Computational Challenges in Modeling of Representative Bioimaging Proteins: GFP-Like Proteins, Flavoproteins, and Phytochromes DOI
Alexander V. Nemukhin, Bella L. Grigorenko, Maria G. Khrenova

et al.

The Journal of Physical Chemistry B, Journal Year: 2019, Volume and Issue: 123(29), P. 6133 - 6149

Published: May 1, 2019

Remarkable success in engineering novel efficient biomarkers based on fluorescent and photoactive proteins provokes a question of whether computational modeling their properties can contribute to this important field. In Feature Article, we analyze selected papers devoted computer simulations three types systems: the green protein its derivatives, flavin-binding proteins, phytochrome domains. The main emphasis is structures, optical spectra, chemical reactions chromophore-containing pockets. Quantum chemistry, quantum mechanics/molecular mechanics, molecular dynamics methods are effective tools these simulations. We highlight both stories persisting challenges, discussing ways elevating theoretical approaches level testable predictions.

Language: Английский

Singlet Oxygen Photophysics: From Liquid Solvents to Mammalian Cells DOI
Mikkel Bregnhøj, Frederik Thorning, Peter R. Ogilby

et al.

Chemical Reviews, Journal Year: 2024, Volume and Issue: 124(17), P. 9949 - 10051

Published: Aug. 6, 2024

Molecular oxygen, O

Language: Английский

Citations

12
Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment DOI Creative Commons
Andrey V. Solov’yov, Alexey V. Verkhovtsev, N. J. Mason

et al.

Chemical Reviews, Journal Year: 2024, Volume and Issue: 124(13), P. 8014 - 8129

Published: June 6, 2024

This roadmap reviews the new, highly interdisciplinary research field studying behavior of condensed matter systems exposed to radiation.The Review highlights several recent advances in and provides a for development over next decade.Condensed radiation can be inorganic, organic, or biological, finite infinite, composed different molecular species materials, exist phases, operate under thermodynamic conditions.Many key phenomena related irradiated are very similar understood based on same fundamental theoretical principles computational approaches.The multiscale nature such requires quantitative description radiation-induced effects occurring at spatial temporal scales, ranging from atomic macroscopic, interlinks between descriptions.The similarity their manifestation origins necessarily bring together disciplines, as physics, chemistry, biology, materials science, nanoscience, biomedical research, demonstrating numerous commonalities them.This is relevant many novel emerging technologies medical applications.

Language: Английский

Citations

9
Interfacing with the Brain: How Nanotechnology Can Contribute DOI Creative Commons
Abdullah Ahmed Ali Ahmed, Núria Alegret, Bethany Almeida

et al.

ACS Nano, Journal Year: 2025, Volume and Issue: unknown

Published: March 10, 2025

Interfacing artificial devices with the human brain is central goal of neurotechnology. Yet, our imaginations are often limited by currently available paradigms and technologies. Suggestions for brain-machine interfaces have changed over time, along technology. Mechanical levers cable winches were used to move parts during mechanical age. Sophisticated electronic wiring remote control arisen age, ultimately leading plug-and-play computer interfaces. Nonetheless, brains so complex that these visions, until recently, largely remained unreachable dreams. The general problem, thus far, most technology mechanically and/or electrically engineered, whereas a living, dynamic entity. As result, worlds difficult interface one another. Nanotechnology, which encompasses engineered solid-state objects integrated circuits, excels at small length scales single few hundred nanometers and, thus, matches sizes biomolecules, biomolecular assemblies, cells. Consequently, we envision nanomaterials nanotools as opportunities in alternative ways. Here, review existing literature on use nanotechnology look forward discussing perspectives limitations based authors' expertise across range complementary disciplines─from neuroscience, engineering, physics, chemistry biology medicine, science mathematics, social jurisprudence. We focus but also include information from related fields when useful complementary.

