By data-mining very large datasets, this study establishes that rather low-abundant events can be analyzed by cryo-ET and paves the way toward broader applications.
Abstract
The chaperonin T-complex protein ring complex (TRiC) is an essential protein-folding machine in eukaryotic cells. Although its cytosolic role in folding newly synthesized proteins is well established, nuclear TRiC remains less well described. Here, we combined cryo-electron tomography (cryo-ET), cross-linking and affinity purification mass spectrometry with AlphaFold3 (AF3)-based structural modeling to examine nuclear TRiC in human cells. We detected intermediates of the TRiC duty cycle in the nucleus and identified several nuclear proteins that bind to TRiC. The respective AF3 models suggest interaction surfaces at the inside of the TRiC chamber. Our findings point toward compartment-specific roles of TRiC and a potential function in maintaining nuclear proteostasis. By data-mining very large datasets, our study establishes that rather low-abundant events can be analyzed by cryo-ET. It thus paves the way toward broader applications.
The comparison of adopter and non-adopter sample reveals three potential adoption inhibitor, security, data privacy, and portability, which underlines the importance of the technical and security perspectives for research investigating the adoption of technology.
Nattakarn Phaphoom, Xiaofeng Wang, S. Samuel et al.· Journal of Systems and Softw...· 111 citations· ⚡8
This study investigates how Lean internal startup facilitates software product innovation in large companies and identifies its enablers and inhibitors, and shows the potential of the method-in-action framework to investigate the Lean startup approach in non-startup context.
Henry Edison, Nina M. Smørsgård, Xiaofeng Wang et al.· Journal of Systems and Softw...· 78 citations· ⚡6
This paper highlights the challenges to conduct proper affect-related studies with psychology, provides a comprehensive literature review in affect theory, and proposes guidelines for conducting psychoempirical software engineering.
D. Graziotin, Xiaofeng Wang, P. Abrahamsson· SSE@SIGSOFT FSE· 56 citations· ⚡4
This study conducts a multiple case study on twenty European software startups and proposes a prototype-centric learning model in early stage software startups, and identifies factors that occur as barriers but also facilitators for prototyping in earlystage software startups.
Anh Nguyen-Duc, Xiaofeng Wang, P. Abrahamsson· International Conference on...· 44 citations· ⚡5
It is demonstrated that linker-free PROTACs can outperform traditional designs, marking a paradigm shift in PROTAC development for targeted protein degradation.
Pinal, a 16-billion-parameter foundation model that produces protein candidates from natural-language functional descriptions, supports natural language as a high-level interface for candidate generation in protein design, enabling programmable exploration with reduced reliance on manually specified structural or seque...
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
