs boast attractive characteristics both for therapeutic use in various disease indications, and as versatile reagents in research and diagnostics. To further increase the versatility of VHHs, we ... ...

    Abstract As small and stable high-affinity antigen binders, VHHs boast attractive characteristics both for therapeutic use in various disease indications, and as versatile reagents in research and diagnostics. To further increase the versatility of VHHs, we explored the VHH scaffold in a structure-guided approach to select regions where the introduction of an N-glycosylation N-X-T sequon and its associated glycan should not interfere with protein folding or epitope recognition. We expressed variants of such glycoengineered VHHs in the
    MeSH term(s) Single-Domain Antibodies/genetics ; Antigens ; Epitopes ; Macrophages
    Chemical Substances Single-Domain Antibodies ; Antigens ; Epitopes
    Language English
    Publishing date 2023-05-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2537838-7
    ISSN 1942-0870 ; 1942-0870
    ISSN (online) 1942-0870
    ISSN 1942-0870
    DOI 10.1080/19420862.2023.2210709
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Yeast-based production platform for potent and stable heavy chain-only antibodies

    Lonigro, Chiara / Eeckhaut, Hannah / Symakani, Royan Alipour / Roose, Kenny / Schepens, Bert / Sedeyn, Koen / De Smet, Anne-Sophie / Zavala Marchan, Jackeline Cecilia / Vanhaverbeke, Pieter / Vanmarcke, Sandrine / Claes, Katrien / De Cae, Sieglinde / Demol, Hans / Devos, Simon / Fijalkowska, Daria / Nerinckx, Wim / Rossey, Iebe / Weyts, Wannes / Abdelnabi, Rana /
    Jochmans, Dirk / Neyts, Johan / Saelens, Xavier / van Schie, Loes / Callewaert, Nico

    bioRxiv

    Abstract: Monoclonal antibodies are the leading drug of the biopharmaceutical market because of their high specificity and tolerability, but the current CHO-based manufacturing platform remains expensive and time-consuming leading to limited accessibility, ... ...

    Abstract Monoclonal antibodies are the leading drug of the biopharmaceutical market because of their high specificity and tolerability, but the current CHO-based manufacturing platform remains expensive and time-consuming leading to limited accessibility, especially in the case of diseases with high incidence and pandemics. Therefore, there is an urgent need for an alternative production system. In this study, we present a rapid and cost-effective microbial platform for heavy chain-only antibodies (VHH-Fc) in the methylotrophic yeast Komagataella phaffii (aka Pichia pastoris). We demonstrate the potential of this platform using a simplified single-gene VHH-Fc fusion construct instead of the conventional monoclonal antibody format, as this is more easily expressed in Pichia pastoris. We demonstrate that the Pichia-produced VHH-Fc fusion construct is stable and that a Pichia-produced VHH-Fc directed against the SARS-CoV-2 spike has potent SARS-CoV-2 neutralizing activity in vitro and in vivo. We expect that this platform will pave the way towards faster and cheaper development and production of broadly neutralizing single-chain antibodies in yeast.
    Keywords covid19
    Language English
    Publishing date 2024-03-05
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2024.03.04.580093
    Database COVID19

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  3. Article ; Online: Sudan-β-d-glucuronides and their use for the histochemical localization of β-glucuronidase activity in transgenic plants.

    Van der Eycken, E / Terryn, N / Goeman, J L / Carlens, G / Nerinckx, W / Claeyssens, M / Van der Eycken, J / Van Montagu, M / Brito-Arias, M / Engler, G

    Plant cell reports

    2019  Volume 19, Issue 10, Page(s) 966–970

    Abstract: Synthesis of five different Sudan-β-D-glucuronides (I, II, III, IV, and RedB) was performed by condensation of a set of red Sudan diazo dyes with methyl (1-deoxy-2,3,4-tri-O-acetyl-1-trichloroacetimidoyl-α-D-glucopyran)uronate. After the acid and alcohol ...

