Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 55

1.

Target highlights in CASP13: Experimental target structures through the eyes of their authors.

Lepore R, Kryshtafovych A, Alahuhta M, Veraszto HA, Bomble YJ, Bufton JC, Bullock AN, Caba C, Cao H, Davies OR, Desfosses A, Dunne M, Fidelis K, Goulding CW, Gurusaran M, Gutsche I, Harding CJ, Hartmann MD, Hayes CS, Joachimiak A, Leiman PG, Loppnau P, Lovering AL, Lunin VV, Michalska K, Mir-Sanchis I, Mitra A, Moult J, Phillips GN Jr, Pinkas DM, Rice PA, Tong Y, Topf M, Walton JD, Schwede T.

Proteins. 2019 Aug 23. doi: 10.1002/prot.25805. [Epub ahead of print]

PMID:
31442339
2.

Approaches to Computational Strain Design in the Multiomics Era.

St John PC, Bomble YJ.

Front Microbiol. 2019 Apr 5;10:597. doi: 10.3389/fmicb.2019.00597. eCollection 2019.

3.

Creation of a functional hyperthermostable designer cellulosome.

Kahn A, Moraïs S, Galanopoulou AP, Chung D, Sarai NS, Hengge N, Hatzinikolaou DG, Himmel ME, Bomble YJ, Bayer EA.

Biotechnol Biofuels. 2019 Feb 28;12:44. doi: 10.1186/s13068-019-1386-y. eCollection 2019.

4.

Heterologous co-expression of two β-glucanases and a cellobiose phosphorylase resulted in a significant increase in the cellulolytic activity of the Caldicellulosiruptor bescii exoproteome.

Kim SK, Chung D, Himmel ME, Bomble YJ, Westpheling J.

J Ind Microbiol Biotechnol. 2019 May;46(5):687-695. doi: 10.1007/s10295-019-02150-0. Epub 2019 Feb 20.

PMID:
30783893
5.

Comparative Biochemical and Structural Analysis of Novel Cellulose Binding Proteins (Tāpirins) from Extremely Thermophilic Caldicellulosiruptor Species.

Lee LL, Hart WS, Lunin VV, Alahuhta M, Bomble YJ, Himmel ME, Blumer-Schuette SE, Adams MWW, Kelly RM.

Appl Environ Microbiol. 2019 Jan 23;85(3). pii: e01983-18. doi: 10.1128/AEM.01983-18. Print 2019 Feb 1.

6.

Deletion of a single glycosyltransferase in Caldicellulosiruptor bescii eliminates protein glycosylation and growth on crystalline cellulose.

Russell J, Kim SK, Duma J, Nothaft H, Himmel ME, Bomble YJ, Szymanski CM, Westpheling J.

Biotechnol Biofuels. 2018 Sep 24;11:259. doi: 10.1186/s13068-018-1266-x. eCollection 2018.

7.

An iterative computational design approach to increase the thermal endurance of a mesophilic enzyme.

Sammond DW, Kastelowitz N, Donohoe BS, Alahuhta M, Lunin VV, Chung D, Sarai NS, Yin H, Mittal A, Himmel ME, Guss AM, Bomble YJ.

Biotechnol Biofuels. 2018 Jul 9;11:189. doi: 10.1186/s13068-018-1178-9. eCollection 2018.

8.

High activity CAZyme cassette for improving biomass degradation in thermophiles.

Brunecky R, Chung D, Sarai NS, Hengge N, Russell JF, Young J, Mittal A, Pason P, Vander Wall T, Michener W, Shollenberger T, Westpheling J, Himmel ME, Bomble YJ.

Biotechnol Biofuels. 2018 Feb 1;11:22. doi: 10.1186/s13068-018-1014-2. eCollection 2018.

9.

Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes.

Nag A, St John PC, Crowley MF, Bomble YJ.

PLoS One. 2018 Jan 30;13(1):e0189144. doi: 10.1371/journal.pone.0189144. eCollection 2018.

10.

Natural diversity of glycoside hydrolase family 48 exoglucanases: insights from structure.

Brunecky R, Alahuhta M, Sammond DW, Xu Q, Chen M, Wilson DB, Brady JW, Himmel ME, Bomble YJ, Lunin VV.

