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Use of Nanostructure-Initiator Mass Spectrometry to Deduce Selectivity of Reaction in Glycoside Hydrolases.

Frontiers in bioengineering and biotechnology

Deng K, Takasuka TE, Bianchetti CM, Bergeman LF, Adams PD, Northen TR, Fox BG.
PMID: 26579511
Front Bioeng Biotechnol. 2015 Oct 27;3:165. doi: 10.3389/fbioe.2015.00165. eCollection 2015.

Chemically synthesized nanostructure-initiator mass spectrometry (NIMS) probes derivatized with tetrasaccharides were used to study the reactivity of representative Clostridium thermocellum β-glucosidase, endoglucanases, and cellobiohydrolase. Diagnostic patterns for reactions of these different classes of enzymes were observed. Results show sequential...

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Deng K, Takasuka TE, Bianchetti CM, et al. Use of Nanostructure-Initiator Mass Spectrometry to Deduce Selectivity of Reaction in Glycoside Hydrolases. Front Bioeng Biotechnol. 2015;3:165doi: 10.3389/fbioe.2015.00165.
Deng, K., Takasuka, T. E., Bianchetti, C. M., Bergeman, L. F., Adams, P. D., Northen, T. R., & Fox, B. G. (2015). Use of Nanostructure-Initiator Mass Spectrometry to Deduce Selectivity of Reaction in Glycoside Hydrolases. Frontiers in bioengineering and biotechnology, 3165. https://doi.org/10.3389/fbioe.2015.00165
Deng, Kai, et al. "Use of Nanostructure-Initiator Mass Spectrometry to Deduce Selectivity of Reaction in Glycoside Hydrolases." Frontiers in bioengineering and biotechnology vol. 3 (2015): 165. doi: https://doi.org/10.3389/fbioe.2015.00165
Deng K, Takasuka TE, Bianchetti CM, Bergeman LF, Adams PD, Northen TR, Fox BG. Use of Nanostructure-Initiator Mass Spectrometry to Deduce Selectivity of Reaction in Glycoside Hydrolases. Front Bioeng Biotechnol. 2015 Oct 27;3:165. doi: 10.3389/fbioe.2015.00165. eCollection 2015. PMID: 26579511; PMCID: PMC4621489.
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The hemicellulose-degrading enzyme system of the thermophilic bacterium .

Biotechnology for biofuels

Broeker J, Mechelke M, Baudrexl M, Mennerich D, Hornburg D, Mann M, Schwarz WH, Liebl W, Zverlov VV.
PMID: 30159029
Biotechnol Biofuels. 2018 Aug 23;11:229. doi: 10.1186/s13068-018-1228-3. eCollection 2018.

BACKGROUND: The bioconversion of lignocellulosic biomass in various industrial processes, such as the production of biofuels, requires the degradation of hemicellulose. RESULTS: To reveal the hemicellulose-degrading potential of 50 glycoside hydrolases, they were recombinantly produced and characterised. 46 of...

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Broeker J, Mechelke M, Baudrexl M, et al. The hemicellulose-degrading enzyme system of the thermophilic bacterium . Biotechnol Biofuels. 2018;11:229doi: 10.1186/s13068-018-1228-3.
Broeker, J., Mechelke, M., Baudrexl, M., Mennerich, D., Hornburg, D., Mann, M., Schwarz, W. H., Liebl, W., & Zverlov, V. V. (2018). The hemicellulose-degrading enzyme system of the thermophilic bacterium . Biotechnology for biofuels, 11229. https://doi.org/10.1186/s13068-018-1228-3
Broeker, Jannis, et al. "The hemicellulose-degrading enzyme system of the thermophilic bacterium ." Biotechnology for biofuels vol. 11 (2018): 229. doi: https://doi.org/10.1186/s13068-018-1228-3
Broeker J, Mechelke M, Baudrexl M, Mennerich D, Hornburg D, Mann M, Schwarz WH, Liebl W, Zverlov VV. The hemicellulose-degrading enzyme system of the thermophilic bacterium . Biotechnol Biofuels. 2018 Aug 23;11:229. doi: 10.1186/s13068-018-1228-3. eCollection 2018. PMID: 30159029; PMCID: PMC6106730.
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A Structural and Functional Elucidation of the Rumen Microbiome Influenced by Various Diets and Microenvironments.

