Publications related to Who Activates the Nucleophile in Ribozyme Catalysis? An Answer from the Splicing Mechanism of Group II Introns

Related publications (33)

Rate-Determining Step for Electrochemical Reduction of Carbon Dioxide into Carbon Monoxide at Silver Electrodes

Silver is one of the most studied electrode materials for the electrochemical reduction of carbon dioxide into carbon monoxide, a product with many industrial applications. There is a growing number of reports in which silver is implemented in gas diffusio ...

2024

Probing Catalytic Sites and Adsorbate Spillover on Ultrathin FeO2-x Film on Ir(111) during CO Oxidation

Harald Brune, Hao Yin

The spatially resolved identification of active sites on the heterogeneous catalyst surface is an essential step toward directly visualizing a catalytic reaction with atomic scale. To date, ferrous centers on platinum group metals have shown promising pote ...

Amer Chemical Soc2024

Encoding quantum-chemical knowledge into machine-learning models of complex molecular properties

Ksenia Briling

Statistical (machine-learning, ML) models are more and more often used in computational chemistry as a substitute to more expensive ab initio and parametrizable methods. While the ML algorithms are capable of learning physical laws implicitly from data, ad ...

EPFL2024

Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations

Vassily Hatzimanikatis, Daniel Robert Weilandt, Asli Sahin

One of the main challenges hampering the development of kinetic models is the lack of kinetic parameters for many enzymatic reactions. Here, the authors introduce a framework to explore the catalytically optimal operating conditions of any complex enzyme m ...

Nature Portfolio2023

RNA-based nanomedicines and their clinical applications

Yi Wang

RNA-based nanomedicines encompass a range of therapeutic approaches that utilize RNA molecules or molecules that target RNAs for the treatment or prevention of diseases. These include antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs), endo ...

Tsinghua Univ Press2023

Reactivity of Bromine Radical with Dissolved Organic Matter Moieties and Monochloramine: Effect on Bromate Formation during Ozonation

Urs von Gunten, Sung Eun Lim

Bromine radical (Br center dot) has been hypothesized to be a key intermediate of bromate formation during ozonation. Once formed, Br center dot further reacts with ozone to eventually form bromate. However, this reaction competes with the reaction of Br c ...

AMER CHEMICAL SOC2023

Inferring free-energy barriers and kinetic rates from molecular dynamics via underdamped Langevin models

David Daniel Girardier, Fabio Pietrucci, Sara Bonella

Rare events include many of the most interesting transformation processes in condensed matter, from phase transitions to biomolecular conformational changes to chemical reactions. Access to the corresponding mechanisms, free-energy landscapes and kinetic r ...

Aip Publishing2023

Kinetic Network Modeling of the Catalytic Upgrading of Biomass's Acetate Fraction to Aromatics

Jeremy Luterbacher, Jher Hau Yeap, Bartosz Rozmyslowicz

The acetate fraction is the fourth most abundant fraction by weight in many plant species and can be easily extracted as acetic acid in high yields. We have previously shown that acetic acid obtained from steam pretreated beech wood could be upgraded in a ...

Amer Chemical Soc2023

Efficient and sensitive profiling of RNA–protein interactions using TLC-CLIP

Didier Trono, Julien Léonard Duc, Christina Ernst

RNA-binding proteins are instrumental for post-transcriptional gene regulation, controlling all aspects throughout the lifecycle of RNA molecules. However, transcriptome-wide methods to profile RNA-protein interactions in vivo remain technically challengin ...

2023

Computational Studies for the Design of Metalloenzyme Mimics

Guido Frisari

At present, there is no general standard automated method for engineering metalloenzymes, industrially-relevant systems able to catalyze environmentally friendly reactions. One of the most studied natural metalloenzymes is the second isoform of human carbo ...

EPFL2023

cgNA plus web : A Visual Interface to the cgNA plus Sequence-dependent Statistical Mechanics Model of Double-stranded Nucleic Acids

John Maddocks, Rahul Sharma, Alessandro Samuele Patelli, Lennart de Bruin

The sequence-dependent statistical mechanics of double-stranded nucleic acid, or dsNA, is believed to be essential in its biological functions. In turn, the equilibrium statistical mechanics behaviour of dsNA depends strongly both on sequence-dependent per ...