Biotechnol Biofuels. 2017 Nov 30;10:274. doi: 10.1186/s13068-017-0951-5. eCollection 2017.

11.

Structure of a Thermobifida fusca lytic polysaccharide monooxygenase and mutagenesis of key residues.

Kruer-Zerhusen N, Alahuhta M, Lunin VV, Himmel ME, Bomble YJ, Wilson DB.

Biotechnol Biofuels. 2017 Nov 30;10:243. doi: 10.1186/s13068-017-0925-7. eCollection 2017.

12.

Undefined cellulase formulations hinder scientific reproducibility.

Himmel ME, Abbas CA, Baker JO, Bayer EA, Bomble YJ, Brunecky R, Chen X, Felby C, Jeoh T, Kumar R, McCleary BV, Pletschke BI, Tucker MP, Wyman CE, Decker SR.

Biotechnol Biofuels. 2017 Nov 28;10:283. doi: 10.1186/s13068-017-0974-y. eCollection 2017.

13.

Expression of a Cellobiose Phosphorylase from Thermotoga maritima in Caldicellulosiruptor bescii Improves the Phosphorolytic Pathway and Results in a Dramatic Increase in Cellulolytic Activity.

Kim SK, Himmel ME, Bomble YJ, Westpheling J.

Appl Environ Microbiol. 2018 Jan 17;84(3). pii: e02348-17. doi: 10.1128/AEM.02348-17. Print 2018 Feb 1.

14.

Lignocellulose deconstruction in the biosphere.

Bomble YJ, Lin CY, Amore A, Wei H, Holwerda EK, Ciesielski PN, Donohoe BS, Decker SR, Lynd LR, Himmel ME.

Curr Opin Chem Biol. 2017 Dec;41:61-70. doi: 10.1016/j.cbpa.2017.10.013. Epub 2017 Nov 2. Review.

PMID:
29100023
15.

Heterologous expression of a β-D-glucosidase in Caldicellulosiruptor bescii has a surprisingly modest effect on the activity of the exoproteome and growth on crystalline cellulose.

Kim SK, Chung D, Himmel ME, Bomble YJ, Westpheling J.

J Ind Microbiol Biotechnol. 2017 Dec;44(12):1643-1651. doi: 10.1007/s10295-017-1982-4. Epub 2017 Sep 23.

PMID:
28942503
16.

The Multi Domain Caldicellulosiruptor bescii CelA Cellulase Excels at the Hydrolysis of Crystalline Cellulose.

Brunecky R, Donohoe BS, Yarbrough JM, Mittal A, Scott BR, Ding H, Taylor Ii LE, Russell JF, Chung D, Westpheling J, Teter SA, Himmel ME, Bomble YJ.

Sci Rep. 2017 Aug 29;7(1):9622. doi: 10.1038/s41598-017-08985-w.

17.

Structural, mutagenic and in silico studies of xyloglucan fucosylation in Arabidopsis thaliana suggest a water-mediated mechanism.

Urbanowicz BR, Bharadwaj VS, Alahuhta M, Peña MJ, Lunin VV, Bomble YJ, Wang S, Yang JY, Tuomivaara ST, Himmel ME, Moremen KW, York WS, Crowley MF.

Plant J. 2017 Sep;91(6):931-949. doi: 10.1111/tpj.13628. Epub 2017 Aug 28.

18.

In vivo synergistic activity of a CAZyme cassette from Acidothermus cellulolyticus significantly improves the cellulolytic activity of the C. bescii exoproteome.

Kim SK, Chung D, Himmel ME, Bomble YJ, Westpheling J.

Biotechnol Bioeng. 2017 Nov;114(11):2474-2480. doi: 10.1002/bit.26366. Epub 2017 Aug 3.

PMID:
28650071
19.

Metabolic Engineering of Actinobacillus succinogenes Provides Insights into Succinic Acid Biosynthesis.

Guarnieri MT, Chou YC, Salvachúa D, Mohagheghi A, St John PC, Peterson DJ, Bomble YJ, Beckham GT.