    Abstract Synthesis of five different Sudan-β-D-glucuronides (I, II, III, IV, and RedB) was performed by condensation of a set of red Sudan diazo dyes with methyl (1-deoxy-2,3,4-tri-O-acetyl-1-trichloroacetimidoyl-α-D-glucopyran)uronate. After the acid and alcohol groups had been deprotected, the resulting compounds were used for histochemical localization of β-glucuronidase (GUS) activity in transgenic plants (Petunia hybrida, Arabidopsis thaliana, and Nicotiana tabacum) that contained the GUS reporter system. Because the cleavage of the β-glucuronide results in the liberation of an insoluble Sudan dye, Sudan substrates gave no diffusion artifacts as described for the commonly used 5-bromo-4-chloro-3-indolyl-β-D-glucuronide (X-gluc). A comparison of assays with different Sudan glucuronides and X-gluc demonstrated that the SudanIV variant is a valuable glucuronide substrate for the precise histochemical localization of GUS activity in transgenic plants.
    Language English
    Publishing date 2019-02-11
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 8397-5
    ISSN 1432-203X ; 0721-085X ; 0721-7714
    ISSN (online) 1432-203X
    ISSN 0721-085X ; 0721-7714
    DOI 10.1007/s002990000219
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: When PERK inhibitors turn out to be new potent RIPK1 inhibitors: critical issues on the specificity and use of GSK2606414 and GSK2656157.

    Rojas-Rivera, Diego / Delvaeye, Tinneke / Roelandt, Ria / Nerinckx, Wim / Augustyns, Koen / Vandenabeele, Peter / Bertrand, Mathieu J M

    Cell death and differentiation

    2017  Volume 24, Issue 6, Page(s) 1100–1110

    Abstract: Accumulation of unfolded proteins in the endoplasmic reticulum (ER) causes a state of cellular stress known as ER stress. The cells respond to ER stress by activating the unfolded protein response (UPR), a signaling network emerging from the ER-anchored ... ...

    Abstract Accumulation of unfolded proteins in the endoplasmic reticulum (ER) causes a state of cellular stress known as ER stress. The cells respond to ER stress by activating the unfolded protein response (UPR), a signaling network emerging from the ER-anchored receptors IRE1α, PERK and ATF6. The UPR aims at restoring ER protein-folding homeostasis, but turns into a toxic signal when the stress is too severe or prolonged. Recent studies have demonstrated links between the UPR and inflammation. Consequently, small molecule inhibitors of IRE1α and PERK have become attractive tools for the potential therapeutic manipulation of the UPR in inflammatory conditions. TNF is a master pro-inflammatory cytokine that drives inflammation either directly by promoting gene activation, or indirectly by inducing RIPK1 kinase-dependent cell death, in the form of apoptosis or necroptosis. To evaluate the potential contribution of the UPR to TNF-induced cell death, we tested the effects of two commonly used PERK inhibitors, GSK2606414 and GSK2656157. Surprisingly, we observed that both compounds completely repressed TNF-mediated RIPK1 kinase-dependent death, but found that this effect was independent of PERK inactivation. Indeed, these two compounds turned out to be direct RIPK1 inhibitors, with comparable potency to the recently developed RIPK1 inhibitor GSK'963 (about 100 times more potent than NEC-1s). Importantly, these compounds completely inhibited TNF-mediated RIPK1-dependent cell death at a concentration that did not affect PERK activity in cells. In vivo, GSK2656157 administration protected mice from lethal doses of TNF independently of PERK inhibition and as efficiently as GSK'963. Together, our results not only report on new and very potent RIPK1 inhibitors but also highlight the risk of misinterpretation when using these two PERK inhibitors in the context of ER stress, cell death and inflammation.
    Language English
    Publishing date 2017-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 1225672-9
    ISSN 1476-5403 ; 1350-9047
    ISSN (online) 1476-5403
    ISSN 1350-9047
    DOI 10.1038/cdd.2017.58
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Selective Engagement of FcγRIV by a M2e-Specific Single Domain Antibody Construct Protects Against Influenza A Virus Infection.

    De Vlieger, Dorien / Hoffmann, Katja / Van Molle, Inge / Nerinckx, Wim / Van Hoecke, Lien / Ballegeer, Marlies / Creytens, Sarah / Remaut, Han / Hengel, Hartmut / Schepens, Bert / Saelens, Xavier

    Frontiers in immunology

    2019  Volume 10, Page(s) 2920

    Abstract: Lower respiratory tract infections, such as infections caused by influenza A viruses, are a constant threat for public health. Antivirals are indispensable to control disease caused by epidemic as well as pandemic influenza A. We developed a novel anti- ... ...