Language: Английский

Citations

1
Signal transduction in photoreceptor histidine kinases DOI Creative Commons
Andreas Möglich

Protein Science, Journal Year: 2019, Volume and Issue: 28(11), P. 1923 - 1946

Published: Aug. 9, 2019

Abstract Two‐component systems (TCS) constitute the predominant means by which prokaryotes read out and adapt to their environment. Canonical TCSs comprise a sensor histidine kinase (SHK), usually transmembrane receptor, response regulator (RR). In signal‐dependent manner, SHK autophosphorylates in turn transfers phosphoryl group RR then elicits downstream responses, often form of altered gene expression. SHKs also catalyze hydrolysis phospho‐RR, hence, tightly adjusting overall degree phosphorylation. Photoreceptor kinases are subset mostly soluble, cytosolic that sense light near‐ultraviolet near‐infrared spectral range. Owing experimental tractability, photoreceptor serve as paradigms provide unusually detailed molecular insight into signal detection, decoding, regulation activity. The synthesis recent results on receptors with light‐oxygen‐voltage, bacteriophytochrome microbial rhodopsin units identifies recurring, joint signaling strategies. Light signals initially absorbed module converted subtle rearrangements α helices, through pivoting rotation. These conformational transitions propagate parallel coiled‐coil linkers effector unit changes left‐handed superhelical winding. Within effector, conformations triggered modulate solvent accessibility residues engaged phosphatase activities. Taken together, consistent view entire trajectory from detection output emerges. underlying allosteric mechanisms could widely apply TCS general.

Language: Английский

Citations

69
Light‐Induced Dimerization Approaches to Control Cellular Processes DOI Creative Commons

Laura Klewer,

Yao‐Wen Wu

Chemistry - A European Journal, Journal Year: 2019, Volume and Issue: 25(54), P. 12452 - 12463

Published: July 15, 2019

Abstract Light‐inducible approaches provide a means to control biological systems with spatial and temporal resolution that is unmatched by traditional genetic perturbations. Recent developments of optogenetic chemo‐optogenetic for induced proximity in cells facilitate rapid reversible manipulation highly dynamic cellular processes have become valuable tools diverse applications. New expansions the toolbox signal transduction, genome editing, “painting” patterns active molecules onto membranes, light‐induced cell cycle control. A combination light‐ chemically dimerization also seen interesting progress. Herein, an overview emerging provided, recent applications tackling complex problems are discussed.

Language: Английский

Citations

63
Optogenetic control of mRNA localization and translation in live cells DOI

Na Yeon Kim,

Sangkyu Lee, Jeonghye Yu

et al.

Nature Cell Biology, Journal Year: 2020, Volume and Issue: 22(3), P. 341 - 352

Published: Feb. 17, 2020

Language: Английский

Citations

58
Optimized Vivid-derived Magnets photodimerizers for subcellular optogenetics in mammalian cells DOI Creative Commons
Lorena Benedetti, Jonathan S. Marvin, Hanieh Falahati

et al.

eLife, Journal Year: 2020, Volume and Issue: 9

Published: Nov. 11, 2020

Light-inducible dimerization protein modules enable precise temporal and spatial control of biological processes in non-invasive fashion. Among them, Magnets are small engineered from the Neurospora crassa photoreceptor Vivid by orthogonalizing homodimerization interface into complementary heterodimers. Both components, which well-tolerated as fusion partners, photoreceptors requiring simultaneous photoactivation to interact, enabling high spatiotemporal confinement with a single excitation wavelength. However, require concatemerization for efficient responses cell preincubation at 28°C be functional. Here we overcome these limitations engineering an optimized pair neither nor low temperature preincubation. We validated ‘enhanced’ (eMags) using them rapidly reversibly recruit proteins subcellular organelles, induce organelle contacts, reconstitute OSBP-VAP ER-Golgi tethering implicated phosphatidylinositol-4-phosphate transport metabolism. eMags represent very effective tool optogenetically manipulate physiological over whole cells or volumes.

