Publications related to Directed evolution of the suicide protein O⁶-alkylguanine-DNA alkyltransferase for increased reactivity results in an alkylated protein with exceptional stability

Optimality principles for the analysis of biological processes across scales: From enzyme kinetics to microbiome dynamics

Microorganisms are essential for life on Earth, performing key roles in numerous biological processes. Their influence extends across a wide spectrum, from human health and ecological balance to advancements in biotechnology and industrial applications. Th ...

EPFL2024

Development of cysteine cathepsin inhibitors combined with cell type-specific delivery for the treatment of B-cell lymphoma and solid tumors

Aaron Simone Petruzzella

Cysteine cathepsins proteases are enzymes that play essential physiological roles, but their activity is also associated to different aspects of cancer progression and to the development of other diseases. Therefore, cysteine cathepsins are relevant and pr ...

EPFL2024

A chemical biology approach to decipher chromatin ubiquitylation by RNF168

Pauline Franz

DNA damage signaling following DNA double-strand breaks (DSBs) involves numerous regulating proteins, which dynamically recognize ('read') and alter ('write' or 'erase') histone post-translational modifications (PTMs). Among these PTMs, the ubiquitin syste ...

EPFL2024

Variational quantum time evolution without the quantum geometric tensor

Giuseppe Carleo, Riccardo Rossi, Julien Sebastian Gacon, Stefan Woerner, Jannes Willy E. Nys

Realand imaginary -time quantum state evolutions are crucial in physics and chemistry for exploring quantum dynamics, preparing ground states, and computing thermodynamic observables. On near -term devices, variational quantum time evolution is a promising ...

Amer Physical Soc2024

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

Telomere protection against oxidative stress

Thu Trang Nguyen

Telomeres are nucleoprotein structures at the ends of linear chromosomes, being essential for the maintenance of genomic integrity. Telomeres have a unique structure which distinguishes chromosome termini from DNA damage sites. Shelterin complexes are the ...

EPFL2023

Preomic profile of BxPC-3 cells after treatment with BRC4

Andrea Cavalli

BRCA2 and RAD51 are two proteins that play a central role in homologous recombination (HR) and DNA double strand break (DSB) repair. BRCA2 assists RAD51 fibrillation and defibrillation through binding with its eight BRC repeats, with BRC4 being one of the ...

ELSEVIER2023

Identification and characterization of proteins that protect human telomeres from fragility

Anna Christina Näger

Difficulties to replicate telomeres - the ends of our chromosomes - can cause telomere shortening and genome instability. These difficulties are due to the repetitive DNA sequence and distinct structures at telomeres that challenge the semi-conservative DN ...

EPFL2022

Protein Engineering for Personalized therapy and diagnosis

Lixia Wei

Protein Engineering, especially protein post-translational modification (PTM), ex-tends proteomes in a more complex way than one can expect from analysis of their encod-ing genomes. It can activate or deactivate certain catalytic functions, add new desired ...

EPFL2022

Directed evolution of DNA-wrapped single-walled carbon nanotube complexes for optical sensing

Benjamin Paul Johanès Gabriel Lambert

Single-walled carbon nanotubes (SWCNTs) have garnered significant interest for their applications in optical biosensing. SWCNTs exhibit a sensitive and photostable fluorescence in the near-infrared (NIR) range, allowing for the continuous monitoring of tar ...

EPFL2021

The phase separation-dependent FUS interactome reveals nuclear and cytoplasmic function of liquid-liquid phase separation

Helen Lindsay

Liquid-liquid phase separation (LLPS) of proteins and RNAs has emerged as the driving force underlying the formation of membrane-less organelles. Such biomolecular condensates have various biological functions and have been linked to disease. The protein F ...

2021

Organohalide respiration in Firmicutes: energy metabolism and transcription regulation

Mathilde Stéphanie Willemin

Organohalides are a class of compounds often considered as persistent pollutants and harmful to environmental and human health. Some bacteria, among which are representatives from the Firmicutes phylum, are capable of using these compounds as terminal acce ...

EPFL2021

Requirements for DNA bubble structure for efficient cleavage by helix-two-turn-helix DNA glycosylases

Kristina Makasheva

Oxidative DNA lesions, constantly generated by both endogenous and environmentally induced reactive oxygen species, are removed via the base excision repair pathway. In bacteria, Fpg and Nei DNA glycosylases, belonging to the helix-two-turn-helix (H2TH) st ...

2020

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

Yimon Aye, Alexandra Krina Van Hall-Beauvais

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

Common Gene Expression Patterns in Environmental Model Organisms Exposed to Engineered Nanomaterials: A Meta-Analysis

Kristin Schirmer, Anze Zupanic

The use of omics is gaining importance in the field of nanoecotoxicology; an increasing number of studies are aiming to investigate the effects and modes of action of engineered nanomaterials (ENMs) in this way. However, a systematic synthesis of the outco ...

AMER CHEMICAL SOC2020

Modeling biochemical reaction networks in complex intracellular environments

Daniel Robert Weilandt

Whether one aims to design treatments for diseases such as cancer or diabetes, engineer cells to produce valuable biochemicals sustainably, or to grasp the behavior of living organisms, it is essential to understand how cells react to genetic, environmenta ...

EPFL2020

Modeling, predicting and mining metabolism at atom-level resolution

Jasmin Maria Hafner

Living organisms can catalyze many thousands of biochemical reactions that they use to convert energy and matter, which provides them with the essentials for life. The sum of these chemical reactions happening in an organism is called metabo-lism. Understa ...

EPFL2020

Generation of chiral asymmetry via helical magnetic fields

Ruth Durrer, Jennifer Waltraud Schober

It is well known that helical magnetic fields undergo a so-called inverse cascade by which their correlation length grows due to the conservation of magnetic helicity in classical ideal magnetohydro-dynamics (MHD). At high energies above approximately 10 M ...

American Physical Society2020

The evolution of the type VI secretion system as a disintegration weapon

Julius Hans Bernd Winter

The type VI secretion system (T6SS) is a nanomachine used by many bacteria to drive a toxin-laden needle into other bacterial cells. Although the potential to influence bacterial competition is clear, the fitness impacts of wielding a T6SS are not well und ...

PUBLIC LIBRARY SCIENCE2020

Sirt6 deletion in bone marrow-derived cells increases atherosclerosis - Central role of macrophage scavenger receptor 1

Matthias Alexander Sokrates Stein, Johan Auwerx, Julien Weber, Tasneem Arsiwala

Aims: Sirtuin 6 (Sirt6) is a NAD(+)-dependent deacetylase that plays a key role in DNA repair, inflammation and lipid regulation. Sirt6-null mice show severe metabolic defects and accelerated aging. Macrophage-foam cell formation via scavenger receptors is ...

2020