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The hydrolysis mechanism of a GH45 cellulase and its potential relation to lytic transglycosylase and expansin function.

Bharadwaj VS, Knott BC, Ståhlberg J, Beckham GT, Crowley MF.

J Biol Chem. 2020 Feb 13. pii: jbc.RA119.011406. doi: 10.1074/jbc.RA119.011406. [Epub ahead of print]


Catalytic Mechanism of Aryl-Ether Bond Cleavage in Lignin by LigF and LigG.

Prates ET, Crowley MF, Skaf MS, Beckham GT.

J Phys Chem B. 2019 Dec 5;123(48):10142-10151. doi: 10.1021/acs.jpcb.9b06243. Epub 2019 Nov 19.


The dissociation mechanism of processive cellulases.

Vermaas JV, Kont R, Beckham GT, Crowley MF, Gudmundsson M, Sandgren M, Ståhlberg J, Väljamäe P, Knott BC.

Proc Natl Acad Sci U S A. 2019 Nov 12;116(46):23061-23067. doi: 10.1073/pnas.1913398116. Epub 2019 Oct 30.


Passive membrane transport of lignin-related compounds.

Vermaas JV, Dixon RA, Chen F, Mansfield SD, Boerjan W, Ralph J, Crowley MF, Beckham GT.

Proc Natl Acad Sci U S A. 2019 Nov 12;116(46):23117-23123. doi: 10.1073/pnas.1904643116. Epub 2019 Oct 28.


Enabling microbial syringol conversion through structure-guided protein engineering.

Machovina MM, Mallinson SJB, Knott BC, Meyers AW, Garcia-Borràs M, Bu L, Gado JE, Oliver A, Schmidt GP, Hinchen DJ, Crowley MF, Johnson CW, Neidle EL, Payne CM, Houk KN, Beckham GT, McGeehan JE, DuBois JL.

Proc Natl Acad Sci U S A. 2019 Jul 9;116(28):13970-13976. doi: 10.1073/pnas.1820001116. Epub 2019 Jun 24.


Message-passing neural networks for high-throughput polymer screening.

St John PC, Phillips C, Kemper TW, Wilson AN, Guan Y, Crowley MF, Nimlos MR, Larsen RE.

J Chem Phys. 2019 Jun 21;150(23):234111. doi: 10.1063/1.5099132.


Nanomechanics of cellulose deformation reveal molecular defects that facilitate natural deconstruction.

Ciesielski PN, Wagner R, Bharadwaj VS, Killgore J, Mittal A, Beckham GT, Decker SR, Himmel ME, Crowley MF.

Proc Natl Acad Sci U S A. 2019 May 14;116(20):9825-9830. doi: 10.1073/pnas.1900161116. Epub 2019 Apr 29.


Membrane Permeability of Terpenoids Explored with Molecular Simulation.

Vermaas JV, Bentley GJ, Beckham GT, Crowley MF.

J Phys Chem B. 2018 Nov 15;122(45):10349-10361. doi: 10.1021/acs.jpcb.8b08688. Epub 2018 Nov 1.


Different Behaviors of a Substrate in P450 Decarboxylase and Hydroxylase Reveal Reactivity-Enabling Actors.

Bharadwaj VS, Kim S, Guarnieri MT, Crowley MF.

Sci Rep. 2018 Aug 27;8(1):12826. doi: 10.1038/s41598-018-31237-4.


A promiscuous cytochrome P450 aromatic O-demethylase for lignin bioconversion.

Mallinson SJB, Machovina MM, Silveira RL, Garcia-Borràs M, Gallup N, Johnson CW, Allen MD, Skaf MS, Crowley MF, Neidle EL, Houk KN, Beckham GT, DuBois JL, McGeehan JE.

Nat Commun. 2018 Jun 27;9(1):2487. doi: 10.1038/s41467-018-04878-2.


The impact of O-glycan chemistry on the stability of intrinsically disordered proteins.

Prates ET, Guan X, Li Y, Wang X, Chaffey PK, Skaf MS, Crowley MF, Tan Z, Beckham GT.

Chem Sci. 2018 Mar 20;9(15):3710-3715. doi: 10.1039/c7sc05016j. eCollection 2018 Apr 21.


Iodine-Catalyzed Isomerization of Dimethyl Muconate.

Settle AE, Berstis L, Zhang S, Rorrer NA, Hu H, Richards RM, Beckham GT, Crowley MF, Vardon DR.

ChemSusChem. 2018 Jun 11;11(11):1768-1780. doi: 10.1002/cssc.201800606. Epub 2018 May 9.


Characterization and engineering of a plastic-degrading aromatic polyesterase.

Austin HP, Allen MD, Donohoe BS, Rorrer NA, Kearns FL, Silveira RL, Pollard BC, Dominick G, Duman R, El Omari K, Mykhaylyk V, Wagner A, Michener WE, Amore A, Skaf MS, Crowley MF, Thorne AW, Johnson CW, Woodcock HL, McGeehan JE, Beckham GT.

