Optimization of Conformational Dynamics in an Epistatic Evolutionary Trajectory

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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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

Background: Reproductive isolation can result from adaptive processes (e.g., ecological speciation and mutation-order speciation) or stochastic processes such as "system drift" model. Ecological speciation predicts barriers to gene flow between populations ...

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 ...

We study the drainage of a viscous liquid film coating the outside of a solid horizontal cylinder, where gravity acts vertically. We focus on the limit of large Ohnesorge numbers Oh, where inertia is negligible compared to viscous effects. We first study t ...

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 ...

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 ...

Background: We previously described the KINSSHIP syndrome, an autosomal dominant disorder associated with intellectual disability (ID), mesomelic dysplasia and horseshoe kidney,caused by de novo variants in the degron of AFF3. Mouse knock-ins and overexpre ...

In high elevation Alpine areas, characterised by high snow accumulation and radiation-driven melt processes, the formation of peculiar ablation features called sun cups can be observed. Sun cups likely influence the energy and mass balance of the wet snowp ...

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 ...

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, ...

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 ...

We propose an adaptive quantum algorithm to prepare accurate variational time evolved wave functions. The method is based on the projected variational quantum dynamics (pVQD) algorithm, that performs a global optimization with linear scaling in the number ...

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 ...

Optimization of Conformational Dynamics in an Epistatic Evolutionary Trajectory

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

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

Variational quantum time evolution without the quantum geometric tensor

Microsecond Time-Resolved Cryo-Electron Microscopy

Microsecond time-resolved cryo-electron microscopy

Predicting protein interactions using geometric deep learning on protein surfaces

Reproductive isolation arises during laboratory adaptation to a novel hot environment

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

Stability of a liquid layer draining around a horizontal cylinder: Interplay of capillary and gravity forces

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

Mechanisms and functions of protein S-acylation

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

Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles

Influence of sun cups on surface albedo of wet Alpine snowpack

Structural heterogeneity of the ion and lipid channel TMEM16F

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

Recording physiological history of cells with chemical labeling

Adaptive projected variational quantum dynamics

Computational drug development for membrane protein targets