The interplay of descriptor-based computational analysis with pharmacophore modeling builds the basis for a novel classification scheme for feruloyl esterases

One of the most intriguing groups of enzymes, the feruloyl esterases (FAEs), is ubiquitous in both simple and complex organisms. FAEs have gained importance in biofuel, medicine and food industries due to their capability of acting on a large range of substrates for cleaving ester bonds and synthesizing high-added value molecules through esterification and transesterification reactions. During the past two decades extensive studies have been carried out on the production and partial characterization of FAEs from fungi, while much less is known about FAEs of bacterial or plant origin. Initial classification studies on FAEs were restricted on sequence similarity and substrate specificity on just four model substrates and considered only a handful of FAEs belonging to the fungal kingdom. This study centers on the descriptor-based classification and structural analysis of experimentally verified and putative FAEs; nevertheless, the framework presented here is applicable to every poorly characterized enzyme family. 365 FAE-related sequences of fungal, bacterial and plantae origin were collected and they were clustered using Self Organizing Maps followed by k-means clustering into distinct groups based on amino acid composition and physico-chemical composition descriptors derived from the respective amino acid sequence. A Support Vector Machine model was subsequently constructed for the classification of new FAEs into the pre-assigned clusters. The model successfully recognized 98.2% of the training sequences and all the sequences of the blind test. The underlying functionality of the 12 proposed FAE families was validated against a combination of prediction tools and published experimental data. Another important aspect of the present work involves the development of pharmacophore models for the new FAE families, for which sufficient information on known substrates existed. Knowing the pharmacophoric features of a small molecule that are essential for binding to the members of a certain family opens a window of opportunities for tailored applications of FAEs

Immobilization of feruloyl esterases in mesoporous silica

Mesoporous silica materials have become popular as immobilization support for enzymes due to advantages such as high protein loading capacity and enhanced enzyme activity because of confinement into pores. Immobilization of enzymes is often required for sufficient enzyme stability and to enable recovery in industrially feasible and efficient processes. Feruloyl esterases is a class of enzymes used in biocatalysis for refinement of hydroxycinnamic acids. These compounds have shown to have antioxidant and antibacterial properties, though modification of solubility is necessary for the compounds to be of interest in different commercial products. Previous work has showed that mesoporous silica is a robust immobilization support for feruloyl esterases and that transesterification activity was favored over hydrolysis. Immobilization of feruloyl esterases (FoFAEC) in SBA-15 mesoporous silica showed to be highly affected by pH. Testing the immobilized enzymes for transesterification of methyl ferulate to butyl ferulate showed that the specific activity was affected by the pH at which the enzymes had been immobilized. Consequently there is a pH memory effect, which could be reverted by subsequent washing with a buffer of different pH. The current work involves testing a pH probe bound to the enzyme which will give information of the microenvironment pH close to the enzyme. Additionally, an in silico model of FoFAEC has been developed so that the dimensions of the enzyme can be related to the pore size. The model will also be used to simulate the enzyme structure at different pH, predict orientation and adsorption behavior. The aim is to understand how mesoporous materials can be used to alter the enzymatic activity upon immobilization and in the end develop improved feruloyl esterase biocatalysts that allow customization of the antioxidant properties of hydroxycinnamic acids

Understanding the pH-dependent immobilization efficacy of feruloyl esterase-C on mesoporous silica and its structure activity changes

The purpose of the present investigation was to study the pH dependence of both the immobilization process and the enzyme activity of a feruloyl esterase (FoFaeC from Fusarium oxysporum) immobilized in mesoporous silica. This was done by interpreting experimental results with theoretical molecular modeling of the enzyme structure. Modeling of the 3D structure of the enzyme together with calculations of the electrostatic surface potential showed that changes in the electrostatic potential of the protein surface were correlated with the pH dependence of the immobilization process. High immobilization yields were associated with an increase in pH. The transesterification activity of both immobilized and free enzyme was studied at different values of pH and the optimal pH of the immobilized enzyme was found to be one unit lower than that for the free enzyme. The surface charge distribution around the binding pocket was identified as being a crucial factor for the accessibility of the active site of the immobilized enzyme, indicating that the orientation of the enzyme inside the pores is pH dependent. Interestingly, it was observed that the immobilization pH affects the specific activity, irrespective of the changes in reaction pH. This was identified as a pH memory effect for the immobilized enzyme. On the other hand, a change in product selectivity of the immobilized enzyme was also observed when the transesterification reaction was run in MOPS buffer instead of citrate phosphate buffer. Molecular docking studies revealed that the MOPS buffer molecule can bind to the enzyme binding pocket, and can therefore be assumed to modulate the product selectivity of the immobilized enzyme toward transesterification

Structure and function of a CE4 deacetylase isolated from a marine environment

Chitin, a polymer of β(1–4)-linked N-acetylglucosamine found in e.g. arthropods, is a valuable resource that may be used to produce chitosan and chitooligosaccharides, two compounds with considerable industrial and biomedical potential. Deacetylating enzymes may be used to tailor the properties of chitin and its derived products. Here, we describe a novel CE4 enzyme originating from a marine Arthrobacter species (ArCE4A). Crystal structures of this novel deacetylase were determined, with and without bound chitobiose [(GlcNAc)2], and refined to 2.1 Å and 1.6 Å, respectively. In-depth biochemical characterization showed that ArCE4A has broad substrate specificity, with higher activity against longer oligosaccharides. Mass spectrometry-based sequencing of reaction products generated from a fully acetylated pentamer showed that internal sugars are more prone to deacetylation than the ends. These enzyme properties are discussed in the light of the structure of the enzyme-ligand complex, which adds valuable information to our still rather limited knowledge on enzyme-substrate interactions in the CE4 family