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Proceedings of the National Academy of... Mar 2021Hole hopping through tryptophan/tyrosine chains enables rapid unidirectional charge transport over long distances. We have elucidated structural and dynamical factors...
Hole hopping through tryptophan/tyrosine chains enables rapid unidirectional charge transport over long distances. We have elucidated structural and dynamical factors controlling hopping speed and efficiency in two modified azurin constructs that include a rhenium(I) sensitizer, Re(His)(CO)(dmp), and one or two tryptophans (W, W). Experimental kinetics investigations showed that the two closely spaced (3 to 4 Å) intervening tryptophans dramatically accelerated long-range electron transfer (ET) from Cu to the photoexcited sensitizer. In our theoretical work, we found that time-dependent density-functional theory (TDDFT) quantum mechanics/molecular mechanics/molecular dynamics (QM/MM/MD) trajectories of low-lying triplet excited states of Re(His)(CO)(dmp)-W(-W) exhibited crossings between sensitizer-localized (*Re) and charge-separated [Re(His)(CO)(dmp)/(W or W)] (CS1 or CS2) states. Our analysis revealed that the distances, angles, and mutual orientations of ET-active cofactors fluctuate in a relatively narrow range in which the cofactors are strongly coupled, enabling adiabatic ET. Water-dominated electrostatic field fluctuations bring *Re and CS1 states to a crossing where *Re(CO)(dmp)←W ET occurs, and CS1 becomes the lowest triplet state. ET is promoted by solvation dynamics around *Re(CO)(dmp)(W); and CS1 is stabilized by Re(dmp)/W electron/hole interaction and enhanced W solvation. The second hop, W←W, is facilitated by water fluctuations near the W/W unit, taking place when the electrostatic potential at W drops well below that at W Insufficient solvation and reorganization around W make W←W ET endergonic, shifting the equilibrium toward W and decreasing the charge-separation yield. We suggest that multiscale TDDFT/MM/MD is a suitable technique to model the simultaneous evolution of photogenerated excited-state manifolds.
Topics: Azurin; Electron Transport; Electrons; Molecular Dynamics Simulation; Oxidation-Reduction; Photochemistry; Pseudomonas aeruginosa; Quantum Theory; Rhenium; Static Electricity; Tryptophan; Water
PubMed: 33836608
DOI: 10.1073/pnas.2024627118 -
Molecules (Basel, Switzerland) Aug 2020This review focuses on the description of several examples of supramolecular assemblies of phthalocyanine derivatives differently functionalized and interfaced with... (Review)
Review
This review focuses on the description of several examples of supramolecular assemblies of phthalocyanine derivatives differently functionalized and interfaced with diverse kinds of chemical species for photo-induced phenomena applications. In fact, the role of different substituents was investigated in order to tune peculiar aggregates formation as well as, with the same aim, the possibility to interface these derivatives with other molecular species, as electron donor and acceptor, carbon allotropes, cyclodextrins, protein cages, drugs. Phthalocyanine photo-physical features are indeed really interesting and appealing but need to be preserved and optimized. Here, we highlight that the supramolecular approach is a versatile method to build up very complex and functional architectures. Further, the possibility to minimize the organization energy and to facilitate the spontaneous assembly of the molecules, in numerous examples, has been demonstrated to be more useful and performing than the covalent approach.
Topics: Electron Transport; Indoles; Isoindoles; Light; Photochemistry; Polymers; Thermodynamics
PubMed: 32824375
DOI: 10.3390/molecules25163742 -
Biochemistry Jan 2018Adduction of an electrophile to privileged sensor proteins and the resulting phenotypically dominant responses are increasingly appreciated as being essential for...
Adduction of an electrophile to privileged sensor proteins and the resulting phenotypically dominant responses are increasingly appreciated as being essential for metazoan health. Functional similarities between the biological electrophiles and electrophilic pharmacophores commonly found in covalent drugs further fortify the translational relevance of these small-molecule signals. Genetically encodable or small-molecule-based fluorescent reporters and redox proteomics have revolutionized the observation and profiling of cellular redox states and electrophile-sensor proteins, respectively. However, precision mapping between specific redox-modified targets and specific responses has only recently begun to be addressed, and systems tractable to both genetic manipulation and on-target redox signaling in vivo remain largely limited. Here we engineer transgenic Caenorhabditis elegans expressing functional HaloTagged fusion proteins and use this system to develop a generalizable light-controlled approach to tagging a prototypical electrophile-sensor protein with native electrophiles in vivo. The method circumvents issues associated with low uptake/distribution and toxicity/promiscuity. Given the validated success of C. elegans in aging studies, this optimized platform offers a new lens with which to scrutinize how on-target electrophile signaling influences redox-dependent life span regulation.
