Publication

The disulfide bond in the Aeromonas hydrophila lipase/acyltransferase stabilizes the structure but is not required for secretion or activity

Publications associées (51)

An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification

Assigning or proposing a catalysing enzyme given a chemical or biochemical reaction is of great interest to life sciences and chemistry alike. The exploration and design of metabolic pathways and the challenge of finding more sustainable enzyme-catalysed a ...

2023

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

Investigation of Carboxylic Acid Isosteres and Prodrugs for Inhibition of the Human SIRT5 Lysine Deacylase Enzyme

Alexander Lund Nielsen

Sirtuin 5 (SIRT5) is a protein lysine deacylase enzyme that regulates diverse biology by hydrolyzing epsilon-N-carboxyacyllysine posttranslational modifications in the cell. Inhibition of SIRT5 has been linked to potential treatment of several cancers but ...

2022

Model-based scale-up of a continuously operated consolidated bioprocess based on a microbial consortium for the production of ethanol

David Beat Dempfle

This work demonstrated that consolidated bioprocessing is a promising concept for conversion of lignocellulose to ethanol at industrial scale. CBP offers great cost saving potential, is feasible to be operated continuously and may be scaled up due to exten ...

EPFL2022

The more the merrier: how homo-oligomerization alters the interactome and function of ribonucleotide reductase

Yimon Aye

Stereotyped as a nexus of dNTP synthesis, the dual-subunit enzyme - ribonucleotide reductase (RNR) - is coming into view as a paradigm of oligomerization and moonlighting behavior. In the present issue of `omics', we discuss what makes the larger subunit o ...

ELSEVIER SCI LTD2020

Engineering of ecological niches to create stable artificial consortia for complex biotransformations

Jeremy Luterbacher

The design of controllable artificial microbial consortia has attracted considerable interest in recent years to capitalize on the inherent advantages in comparison to monocultures such as the distribution of the metabolic burden by division of labor, the ...

2020

Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites

Vassily Hatzimanikatis, Ljubisa Miskovic, Noushin Hadadi, Marianne Seijo

Thousands of biochemical reactions with characterized activities are “orphan,” meaning they cannot be assigned to a specific enzyme, leaving gaps in metabolic pathways. Novel reactions predicted by pathway-generation tools also lack associated sequences, l ...

PNAS2019

Single-Molecule Imaging of Active Mitochondrial Nitroreductases Using a Photo-Crosslinking Fluorescent Sensor

Pablo Rivera Fuentes, Zacharias Thiel

Many biomacromols. are known to cluster in microdomains with specific subcellular localization. In the case of enzymes, this clustering greatly defines their biol. functions. Nitroreductases are enzymes capable of reducing nitro groups to amines, and play ...

2019

Portable bioluminescence systems and methods for in vivo monitoring of molecular and metabolic events in animals

Aurélien Godinat, Elena Goun, Aleksey Yevtodiyenko

A system for monitoring biological processes in vivo is provided. The system comprises an implantable luciferase biosensor comprising luciferase in a biocompatible matrix and a caged luciferin probe. The caged luciferin probe can be administered to a livin ...

2018

Design of novel enzyme-catalyzed reactions linked to protein sequences for finding enzyme engineering targets

Vassily Hatzimanikatis, Jasmin Maria Hafner, Homa Mohammadi Peyhani, Noushin Hadadi

A key challenge in metabolic engineering is to find and to improve biosynthetic pathways that lead to the cellular production of a given industrial, pharmaceutical or specialty chemical compound. In many cases, the enzymatic reactions required for bio-prod ...

2017

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