Frontiers in microbiology

Deusch S, Camarinha-Silva A, Conrad J, Beifuss U, Rodehutscord M, Seifert J.
PMID: 28883813
Front Microbiol. 2017 Aug 24;8:1605. doi: 10.3389/fmicb.2017.01605. eCollection 2017.

The structure and function of the microbiome inhabiting the rumen are, amongst other factors, mainly shaped by the animal's feed intake. Describing the influence of different diets on the inherent community arrangement and associated metabolic activities of the most...

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Deusch S, Camarinha-Silva A, Conrad J, et al. A Structural and Functional Elucidation of the Rumen Microbiome Influenced by Various Diets and Microenvironments. Front Microbiol. 2017;8:1605doi: 10.3389/fmicb.2017.01605.
Deusch, S., Camarinha-Silva, A., Conrad, J., Beifuss, U., Rodehutscord, M., & Seifert, J. (2017). A Structural and Functional Elucidation of the Rumen Microbiome Influenced by Various Diets and Microenvironments. Frontiers in microbiology, 81605. https://doi.org/10.3389/fmicb.2017.01605
Deusch, Simon, et al. "A Structural and Functional Elucidation of the Rumen Microbiome Influenced by Various Diets and Microenvironments." Frontiers in microbiology vol. 8 (2017): 1605. doi: https://doi.org/10.3389/fmicb.2017.01605
Deusch S, Camarinha-Silva A, Conrad J, Beifuss U, Rodehutscord M, Seifert J. A Structural and Functional Elucidation of the Rumen Microbiome Influenced by Various Diets and Microenvironments. Front Microbiol. 2017 Aug 24;8:1605. doi: 10.3389/fmicb.2017.01605. eCollection 2017. PMID: 28883813; PMCID: PMC5573736.
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Impaired coordination of nucleophile and increased hydrophobicity in the +1 subsite shift levansucrase activity towards transfructosylation.

Glycobiology

Ortiz-Soto ME, Possiel C, Görl J, Vogel A, Schmiedel R, Seibel J.
PMID: 28575294
Glycobiology. 2017 Aug 01;27(8):755-765. doi: 10.1093/glycob/cwx050.

Bacterial levansucrases produce β(2,6)-linked levan-type polysaccharides using sucrose or sucrose analogs as donor/acceptor substrates. However, the dominant reaction of Bacillus megaterium levansucrase (Bm-LS) is hydrolysis. Single domain levansucrases from Gram-positive bacteria display a wide substrate-binding pocket with open access...

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Ortiz-Soto ME, Possiel C, Görl J, et al. Impaired coordination of nucleophile and increased hydrophobicity in the +1 subsite shift levansucrase activity towards transfructosylation. Glycobiology. 2017;27(8):755-765doi: 10.1093/glycob/cwx050.
Ortiz-Soto, M. E., Possiel, C., Görl, J., Vogel, A., Schmiedel, R., & Seibel, J. (2017). Impaired coordination of nucleophile and increased hydrophobicity in the +1 subsite shift levansucrase activity towards transfructosylation. Glycobiology, 27(8), 755-765. https://doi.org/10.1093/glycob/cwx050
Ortiz-Soto, Maria Elena, et al. "Impaired coordination of nucleophile and increased hydrophobicity in the +1 subsite shift levansucrase activity towards transfructosylation." Glycobiology vol. 27,8 (2017): 755-765. doi: https://doi.org/10.1093/glycob/cwx050
Ortiz-Soto ME, Possiel C, Görl J, Vogel A, Schmiedel R, Seibel J. Impaired coordination of nucleophile and increased hydrophobicity in the +1 subsite shift levansucrase activity towards transfructosylation. Glycobiology. 2017 Aug 01;27(8):755-765. doi: 10.1093/glycob/cwx050. PMID: 28575294; PMCID: PMC5881714.
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FiberGrowth Pipeline: A Framework Toward Predicting Fiber-Specific Growth From Human Gut Bacteroidetes Genomes.

