Protein folding is initiated with a volume contraction called collapse. While the microsecond collapse of horse cyt c has been intensely studied, its molecular mechanism remains elusive. To characterize the structural change, we prepared three cyt c variants labeled with a fluorescent dye at distinct sites (D50, A83, and E104). We track their dynamics via FRET between the dye and the heme by two-dimensional fluorescence lifetime correlation spectroscopy (2D FLCS), which has single-molecule sensitivity and sub-microsecond time resolution. The results reveal that the collapse exhibits two-state dynamics between structurally distributed ensembles, occurring on a time scale of tens of microseconds across all variants. This indicates a global contraction of the whole protein structure with a substantial free energy barrier. A slight delay observed for the D50 variant suggests the late folding of its associated loop. This study demonstrates the capability of 2D FLCS to characterize a small free-energy barrier in complex biophysical processes.
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 sequence constraints.
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.
