Frontiers in multiscale modeling of photoreceptor proteins

M Mroginski, S Adam, GS Amoyal… - Photochemistry and …, 2021 - Wiley Online Library
This perspective article highlights the challenges in the theoretical description of
photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in …

Progress of Molecular Display Technology Using Saccharomyces cerevisiae to Achieve Sustainable Development Goals

S Shibasaki, M Ueda - Microorganisms, 2023 - mdpi.com
In the long history of microorganism use, yeasts have been developed as hosts for
producing biologically active compounds or for conventional fermentation. Since the …

Photophysical engineering of fluorescent proteins: Accomplishments and challenges of physical chemistry strategies

S Mukherjee, R Jimenez - The Journal of Physical Chemistry B, 2022 - ACS Publications
Fluorescent proteins (FPs) have become ubiquitous tools for biological research and
concomitantly they are intriguing molecules that are amenable to study with a wide range of …

How reproducible are QM/MM simulations? Lessons from computational studies of the covalent inhibition of the SARS-CoV-2 main protease by carmofur

G Giudetti, I Polyakov, BL Grigorenko… - Journal of Chemical …, 2022 - ACS Publications
This work explores the level of transparency in reporting the details of computational
protocols that is required for practical reproducibility of quantum mechanics/molecular …

Interplay between locally excited and charge transfer states governs the photoswitching mechanism in the fluorescent protein Dreiklang

T Sen, Y Ma, IV Polyakov, BL Grigorenko… - The Journal of …, 2021 - ACS Publications
We present the results of high-level electronic structure and dynamics simulations of the
photoactive protein Dreiklang. With the goal of understanding the details of the Dreiklang …

Engineering high-activity crosslinked enzyme aggregates via SpyCatcher/SpyTag-mediated self-assembly

X Ma, Y Yang, M Wang, Y Zhang, B Zhao, S Hao… - International Journal of …, 2025 - Elsevier
Abstract Crosslinked Enzyme Aggregates (CLEAs) are favored for their operational stability
and recyclability. However, the traditional CLEAs preparation may distort the enzyme's …

Ultrafast excited state relaxation of a model green fluorescent protein chromophore: Femtosecond fluorescence and transient absorption study

BK Rajbongshi, SR Rather, S Bhowmik… - Journal of Molecular …, 2023 - Elsevier
The intrinsic excited state properties of green fluorescent protein (GFP) chromophore have
inspired syntheses of its structural analogues with a motivation to replicate or improve its …

[HTML][HTML] Overview on Current Selectable Marker Systems and Novel Marker Free Approaches in Fruit Tree Genetic Engineering

V Súnico, I Piunti, M Bhattacharjee, B Mezzetti… - International Journal of …, 2024 - mdpi.com
Selectable marker genes are useful for recognizing which cells have integrated specific
sequences in their genome after genetic transformation processes. They are especially …

Stalling chromophore synthesis of the fluorescent protein Venus reveals the molecular basis of the final oxidation step

HS Auhim, BL Grigorenko, TK Harris, OE Aksakal… - Chemical …, 2021 - pubs.rsc.org
Fluorescent proteins (FPs) have revolutionised the life sciences, but the mechanism of
chromophore maturation is still not fully understood. Here we show that incorporation of a …

[HTML][HTML] Calcium Indicators with Fluorescence Lifetime-Based Signal Readout: A Structure–Function Study

TR Simonyan, LA Varfolomeeva… - International Journal of …, 2024 - mdpi.com
The calcium cation is a crucial signaling molecule involved in numerous cellular pathways.
Beyond its role as a messenger or modulator in intracellular cascades, calcium's function in …