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Items: 49


Starch Digestion by Gut Bacteria: Crowdsourcing for Carbs.

Cerqueira FM, Photenhauer AL, Pollet RM, Brown HA, Koropatkin NM.

Trends Microbiol. 2020 Feb;28(2):95-108. doi: 10.1016/j.tim.2019.09.004. Epub 2019 Oct 14. Review.


Structural and biochemical characterization of 20β-hydroxysteroid dehydrogenase from Bifidobacterium adolescentis strain L2-32.

Doden HL, Pollet RM, Mythen SM, Wawrzak Z, Devendran S, Cann I, Koropatkin NM, Ridlon JM.

J Biol Chem. 2019 Aug 9;294(32):12040-12053. doi: 10.1074/jbc.RA119.009390. Epub 2019 Jun 17.


Erratum for Baxter et al., "The Glucoamylase Inhibitor Acarbose Has a Diet-Dependent and Reversible Effect on the Murine Gut Microbiome".

Baxter NT, Lesniak NA, Sinani H, Schloss PD, Koropatkin NM.

mSphere. 2019 May 22;4(3). pii: e00347-19. doi: 10.1128/mSphere.00347-19. No abstract available.


Surface glycan-binding proteins are essential for cereal beta-glucan utilization by the human gut symbiont Bacteroides ovatus.

Tamura K, Foley MH, Gardill BR, Dejean G, Schnizlein M, Bahr CME, Louise Creagh A, van Petegem F, Koropatkin NM, Brumer H.

Cell Mol Life Sci. 2019 Nov;76(21):4319-4340. doi: 10.1007/s00018-019-03115-3. Epub 2019 May 6.


The Glucoamylase Inhibitor Acarbose Has a Diet-Dependent and Reversible Effect on the Murine Gut Microbiome.

Baxter NT, Lesniak NA, Sinani H, Schloss PD, Koropatkin NM.

mSphere. 2019 Feb 6;4(1). pii: e00528-18. doi: 10.1128/mSphere.00528-18. Erratum in: mSphere. 2019 May 22;4(3):.


A Cell-Surface GH9 Endo-Glucanase Coordinates with Surface Glycan-Binding Proteins to Mediate Xyloglucan Uptake in the Gut Symbiont Bacteroides ovatus.

Foley MH, Déjean G, Hemsworth GR, Davies GJ, Brumer H, Koropatkin NM.

J Mol Biol. 2019 Mar 1;431(5):981-995. doi: 10.1016/j.jmb.2019.01.008. Epub 2019 Jan 19.


Structural basis of Toxoplasma gondii perforin-like protein 1 membrane interaction and activity during egress.

Guerra AJ, Zhang O, Bahr CME, Huynh MH, DelProposto J, Brown WC, Wawrzak Z, Koropatkin NM, Carruthers VB.

PLoS Pathog. 2018 Dec 4;14(12):e1007476. doi: 10.1371/journal.ppat.1007476. eCollection 2018 Dec.


Structural basis for the flexible recognition of α-glucan substrates by Bacteroides thetaiotaomicron SusG.

Arnal G, Cockburn DW, Brumer H, Koropatkin NM.

Protein Sci. 2018 Jun;27(6):1093-1101. doi: 10.1002/pro.3410. Epub 2018 Apr 17.


SusE facilitates starch uptake independent of starch binding in B. thetaiotaomicron.

Foley MH, Martens EC, Koropatkin NM.

Mol Microbiol. 2018 Jun;108(5):551-566. doi: 10.1111/mmi.13949. Epub 2018 Apr 14.


"Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system.

Naas AE, Solden LM, Norbeck AD, Brewer H, Hagen LH, Heggenes IM, McHardy AC, Mackie RI, Paša-Tolić L, Arntzen MØ, Eijsink VGH, Koropatkin NM, Hess M, Wrighton KC, Pope PB.

Microbiome. 2018 Mar 1;6(1):44. doi: 10.1186/s40168-018-0421-8.


The Starch Utilization System Assembles around Stationary Starch-Binding Proteins.

Tuson HH, Foley MH, Koropatkin NM, Biteen JS.

Biophys J. 2018 Jul 17;115(2):242-250. doi: 10.1016/j.bpj.2017.12.015. Epub 2018 Jan 12.


Sporulation capability and amylosome conservation among diverse human colonic and rumen isolates of the keystone starch-degrader Ruminococcus bromii.