Appl Environ Microbiol. 2017 Aug 17;83(17). pii: e00996-17. doi: 10.1128/AEM.00996-17. Print 2017 Sep 1.

20.

Multifunctional Cellulolytic Enzymes Outperform Processive Fungal Cellulases for Coproduction of Nanocellulose and Biofuels.

Yarbrough JM, Zhang R, Mittal A, Vander Wall T, Bomble YJ, Decker SR, Himmel ME, Ciesielski PN.

ACS Nano. 2017 Mar 28;11(3):3101-3109. doi: 10.1021/acsnano.7b00086. Epub 2017 Mar 10.

PMID:
28267923
21.

Efficient estimation of the maximum metabolic productivity of batch systems.

St John PC, Crowley MF, Bomble YJ.

Biotechnol Biofuels. 2017 Jan 31;10:28. doi: 10.1186/s13068-017-0709-0. eCollection 2017.

22.

Engineering the N-terminal end of CelA results in improved performance and growth of Caldicellulosiruptor bescii on crystalline cellulose.

Kim SK, Chung D, Himmel ME, Bomble YJ, Westpheling J.

Biotechnol Bioeng. 2017 May;114(5):945-950. doi: 10.1002/bit.26242.

PMID:
28019666
23.

Heterologous expression of family 10 xylanases from Acidothermus cellulolyticus enhances the exoproteome of Caldicellulosiruptor bescii and growth on xylan substrates.

Kim SK, Chung D, Himmel ME, Bomble YJ, Westpheling J.

Biotechnol Biofuels. 2016 Aug 22;9(1):176. doi: 10.1186/s13068-016-0588-9. eCollection 2016.

24.

Dramatic performance of Clostridium thermocellum explained by its wide range of cellulase modalities.

Xu Q, Resch MG, Podkaminer K, Yang S, Baker JO, Donohoe BS, Wilson C, Klingeman DM, Olson DG, Decker SR, Giannone RJ, Hettich RL, Brown SD, Lynd LR, Bayer EA, Himmel ME, Bomble YJ.

Sci Adv. 2016 Feb 5;2(2):e1501254. doi: 10.1126/sciadv.1501254. eCollection 2016 Feb.

25.

Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms.

Sammond DW, Kastelowitz N, Himmel ME, Yin H, Crowley MF, Bomble YJ.

PLoS One. 2016 Jan 7;11(1):e0145848. doi: 10.1371/journal.pone.0145848. eCollection 2016.

26.

New perspective on glycoside hydrolase binding to lignin from pretreated corn stover.

Yarbrough JM, Mittal A, Mansfield E, Taylor LE 2nd, Hobdey SE, Sammond DW, Bomble YJ, Crowley MF, Decker SR, Himmel ME, Vinzant TB.

Biotechnol Biofuels. 2015 Dec 18;8:214. doi: 10.1186/s13068-015-0397-6. eCollection 2015.

27.

Strategies to reduce end-product inhibition in family 48 glycoside hydrolases.

Chen M, Bu L, Alahuhta M, Brunecky R, Xu Q, Lunin VV, Brady JW, Crowley MF, Himmel ME, Bomble YJ.

Proteins. 2016 Mar;84(3):295-304. doi: 10.1002/prot.24965. Epub 2016 Feb 1.

PMID:
26572060
28.

The catalytic mechanism and unique low pH optimum of Caldicellulosiruptor bescii family 3 pectate lyase.

Alahuhta M, Taylor LE 2nd, Brunecky R, Sammond DW, Michener W, Adams MW, Himmel ME, Bomble YJ, Lunin V.

Acta Crystallogr D Biol Crystallogr. 2015 Sep;71(Pt 9):1946-54. doi: 10.1107/S1399004715013760. Epub 2015 Aug 25.

29.

Expression of the Acidothermus cellulolyticus E1 endoglucanase in Caldicellulosiruptor bescii enhances its ability to deconstruct crystalline cellulose.

Chung D, Young J, Cha M, Brunecky R, Bomble YJ, Himmel ME, Westpheling J.

Biotechnol Biofuels. 2015 Aug 13;8:113. doi: 10.1186/s13068-015-0296-x. eCollection 2015.

30.