Proc Natl Acad Sci U S A. 2018 May 8;115(19):E4350-E4357. doi: 10.1073/pnas.1718804115. Epub 2018 Apr 17.


Structural and molecular dynamics studies of a C1-oxidizing lytic polysaccharide monooxygenase from Heterobasidion irregulare reveal amino acids important for substrate recognition.

Liu B, Kognole AA, Wu M, Westereng B, Crowley MF, Kim S, Dimarogona M, Payne CM, Sandgren M.

FEBS J. 2018 Jun;285(12):2225-2242. doi: 10.1111/febs.14472. Epub 2018 Apr 24.


Engineering enhanced cellobiohydrolase activity.

Taylor LE 2nd, Knott BC, Baker JO, Alahuhta PM, Hobdey SE, Linger JG, Lunin VV, Amore A, Subramanian V, Podkaminer K, Xu Q, VanderWall TA, Schuster LA, Chaudhari YB, Adney WS, Crowley MF, Himmel ME, Decker SR, Beckham GT.

Nat Commun. 2018 Mar 22;9(1):1186. doi: 10.1038/s41467-018-03501-8.


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.


Distinct roles of N- and O-glycans in cellulase activity and stability.

Amore A, Knott BC, Supekar NT, Shajahan A, Azadi P, Zhao P, Wells L, Linger JG, Hobdey SE, Vander Wall TA, Shollenberger T, Yarbrough JM, Tan Z, Crowley MF, Himmel ME, Decker SR, Beckham GT, Taylor LE 2nd.

Proc Natl Acad Sci U S A. 2017 Dec 26;114(52):13667-13672. doi: 10.1073/pnas.1714249114. Epub 2017 Dec 11.


Membrane Permeability of Fatty Acyl Compounds Studied via Molecular Simulation.

Vermaas JV, Beckham GT, Crowley MF.

J Phys Chem B. 2017 Dec 21;121(50):11311-11324. doi: 10.1021/acs.jpcb.7b08233. Epub 2017 Nov 1.


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.


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.


Who's on base? Revealing the catalytic mechanism of inverting family 6 glycoside hydrolases.

Mayes HB, Knott BC, Crowley MF, Broadbelt LJ, Ståhlberg J, Beckham GT.

Chem Sci. 2016 Sep 1;7(9):5955-5968. doi: 10.1039/c6sc00571c. Epub 2016 Jun 1.


Coupling and Reactions of 5-Hydroxyconiferyl Alcohol in Lignin Formation.

Elder T, Berstis L, Beckham GT, Crowley MF.

J Agric Food Chem. 2016 Jun 15;64(23):4742-50. doi: 10.1021/acs.jafc.6b02234. Epub 2016 Jun 3.


Simulations of cellulose translocation in the bacterial cellulose synthase suggest a regulatory mechanism for the dimeric structure of cellulose.

Knott BC, Crowley MF, Himmel ME, Zimmer J, Beckham GT.

Chem Sci. 2016 May 1;7(5):3108-3116. Epub 2016 Jan 29.


Comparison of the simulations of cellulosic crystals with three carbohydrate force fields.

Miyamoto H, Schnupf U, Crowley MF, Brady JW.

Carbohydr Res. 2016 Mar 3;422:17-23. doi: 10.1016/j.carres.2016.01.001. Epub 2016 Jan 11.


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.


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.


Electronic coupling through natural amino acids.

Berstis L, Beckham GT, Crowley MF.

J Chem Phys. 2015 Dec 14;143(22):225102. doi: 10.1063/1.4936588.


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.


O-glycosylation effects on family 1 carbohydrate-binding module solution structures.

Happs RM, Guan X, Resch MG, Davis MF, Beckham GT, Tan Z, Crowley MF.

FEBS J. 2015 Nov;282(22):4341-56. doi: 10.1111/febs.13500. Epub 2015 Sep 21.


The molecular origins of twist in cellulose I-beta.

Bu L, Himmel ME, Crowley MF.

Carbohydr Polym. 2015 Jul 10;125:146-52. doi: 10.1016/j.carbpol.2015.02.023. Epub 2015 Feb 21.


Effects of lytic polysaccharide monooxygenase oxidation on cellulose structure and binding of oxidized cellulose oligomers to cellulases.

Vermaas JV, Crowley MF, Beckham GT, Payne CM.

J Phys Chem B. 2015 May 21;119(20):6129-43. doi: 10.1021/acs.jpcb.5b00778. Epub 2015 Apr 2.


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.


Carbohydrate-protein interactions that drive processive polysaccharide translocation in enzymes revealed from a computational study of cellobiohydrolase processivity.

Knott BC, Crowley MF, Himmel ME, Ståhlberg J, Beckham GT.

J Am Chem Soc. 2014 Jun 18;136(24):8810-9. doi: 10.1021/ja504074g. Epub 2014 Jun 6.


Towards a molecular-level theory of carbohydrate processivity in glycoside hydrolases.

Beckham GT, Ståhlberg J, Knott BC, Himmel ME, Crowley MF, Sandgren M, Sørlie M, Payne CM.