Frontiers in microbiology

Colnet B, Sieber CMK, Perraudeau F, Leclerc M.
PMID: 34690938
Front Microbiol. 2021 Oct 06;12:632567. doi: 10.3389/fmicb.2021.632567. eCollection 2021.

Dietary fibers impact gut colonic health, through the production of short-chain fatty acids. A low-fiber diet has been linked to lower bacterial diversity, obesity, type 2 diabetes, and promotion of mucosal pathogens. Glycoside hydrolases (GHs) are important enzymes involved...

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Colnet B, Sieber CMK, Perraudeau F, et al. FiberGrowth Pipeline: A Framework Toward Predicting Fiber-Specific Growth From Human Gut Bacteroidetes Genomes. Front Microbiol. 2021;12:632567doi: 10.3389/fmicb.2021.632567.
Colnet, B., Sieber, C. M. K., Perraudeau, F., & Leclerc, M. (2021). FiberGrowth Pipeline: A Framework Toward Predicting Fiber-Specific Growth From Human Gut Bacteroidetes Genomes. Frontiers in microbiology, 12632567. https://doi.org/10.3389/fmicb.2021.632567
Colnet, Bénédicte, et al. "FiberGrowth Pipeline: A Framework Toward Predicting Fiber-Specific Growth From Human Gut Bacteroidetes Genomes." Frontiers in microbiology vol. 12 (2021): 632567. doi: https://doi.org/10.3389/fmicb.2021.632567
Colnet B, Sieber CMK, Perraudeau F, Leclerc M. FiberGrowth Pipeline: A Framework Toward Predicting Fiber-Specific Growth From Human Gut Bacteroidetes Genomes. Front Microbiol. 2021 Oct 06;12:632567. doi: 10.3389/fmicb.2021.632567. eCollection 2021. PMID: 34690938; PMCID: PMC8527192.
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The Second Chromosome Promotes the Adaptation of the Genus .

Microbiology spectrum

Feng Z, Zhang Z, Liu Y, Gu J, Cheng Y, Hu W, Li Y, Han W.
PMID: 34878294
Microbiol Spectr. 2021 Dec 22;9(3):e0098021. doi: 10.1128/Spectrum.00980-21. Epub 2021 Dec 08.

Approximately 10% of bacterial strains contain more than one chromosome; however, in contrast to the primary chromosomes, the mechanisms underlying the formation of the second chromosomes and the significance of their existence remain unclear. Species of the genus Flammeovirga...

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Feng Z, Zhang Z, Liu Y, et al. The Second Chromosome Promotes the Adaptation of the Genus . Microbiol Spectr. 2021;9(3):e0098021doi: 10.1128/Spectrum.00980-21.
Feng, Z., Zhang, Z., Liu, Y., Gu, J., Cheng, Y., Hu, W., Li, Y., & Han, W. (2021). The Second Chromosome Promotes the Adaptation of the Genus . Microbiology spectrum, 9(3), e0098021. https://doi.org/10.1128/Spectrum.00980-21
Feng, Zewei, et al. "The Second Chromosome Promotes the Adaptation of the Genus ." Microbiology spectrum vol. 9,3 (2021): e0098021. doi: https://doi.org/10.1128/Spectrum.00980-21
Feng Z, Zhang Z, Liu Y, Gu J, Cheng Y, Hu W, Li Y, Han W. The Second Chromosome Promotes the Adaptation of the Genus . Microbiol Spectr. 2021 Dec 22;9(3):e0098021. doi: 10.1128/Spectrum.00980-21. Epub 2021 Dec 08. PMID: 34878294; PMCID: PMC8653839.
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Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in .