Cofactor Specificity of the Bifunctional Alcohol and Aldehyde Dehydrogenase (AdhE) in Wild-Type and Mutant Clostridium thermocellum and Thermoanaerobacterium saccharolyticum.

Zheng T, Olson DG, Tian L, Bomble YJ, Himmel ME, Lo J, Hon S, Shaw AJ, van Dijken JP, Lynd LR.

J Bacteriol. 2015 Aug 1;197(15):2610-9. doi: 10.1128/JB.00232-15. Epub 2015 May 26.

31.

Homologous expression of the Caldicellulosiruptor bescii CelA reveals that the extracellular protein is glycosylated.

Chung D, Young J, Bomble YJ, Vander Wall TA, Groom J, Himmel ME, Westpheling J.

PLoS One. 2015 Mar 23;10(3):e0119508. doi: 10.1371/journal.pone.0119508. eCollection 2015.

32.

Deletion of Caldicellulosiruptor bescii CelA reveals its crucial role in the deconstruction of lignocellulosic biomass.

Young J, Chung D, Bomble YJ, Himmel ME, Westpheling J.

Biotechnol Biofuels. 2014 Oct 9;7(1):142. doi: 10.1186/s13068-014-0142-6. eCollection 2014.

33.

Predicting enzyme adsorption to lignin films by calculating enzyme surface hydrophobicity.

Sammond DW, Yarbrough JM, Mansfield E, Bomble YJ, Hobdey SE, Decker SR, Taylor LE, Resch MG, Bozell JJ, Himmel ME, Vinzant TB, Crowley MF.

J Biol Chem. 2014 Jul 25;289(30):20960-9. doi: 10.1074/jbc.M114.573642. Epub 2014 May 29.

34.

Response to Comment on "Revealing nature's cellulase diversity: the digestion mechanism of Caldicellulosiruptor bescii CelA".

Brunecky R, Alahuhta M, Xu Q, Donohoe BS, Crowley MF, Kataeva IA, Yang SJ, Resch MG, Adams MW, Lunin VV, Himmel ME, Bomble YJ.

Science. 2014 May 9;344(6184):578. doi: 10.1126/science.1251701.

35.

Experimental and modeling studies of an unusual water-filled pore structure with possible mechanistic implications in family 48 cellulases.

Chen M, Kostylev M, Bomble YJ, Crowley MF, Himmel ME, Wilson DB, Brady JW.

J Phys Chem B. 2014 Mar 6;118(9):2306-15. doi: 10.1021/jp408767j. Epub 2014 Feb 19.

PMID:
24471470
36.

Revealing nature's cellulase diversity: the digestion mechanism of Caldicellulosiruptor bescii CelA.

Brunecky R, Alahuhta M, Xu Q, Donohoe BS, Crowley MF, Kataeva IA, Yang SJ, Resch MG, Adams MW, Lunin VV, Himmel ME, Bomble YJ.

Science. 2013 Dec 20;342(6165):1513-6. doi: 10.1126/science.1244273.

PMID:
24357319
37.

Improving activity of minicellulosomes by integration of intra- and intermolecular synergies.

Xu Q, Ding SY, Brunecky R, Bomble YJ, Himmel ME, Baker JO.

Biotechnol Biofuels. 2013 Aug 30;6(1):126. doi: 10.1186/1754-6834-6-126.

38.

Structure and function of the Clostridium thermocellum cellobiohydrolase A X1-module repeat: enhancement through stabilization of the CbhA complex.

Brunecky R, Alahuhta M, Bomble YJ, Xu Q, Baker JO, Ding SY, Himmel ME, Lunin VV.

Acta Crystallogr D Biol Crystallogr. 2012 Mar;68(Pt 3):292-9. doi: 10.1107/S0907444912001680. Epub 2012 Feb 14.

PMID:
22349231
39.

Molecular dynamics simulations of the interaction of glucose with imidazole in aqueous solution.

Chen M, Bomble YJ, Himmel ME, Brady JW.

Carbohydr Res. 2012 Feb 15;349:73-7. doi: 10.1016/j.carres.2011.12.008. Epub 2011 Dec 16.

PMID:
22248861
40.

