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1. Site-directed spin labeling-electron paramagnetic resonance spectroscopy in biocatalysis: Enzyme orientation and dynamics in nanoscale confinement

   https://doi.org/https://doi.org/10.1016/j.checat.2021.03.005  

   Pan, Y. ; Li, H. ; Li, Q. ; Lenertz, M. ; Zhu, X. ; Chen, B. ; Yang, Z. ( April 2021 , Chem catalysis)

   null (Ed.)

   Site-directed spin labeling (SDSL) in combination with electron paramagnetic resonance (EPR) spectroscopy probes the otherwise inaccessible structural information in complex biological systems. We recently extended SDSL-EPR to reveal the relative orientation and backbone dynamics of enzymes upon encapsulation in mesoporous nanostructures, which set the structural basis underlying the observed biocatalytic activity. Our strategy had generated interest in the biocatalysis community, and thus in this resource article, we contribute an introduction to the principles and experimental procedure that generalize SDSL-EPR to heterogeneous biocatalysis. We will focus on enzymes in mesoporous materials with examples demonstrating the methods and cautions of potential pitfalls. The ultimate goal is to provide the biocatalysis community with a powerful resource to fill in a long-standing knowledge gap in heterogeneous biocatalysis and the structure-function relationship of enzymes at the interface of enzyme-mesoporous materials and utilize the structural insights to guide the rational design of porous platforms for enzyme immobilization. 

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2. Enzyme purification and sustained enzyme activity for pharmaceutical biocatalysis by fusion with phase‐separating intrinsically disordered protein

   https://doi.org/10.1002/bit.28787  

   Li, Xinyi ; Kuchinski, Liam_M ; Park, Augene ; Murphy, Grant_S ; Soto, Karla_Camacho ; Schuster, Benjamin_S ( July 2024 , Biotechnology and Bioengineering)

   In recent decades, biocatalysis has emerged as an important alternative to chemical catalysis in pharmaceutical manufacturing. Biocatalysis is attractive because enzymatic cascades can synthesize complex molecules with incredible selectivity, yield, and in an environmentally benign manner. Enzymes for pharmaceutical biocatalysis are typically used in their unpurified state, since it is time‐consuming and cost‐prohibitive to purify enzymes using conventional chromatographic processes at scale. However, impurities present in crude enzyme preparations can consume substrate, generate unwanted byproducts, as well as make the isolation of desired products more cumbersome. Hence, a facile, nonchromatographic purification method would greatly benefit pharmaceutical biocatalysis. To address this issue, here we have captured enzymes into membraneless compartments by fusing enzymes with an intrinsically disordered protein region, the RGG domain from LAF‐1. The RGG domain can undergo liquid–liquid phase separation, forming liquid condensates triggered by changes in temperature or salt concentration. By centrifuging these liquid condensates, we have successfully purified enzyme‐RGG fusions, resulting in significantly enhanced purity compared to cell lysate. Furthermore, we performed enzymatic reactions utilizing purified fusion proteins to assay enzyme activity. Results from the enzyme assays indicate that enzyme‐RGG fusions purified by the centrifugation method retain enzymatic activity, with greatly reduced background activity compared to crude enzyme preparations. Our work focused on three different enzymes—a kinase, a phosphorylase, and an ATP‐dependent ligase. The kinase and phosphorylase are components of the biocatalytic cascade for manufacturing molnupiravir, and we demonstrated facile co‐purification of these two enzymes by co‐phase separation. To conclude, enzyme capture by RGG tagging promises to overcome difficulties in bioseparations and biocatalysis for pharmaceutical synthesis.

    

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3. One-pot synthesis of enzyme@metal–organic material (MOM) biocomposites for enzyme biocatalysis

   https://doi.org/DOI https://doi.org/10.1039/D1GC00775K  

   Pan, Y. ; Li, H. ; Lenertz, M. ; Han, Y. ; Ugrinov, A. ; Kilin, D. ; Chen, B. ; Yang, Z. ( March 2021 , Green chemistry)

   null (Ed.)