Computational and structural biotechnology journal

Briganti L, Capetti C, Pellegrini VOA, Ghio S, Campos E, Nascimento AS, Polikarpov I.
PMID: 33815691
Comput Struct Biotechnol J. 2021 Mar 07;19:1557-1566. doi: 10.1016/j.csbj.2021.03.002. eCollection 2021.

Glycoside hydrolases (GHs) are essential for plant biomass deconstruction. GH11 family consist of endo-β-1,4-xylanases which hydrolyze xylan, the second most abundant cell wall biopolymer after cellulose, into small bioavailable oligomers. Structural requirements for enzymatic mechanism of xylan hydrolysis is...

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Briganti L, Capetti C, Pellegrini VOA, et al. Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in . Comput Struct Biotechnol J. 2021;19:1557-1566doi: 10.1016/j.csbj.2021.03.002.
Briganti, L., Capetti, C., Pellegrini, V. O. A., Ghio, S., Campos, E., Nascimento, A. S., & Polikarpov, I. (2021). Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in . Computational and structural biotechnology journal, 191557-1566. https://doi.org/10.1016/j.csbj.2021.03.002
Briganti, Lorenzo, et al. "Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in ." Computational and structural biotechnology journal vol. 19 (2021): 1557-1566. doi: https://doi.org/10.1016/j.csbj.2021.03.002
Briganti L, Capetti C, Pellegrini VOA, Ghio S, Campos E, Nascimento AS, Polikarpov I. Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in . Comput Struct Biotechnol J. 2021 Mar 07;19:1557-1566. doi: 10.1016/j.csbj.2021.03.002. eCollection 2021. PMID: 33815691; PMCID: PMC7994722.
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[No title available]

ACS applied bio materials

Thorn CR, Prestidge CA, Boyd BJ, Thomas N.
PMID: 35016391
ACS Appl Bio Mater. 2018 Aug 20;1(2):281-288. doi: 10.1021/acsabm.8b00062. Epub 2018 Jul 13.

Bacterial biofilms account for up to 80% of all community-acquired infections for which bacterial eradication is currently not achievable using conventional antimicrobial treatments. The protective matrix that engulfs biofilm-associated bacteria frequently renders antibiotics ineffective. Glycoside hydrolases are a class...

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Thorn CR, Prestidge CA, Boyd BJ, et al. . ACS Appl Bio Mater. 2018;1(2):281-288doi: 10.1021/acsabm.8b00062.
Thorn, C. R., Prestidge, C. A., Boyd, B. J., & Thomas, N. (2018). . ACS applied bio materials, 1(2), 281-288. https://doi.org/10.1021/acsabm.8b00062
Thorn, Chelsea R, et al. "." ACS applied bio materials vol. 1,2 (2018): 281-288. doi: https://doi.org/10.1021/acsabm.8b00062
Thorn CR, Prestidge CA, Boyd BJ, Thomas N. . ACS Appl Bio Mater. 2018 Aug 20;1(2):281-288. doi: 10.1021/acsabm.8b00062. Epub 2018 Jul 13. PMID: 35016391.
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Thermoascus aurantiacus is a promising source of enzymes for biomass deconstruction under thermophilic conditions.

Biotechnology for biofuels

McClendon SD, Batth T, Petzold CJ, Adams PD, Simmons BA, Singer SW.
PMID: 22839529
Biotechnol Biofuels. 2012 Jul 28;5(1):54. doi: 10.1186/1754-6834-5-54.

BACKGROUND: Thermophilic fungi have attracted increased interest for their ability to secrete enzymes that deconstruct biomass at high temperatures. However, development of thermophilic fungi as enzyme producers for biomass deconstruction has not been thoroughly investigated. Comparing the enzymatic activities...