Multiple functions of aromatic-carbohydrate interactions in a processive cellulase examined with molecular simulation.

Payne CM, Bomble YJ, Taylor CB, McCabe C, Himmel ME, Crowley MF, Beckham GT.

J Biol Chem. 2011 Nov 25;286(47):41028-35. doi: 10.1074/jbc.M111.297713. Epub 2011 Sep 29.

41.

Molecular-level origins of biomass recalcitrance: decrystallization free energies for four common cellulose polymorphs.

Beckham GT, Matthews JF, Peters B, Bomble YJ, Himmel ME, Crowley MF.

J Phys Chem B. 2011 Apr 14;115(14):4118-27. doi: 10.1021/jp1106394. Epub 2011 Mar 22.

PMID:
21425804
42.

Applications of computational science for understanding enzymatic deconstruction of cellulose.

Beckham GT, Bomble YJ, Bayer EA, Himmel ME, Crowley MF.

Curr Opin Biotechnol. 2011 Apr;22(2):231-8. doi: 10.1016/j.copbio.2010.11.005. Epub 2010 Dec 17. Review.

PMID:
21168322
43.

The O-glycosylated linker from the Trichoderma reesei Family 7 cellulase is a flexible, disordered protein.

Beckham GT, Bomble YJ, Matthews JF, Taylor CB, Resch MG, Yarbrough JM, Decker SR, Bu L, Zhao X, McCabe C, Wohlert J, Bergenstråhle M, Brady JW, Adney WS, Himmel ME, Crowley MF.

Biophys J. 2010 Dec 1;99(11):3773-81. doi: 10.1016/j.bpj.2010.10.032.

44.

Modeling the self-assembly of the cellulosome enzyme complex.

Bomble YJ, Beckham GT, Matthews JF, Nimlos MR, Himmel ME, Crowley MF.

J Biol Chem. 2011 Feb 18;286(7):5614-23. doi: 10.1074/jbc.M110.186031. Epub 2010 Nov 22.

45.

The unique binding mode of cellulosomal CBM4 from Clostridium thermocellum cellobiohydrolase A.

Alahuhta M, Xu Q, Bomble YJ, Brunecky R, Adney WS, Ding SY, Himmel ME, Lunin VV.

J Mol Biol. 2010 Sep 17;402(2):374-87. doi: 10.1016/j.jmb.2010.07.028. Epub 2010 Jul 21.

PMID:
20654622
46.

Identification of amino acids responsible for processivity in a Family 1 carbohydrate-binding module from a fungal cellulase.

Beckham GT, Matthews JF, Bomble YJ, Bu L, Adney WS, Himmel ME, Nimlos MR, Crowley MF.

J Phys Chem B. 2010 Jan 28;114(3):1447-53. doi: 10.1021/jp908810a.

PMID:
20050714
47.

The energy landscape for the interaction of the family 1 carbohydrate-binding module and the cellulose surface is altered by hydrolyzed glycosidic bonds.

Bu L, Beckham GT, Crowley MF, Chang CH, Matthews JF, Bomble YJ, Adney WS, Himmel ME, Nimlos MR.

J Phys Chem B. 2009 Aug 6;113(31):10994-1002. doi: 10.1021/jp904003z.

PMID:
19594145
48.

Multiscale modeling of nucleic acids: insights into DNA flexibility.

Bomble YJ, Case DA.

Biopolymers. 2008 Sep;89(9):722-31. doi: 10.1002/bip.21000.

49.

Factors Contributing to the Accuracy of Harmonic Force Field Calculations for Water.

Cortez MH, Brinkmann NR, Polik WF, Taylor PR, Bomble YJ, Stanton JF.

J Chem Theory Comput. 2007 Jul;3(4):1267-74. doi: 10.1021/ct600347e.

PMID:
26633200
50.

Thermochemistry of key soot formation intermediates: C3H3 isomers.

Wheeler SE, Robertson KA, Allen WD, Schaefer HF 3rd, Bomble YJ, Stanton JF.

J Phys Chem A. 2007 May 17;111(19):3819-30. Epub 2007 Apr 3.

PMID:
17402717

Supplemental Content

Loading ...
Support Center