Chem

Journal: Chem

Publisher

Elsevier

ISSN

2451-9294
2451-9308

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Publications 1 - 8 of 8

Exploring mechanism of enzyme catalysis by on-chip transient kinetics coupled with global data analysis and molecular modeling
Hess, David; Dockalova, Veronika; Kokkonen, Piia; et al. (2021)
Chem
The ability to engineer enzymes for industrial and biomedical applications is primarily limited by a paucity of mechanistic understanding. To gain insight into the mechanisms of enzyme catalysis, one must screen enormous numbers of discrete reaction conditions, which is a laborious task using conventional technologies. To address such limitations, we develop a droplet-based microfluidic platform for high-throughput acquisition of transient kinetic data over a range of substrate concentrations and temperatures. When compared with conventional methods, our platform reduces assay volumes by six orders of magnitude and increases throughput to 9,000 reactions/min. To demonstrate their utility, we measure the transient kinetics of three model enzymes, namely, β-galactosidase, horseradish peroxidase, and microperoxidase. Additionally, we conduct a complex kinetic and thermodynamic study of engineered variants of haloalkane dehalogenases. Datasets are globally analyzed and complemented by molecular dynamics simulations, providing new insights into the molecular basis of substrate specificity and the role of hydration-related entropy.
Animal-associated marine Acidobacteria with a rich natural-product repertoire
Leopold-Messer, Stefan; Chepkirui, Clara; Mabesoone, Mathijs F.J.; et al. (2023)
Chem
Sponges are well known as rich sources of bioactive natural products. Various studies suggest that many of these compounds are produced by symbiotic bacteria. However, substance supplies and functional insights about the producers remain limited because cultivation remains unsuccessful. To identify alternative, sustainable sources of sponge-derived polyketides, we computationally analyzed 5,289 characterized and orphan trans-acyltransferase polyketide synthases, enzymes with widespread roles in polyketide biosynthesis by bacterial symbionts. The workflow predicted animal-derived marine Acidobacteria of the family Acanthopleuribacteraceae with large sets of biosynthetic gene clusters to be enriched in sponge-type chemistry. Targeted compound isolation from a chiton-associated strain yielded congeners of the phorboxazoles and calyculins, potent and scarce cytotoxins exclusively known from sponges, and depsipeptides named acidobactamides. These first natural products of Acidobacteria and new fire coral metagenomic data on a third family member suggest animal-associated Acanthopleuribacteraceae as a rich source of sponge-type and other metabolites.
Small but Perfectly Formed? Successes, Challenges, and Opportunities for Microfluidics in the Chemical and Biological Sciences
Chiu, Daniel T.; deMello, Andrew J.; Di Carlo, Dino; et al. (2017)
Chem
Dinitrogen Coupling to a Terpyridine-Molybdenum Chromophore Is Switched on by Fermi Resonance
Rafiq, Shahnawaz; Bezdek, Máté; Chirik, Paul J.; et al. (2019)
Chem
Laser-Microstructured Copper Reveals Selectivity Patterns in the Electrocatalytic Reduction of CO2
Veenstra, Florentine L.P.; Ackerl, Norbert; Martín, Antonio J.; et al. (2020)
Chem
The strategy of engineering the local chemical environment to direct selectivity in the electroreduction of CO2 toward value-added products is only qualitatively understood. The unfeasibility of local concentration measurements and the limited applicability of simulations to practical systems hinder more precise guidelines. Herein, we quantify the impact of the (electro)chemical environment on the selectivity pattern using microstructured Cu electrodes prepared by ultrashort pulse laser ablation. We created regularly distributed micro-probes and assessed their product distributions at distinct overpotentials. The regular geometry enabled the accurate simulation of the local pH and CO2 concentration. Selectivity maps useful for mechanistic and applied studies emerged. They reveal clear patterns for C1-C3 products suggesting novel insights such as the presence of two reaction mechanisms for propanol. The effect on the selectivity pattern of operation parameters such as enhanced mass transport and electrolyte composition was also predicted by the maps.
Porous polyisothiocyanurates for selective palladium recovery and heterogeneous catalysis
Song, Kyung Seob; Ashirov, Timur; Talapaneni, Siddulu Naidu; et al. (2022)
Chem
Palladium is an indispensable metal due to its wide range of industrial applications. Pd refining, however, is an extremely energy-intensive process with a serious environmental impact. Thus, the selective recovery of Pd from secondary sources is rather important. In this direction, solid sorbents are promising candidates owing to their reusability. Here, we report the synthesis of porous polyisothiocyanurates through the trimerization of 1,4-phenyldiisothiocyanate under ionothermal conditions, named covalent isothiocyanurate frameworks (CITCFs), bearing in situ generated thiourea moieties as binding sites for Pd. High surface area of CICTFs, 1,589 m2 g−1, along with the presence of abundant sulfur atoms within a hierarchically porous network, enabled an exceptional Pd(II) uptake capacity of 909 mg g−1, fast adsorption kinetics, stable uptake over a wide pH range, and selective Pd(II) recovery from wastewater conditions. Moreover, the reduction of recovered Pd(II) within the polymer network led to highly efficient heterogeneous catalysis for the Suzuki-Miyaura cross-coupling reaction.
Electrocatalytic reduction of nitrogen: from Haber-Bosch to Ammonia artificial leaf
Martín, Antonio J.; Shinagawa, Tatsuya; Pérez-Ramírez, Javier (2019)
Chem
Widespread microbial utilization of ribosomal β-amino acid-containing peptides and proteins
Scott, Thomas A.; Verest, Marjan; Farnung, Jakob; et al. (2022)
Chem
β-Amino residues are regarded as extremely rare features among ribosomal products. They can be installed by a remarkable non-canonical enzymatic splicing process occurring in some Nif11-type ribosomally synthesized and posttranslationally modified peptide (RiPP) pathways from select cyanobacteria. The functions of the final pathway products remained unknown. Here, a global bioinformatic analysis suggested an unexpectedly broad distribution of ribosomal β-amino acid products in diverse bacterial lineages as well as archaea. Characterization of 27 bacterial splicease-substrate pairs confirmed the modification in all cases. The “spliceotide” products include many previously unrecognized RiPP types as well as proteins, contain 35 to >600 residues, and feature single to multiple α-keto-β-amino acid moieties, with 15 different naturally occurring β units characterized and 20 predicted. Of three tested spliceotides, all exhibited exceptionally potent protease inhibitory activity, providing a potential rationale for the widespread splicease chemistry in prokaryotes and highlighting substantial potential for drug discovery and gene-based biomolecule diversification.

Publications 1 - 8 of 8

Journal: Chem

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