Mukhopadhya I, Moraïs S, Laverde-Gomez J, Sheridan PO, Walker AW, Kelly W, Klieve AV, Ouwerkerk D, Duncan SH, Louis P, Koropatkin N, Cockburn D, Kibler R, Cooper PJ, Sandoval C, Crost E, Juge N, Bayer EA, Flint HJ.

Environ Microbiol. 2018 Jan;20(1):324-336. doi: 10.1111/1462-2920.14000. Epub 2017 Dec 7.


Novel carbohydrate binding modules in the surface anchored α-amylase of Eubacterium rectale provide a molecular rationale for the range of starches used by this organism in the human gut.

Cockburn DW, Suh C, Medina KP, Duvall RM, Wawrzak Z, Henrissat B, Koropatkin NM.

Mol Microbiol. 2018 Jan;107(2):249-264. doi: 10.1111/mmi.13881. Epub 2017 Dec 1.


Meds Modify Microbiome, Mediating Their Effects.

Koropatkin NM, Martens EC.

Cell Metab. 2017 Sep 5;26(3):456-457. doi: 10.1016/j.cmet.2017.08.022.


Biochemical and Structural Analyses of Two Cryptic Esterases in Bacteroides intestinalis and their Synergistic Activities with Cognate Xylanases.

Wefers D, Cavalcante JJV, Schendel RR, Deveryshetty J, Wang K, Wawrzak Z, Mackie RI, Koropatkin NM, Cann I.

J Mol Biol. 2017 Aug 4;429(16):2509-2527. doi: 10.1016/j.jmb.2017.06.017. Epub 2017 Jun 29.


A polysaccharide utilization locus from Flavobacterium johnsoniae enables conversion of recalcitrant chitin.

Larsbrink J, Zhu Y, Kharade SS, Kwiatkowski KJ, Eijsink VG, Koropatkin NM, McBride MJ, Pope PB.

Biotechnol Biofuels. 2016 Nov 28;9:260. eCollection 2016.


Galactomannan Catabolism Conferred by a Polysaccharide Utilization Locus of Bacteroides ovatus: ENZYME SYNERGY AND CRYSTAL STRUCTURE OF A β-MANNANASE.

Bågenholm V, Reddy SK, Bouraoui H, Morrill J, Kulcinskaja E, Bahr CM, Aurelius O, Rogers T, Xiao Y, Logan DT, Martens EC, Koropatkin NM, Stålbrand H.

J Biol Chem. 2017 Jan 6;292(1):229-243. doi: 10.1074/jbc.M116.746438. Epub 2016 Nov 21.


A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility.

Desai MS, Seekatz AM, Koropatkin NM, Kamada N, Hickey CA, Wolter M, Pudlo NA, Kitamoto S, Terrapon N, Muller A, Young VB, Henrissat B, Wilmes P, Stappenbeck TS, Núñez G, Martens EC.

Cell. 2016 Nov 17;167(5):1339-1353.e21. doi: 10.1016/j.cell.2016.10.043.


Corrigendum: Determining crystal structures through crowdsourcing and coursework.

Horowitz S, Koepnick B, Martin R, Tymieniecki A, Winburn AA, Cooper S, Flatten J, Rogawski DS, Koropatkin NM, Hailu TT, Jain N, Koldewey P, Ahlstrom LS, Chapman MR, Sikkema AP, Skiba MA, Maloney FP, Beinlich FR; Foldit Players; University of Michigan students, Popović Z, Baker D, Khatib F, Bardwell JC.

Nat Commun. 2016 Oct 25;7:13392. doi: 10.1038/ncomms13392. No abstract available.


Determining crystal structures through crowdsourcing and coursework.

Horowitz S, Koepnick B, Martin R, Tymieniecki A, Winburn AA, Cooper S, Flatten J, Rogawski DS, Koropatkin NM, Hailu TT, Jain N, Koldewey P, Ahlstrom LS, Chapman MR, Sikkema AP, Skiba MA, Maloney FP, Beinlich FR; Foldit Players; University of Michigan students, Popović Z, Baker D, Khatib F, Bardwell JC.

Nat Commun. 2016 Sep 16;7:12549. doi: 10.1038/ncomms12549. Erratum in: Nat Commun. 2016 Oct 25;7:13392.


Lysozyme activity of the Ruminococcus champanellensis cellulosome.

Moraïs S, Cockburn DW, Ben-David Y, Koropatkin NM, Martens EC, Duncan SH, Flint HJ, Mizrahi I, Bayer EA.

Environ Microbiol. 2016 Dec;18(12):5112-5122. doi: 10.1111/1462-2920.13501. Epub 2016 Sep 7.


