Physical constraints and functional plasticity of cellulases

Kari, Jeppe; Molina, Gustavo A.; Schaller, Kay; Schiano‐di‐Cola, Corinna; Christensen, Stefan Jarl; Badino, Silke Flindt; Sørensen, Trine Holst; Røjel, Nanna Sandager; Keller, Malene B.; Sørensen, Nanna Rolsted; Kołaczkowski, Bartłomiej M; Olsen, Johan P.; Krogh, Kristian B. R. M.; Jensen, Kenneth; Cavaleiro, Ana Mafalda; Peters, Günther H.J.; Spodsberg, Nikolaj; Borch, Kim

doi:10.1038/s41467-021-24075-y

Cited by 27 publications

(52 citation statements)

References 65 publications

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“…21 This type of tradeoff between binding strength and rate is well-known within inorganic, heterogeneous catalysis, and was originally coined as the Sabatier principle, which states that efficient catalysis occurs when the catalyst binds its reactant with intermediate strength. 22,23 The Sabatier principle has recently proven useful for predicting and rationalizing catalytic properties of cellulases 24,25 and as a guide for computer-aided enzyme design and discovery. 26…”

Section: Introductionmentioning

confidence: 99%

Sabatier principle for rationalizing enzymatic hydrolysis of a synthetic polyester

Bååth

Jensen

Borch

et al. 2022

Preprint

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Interfacial enzyme reactions are common in nature and in industrial settings, including the enzymatic deconstruction of poly(ethylene terephthalate) (PET) waste. Kinetic descriptions of PET hydrolases are necessary for both comparative analyses, discussions of structure-function relations and rational optimization of technical processes. We investigated whether the Sabatier principle could be used for this purpose. Specifically, we compared the kinetics of two well-known PET hydrolases, leaf-branch compost cutinase (LCC) and a cutinase from the bacterium T. fusca (TfC) when adding different concentrations of the surfactant cetyltrimethylammonium bromide (CTAB). We found that CTAB consistently lowered the strength of enzyme-PET interactions, while its effect on enzymatic turnover was strongly biphasic. Thus, at gradually increasing CTAB concentrations, turnover was initially promoted and subsequently suppressed. This correlation with maximal turnover at an intermediate binding strength is in accordance with the Sabatier principle. One consequence of these results is that both enzymes had too strong intrinsic interaction with PET for optimal turnover, especially TfC, which showed a 20-fold improvement of kcat at the maximum. LCC on the other hand had an intrinsic substrate affinity closer to the Sabatier optimum and the turnover rate was 5-fold improved at weakened substrate binding. Our results show that the Sabatier principle may indeed rationalize enzymatic PET degradation and support process optimization. Finally, we suggest that future discovery efforts should consider enzymes with weakened substrate binding, since strong adsorption seems to limit their catalytic performance.

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Section: Introductionmentioning

confidence: 99%

Sabatier principle for rationalizing enzymatic hydrolysis of a synthetic polyester

Bååth

Jensen

Borch

et al. 2022

Preprint

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“…100 cellulases with experimental binding values. 3 For a more efficient training, all binding energies were linearly scaled with a minimum value of −13 kJ/mol and a maximum value of 17 kJ/mol, resulting in values well between 0-1 for all datasets.…”

Section: Experimental Procedures Data Set and Data Curationmentioning

confidence: 99%

“…It is known that the residues W38 and W40 are critical for binding and that their mutation to alanine leads to a drastic decrease in binding energy. 3,19 Software The deep learning model was built with Tensorflow (2.4) using python (3.8.11), CUDA (11.3), scikit-learn (0.24.2). 20,21 The module 3D-GuidedGradCAM was used to perform guided back-propagation.…”

Section: Transfer-learning For Classification Modelmentioning

confidence: 99%

“…2 Previous work showed that the binding of the whole complex could be approximated by the binding of the CD towards a threaded chain and binding of the CBM on the crystalline surface (right). [3][4][5] Cellulases are typically modular, consisting of a catalytic domain (CD) and a carbohydratebinding module (CBM) connected by a flexible linker (see Fig. 1).…”

Section: Introductionmentioning

confidence: 99%

“…1). [3][4][5] This simplifies the setup drastically, as crystal structures of the CD in complex with threaded substrate exists and the interactions of the CBM towards the crystal surface are well studied. 2 Building up on this approximation, we recently proposed a cheap computational method based on molecular dynamics (MD) simulation.…”

Section: Introductionmentioning

confidence: 99%

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Binding prediction of multi-domain cellulases with a dual-CNN

Schaller¹,

Kari²,

Borch³

et al. 2022

Preprint

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Cellulases hold great promise for the production of biofuels and biochemicals. However, they are modular enzymes acting on a complex heterogeneous substrate. Because of this complexity, the computational prediction of their catalytic properties remains scarce, which restricts both enzyme discovery and enzyme design. Here, we present a dual-input convolutional neural network to predict the binding of multi-domain enzymes. This regression model outperformed previous molecular dynamics-based methods for binding prediction for cellulases in a fraction of the time. Also, we show that when changed to a classification problem, the same network can be back-propagated to suggest mutations to improve enzyme binding. A similar approach could increase our understanding of the structure-activity relationship of enzymes, and suggest new promising mutations for enzyme design using explainable artificial intelligence.

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Rationalizing the Influence of the Binding Affinity on the Activity of Phosphoserine Phosphatases

Chiba,

Ooka,

Wintzer

et al. 2024

Angewandte Chemie

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The Sabatier principle states that catalytic activity can be maximized when the substrate binding affinity is neither too strong nor too weak. Recent studies have shown that the activity of several hydrolases is maximized at intermediate values of the binding affinity (Michaelis–Menten constant: Km). However, it remains unclear whether this concept of artificial catalysis is applicable to enzymes in general, especially for those which have evolved under different reaction environments. Herein, we show that the activity of phosphoserine phosphatase is also enhanced at an intermediate Km value of approximately 0.5 mM. Within our dataset, the variation of Km by three orders of magnitude accounted for a roughly 18‐fold variation in the activity. Owing to the high phylogenetic and physiological diversity of our dataset, our results support the importance of optimizing Km for enzymes in general. On the other hand, a 77‐fold variation in the activity was attributed to other physicochemical parameters, such as the Arrhenius prefactor of kcat, and could not be explained by the Sabatier principle. Therefore, while tuning the binding affinity according to the Sabatier principle is an important consideration, the Km value is only one of many physicochemical parameters which must be optimized to maximize enzymatic activity.

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Physical constraints and functional plasticity of cellulases

Cited by 27 publications

References 65 publications

Sabatier principle for rationalizing enzymatic hydrolysis of a synthetic polyester

Sabatier principle for rationalizing enzymatic hydrolysis of a synthetic polyester

Binding prediction of multi-domain cellulases with a dual-CNN

Rationalizing the Influence of the Binding Affinity on the Activity of Phosphoserine Phosphatases

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