User:Darrell Cockburn

Darrell Cockburn received his BSc. and PhD from the University of Guelph in Ontario, Canada. During his PhD under his adviser Anthony Clarke, Darrell primarily studied the structure function relationships within the endoglucanase family GH6. In 2010 Darrell moved to Denmark to take an H.C. Ørsted fellowship with Birte Svensson at the Technical University of Denmark. There he studied Surface Binding Sites in a variety of carbohydrate active enzymes, with a particular focus on GH13. In 2013 Darrell moved to the University of Michigan to continue his Postdoctoral training with Nicole Koropatkin, studying the amylolytic systems of the gut bacteria Eubacterium rectale and Ruminococcus bromii. In 2017 Darrell started his own lab at Penn State University in the Department of Food Science, focusing on resistant starch degradation by the human gut microbiome.

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1. Arnal G, Cockburn DW, Brumer H, and Koropatkin NM. (2018). Structural basis for the flexible recognition of α-glucan substrates by Bacteroides thetaiotaomicron SusG. Protein Sci. 2018;27(6):1093-1101. DOI:10.1002/pro.3410 |
2. 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, and Flint HJ. (2018). Sporulation capability and amylosome conservation among diverse human colonic and rumen isolates of the keystone starch-degrader Ruminococcus bromii. Environ Microbiol. 2018;20(1):324-336. DOI:10.1111/1462-2920.14000 |
3. Cockburn DW, Suh C, Medina KP, Duvall RM, Wawrzak Z, Henrissat B, and Koropatkin NM. (2018). 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. Mol Microbiol. 2018;107(2):249-264. DOI:10.1111/mmi.13881 |
4. Cockburn D, Wilkens C, and Svensson B. (2017). Affinity Electrophoresis for Analysis of Catalytic Module-Carbohydrate Interactions. Methods Mol Biol. 2017;1588:119-127. DOI:10.1007/978-1-4939-6899-2_9 |
5. Moraïs S, Cockburn DW, Ben-David Y, Koropatkin NM, Martens EC, Duncan SH, Flint HJ, Mizrahi I, and Bayer EA. (2016). Lysozyme activity of the Ruminococcus champanellensis cellulosome. Environ Microbiol. 2016;18(12):5112-5122. DOI:10.1111/1462-2920.13501 |
6. Cockburn DW and Koropatkin NM. (2016). Polysaccharide Degradation by the Intestinal Microbiota and Its Influence on Human Health and Disease. J Mol Biol. 2016;428(16):3230-3252. DOI:10.1016/j.jmb.2016.06.021 |
7. Cockburn D, Wilkens C, Dilokpimol A, Nakai H, Lewińska A, Abou Hachem M, and Svensson B. (2016). Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes. PLoS One. 2016;11(8):e0160112. DOI:10.1371/journal.pone.0160112 |
8. Wilkens C, Andersen S, Petersen BO, Li A, Busse-Wicher M, Birch J, Cockburn D, Nakai H, Christensen HEM, Kragelund BB, Dupree P, McCleary B, Hindsgaul O, Hachem MA, and Svensson B. (2016). An efficient arabinoxylan-debranching α-L-arabinofuranosidase of family GH62 from Aspergillus nidulans contains a secondary carbohydrate binding site. Appl Microbiol Biotechnol. 2016;100(14):6265-6277. DOI:10.1007/s00253-016-7417-8 |
9. Foley MH, Cockburn DW, and Koropatkin NM. (2016). The Sus operon: a model system for starch uptake by the human gut Bacteroidetes. Cell Mol Life Sci. 2016;73(14):2603-17. DOI:10.1007/s00018-016-2242-x |
10. Cockburn D, Nielsen MM, Christiansen C, Andersen JM, Rannes JB, Blennow A, and Svensson B. (2015). Surface binding sites in amylase have distinct roles in recognition of starch structure motifs and degradation. Int J Biol Macromol. 2015;75:338-45. DOI:10.1016/j.ijbiomac.2015.01.054 |
11. Cockburn DW, Orlovsky NI, Foley MH, Kwiatkowski KJ, Bahr CM, Maynard M, Demeler B, and Koropatkin NM. (2015). Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale. Mol Microbiol. 2015;95(2):209-30. DOI:10.1111/mmi.12859 |