Topics: Aldehydes; Animals; Animals, Genetically Modified; Bacterial Proteins; Caenorhabditis elegans; Caenorhabditis elegans Proteins; Electrochemistry; Hydrolases; Kelch-Like ECH-Associated Protein 1; Longevity; Luminescent Proteins; Oxidation-Reduction; Photochemistry; Protein Processing, Post-Translational; Recombinant Fusion Proteins; Transgenes; Red Fluorescent Protein
PubMed: 28857552
DOI: 10.1021/acs.biochem.7b00642 -
International Journal of Molecular... Mar 2019Protein phosphorylation regulated by protein kinases, as well as their dephosphorylation, is one of the most common post-translational modifications, and plays important... (Review)
Review
Protein phosphorylation regulated by protein kinases, as well as their dephosphorylation, is one of the most common post-translational modifications, and plays important roles in physiological activities, such as intracellular signal communications, gene transcription, cell proliferation and apoptosis. Over-expression of protein kinases is closely associated with various diseases. Consequently, accurate detection of protein kinases activities and their relevant inhibitors screening is critically important, not only to the biochemical research, but also to the clinical diagnosis and therapy. Nanomaterials, taking advantage of large surface areas, as well as excellent electrical, catalytic, magnetic and optical properties, have been utilized as target concentrators, recognition components, signal transducer or amplification elements in protein kinase related assays. This review summarizes the recent representative works to highlight the applications of nanomaterials in different biosensor technologies for protein kinases activities detection and their inhibitors screening. First, different nanomaterials developed for phosphoprotein/phosphopeptide enrichment and phosphate recognition are introduced. Next, representative works are selected that mainly focus on the utilization of nanomaterials as signal transducer or amplification elements in various protein kinases sensing platforms, such as electrochemical, colorimetric, fluorescent, and mass spectroscopy-based approaches. Finally, the major challenges and perspectives of nanomaterials being applied in protein kinases related assays are discussed.
Topics: Animals; Biosensing Techniques; Colorimetry; Electrochemical Techniques; Enzyme Activation; Humans; Nanostructures; Nanotechnology; Phosphates; Phosphoproteins; Phosphorylation; Photochemistry; Protein Binding; Protein Kinases; Signal Transduction
PubMed: 30901923
DOI: 10.3390/ijms20061440 -
BBA Advances 2023The present Review is an attempt by projecting the basic knowledge on photochemical proton transfer to achieve consistent understanding of proton motions in...
The present Review is an attempt by projecting the basic knowledge on photochemical proton transfer to achieve consistent understanding of proton motions in biocatalysis, photobiocatalysis, operation of selective proton channels and systems of photosynthesis and cellular respiration. The basic mechanisms of proton transfer are in active research in the electronic excited states of organic molecules. This allows observing the reactions directly in real time, providing their dynamic and thermodynamic description and coupling with structural and energetic variables. These achievements lay the background for understanding the proton transfers in biochemical reactions, where such ultrafast events are not only 'optically silent' but are hidden under much slower rate-limiting steps, such as protein conformational changes, substrate binding and product release. The mechanistic description of biocatalytic and transmembrane proton transport is shown as a multi-step proton migration that is available for modeling in photochemical reactions. For explaining the formation of transmembrane proton gradients, a simple 'proton lift' concept is presented that may be the basis of further research and analysis.
PubMed: 37378355
DOI: 10.1016/j.bbadva.2023.100085 -
Current status and future prospects for enabling chemistry technology in the drug discovery process.F1000Research 2016This review covers recent advances in the implementation of enabling chemistry technologies into the drug discovery process. Areas covered include parallel synthesis... (Review)
Review
This review covers recent advances in the implementation of enabling chemistry technologies into the drug discovery process. Areas covered include parallel synthesis chemistry, high-throughput experimentation, automated synthesis and purification methods, flow chemistry methodology including photochemistry, electrochemistry, and the handling of "dangerous" reagents. Also featured are advances in the "computer-assisted drug design" area and the expanding application of novel mass spectrometry-based techniques to a wide range of drug discovery activities.