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McClendon SD, Batth T, Petzold CJ, et al. Thermoascus aurantiacus is a promising source of enzymes for biomass deconstruction under thermophilic conditions. Biotechnol Biofuels. 2012;5(1):54doi: 10.1186/1754-6834-5-54.
McClendon, S. D., Batth, T., Petzold, C. J., Adams, P. D., Simmons, B. A., & Singer, S. W. (2012). Thermoascus aurantiacus is a promising source of enzymes for biomass deconstruction under thermophilic conditions. Biotechnology for biofuels, 5(1), 54. https://doi.org/10.1186/1754-6834-5-54
McClendon, Shara D, et al. "Thermoascus aurantiacus is a promising source of enzymes for biomass deconstruction under thermophilic conditions." Biotechnology for biofuels vol. 5,1 (2012): 54. doi: https://doi.org/10.1186/1754-6834-5-54
McClendon SD, Batth T, Petzold CJ, Adams PD, Simmons BA, Singer SW. Thermoascus aurantiacus is a promising source of enzymes for biomass deconstruction under thermophilic conditions. Biotechnol Biofuels. 2012 Jul 28;5(1):54. doi: 10.1186/1754-6834-5-54. PMID: 22839529; PMCID: PMC3507748.
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Expanded analyses of the functional correlations within structural classifications of glycoside hydrolases.

Computational and structural biotechnology journal

Li DD, Wang JL, Liu Y, Li YZ, Zhang Z.
PMID: 34849197
Comput Struct Biotechnol J. 2021 Nov 02;19:5931-5942. doi: 10.1016/j.csbj.2021.10.039. eCollection 2021.

Glycoside hydrolases (GHs) are greatly diverse in sequences and functions, but systematic studies of GH relationships based on structural information are lacking. Here, we report that GHs have multiple evolutionary origins and are structurally derived from 27 homologous superfamilies...

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Li DD, Wang JL, Liu Y, et al. Expanded analyses of the functional correlations within structural classifications of glycoside hydrolases. Comput Struct Biotechnol J. 2021;19:5931-5942doi: 10.1016/j.csbj.2021.10.039.
Li, D. D., Wang, J. L., Liu, Y., Li, Y. Z., & Zhang, Z. (2021). Expanded analyses of the functional correlations within structural classifications of glycoside hydrolases. Computational and structural biotechnology journal, 195931-5942. https://doi.org/10.1016/j.csbj.2021.10.039
Li, Dan-Dan, et al. "Expanded analyses of the functional correlations within structural classifications of glycoside hydrolases." Computational and structural biotechnology journal vol. 19 (2021): 5931-5942. doi: https://doi.org/10.1016/j.csbj.2021.10.039
Li DD, Wang JL, Liu Y, Li YZ, Zhang Z. Expanded analyses of the functional correlations within structural classifications of glycoside hydrolases. Comput Struct Biotechnol J. 2021 Nov 02;19:5931-5942. doi: 10.1016/j.csbj.2021.10.039. eCollection 2021. PMID: 34849197; PMCID: PMC8602953.
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Engineering the substrate binding site of the hyperthermostable archaeal endo-β-1,4-galactanase from Ignisphaera aggregans.

Biotechnology for biofuels

Muderspach SJ, Fredslund F, Volf V, Poulsen JN, Blicher TH, Clausen MH, Rasmussen KK, Krogh KBRM, Jensen K, Lo Leggio L.
PMID: 34530892
Biotechnol Biofuels. 2021 Sep 16;14(1):183. doi: 10.1186/s13068-021-02025-6.

BACKGROUND: Endo-β-1,4-galactanases are glycoside hydrolases (GH) from the GH53 family belonging to the largest clan of GHs, clan GH-A. GHs are ubiquitous and involved in a myriad of biological functions as well as being widely used industrially. Endo-β-1,4-galactanases, in...