    Abstract Lower respiratory tract infections, such as infections caused by influenza A viruses, are a constant threat for public health. Antivirals are indispensable to control disease caused by epidemic as well as pandemic influenza A. We developed a novel anti-influenza A virus approach based on an engineered single-domain antibody (VHH) construct that can selectively recruit innate immune cells to the sites of virus replication. This protective construct comprises two VHHs. One VHH binds with nanomolar affinity to the conserved influenza A matrix protein 2 (M2) ectodomain (M2e). Co-crystal structure analysis revealed that the complementarity determining regions 2 and 3 of this VHH embrace M2e. The second selected VHH specifically binds to the mouse Fcγ Receptor IV (FcγRIV) and was genetically fused to the M2e-specific VHH, which resulted in a bi-specific VHH-based construct that could be efficiently expressed in
    MeSH term(s) Amino Acid Sequence ; Animals ; Antibodies, Bispecific/chemistry ; Antibodies, Bispecific/immunology ; Antibodies, Viral/chemistry ; Antibodies, Viral/immunology ; Cell Line ; Humans ; Influenza A virus/immunology ; Influenza, Human/immunology ; Influenza, Human/metabolism ; Influenza, Human/virology ; Mice ; Models, Molecular ; Peptides/chemistry ; Peptides/immunology ; Protein Conformation ; Receptors, IgG/chemistry ; Receptors, IgG/metabolism ; Single-Domain Antibodies/chemistry ; Single-Domain Antibodies/immunology ; Structure-Activity Relationship ; Viral Matrix Proteins/chemistry ; Viral Matrix Proteins/immunology
    Chemical Substances Antibodies, Bispecific ; Antibodies, Viral ; FCGR3A protein, human ; M2 protein, Influenza A virus ; Peptides ; Receptors, IgG ; Single-Domain Antibodies ; Viral Matrix Proteins
    Language English
    Publishing date 2019-12-12
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2019.02920
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Intravitreal antisense oligonucleotide sepofarsen in Leber congenital amaurosis type 10: a phase 1b/2 trial.

    Russell, Stephen R / Drack, Arlene V / Cideciyan, Artur V / Jacobson, Samuel G / Leroy, Bart P / Van Cauwenbergh, Caroline / Ho, Allen C / Dumitrescu, Alina V / Han, Ian C / Martin, Mitchell / Pfeifer, Wanda L / Sohn, Elliott H / Walshire, Jean / Garafalo, Alexandra V / Krishnan, Arun K / Powers, Christian A / Sumaroka, Alexander / Roman, Alejandro J / Vanhonsebrouck, Eva /
    Jones, Eltanara / Nerinckx, Fanny / De Zaeytijd, Julie / Collin, Rob W J / Hoyng, Carel / Adamson, Peter / Cheetham, Michael E / Schwartz, Michael R / den Hollander, Wilhelmina / Asmus, Friedrich / Platenburg, Gerard / Rodman, David / Girach, Aniz

    Nature medicine

    2022  Volume 28, Issue 5, Page(s) 1014–1021

    Abstract: CEP290-associated Leber congenital amaurosis type 10 (LCA10) is a retinal disease resulting in childhood blindness. Sepofarsen is an RNA antisense oligonucleotide targeting the c.2991+1655A>G variant in the CEP290 gene to treat LCA10. In this open-label, ...

