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- Crnjar, Alessandro, et al.
(author)
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Conformational Selection of a Tryptophan Side Chain Drives the Generalized Increase in Activity of PET Hydrolases through a Ser/Ile Double Mutation
- 2023
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In: ACS ORGANIC & INORGANIC AU. - : American Chemical Society (ACS). - 2694-247X. ; 3:2, s. 109-119
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Journal article (peer-reviewed)abstract
- Poly(ethylene terephthalate) (PET) is the most common polyester plastic in the packaging industry and a major source of environmental pollution due to its single use. Several enzymes, termed PET hydrolases, have been found to hydrolyze this polymer at different temperatures, with the enzyme from Ideonella sakaiensis (IsPETase) having optimal catalytic activity at 30-35 degrees C. Crystal structures of IsPETase have revealed that the side chain of a conserved tryptophan residue within an active site loop (W185) shifts between three conformations to enable substrate binding and product release. This is facilitated by two residues unique to IsPETase, S214 and I218. When these residues are inserted into other PET hydrolases in place of the otherwise strictly conserved histidine and phenylalanine residues found at their respective positions, they enhance activity and decrease Topt. Herein, we combine molecular dynamics and well-tempered metadynamics simulations to investigate dynamic changes of the S214/I218 and H214/F218 variants of IsPETase, as well as three other mesophilic and thermophilic PET hydrolases, at their respective temperature and pH optima. Our simulations show that the S214/I218 insertion both increases the flexibility of active site loop regions harboring key catalytic residues and the conserved tryptophan and expands the conformational plasticity of this tryptophan side chain, enabling the conformational transitions that allow for substrate binding and product release in IsPETase. The observed catalytic enhancement caused by this substitution in other PET hydrolases appears to be due to conformational selection, by capturing the conformational ensemble observed in IsPETase.
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| 2. |
- Hintzen, Jordi, 1994, et al.
(author)
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Fluorescence Labeling of Peptides: Finding the Optimal Protocol for Coupling Various Dyes to ATCUN-like Structures
- 2024
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In: ACS ORGANIC & INORGANIC AU. - 2694-247X.
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Journal article (peer-reviewed)abstract
- Labeling of peptides and proteins with fluorescent dyes is a key step in functionalizing these structures for a wide array of biological assays. However, coupling strategies of such dyes have not been optimized for the most common compounds, while this step is typically the most precious and costly of the whole synthesis. We searched for the best conditions for attachment of the most widely used fluorescent dyes such as 6-carboxyfluorescein, Rhodamine B, and BODIPY-FL to peptides, where amino terminal Cu(II) and Ni(II) binding site (ATCUN) peptides were used as a model system. Surprisingly, conventional methods of dye attachment proved to not be satisfactory and yielded poor efficiency results. We have discovered that when labeling primary amines on peptides, the uncommon synthesis of activated pentafluorophenol (PFP) esters is the most efficient strategy, expedited by microwave irradiation. Coupling to secondary amines is achieved most efficiently through conventional coupling reagents such as HATU and PyBOP. Furthermore, we have employed our fluorescently labeled ATCUN peptides in studies for Cu(II) and Ni(II) sensing, showing that changing the fluorophore does not significantly affect the fluorescence quenching process and discovering the optimal linker length between the ATCUN core and the dye, expanding the repertoire of fluorophores that can be used in this application.
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| 3. |
- Lindroth, Rickard, et al.
(author)
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Sustainable Ir-Photoredox Catalysis by Means of Heterogenization
- 2022
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In: ACS ORGANIC & INORGANIC AU. - : American Chemical Society (ACS). - 2694-247X. ; 2:5, s. 427-432
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Journal article (peer-reviewed)abstract
- A heterogenized iridium catalyst was employed to perform photoredox catalysis for a collection of mechanistically orthogonal reactions using very low quantities of iridium (0.01-0.1 mol %). The heterogenized construct consists of an organometallic iridium coordination complex bonded to an aluminum metal oxide solid-state support via an anchoring group. The solid-state support allows for easy recovery and reusability of the catalyst. Evaluation of the catalytic activity was performed with five different reactions, showing broad applicability and demonstrating the general potential for a heterogenized strategy. Moreover, the heterogenized catalyst was shown to be reusable up to five times and also mediated the reactions with much higher efficiency than the original processes by employing the corresponding homogeneous catalyst. As a result of the low catalyst loadings employed, the feasibility of reusage, and faster reaction times, this catalyst offers a more sustainable option when precious metal catalysts are used in organic synthesis. Finally, the catalyst was successfully applied to a gram-scale reaction, showing it is susceptible to scalability.
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