   Metal–organic frameworks/materials (MOFs/MOMs) are advanced enzyme immobilization platforms that improve biocatalysis, materials science, and protein biophysics. A unique way to immobilize enzymes is co-crystallization/co-precipitation, which removes the limitation on enzyme/substrate size. Thus far, most enzyme@MOF composites rely on the use of non-sustainable chemicals and, in certain cases, heavy metals, which not only creates concerns regarding environmental conservation but also limits their applications in nutrition and biomedicine. Here, we show that a dimeric compound derived from lignin, 5,5′-dehydrodivanillate (DDVA), co-precipitates with enzymes and low-toxicity metals, Ca2+ and Zn2+, and forms stable enzyme@Ca/Zn–MOM composites. We demonstrated this strategy on four enzymes with different isoelectric points (IEPs), molecular weights, and substrate sizes. Furthermore, we found that all enzymes displayed slightly different but reasonable catalytic efficiencies upon immobilization in the Ca–DDVA and Zn–DDVA MOMs, as well as reasonable reusability in both composites. We then probed the structural basis of such differences using a representative enzyme and found enhanced restriction of enzymes in Zn–DDVA than in Ca–DDVA, which might have caused the activity difference. To the best of our knowledge, this is the first aqueous-phase, one-pot synthesis of a lignin-derived “green” enzyme@MOF/MOM platform that can host enzymes without any limitations on enzyme IEP, molecular weight, and substrate size. The different morphologies and crystallinities of the composites formed by Ca–DDVA and Zn–DDVA MOMs broaden their applications depending on the problem of interest. Our approach of enzyme immobilization not only improves the sustainability/reusability of almost all enzymes but also reduces/eliminates the use of non-sustainable resources. This synthesis method has a negligible environmental impact while the products are non-toxic to living things and the environment. The biocompatibility also makes it possible to carry out enzyme delivery/release for nutritional or biomedical applications via our “green” biocomposites. 

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4. Protein Mediated Enzyme Immobilization

   https://doi.org/10.1002/smll.202106425  

   Caparco, Adam A. ; Dautel, Dylan R. ; Champion, Julie A. ( February 2022 , Small)

   Enzyme immobilization is an essential technology for commercializing biocatalysis. It imparts stability, recoverability, and other valuable features that improve the effectiveness of biocatalysts. While many avenues to join an enzyme to solid phases exist, protein‐mediated immobilization is rapidly developing and has many advantages. Protein‐mediated immobilization allows for the binding interaction to be genetically coded, can be used to create artificial multienzyme cascades, and enables modular designs that expand the variety of enzymes immobilized. By designing around binding interactions between protein domains, they can be integrated into functional materials for protein immobilization. These materials are framed within the context of biocatalytic performance, immobilization efficiency, and stability of the materials. In this review, supports composed entirely of protein are discussed first, with systems such as cellulosomes and protein cages being discussed alongside newer technologies like spore‐based biocatalysts and forizymes. Protein‐composite materials such as polymersomes and protein–inorganic supraparticles are then discussed to demonstrate how protein‐mediated strategies are applied to many classes of solid materials. Critical analysis and future directions of protein‐based immobilization are then discussed, with a particular focus on both computational and design strategies to advance this area of research and make it more broadly applicable to many classes of enzymes.

    

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5. In situ monitoring of protein transfer into nanoscale channels

   https://doi.org/doi.org/10.1016/j.xcrp.2021.100576  

   Pan, Y. ; Wang, X. ; Li, H. ; Ren, J. ; Zhang, Y. ; Jordahl, D. ; Schuster, I. ; Farmakes, J. ; Hong, H. ; Yang, Z. ; et al ( September 2021 , Cell reports physical science)

   null (Ed.)

   Protein transfer into nanoscale compartments is critical for many cellular/life processes, yet there are few reports on how compartment properties impact the protein orientation during a transfer. Such a knowledge gap limits a deeper understanding of the protein transfer mechanism, which could be bridged using nanoporous materials. Here, we use a mesoporous silica, a covalent organic framework, and a metal-organic framework with charged, hydrophobic, and neutral surfaces, respectively, to elucidate the impact of channel properties on the transfer of a model protein, lysozyme. Using site-directed spin labeling and time-resolved electron paramagnetic resonance spectroscopy, we reveal that the transfer can be a multi-step process depending on channel properties and depict the relative orientation changes of lysozyme upon transfer into each channel. To the best of our knowledge, this is the first structural insight into protein orientation upon transfer into different compartments, meaningful for the rational design of synthetic materials to host enzymes or mimic the cellular compartments. 

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