Polysaccharide Degradation by the Intestinal Microbiota and Its Influence on Human Health and Disease.

Cockburn DW, Koropatkin NM.

J Mol Biol. 2016 Aug 14;428(16):3230-3252. doi: 10.1016/j.jmb.2016.06.021. Epub 2016 Jul 6. Review.


A β-mannan utilization locus in Bacteroides ovatus involves a GH36 α-galactosidase active on galactomannans.

Reddy SK, Bågenholm V, Pudlo NA, Bouraoui H, Koropatkin NM, Martens EC, Stålbrand H.

FEBS Lett. 2016 Jul;590(14):2106-18. doi: 10.1002/1873-3468.12250. Epub 2016 Jun 28.


The Sus operon: a model system for starch uptake by the human gut Bacteroidetes.

Foley MH, Cockburn DW, Koropatkin NM.

Cell Mol Life Sci. 2016 Jul;73(14):2603-17. doi: 10.1007/s00018-016-2242-x. Epub 2016 May 2. Review.


Molecular Dissection of Xyloglucan Recognition in a Prominent Human Gut Symbiont.

Tauzin AS, Kwiatkowski KJ, Orlovsky NI, Smith CJ, Creagh AL, Haynes CA, Wawrzak Z, Brumer H, Koropatkin NM.

mBio. 2016 Apr 26;7(2):e02134-15. doi: 10.1128/mBio.02134-15.


Unique Organization of Extracellular Amylases into Amylosomes in the Resistant Starch-Utilizing Human Colonic Firmicutes Bacterium Ruminococcus bromii.

Ze X, Ben David Y, Laverde-Gomez JA, Dassa B, Sheridan PO, Duncan SH, Louis P, Henrissat B, Juge N, Koropatkin NM, Bayer EA, Flint HJ.

mBio. 2015 Sep 29;6(5):e01058-15. doi: 10.1128/mBio.01058-15.


Enzymatic profiling of cellulosomal enzymes from the human gut bacterium, Ruminococcus champanellensis, reveals a fine-tuned system for cohesin-dockerin recognition.

Moraïs S, Ben David Y, Bensoussan L, Duncan SH, Koropatkin NM, Martens EC, Flint HJ, Bayer EA.

Environ Microbiol. 2016 Feb;18(2):542-56. doi: 10.1111/1462-2920.13047. Epub 2015 Oct 14.


Outer membrane proteins related to SusC and SusD are not required for Cytophaga hutchinsonii cellulose utilization.

Zhu Y, Kwiatkowski KJ, Yang T, Kharade SS, Bahr CM, Koropatkin NM, Liu W, McBride MJ.

Appl Microbiol Biotechnol. 2015 Aug;99(15):6339-50. doi: 10.1007/s00253-015-6555-8. Epub 2015 Apr 7.


Ruminococcal cellulosome systems from rumen to human.

Ben David Y, Dassa B, Borovok I, Lamed R, Koropatkin NM, Martens EC, White BA, Bernalier-Donadille A, Duncan SH, Flint HJ, Bayer EA, Moraïs S.

Environ Microbiol. 2015 Sep;17(9):3407-26. doi: 10.1111/1462-2920.12868. Epub 2015 May 7.


Superresolution imaging captures carbohydrate utilization dynamics in human gut symbionts.

Karunatilaka KS, Cameron EA, Martens EC, Koropatkin NM, Biteen JS.

mBio. 2014 Nov 11;5(6):e02172. doi: 10.1128/mBio.02172-14.


Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale.

Cockburn DW, Orlovsky NI, Foley MH, Kwiatkowski KJ, Bahr CM, Maynard M, Demeler B, Koropatkin NM.

Mol Microbiol. 2015 Jan;95(2):209-30. doi: 10.1111/mmi.12859. Epub 2014 Dec 19.


Multifunctional nutrient-binding proteins adapt human symbiotic bacteria for glycan competition in the gut by separately promoting enhanced sensing and catalysis.

Cameron EA, Kwiatkowski KJ, Lee BH, Hamaker BR, Koropatkin NM, Martens EC.

mBio. 2014 Sep 9;5(5):e01441-14. doi: 10.1128/mBio.01441-14.


A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes.

Larsbrink J, Rogers TE, Hemsworth GR, McKee LS, Tauzin AS, Spadiut O, Klinter S, Pudlo NA, Urs K, Koropatkin NM, Creagh AL, Haynes CA, Kelly AG, Cederholm SN, Davies GJ, Martens EC, Brumer H.