    Abstract CEP290-associated Leber congenital amaurosis type 10 (LCA10) is a retinal disease resulting in childhood blindness. Sepofarsen is an RNA antisense oligonucleotide targeting the c.2991+1655A>G variant in the CEP290 gene to treat LCA10. In this open-label, phase 1b/2 ( NCT03140969 ), 12-month, multicenter, multiple-dose, dose-escalation trial, six adult patients and five pediatric patients received ≤4 doses of intravitreal sepofarsen into the worse-seeing eye. The primary objective was to evaluate sepofarsen safety and tolerability via the frequency and severity of ocular adverse events (AEs); secondary objectives were to evaluate pharmacokinetics and efficacy via changes in functional outcomes. Six patients received sepofarsen 160 µg/80 µg, and five patients received sepofarsen 320 µg/160 µg. Ten of 11 (90.9%) patients developed ocular AEs in the treated eye (5/6 with 160 µg/80 µg; 5/5 with 320 µg/160 µg) versus one of 11 (9.1%) in the untreated eye; most were mild in severity and dose dependent. Eight patients developed cataracts, of which six (75.0%) were categorized as serious (2/3 with 160 µg/80 µg; 4/5 with 320 µg/160 µg), as lens replacement was required. As the 160-µg/80-µg group showed a better benefit-risk profile, higher doses were discontinued or not initiated. Statistically significant improvements in visual acuity and retinal sensitivity were reported (post hoc analysis). The manageable safety profile and improvements reported in this trial support the continuation of sepofarsen development.
    MeSH term(s) Adult ; Antigens, Neoplasm/genetics ; Blindness/genetics ; Cell Cycle Proteins/genetics ; Child ; Cytoskeletal Proteins/metabolism ; Humans ; Leber Congenital Amaurosis/drug therapy ; Leber Congenital Amaurosis/genetics ; Oligonucleotides, Antisense/adverse effects ; Vision, Ocular
    Chemical Substances Antigens, Neoplasm ; Cell Cycle Proteins ; Cep290 protein, human ; Cytoskeletal Proteins ; Oligonucleotides, Antisense
    Language English
    Publishing date 2022-04-04
    Publishing country United States
    Document type Clinical Trial, Phase I ; Clinical Trial, Phase II ; Journal Article ; Multicenter Study ; Research Support, Non-U.S. Gov't
    ZDB-ID 1220066-9
    ISSN 1546-170X ; 1078-8956
    ISSN (online) 1546-170X
    ISSN 1078-8956
    DOI 10.1038/s41591-022-01755-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: An alternative approach for the synthesis of fluorogenic substrates of endo-beta-(1-->4)-xylanases and some applications.

    Vrsanská, Mária / Nerinckx, Wim / Claeyssens, Marc / Biely, Peter

    Carbohydrate research

    2008  Volume 343, Issue 3, Page(s) 541–548

    Abstract: Fluorogenic substrates of endo-beta-(1-->4)-xylanases (EXs), 4-methylumbelliferyl beta-glycosides of xylobiose and xylotriose were synthesized from fully acetylated oligosaccharides using the alpha-trichloroacetimidate procedure. A commercially available ...

    Abstract Fluorogenic substrates of endo-beta-(1-->4)-xylanases (EXs), 4-methylumbelliferyl beta-glycosides of xylobiose and xylotriose were synthesized from fully acetylated oligosaccharides using the alpha-trichloroacetimidate procedure. A commercially available syrup containing xylose and xylo-oligosaccharides was used as the starting material. Both fluorogenic glycosides were found to be suitable substrates for EXs, particularly for sensitive detection of the enzymes in electrophoretic gels and their in situ localization on sections of fruiting bodies of some plants, such as tomato, potato and eggplant, all of the family Solanaceae.
    MeSH term(s) Disaccharides/chemical synthesis ; Electrophoresis ; Endo-1,4-beta Xylanases/analysis ; Endo-1,4-beta Xylanases/chemistry ; Fluorescent Dyes/chemical synthesis ; Plants/enzymology ; Trisaccharides/chemical synthesis ; Xylose
    Chemical Substances Disaccharides ; Fluorescent Dyes ; Trisaccharides ; xylotriose ; Xylose (A1TA934AKO) ; Endo-1,4-beta Xylanases (EC 3.2.1.8) ; xylobiose (ID02R0EG7P)
    Language English
    Publishing date 2008-02-25
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1435-7
    ISSN 1873-426X ; 0008-6215
    ISSN (online) 1873-426X
    ISSN 0008-6215
    DOI 10.1016/j.carres.2007.11.011
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Theory and computation show that Asp463 is the catalytic proton donor in human endoplasmic reticulum alpha-(1-->2)-mannosidase I.