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Muderspach SJ, Fredslund F, Volf V, et al. Engineering the substrate binding site of the hyperthermostable archaeal endo-β-1,4-galactanase from Ignisphaera aggregans. Biotechnol Biofuels. 2021;14(1):183doi: 10.1186/s13068-021-02025-6.
Muderspach, S. J., Fredslund, F., Volf, V., Poulsen, J. N., Blicher, T. H., Clausen, M. H., Rasmussen, K. K., Krogh, K. B. R. M., Jensen, K., & Lo Leggio, L. (2021). Engineering the substrate binding site of the hyperthermostable archaeal endo-β-1,4-galactanase from Ignisphaera aggregans. Biotechnology for biofuels, 14(1), 183. https://doi.org/10.1186/s13068-021-02025-6
Muderspach, Sebastian J, et al. "Engineering the substrate binding site of the hyperthermostable archaeal endo-β-1,4-galactanase from Ignisphaera aggregans." Biotechnology for biofuels vol. 14,1 (2021): 183. doi: https://doi.org/10.1186/s13068-021-02025-6
Muderspach SJ, Fredslund F, Volf V, Poulsen JN, Blicher TH, Clausen MH, Rasmussen KK, Krogh KBRM, Jensen K, Lo Leggio L. Engineering the substrate binding site of the hyperthermostable archaeal endo-β-1,4-galactanase from Ignisphaera aggregans. Biotechnol Biofuels. 2021 Sep 16;14(1):183. doi: 10.1186/s13068-021-02025-6. PMID: 34530892; PMCID: PMC8447715.
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Structure of a bacterial α-1,2-glucosidase defines mechanisms of hydrolysis and substrate specificity in GH65 family hydrolases.

The Journal of biological chemistry

Nakamura S, Nihira T, Kurata R, Nakai H, Funane K, Park EY, Miyazaki T.
PMID: 34728215
J Biol Chem. 2021 Dec;297(6):101366. doi: 10.1016/j.jbc.2021.101366. Epub 2021 Oct 30.

Glycoside hydrolase family 65 (GH65) comprises glycoside hydrolases (GHs) and glycoside phosphorylases (GPs) that act on α-glucosidic linkages in oligosaccharides. All previously reported bacterial GH65 enzymes are GPs, whereas all eukaryotic GH65 enzymes known are GHs. In addition, to...

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Nakamura S, Nihira T, Kurata R, et al. Structure of a bacterial α-1,2-glucosidase defines mechanisms of hydrolysis and substrate specificity in GH65 family hydrolases. J Biol Chem. 2021;297(6):101366doi: 10.1016/j.jbc.2021.101366.
Nakamura, S., Nihira, T., Kurata, R., Nakai, H., Funane, K., Park, E. Y., & Miyazaki, T. (2021). Structure of a bacterial α-1,2-glucosidase defines mechanisms of hydrolysis and substrate specificity in GH65 family hydrolases. The Journal of biological chemistry, 297(6), 101366. https://doi.org/10.1016/j.jbc.2021.101366
Nakamura, Shuntaro, et al. "Structure of a bacterial α-1,2-glucosidase defines mechanisms of hydrolysis and substrate specificity in GH65 family hydrolases." The Journal of biological chemistry vol. 297,6 (2021): 101366. doi: https://doi.org/10.1016/j.jbc.2021.101366
Nakamura S, Nihira T, Kurata R, Nakai H, Funane K, Park EY, Miyazaki T. Structure of a bacterial α-1,2-glucosidase defines mechanisms of hydrolysis and substrate specificity in GH65 family hydrolases. J Biol Chem. 2021 Dec;297(6):101366. doi: 10.1016/j.jbc.2021.101366. Epub 2021 Oct 30. PMID: 34728215; PMCID: PMC8626586.
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Showing 13 to 24 of 222 entries