Language: Английский

Citations

57
The Red Edge: Bilin-Binding Photoreceptors as Optogenetic Tools and Fluorescence Reporters DOI Creative Commons
Kun Tang, Hannes M. Beyer, Matías D. Zurbriggen

et al.

Chemical Reviews, Journal Year: 2021, Volume and Issue: 121(24), P. 14906 - 14956

Published: Oct. 20, 2021

This review adds the bilin-binding phytochromes to Chemical Reviews thematic issue "Optogenetics and Photopharmacology". The work is structured into two parts. We first outline photochemistry of covalently bound tetrapyrrole chromophore summarize relevant spectroscopic, kinetic, biochemical, physiological properties different families phytochromes. Based on this knowledge, we then describe engineering further improve these chromoproteins as photoswitches their employment in an ever-growing number optogenetic applications. Most applications rely light-controlled complex formation between plant photoreceptor PhyB phytochrome-interacting factors (PIFs) or C-terminal light-regulated domains with enzymatic functions present many bacterial algal Phytochrome-based tools are currently implemented bacteria, yeast, plants, animals achieve light control a wide range biological activities. These cover regulation gene expression, protein transport cell organelles, recruitment phytochrome- PIF-tagged proteins membranes other cellular compartments. compilation illustrates intrinsic advantages compared classes, e.g., bidirectional dual-wavelength enabling instant ON OFF regulation. In particular, long wavelength absorption fluorescence within "transparent window" makes attractive for requiring deep tissue penetration combination blue UV light-sensing photoreceptors. addition variability employing natural engineered phytochromes, also discuss recent progress development bilin-based fluorescent proteins.

Language: Английский

Citations

42
Red Light Optogenetics in Neuroscience DOI Creative Commons
K. Lehtinen, Miriam S. Nokia, Heikki Takala

et al.

Frontiers in Cellular Neuroscience, Journal Year: 2022, Volume and Issue: 15

Published: Jan. 3, 2022

Optogenetics, a field concentrating on controlling cellular functions by means of light-activated proteins, has shown tremendous potential in neuroscience. It possesses superior spatiotemporal resolution compared to the surgical, electrical, and pharmacological methods traditionally used studying brain function. A multitude optogenetic tools for neuroscience have been created that, example, enable control action generation via ion channels. Other proteins brain, long-term potentiation or ablate specific subtypes neurons. In vivo applications, however, majority are operated with blue, green, yellow light, which all limited penetration biological tissues red light especially infrared light. This difference is significant, considering size rodent major research model Our review will focus utilization light-operated We first outline advantages studies. Then we provide brief overview systems new developments field. Finally, highlight different further facilitate use optogenetics

Language: Английский

Citations

38
Signal transduction in light-oxygen-voltage receptors lacking the active-site glutamine DOI Creative Commons
Julia Dietler, Renate Gelfert,

Jennifer Kaiser

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: May 12, 2022

Abstract In nature as in biotechnology, light-oxygen-voltage photoreceptors perceive blue light to elicit spatiotemporally defined cellular responses. Photon absorption drives thioadduct formation between a conserved cysteine and the flavin chromophore. An equally conserved, proximal glutamine processes resultant protonation into downstream hydrogen-bond rearrangements. Here, we report that this glutamine, long deemed essential, is generally dispensable. its absence, several receptors invariably retained productive, if often attenuated, signaling Structures of paradigm at around 1 Å resolution revealed highly similar light-induced conformational changes, irrespective whether present. Naturally occurring, glutamine-deficient likely serve bona fide photoreceptors, showcase for diguanylate cyclase. We propose without water molecules transiently approach chromophore thus propagate downstream. Signaling appears intrinsic receptors, which pertains biotechnological applications suggests evolutionary descendance from redox-active flavoproteins.

Language: Английский

Citations

38