SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions

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Living systems are commonly engineered through an iterative design-build-test process. However, unlike in other engineering disciplines, the systems that synthetic biologists construct are able to evolve. On the one hand, this compromises their long-term s ...

In the domain of computational structural biology, predicting protein interactions based on molecular structure remains a pivotal challenge. This thesis delves into this challenge through a series of interconnected studies. The first chapter introduces th ...

Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...

The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...

De novo design of complex protein folds using solely computational means remains a substantial challenge1. Here we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topologies, ...

Recently, single-particle cryo-electron microscopy emerged as a technique capable of determining protein structures at near-atomic resolution and resolving protein dynamics with a temporal resolution ranging from second to milliseconds. This thesis describ ...

Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome densities, ...

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 phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

This study combined protein modeling methods to generate the prolamins' fractions as precise as possible. Hence, gliadins, zeins, kafirins, hordeins, secalins, avenins and oryzins were generated based on their characteristics and disulfide mapping. Finding ...

As the fundamental machinery orchestrating cellular functions, proteins influence the state of every cell profoundly. As cells exhibit significant variations from one to another, analyzing the proteome on a single-cell level is imperative to unravel their ...

Cartilage homeostasis, crucial for musculoskeletal function, is orchestrated by interconnected biophysical cues. In healthy cartilage, repetitive compressive loading not only elicits a range of mechanical stimuli but also induces a gradual transient temper ...

Over the past two decades, protein S-acylation (often referred to as S-palmitoylation) has emerged as an important regulator of vital signalling pathways. S-Acylation is a reversible post-translational modification that involves the attachment of a fatty a ...

Recordings of the physiological history of cells provide insights into biological processes, yet obtaining such recordings is a challenge. To address this, we introduce a method to record transient cellular events for later analysis. We designed proteins t ...

Microsecond time-resolved cryo-electron microscopy has emerged as a novel approach for directly observing protein dynamics. By providing microsecond temporal and near-atomic spatial resolution, it has the potential to elucidate a wide range of dynamics tha ...

Transmembrane protein 16 F (TMEM16F) is a Ca2+-activated homodimer which functions as an ion channel and a phospholipid scramblase. Despite the availability of several TMEM16F cryogenic electron microscopy (cryo-EM) structures, the mechanism of activation ...

The synthesis of complex sugars is a key aspect of microbial biology. Cyclic beta-1,2-glucan (C beta G) is a circular polysaccharide critical for host interactions of many bacteria, including major pathogens of humans (Brucella) and plants (Agrobacterium). ...

The application of computational biology in drug development for membrane protein targets has experienced a boost from recent developments in deep learning-driven structure prediction, increased speed and resolution of structure elucidation, machine learni ...

Borrowing some quotes from Harper Lee's novel "To Kill A Mockingbird" to help frame our manuscript, we discuss methods to profile local proteomes. We initially focus on chemical biology regimens that function in live organisms and use reactive biotin speci ...

In recent years, there has been a surge of interest in predicting computed activation barriers, to enable the acceleration of the automated exploration of reaction networks. Consequently, various predictive approaches have emerged, ranging from graph-based ...

SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions

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Light-directed evolution of dynamic biological systems

Predicting protein interactions using geometric deep learning on protein surfaces

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

Opportunities and challenges in design and optimization of protein function

Computational design of soluble and functional membrane protein analogues

Microsecond Time-Resolved Cryo-Electron Microscopy

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

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

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Prolamins' 3D structure: A new insight into protein modeling using the language of numbers and shapes

Development of tools and methods for protein identification: From single molecules to in vivo applications

Synergetic Support of Cartilage Homeostasis via Coupled Thermal-Hydrostatic Pressure Stimuli

Mechanisms and functions of protein S-acylation

Recording physiological history of cells with chemical labeling

Microsecond time-resolved cryo-electron microscopy

Structural heterogeneity of the ion and lipid channel TMEM16F

Structure-function analysis of the cyclic β-1,2-glucan synthase from Agrobacterium tumefaciens

Computational drug development for membrane protein targets

Climbing into their Skin to Understand Contextual Protein-Protein Associations and Localizations: Functional Investigations in Transgenic Live Model Organisms

Benchmarking machine-readable vectors of chemical reactions on computed activation barriers