12. Cockburn, D., Wilkens, C., Ruzanski, C., Andersen, S., Willum Nielsen, J., Smith, A.M., Field, R.A., Willemoës, M., Abou Hachem, M., and Svensson B. (2014) Analysis of surface binding sites (SBSs) in carbohydrate active enzymes with focus on glycoside hydrolase families 13 and 77 — a mini-review. Biologia, 69, 705-712. DOI: 10.2478/s11756-014-0373-9

13. Cockburn, D. and Svensson, B. Surface binding sites in carbohydrate active enzymes: an emerging picture of structural and functional diversity. 2013. In: Lindhorst TK, Rauter AP (eds) SPR carbohydrate chemistry—chemical and biological approaches, vol 39. Royal Society of Chemistry, Cambridge. DOI: 10.1039/9781849737173-00204

14. Ruzanski C, Smirnova J, Rejzek M, Cockburn D, Pedersen HL, Pike M, Willats WG, Svensson B, Steup M, Ebenhöh O, Smith AM, and Field RA. (2013). A bacterial glucanotransferase can replace the complex maltose metabolism required for starch to sucrose conversion in leaves at night. J Biol Chem. 2013;288(40):28581-98. DOI:10.1074/jbc.M113.497867 |

15. Møller, M.S., Cockburn, D., Nielsen, J.W., Jensen, J.M., Vester-Christensen, M.B., Nielsen, M.M., Andersen, J.M., Wilkens, C., Rannes, J., Hägglund, P., Henriksen, A., Abou Hachem, M., Willemoës M., and B. Svensson (2013) Surface Binding Sites (SBS), Mechanism and Regulation of 2 Enzymes Degrading Amylopectin and α-limit Dextrins. J. Appl. Glycosci. EPub March 21. DOI: 10.5458/jag.jag.JAG-2012_023

16. Diemer, S.K., Svensson, B., Nygren Babol, L., Cockburn, D., Grijpstra, P., Dijkhuizen, L., Folkenberg, D.M., Garrigues, C., and R. Ipsen (2012) Binding interactions between α-glucans from Lactobacillus reuteri and milk proteins characterised by surface plasmon resonance. Food Biophys. 7: 220-226. DOI: 10.1007/s11483-012-9260-5

17. Cockburn DW and Clarke AJ. (2011). Modulating the pH-activity profile of cellulase A from Cellulomonas fimi by replacement of surface residues. Protein Eng Des Sel. 2011;24(5):429-37. DOI:10.1093/protein/gzr004 |
18. Quirk A, Lipkowski J, Vandenende C, Cockburn D, Clarke AJ, Dutcher JR, and Roscoe SG. (2010). Direct visualization of the enzymatic digestion of a single fiber of native cellulose in an aqueous environment by atomic force microscopy. Langmuir. 2010;26(7):5007-13. DOI:10.1021/la9037028 |
19. Cockburn DW, Vandenende C, and Clarke AJ. (2010). Modulating the pH-activity profile of cellulase by substitution: replacing the general base catalyst aspartate with cysteinesulfinate in cellulase A from Cellulomonas fimi. Biochemistry. 2010;49(9):2042-50. DOI:10.1021/bi1000596 |
20. Jing H, Cockburn D, Zhang Q, and Clarke AJ. (2009). Production and purification of the isolated family 2a carbohydrate-binding module from Cellulomonas fimi. Protein Expr Purif. 2009;64(1):63-8. DOI:10.1016/j.pep.2008.10.015 |
21. Legaree BA, Daniels K, Weadge JT, Cockburn D, and Clarke AJ. (2007). Function of penicillin-binding protein 2 in viability and morphology of Pseudomonas aeruginosa. J Antimicrob Chemother. 2007;59(3):411-24. DOI:10.1093/jac/dkl536 |