How endoglucanase enzymes act on cellulose nanofibrils: role of amorphous regions revealed by atomistic simulations

Orłowski, Adam; Paavilainen, Sami; Manna, Moutusi; Heiskanen, Isto; Backfolk, Kaj; Timonen, J.; Vattulainen, Ilpo

doi:10.1007/s10570-015-0705-0

Cited by 27 publications

(21 citation statements)

References 56 publications

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“…This includes studies on the crystal structure of cellulose microfibrils (Matthews et al 2006;Wada et al 2011;Oehme et al 2015bOehme et al , 2018, and, as mentioned before, various aspects of the microfibril twist (Yui et al 2006;Matthews et al 2006;Yui and Hayashi 2007;Paavilainen et al 2011;Hadden et al 2013;Bu et al 2015;Conley et al 2016;Kannam et al 2017). Other studies have looked at the interactions of microfibrils with water (Yui et al 2006;Bergenstråhle et al 2008;Maurer et al 2013;Kulasinski et al 2015Kulasinski et al , 2017Lindh et al 2016;O'Neill et al 2017), their response to elevated temperatures (Matthews et al 2011(Matthews et al , 2012bZhang et al 2011); their mechanical properties (Paavilainen et al 2012;Saitoh et al 2013;Molnár et al 2018), aggregation and disintegration (Oehme et al 2015a;Paajanen et al 2016;Silveira et al 2016), chemical modification (Wada et al 2011;Paajanen et al 2016), enzymatic degradation (Beckham et al 2011;Orłowski et al 2015), and dissolution in ionic liquids (Gross et al 2011;Uto et al 2018); the pyrolytic degradation of cellulose (Zheng et al 2016;Paajanen and Vaari 2017); and radiation-induced defects (Polvi et al 2012;…”

Section: Computationalmentioning

confidence: 99%

Chirality and bound water in the hierarchical cellulose structure

et al. 2019

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The origins of the unique properties of natural fibres have remained largely unresolved because of the complex interrelations between structural hierarchy, chirality and bound water. In this paper, analysis of the melting endotherms for bleached hardwood pulps indicates that the amount of nonfreezing bound water (0.21 g/g) is roughly half of the amount of freezing bound water (0.42 g/g). We link this result to the two smallest constitutive units, microfibrils and their bundles, using molecular dynamics simulations at both hierarchical levels. The molecular water layers found in the simulations correspond quite accurately to the measured amount of non-freezing and freezing bound water. Disorder that results from the microfibril twist and amphiphilicity prevents co-crystallisation, leaving routes for water molecules to diffuse inside the microfibril bundle. Moreover, the simulations predict correctly the magnitude of the right-handed twist at different hierarchical levels. Significant changes in hydroxymethyl group conformations are seen during twisting that compare well with existing experimental data. Our findings go beyond earlier modelling studies in predicting the twist and structure of the microfibril bundle.

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Section: Computationalmentioning

confidence: 99%

Chirality and bound water in the hierarchical cellulose structure

et al. 2019

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“…We used molecular dynamics (MD) simulations to study the structure, dynamics, and cellulose-binding energetics of a family-III carbohydrate-binding module (CBM3a) 46 from the cellulosomal scaffoldin subunit of Clostridium thermocellum, and of expansin (EXLX1) 41 from Bacillus subtilis. The interactions of these proteins with cellulose were studied by introducing them into two distinct cellulose environments: the crystalline form type Iβ surface [47][48][49] consisting of three layers of cellulose, and nanocellulose fibres with two distinct non-crystalline regions 50 . CBMs can bind to different types of cellulose 24 , including crystalline and amorphous cellulose 78,79 .…”

Section: Computational Models (A) Overview Of the Simulated Complexesmentioning

confidence: 99%

“…Cellulose nanofibers were created from crystalline Iβ with amorphous regions 50 . We created one type of amorphous cellulose model (abbreviated as -aI)…”