Nature. 2014 Feb 27;506(7489):498-502. doi: 10.1038/nature12907. Epub 2014 Jan 19.


Dynamic responses of Bacteroides thetaiotaomicron during growth on glycan mixtures.

Rogers TE, Pudlo NA, Koropatkin NM, Bell JS, Moya Balasch M, Jasker K, Martens EC.

Mol Microbiol. 2013 Jun;88(5):876-90. doi: 10.1111/mmi.12228. Epub 2013 May 5.


Multidomain Carbohydrate-binding Proteins Involved in Bacteroides thetaiotaomicron Starch Metabolism.

Cameron EA, Maynard MA, Smith CJ, Smith TJ, Koropatkin NM, Martens EC.

J Biol Chem. 2012 Oct 5;287(41):34614-25. doi: 10.1074/jbc.M112.397380. Epub 2012 Aug 21.


Glycan recognition by the Bacteroidetes Sus-like systems.

Bolam DN, Koropatkin NM.

Curr Opin Struct Biol. 2012 Oct;22(5):563-9. doi: 10.1016/ Epub 2012 Jul 19. Review.


How glycan metabolism shapes the human gut microbiota.

Koropatkin NM, Cameron EA, Martens EC.

Nat Rev Microbiol. 2012 Apr 11;10(5):323-35. doi: 10.1038/nrmicro2746. Review.


The two faces of ToxR: activator of ompU, co-regulator of toxT in Vibrio cholerae.

Morgan SJ, Felek S, Gadwal S, Koropatkin NM, Perry JW, Bryson AB, Krukonis ES.

Mol Microbiol. 2011 Jul;81(1):113-28. doi: 10.1111/j.1365-2958.2011.07681.x. Epub 2011 Jun 5.


SusG: a unique cell-membrane-associated alpha-amylase from a prominent human gut symbiont targets complex starch molecules.

Koropatkin NM, Smith TJ.

Structure. 2010 Feb 10;18(2):200-15. doi: 10.1016/j.str.2009.12.010.


Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm.

Martens EC, Koropatkin NM, Smith TJ, Gordon JI.

J Biol Chem. 2009 Sep 11;284(37):24673-7. doi: 10.1074/jbc.R109.022848. Epub 2009 Jun 24. Review.


Structure of a SusD homologue, BT1043, involved in mucin O-glycan utilization in a prominent human gut symbiont.

Koropatkin N, Martens EC, Gordon JI, Smith TJ.

Biochemistry. 2009 Feb 24;48(7):1532-42. doi: 10.1021/bi801942a.


Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices.

Koropatkin NM, Martens EC, Gordon JI, Smith TJ.

Structure. 2008 Jul;16(7):1105-15. doi: 10.1016/j.str.2008.03.017.


The structure of the iron-binding protein, FutA1, from Synechocystis 6803.

Koropatkin N, Randich AM, Bhattacharyya-Pakrasi M, Pakrasi HB, Smith TJ.

J Biol Chem. 2007 Sep 14;282(37):27468-77. Epub 2007 Jul 11.


The structure of a cyanobacterial bicarbonate transport protein, CmpA.

Koropatkin NM, Koppenaal DW, Pakrasi HB, Smith TJ.

J Biol Chem. 2007 Jan 26;282(4):2606-14. Epub 2006 Nov 22.


Atomic structure of a nitrate-binding protein crucial for photosynthetic productivity.

Koropatkin NM, Pakrasi HB, Smith TJ.

Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):9820-5. Epub 2006 Jun 15.


Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi complexed with CDP-D-xylose.

Koropatkin NM, Holden HM.

Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):365-73. Epub 2005 Mar 24.


Kinetic and structural analysis of alpha-D-Glucose-1-phosphate cytidylyltransferase from Salmonella typhi.

Koropatkin NM, Cleland WW, Holden HM.

J Biol Chem. 2005 Mar 18;280(11):10774-80. Epub 2005 Jan 5.


Molecular structure of alpha-D-glucose-1-phosphate cytidylyltransferase from Salmonella typhi.

Koropatkin NM, Holden HM.

J Biol Chem. 2004 Oct 15;279(42):44023-9. Epub 2004 Aug 3.


High resolution x-ray structure of tyvelose epimerase from Salmonella typhi.

Koropatkin NM, Liu HW, Holden HM.

J Biol Chem. 2003 Jun 6;278(23):20874-81. Epub 2003 Mar 17.

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