    Cantú, David / Nerinckx, Wim / Reilly, Peter J

    Carbohydrate research

    2008  Volume 343, Issue 13, Page(s) 2235–2242

    Abstract: It has been difficult to identify the proton donor and nucleophilic assistant/base of endoplasmic reticulum alpha-(1-->2)-mannosidase I, a member of glycoside hydrolase Family 47, which cleaves the glycosidic bond between two alpha-(1-->2)-linked ... ...

    Abstract It has been difficult to identify the proton donor and nucleophilic assistant/base of endoplasmic reticulum alpha-(1-->2)-mannosidase I, a member of glycoside hydrolase Family 47, which cleaves the glycosidic bond between two alpha-(1-->2)-linked mannosyl residues by the inverting mechanism, trimming Man(9)GlcNAc(2) to Man(8)GlcNAc(2) isomer B. Part of the difficulty is caused by the enzyme's use of a water molecule to transmit the proton that attacks the glycosidic oxygen atom. We earlier used automated docking to conclusively determine that Glu435 in the yeast enzyme (Glu599 in the corresponding human enzyme) is the nucleophilic assistant. The commonly accepted proton donor has been Glu330 in the human enzyme (Glu132 in the yeast enzyme). However, for theoretical reasons this conclusion is untenable. Theory, automated docking of alpha-d-(3)S(1)-mannopyranosyl-(1-->2)-alpha-d-(4)C(1)-mannopyranose and water molecules associated with candidate proton donors, and estimation of dissociation constants of the latter have shown that the true proton donor is Asp463 in the human enzyme (Asp275 in the yeast enzyme).
    MeSH term(s) Aspartic Acid/chemistry ; Binding Sites ; Carbohydrates/chemistry ; Catalysis ; Crystallography, X-Ray/methods ; Endoplasmic Reticulum/enzymology ; Humans ; Hydrogen-Ion Concentration ; Mannosidases/chemistry ; Models, Chemical ; Molecular Conformation ; Oxygen/chemistry ; Protons ; Static Electricity ; Water/chemistry
    Chemical Substances Carbohydrates ; Protons ; Water (059QF0KO0R) ; Aspartic Acid (30KYC7MIAI) ; Mannosidases (EC 3.2.1.-) ; mannosyl-oligosaccharide 1,2-alpha-mannosidase (EC 3.2.1.113) ; Oxygen (S88TT14065)
    Language English
    Publishing date 2008-09-08
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1435-7
    ISSN 1873-426X ; 0008-6215
    ISSN (online) 1873-426X
    ISSN 0008-6215
    DOI 10.1016/j.carres.2008.05.026
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Rational design, synthesis, evaluation and enzyme-substrate structures of improved fluorogenic substrates for family 6 glycoside hydrolases.

    Wu, Miao / Nerinckx, Wim / Piens, Kathleen / Ishida, Takuya / Hansson, Henrik / Sandgren, Mats / Ståhlberg, Jerry

    The FEBS journal

    2013  Volume 280, Issue 1, Page(s) 184–198

    Abstract: Methylumbelliferyl-β-cellobioside (MUF-G2) is a convenient fluorogenic substrate for certain β-glycoside hydrolases (GH). However, hydrolysis of the aglycone is poor with GH family 6 enzymes (GH6), despite strong binding. Prediction of the orientation of ...