Curr Opin Biotechnol. 2014 Jun;27:96-106. doi: 10.1016/j.copbio.2013.12.002. Epub 2014 Jan 4. Review.


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.


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.


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.


The mechanism of cellulose hydrolysis by a two-step, retaining cellobiohydrolase elucidated by structural and transition path sampling studies.

Knott BC, Haddad Momeni M, Crowley MF, Mackenzie LF, Götz AW, Sandgren M, Withers SG, Ståhlberg J, Beckham GT.

J Am Chem Soc. 2014 Jan 8;136(1):321-9. doi: 10.1021/ja410291u. Epub 2013 Dec 16.


New faster CHARMM molecular dynamics engine.

Hynninen AP, Crowley MF.

J Comput Chem. 2014 Feb 15;35(5):406-13. doi: 10.1002/jcc.23501. Epub 2013 Dec 2.


Glycoside hydrolase processivity is directly related to oligosaccharide binding free energy.

Payne CM, Jiang W, Shirts MR, Himmel ME, Crowley MF, Beckham GT.

J Am Chem Soc. 2013 Dec 18;135(50):18831-9. doi: 10.1021/ja407287f. Epub 2013 Dec 5.


Irreversible transformations of native celluloses, upon exposure to elevated temperatures.

Atalla RS, Crowley MF, Himmel ME, Atalla RH.

Carbohydr Polym. 2014 Jan 16;100:2-8. doi: 10.1016/j.carbpol.2013.06.007. Epub 2013 Jun 15.


Loop motions important to product expulsion in the Thermobifida fusca glycoside hydrolase family 6 cellobiohydrolase from structural and computational studies.

Wu M, Bu L, Vuong TV, Wilson DB, Crowley MF, Sandgren M, Ståhlberg J, Beckham GT, Hansson H.

J Biol Chem. 2013 Nov 15;288(46):33107-17. doi: 10.1074/jbc.M113.502765. Epub 2013 Sep 30.


3D electron tomography of pretreated biomass informs atomic modeling of cellulose microfibrils.

Ciesielski PN, Matthews JF, Tucker MP, Beckham GT, Crowley MF, Himmel ME, Donohoe BS.

ACS Nano. 2013 Sep 24;7(9):8011-9. doi: 10.1021/nn4031542. Epub 2013 Sep 4.


Endoglucanase peripheral loops facilitate complexation of glucan chains on cellulose via adaptive coupling to the emergent substrate structures.

Lin Y, Beckham GT, Himmel ME, Crowley MF, Chu JW.

J Phys Chem B. 2013 Sep 19;117(37):10750-8. doi: 10.1021/jp405897q. Epub 2013 Sep 9.


Glycosylated linkers in multimodular lignocellulose-degrading enzymes dynamically bind to cellulose.

Payne CM, Resch MG, Chen L, Crowley MF, Himmel ME, Taylor LE 2nd, Sandgren M, Ståhlberg J, Stals I, Tan Z, Beckham GT.

Proc Natl Acad Sci U S A. 2013 Sep 3;110(36):14646-51. doi: 10.1073/pnas.1309106110. Epub 2013 Aug 19.


Binding site dynamics and aromatic-carbohydrate interactions in processive and non-processive family 7 glycoside hydrolases.

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

J Phys Chem B. 2013 May 2;117(17):4924-33. doi: 10.1021/jp401410h. Epub 2013 Apr 10.


Crystal structure and computational characterization of the lytic polysaccharide monooxygenase GH61D from the Basidiomycota fungus Phanerochaete chrysosporium.

Wu M, Beckham GT, Larsson AM, Ishida T, Kim S, Payne CM, Himmel ME, Crowley MF, Horn SJ, Westereng B, Igarashi K, Samejima M, Ståhlberg J, Eijsink VG, Sandgren M.

J Biol Chem. 2013 May 3;288(18):12828-39. doi: 10.1074/jbc.M113.459396. Epub 2013 Mar 22.


Computational investigation of the pH dependence of loop flexibility and catalytic function in glycoside hydrolases.

Bu L, Crowley MF, Himmel ME, Beckham GT.

J Biol Chem. 2013 Apr 26;288(17):12175-86. doi: 10.1074/jbc.M113.462465. Epub 2013 Mar 15.


Initial recognition of a cellodextrin chain in the cellulose-binding tunnel may affect cellobiohydrolase directional specificity.

Ghattyvenkatakrishna PK, Alekozai EM, Beckham GT, Schulz R, Crowley MF, Uberbacher EC, Cheng X.

Biophys J. 2013 Feb 19;104(4):904-12. doi: 10.1016/j.bpj.2012.12.052.


Cellulase linkers are optimized based on domain type and function: insights from sequence analysis, biophysical measurements, and molecular simulation.

Sammond DW, Payne CM, Brunecky R, Himmel ME, Crowley MF, Beckham GT.

PLoS One. 2012;7(11):e48615. doi: 10.1371/journal.pone.0048615. Epub 2012 Nov 6.

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