Section: (B) Cellulose Modelsmentioning

confidence: 99%

“…The OPLS all-atom force field was used to describe all molecules 61 in the simulations with amorphous cellulose, and water was modelled using the TIP3P variant that is compatible with the OPLS parameterization , similar to the protocol used to model cellulase binding to cellulose nanofibrils in earlier work 50,54,63 .…”

Section: Simulation Protocols (A) Atomistic Molecular Dynamics Simulamentioning

confidence: 99%

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On the distinct binding modes of expansin and carbohydrate-binding module proteins on crystalline and nanofibrous cellulose: implications for cellulose degradation by designer cellulosomes

Orłowski

Artzi

Cazade

et al. 2018

Phys. Chem. Chem. Phys.

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Transformation of cellulose into monosaccharides can be achieved by hydrolysis of the cellulose chains, carried out by a special group of enzymes known as cellulases. The enzymatic mechanism of cellulases is well described, but the role of non-enzymatic components of the cellulose-degradation machinery is still poorly understood, and difficult to measure using experiments alone. In this study, we use a comprehensive set of atomistic molecular dynamics simulations to probe the molecular details of binding of the family-3a carbohydrate-binding module (CBM3a) and the bacterial expansin protein (EXLX1) to a range of cellulose substrates. Our results suggest that CBM3a behaves in a similar way on both crystalline and amorphous cellulose, whereas binding of the dual-domain expansin protein depends on the substrate crystallinity, and we relate our computed binding modes to the experimentally measured features of CBM and expansin action on cellulose.

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“…There are three kinds of cellulase for hydrolysis of cellulose by synergistic action: endo-b-1,4-glucanase; exo-b-1,4-glucanase; b-glucosidases [23]. Endo-b-1,4-glucanase hydrolyzes internal glycosidic bonds in cellulose with a random, on-off fashion [24,25]. And the catalytic mechanism of endo-b-1,4-glucanase was believed to consist of two reaction steps involving glycosylation and deglycosylation steps [26,27].…”

Section: Introductionmentioning

confidence: 99%

Effective Cleavage of β-1,4-Glycosidic Bond by Functional Micelle with l-Histidine Residue

Liao¹,

Liu

Xiao³

et al. 2016

Catal Lett

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A novel functional surfactant N a -dodecyl-Lhistidine (NDH) was synthesized and its micelle was used as mimic of b-1,4-endoglucanase to catalyzed the hydrolysis of methyl-b-D-cellobioside (MCB) under relatively low temperatures (80-110°C). The results showed that the micelle of NDH displayed excellent catalytic activity for the cleavage of b-1,4-glycosidic bond and the formation ofThe micelle-catalyzed first-order reaction rate constant k m of degradation of MCB was calculated. The conversion of MCB and selectivity of reducing sugars (glucose and fructose) could reach 58.9 and 87.1 %, respectively, for a reaction time of 10 h at pH 4.0 and 110°C. In NDH micelle-catalyzed reaction sugar ester was deduced as the chief product. The reaction pathways of MCB hydrolysis were proposed and the activation energy Ea for the hydrolysis was calculated. Graphical AbstractO OCR OH OH HO HO pH4.0, 90 o C Selectivity>97% O O OH OH HO HO O OH OH OCH 3 HO Glucose Fructose + p H 1 2 . 0 , 2 5 o C O N N H NH HOOC C 12 H 25

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How endoglucanase enzymes act on cellulose nanofibrils: role of amorphous regions revealed by atomistic simulations

Cited by 27 publications

References 56 publications

Chirality and bound water in the hierarchical cellulose structure

Chirality and bound water in the hierarchical cellulose structure

On the distinct binding modes of expansin and carbohydrate-binding module proteins on crystalline and nanofibrous cellulose: implications for cellulose degradation by designer cellulosomes

Effective Cleavage of β-1,4-Glycosidic Bond by Functional Micelle with l-Histidine Residue

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