    Abstract Methylumbelliferyl-β-cellobioside (MUF-G2) is a convenient fluorogenic substrate for certain β-glycoside hydrolases (GH). However, hydrolysis of the aglycone is poor with GH family 6 enzymes (GH6), despite strong binding. Prediction of the orientation of the aglycone of MUF-G2 in the +1 subsite of Hypocrea jecorina Cel6A by automated docking suggested umbelliferyl modifications at C4 and C6 for improved recognition. Four modified umbelliferyl-β-cellobiosides [6-chloro-4-methyl- (ClMUF); 6-chloro-4-trifluoromethyl- (ClF3MUF); 4-phenyl- (PhUF); 6-chloro-4-phenyl- (ClPhUF)] were synthesized and tested with GH6, GH7, GH9, GH5 and GH45 cellulases. Indeed the rate of aglycone release by H. jecorina Cel6A was 10-150 times higher than with MUF-G2, although it was still three orders of magnitude lower than with H. jecorina Cel7B. The 4-phenyl substitution drastically reduced the fluorescence intensity of the free aglycone, while ClMUF-G2 could be used for determination of k(cat) and K(M) for H. jecorina Cel6A and Thermobifida fusca Cel6A. Crystal structures of H. jecorina Cel6A D221A mutant soaked with the MUF-, ClMUF- and ClPhUF-β-cellobioside substrates show that the modifications turned the umbelliferyl group 'upside down', with the glycosidic bond better positioned for protonation than with MUF-G2.
    MeSH term(s) Actinomycetales/enzymology ; Bacterial Proteins/chemistry ; Catalytic Domain ; Cellobiose/analogs & derivatives ; Cellobiose/chemical synthesis ; Cellobiose/chemistry ; Cellulases/chemistry ; Crystallography, X-Ray ; Fluorescent Dyes/chemical synthesis ; Fluorescent Dyes/chemistry ; Fungal Proteins/chemistry ; Hydrolysis ; Hypocrea/enzymology ; Kinetics ; Molecular Docking Simulation ; Protein Binding ; Protein Structure, Secondary ; Spectrometry, Fluorescence
    Chemical Substances Bacterial Proteins ; Fluorescent Dyes ; Fungal Proteins ; Cellobiose (16462-44-5) ; Cellulases (EC 3.2.1.-)
    Language English
    Publishing date 2013-01
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2173655-8
    ISSN 1742-4658 ; 1742-464X
    ISSN (online) 1742-4658
    ISSN 1742-464X
    DOI 10.1111/febs.12060
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: The fate of beta-D-mannopyranose after its formation by endoplasmic reticulum alpha-(1-->2)-mannosidase I catalysis.

    Mulakala, Chandrika / Nerinckx, Wim / Reilly, Peter J

    Carbohydrate research

    2007  Volume 342, Issue 2, Page(s) 163–169

    Abstract: The automated docking program AutoDock was used to dock all 38 characteristic beta-D-mannopyranose ring conformers into the active site of the yeast endoplasmic reticulum alpha-(1-->2)-mannosidase I, a Family 47 glycoside hydrolase that converts ... ...

    Abstract The automated docking program AutoDock was used to dock all 38 characteristic beta-D-mannopyranose ring conformers into the active site of the yeast endoplasmic reticulum alpha-(1-->2)-mannosidase I, a Family 47 glycoside hydrolase that converts Man9GlcNAc2 to Man8GlcNAc2. The subject of this work is to establish the conformational pathway that allows the cleaved glycon product to leave the enzyme active site and eventually reach the ground-state conformation. Twelve of the 38 conformers optimally dock in the active site where the inhibitors 1-deoxymannonojirimycin and kifunensine are found in enzyme crystal structures. A further 23 optimally dock in a second site on the side of the active-site well, while three dock outside the active-site cavity. It appears, through analysis of the internal energies of different ring conformations, of intermolecular energies between the ligands and enzyme, and of forces exerted on the ligands by the enzyme, that beta-D-mannopyranose follows the path 3E-->1C4-->1H2-->B2,5 before being expelled by the enzyme. The highly conserved second site that strongly binds beta-D-mannopyranose-4C1 may exist to prevent competitive inhibition by the product, and is worthy of further investigation.
    MeSH term(s) Binding Sites ; Carbohydrate Conformation ; Catalysis ; Computational Biology ; Endoplasmic Reticulum/metabolism ; Mannose/metabolism ; Mannosidases/chemistry ; Mannosidases/metabolism ; Models, Molecular ; Protein Binding ; Structure-Activity Relationship
    Chemical Substances Mannosidases (EC 3.2.1.-) ; mannosyl-oligosaccharide 1,2-alpha-mannosidase (EC 3.2.1.113) ; Mannose (PHA4727WTP)
    Language English
    Publishing date 2007-02-05
    Publishing country Netherlands
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1435-7
    ISSN 1873-426X ; 0008-6215
    ISSN (online) 1873-426X
    ISSN 0008-6215
    DOI 10.1016/j.carres.2006.11.012
    Database MEDical Literature Analysis and Retrieval System OnLINE

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