Chromatin as a Dynamic Platform for Protein-Protein Interactions

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Chromatin-modifying enzymes target distinct residues within histones to finetune gene expression profiles. SIRT7 is an NAD+-dependent deacylase often deregulated in cancer, which deacetylates either H3 lysine 36 (H3K36) or H3K18 with high specificity withi ...

Proteins are foundational biomolecules of life playing a crucial role in a myriad of biological processes. Their function often requires interplay with other biomolecules, including proteins themselves. Protein-protein interactions (PPIs) are essential for ...

The control of eukaryotic gene expression is intimately connected to highly dynamic chromatin structures. Gene regulation relies on activator and repressor transcription factors (TFs) that induce local chromatin opening and closing. However, it is unclear ...

Protein–ligand interactions (PLIs) determine the efficacy and safety profiles of small molecule drugs. Existing methods rely on either structural information or resource-intensive computations to predict PLI, casting doubt on whether it is possible to perf ...

Protein stabilization has a crucial rule sustaining biological functionality, disease prevention, and pharmaceutical formulation stabilization, and yet its stabilization mechanism by small molecules such as amino acids is not fully understood. In this work ...

Posttranslational modifications (PTMs) of proteins play central roles in regulating the protein structure, interactome, and functions. A notable modification site is the aromatic side chain of Tyr, which undergoes modifications such as phosphorylation and ...

In Nature, most known objects can perform their functions only when in supramolecular self-assembled from, e.g. protein complexes and cell membranes. Here, a dendritic polymer is presented that inhibits severe acute respiratory syndrome coronavirus 2 (SARS ...

Whole genome doubling (WGD) events are drivers of genetic innovation across vertebrate evolution. While generally detrimental to mammalian organisms, WGDs are crucial in the development of various plants and fungi, as well as for the terminal differentiati ...

Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...

The goal of my PhD was the development of a new method for unselective surface labeling, not substrate-specific, that would give access to direct visualization of any surface interactions. In order to achieve this challenging goal, we wanted to develop a g ...

Size of the nucleus, a membrane-bound organelle for DNA replication and transcription in eukaryotic cells, varies to adapt nuclear functions to the surrounding environment. Nuclear size strongly correlates with cytoplasmic size and genomic content. Previou ...

Synucleinopathies such as Parkinson's disease, dementia with Lewy bodies and multiple system atrophy (MSA) are detrimental neurodegenerative diseases. Alpha-synuclein (aSyn), the main aggregating protein found in the pathological inclusions of these ailmen ...

The binding and catalytic functions of proteins are generally mediated by a small number of functional residues held in place by the overall protein structure. Here, we describe deep learning approaches for scaffolding such functional sites without needing ...

Water is one of the most abundant molecules in the universe. It forms a hydrogen bond network with unique structure and dynamics. Hydrogen bonding is highly relevant to many biological processes including membrane formation, protein folding, adsorption, an ...

The work presented in this thesis combines supervised and unsupervised machine learning to examine structure-property relationships in databases of materials. While either supervised learning or unsupervised learning alone can be a powerful tool for assess ...

Thanks to recent advancements in synthetic biology, the dream of creating a synthetic cell has become feasible. However, due to its inherent complexity, one of the fundamental functions of all living systems, i.e., self-replication, remains to be introduce ...

Actin is the most abundant protein in eukaryotic cells and is key to many cellular functions. The filamentous form of actin (F-actin) can be studied with help of natural products that specifically recognize it, as for example fluorophore-labeled probes of ...

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific antibody responses to the spike (S) protein monomer, S protein native trimeric form, or the nucleocapsid (N) proteins were evaluated in cohorts of individuals with acute infection (n = 9 ...

The essential human enzyme lysine specific demethylase 1 (LSD1) silences genes by demethylating mono- and dimethylated lysine 4 in histone H3 (H3K4me1/2). Studies of the minimal requirements for LSD1 activity are complicated by the heterogeneity of histone ...

Many targeted cancer therapies fail to improve the overall survival of patients. Limitations involve low drug selectivity and the rapid development of resistance. Moreover, the majority of oncogenic drivers presently remain considered as undruggable as th ...

Chromatin as a Dynamic Platform for Protein-Protein Interactions

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Structural basis of SIRT7 nucleosome engagement and substrate specificity

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

Individual transcription factors modulate both the micromovement of chromatin and its long-range structure

G–PLIP: Knowledge graph neural network for structure-free protein–ligand bioactivity prediction

Hydrophobic Interaction and its Small Molecule effect

A Versatile Method for Site-Specific Chemical Installation of Aromatic Posttranslational Modification Analogs into Proteins

Supramolecular Architectures of Dendritic Polymers Provide Irreversible Inhibitor to Block Viral Infection

Whole genome doubling promotes tumorigenesis through loss of chromatin segregation and compartment repositioning

De novo designed proteins: a study in engineering novel folds and functions

Azide-Containing Hypervalent Iodine Reagents for Biomolecules Functionalization

Differential contribution of nuclear size scaling mechanisms between Xenopus species

Capturing the heterogeneity of alpha-synuclein pathology in synucleinopathies

Scaffolding protein functional sites using deep learning

Second harmonic scattering of water in a biological context

Structure-Property Relationships in Complex Materials by Combining Supervised and Unsupervised Machine Learning

Towards an artificial cell: Development of a system which self-regenerates the protein components of the PURE system in microfluidic reactors

In Vitro-Evolved Peptides Bind Monomeric Actin and Mimic Actin-Binding Protein Thymosin-β4

Changes in SARS-CoV-2 Spike versus Nucleoprotein Antibody Responses Impact the Estimates of Infections in Population-Based Seroprevalence Studies

Nucleosome Binding by the Lysine Specific Demethylase 1 (LSD1) Enzyme Enables Histone H3 Demethylation

Targeting the oncogenic signaling of the transcription factor STAT3 with potent and selective monobody inhibitors