Elsevier2023

Understanding the growth mechanism of BaZrS3 chalcogenide perovskite thin films from sulfurized oxide precursors

Anna Fontcuberta i Morral, Mirjana Dimitrievska, Elias Zsolt Stutz, Santhanu Panikar Ramanandan, Andrea Giunto

Barium zirconium sulfide (BaZrS3) is an earth-abundant and environmentally friendly chalcogenide perovskite with promising properties for various energy conversion applications. Recently, sulfurization of oxide precursors has been suggested as a viable sol ...

IOP Publishing Ltd2023

Operando identification of a side-on nickel superoxide intermediate and the mechanism of oxygen evolution on nickel oxyhydroxide

Xile Hu, Lichen Bai, Seunghwa Lee

The oxygen evolution reaction (OER) is a key electrochemical reac-tion relevant to energy storage. Ni-containing bimetallic oxyhydrox-ides are among the most active OER catalysts in alkaline medium, but the mechanism of OER on pure Ni oxyhydroxide remains ...

ELSEVIER2023

Chlorination of amides: Kinetics and mechanisms of formation of N-chloramides and their reactions with phenolic compounds

Urs von Gunten, Tianqi Zhang

Amides are common constituents in natural organic matter and synthetic chemicals. In this study, we investi-gated kinetics and mechanisms of the reactions of chlorine with seven amides, including acetamide, N-meth-ylformamide, N-methylacetamide, benzamide, ...

2023

Recombinant Full-Length TDP-43 Oligomers Retain Their Ability to Bind RNAs, Are Not Toxic, and Do Not Seed TDP-43 Aggregation in Vitro

Hilal Lashuel, Yllza Jasiqi, Lixin Yang

TAR DNA-binding protein with 43 kD (TDP-43) is a partially disordered protein that misfolds and accumulates in the brains of patients affected by several neurodegenerative diseases. TDP-43 oligomers have been reported to form due to aberrant misfolding or ...

Amer Chemical Soc2023

Development of next-generation microfluidic systems for enhanced, faster, and cost-effective immunoassays for tissue diagnostics - Ac electrothermal flow & Acoustofluidics

Muaz Salama Abdelmonem Draz

The application of microfluidics in the field of surface-based assays and more specifically, the spatial molecular profiling of tumor tissues has gained a lot of interest, especially with the increased interest in personalized medicine and targeted therapy ...

EPFL2023

CO2 Capture and Release in Amine Solutions: To What Extent Can Molecular Simulations Help Understand the Trends?

Wanda Andreoni, Fabio Pietrucci, Changru Ma

Absorption in amine solutions is a well-established advanced technology for CO2 capture. However, the fundamental aspects of the chemical reactions occurring in solution still appear to be unclear. Our previous investigation of aqueous monoethanolamine (ME ...

2023

Antagonistic interactions among structured domains in the multivalent Bicc1-ANKS3-ANKS6 protein network govern phase transitioning of target mRNAs

Daniel Constam, Benjamin Marcel Daniel Rothé, Simon Fortier, Céline Emmanuelle Schmuziger, Céline Gagnieux

The growing number of diseases linked to aberrant phase transitioning of ribonucleoproteins highlights the need to uncover how the interplay between multivalent protein and RNA interactions is regulated. Cytoplasmic granules of the RNA binding protein Bica ...

CELL PRESS2023

Oxidation of organic micropollutant surrogate functional groups with peracetic acid activated by aqueous Co(II), Cu(II), or Ag(I) and geopolymer-supported Co(II)

Urs von Gunten

Peracetic acid (PAA) in combination with transition metals has recently gained increasing attention for organic micropollutant abatement. In this study, aqueous Co(II), Cu(II), and Ag(I) were compared for their capacity to activate PAA. Co(II) outperformed ...

PERGAMON-ELSEVIER SCIENCE LTD2022

Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver

Felix Naef, Cédric Gobet, Benjamin Dieter Weger, Clémence Yumie Syloun Hurni

In eukaryotes, RNA is synthesised in the nucleus, spliced, and exported to the cytoplasm where it is translated and finally degraded. Any of these steps could be subject to temporal regulation during the circadian cycle, resulting in daily fluctuations of ...

PUBLIC LIBRARY SCIENCE2022