Immobilization of the N-terminal helix stabilizes prefusion paramyxovirus fusion proteins

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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 ...

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 ...

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 ...

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 70 kDa heat shock protein (Hsp70) chaperones control protein homeostasis in all ATP-containing cellular compartments. J-domain proteins (JDPs) coevolved with Hsp70s to trigger ATP hydrolysis and catalytically upload various substrate polypeptides in ne ...

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 ...

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 ...

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 ...

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 ...

G-protein-coupled receptors (GPCRs) are key regulators of human physiology and are the targets of many small-molecule research compounds and therapeutic drugs. While most of these ligands bind to their target GPCR with high affinity, selectivity is often l ...

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 ...

Dataset corresponding to the following manuscript: Slagter, A., Setyadji, J.A., Vogt, E.L. et al. Nanoindentation Hardness and Modulus of Al2O3–SiO2–CaO and MnO–SiO2–FeO Inclusions in Iron. Metall Mater Trans A (2024). https://doi.org/10.1007/s11661-024-0 ...

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 ...

This data set contains the data collected during the FNS project Green Piezo (Grant no. 179064) in association with the recent publication entitled “3D printing of customizable transient bioelectronics and sensors”. This work aims to study and demonstrate ...

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 ...

This paper presents a novel hybrid framework for generating and updating a synthetic population. We call it hybrid because it combines model-based and data-driven approaches. Existing generators produce a snapshot of synthetic data that becomes outdated ov ...

This repository contains microphysics routines, scripts, and processed data from the Weather Research and Forecasting (WRF) model simulations presented in the paper "RaFSIP: Parameterizing ice multiplication in models using a machine learning approach", by ...

We propose a comparative study of three different methods aimed at optimizing existing groundwater monitoring networks. Monitoring piezometric heads in subsurface porous formations is crucial at regional scales to properly characterize the relevant subsurf ...

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 ...

This document contains all the data and the details of the analysis used in the manuscript titled " Control of Ge island coalescence for the formation of nanowires on silicon." https://doi.org/10.1039/D3NH00573A ...

Immobilization of the N-terminal helix stabilizes prefusion paramyxovirus fusion proteins

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

Opportunities and challenges in design and optimization of protein function

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

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

Autorepression of yeast Hsp70 cochaperones by intramolecular interactions involving their J-domains

Computational drug development for membrane protein targets

Predicting protein interactions using geometric deep learning on protein surfaces

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

Recording physiological history of cells with chemical labeling

Antibodies expand the scope of angiotensin receptor pharmacology

Microsecond Time-Resolved Cryo-Electron Microscopy

Nanoindentation hardness and modulus of Al2O3-SiO2-CaO and MnO-SiO2-FeO inclusions in iron

Mechanisms and functions of protein S-acylation

Dataset for '3D printing of customizable transient bioelectronics and sensors'

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

Hybrid Simulator for Capturing Dynamics of Synthetic Populations

Data and scripts for the RaFSIP scheme

Data-driven statistical optimization of a groundwater monitoring network

Microsecond time-resolved cryo-electron microscopy

Data set for control of Ge island coalescence for the formation of nanowires on silicon