PubMed: 27781094
DOI: 10.12688/f1000research.9515.1 -
Molecules (Basel, Switzerland) May 2020The use of light-activated chemical probes to study biological interactions was first discovered in the 1960s, and has since found many applications in studying diseases... (Review)
Review
The use of light-activated chemical probes to study biological interactions was first discovered in the 1960s, and has since found many applications in studying diseases and gaining deeper insight into various cellular mechanisms involving protein-protein, protein-nucleic acid, protein-ligand (drug, probe), and protein-co-factor interactions, among others. This technique, often referred to as photoaffinity labelling, uses radical precursors that react almost instantaneously to yield spatial and temporal information about the nature of the interaction and the interacting partner(s). This review focuses on the recent advances in chemical biology in the use of benzophenones and diazirines, two of the most commonly known light-activatable radical precursors, with a focus on the last three years, and is intended to provide a solid understanding of their chemical and biological principles and their applications.
Topics: Benzophenones; Diazomethane; Photoaffinity Labels; Photochemistry
PubMed: 32414020
DOI: 10.3390/molecules25102285 -
Chemical Reviews Dec 2021This review adds the bilin-binding phytochromes to the thematic issue "Optogenetics and Photopharmacology". The work is structured into two parts. We first outline the... (Review)
Review
This review adds the bilin-binding phytochromes to the thematic issue "Optogenetics and Photopharmacology". The work is structured into two parts. We first outline the photochemistry of the covalently bound tetrapyrrole chromophore and summarize relevant spectroscopic, kinetic, biochemical, and physiological properties of the different families of phytochromes. Based on this knowledge, we then describe the engineering of phytochromes to further improve these chromoproteins as photoswitches and review their employment in an ever-growing number of different optogenetic applications. Most applications rely on the light-controlled complex formation between the plant photoreceptor PhyB and phytochrome-interacting factors (PIFs) or C-terminal light-regulated domains with enzymatic functions present in many bacterial and algal phytochromes. Phytochrome-based optogenetic tools are currently implemented in bacteria, yeast, plants, and animals to achieve light control of a wide range of biological activities. These cover the regulation of gene expression, protein transport into cell organelles, and the recruitment of phytochrome- or PIF-tagged proteins to membranes and other cellular compartments. This compilation illustrates the intrinsic advantages of phytochromes compared to other photoreceptor classes, e.g., their bidirectional dual-wavelength control enabling instant ON and OFF regulation. In particular, the long wavelength range of absorption and fluorescence within the "transparent window" makes phytochromes attractive for complex applications requiring deep tissue penetration or dual-wavelength control in combination with blue and UV light-sensing photoreceptors. In addition to the wide variability of applications employing natural and engineered phytochromes, we also discuss recent progress in the development of bilin-based fluorescent proteins.
Topics: Animals; Bile Pigments; Light; Optogenetics; Photochemistry; Photoreceptor Cells; Phytochrome
PubMed: 34669383
DOI: 10.1021/acs.chemrev.1c00194 -
Open Biology Apr 2019The rapid response of photosynthetic organisms to fluctuations in ambient light intensity is incompletely understood at both the molecular and membrane levels. In this... (Review)
Review
The rapid response of photosynthetic organisms to fluctuations in ambient light intensity is incompletely understood at both the molecular and membrane levels. In this review, we describe research from our group over a 10-year period aimed at identifying the photophysical mechanisms used by plants, algae and mosses to control the efficiency of light harvesting by photosystem II on the seconds-to-minutes time scale. To complement the spectroscopic data, we describe three models capable of describing the measured response at a quantitative level. The review attempts to provide an integrated view that has emerged from our work, and briefly looks forward to future experimental and modelling efforts that will refine and expand our understanding of a process that significantly influences crop yields.
Topics: Algorithms; Chlorophyll; Energy Transfer; Light; Light-Harvesting Protein Complexes; Models, Biological; Photochemistry; Photosynthesis; Photosystem II Protein Complex; Plants
PubMed: 30966997
DOI: 10.1098/rsob.190043 -
SLAS Technology Aug 2018Recently advances in miniaturization and automation have been utilized to rapidly decrease the time to result for microbiology testing in the clinic. These advances have...
Recently advances in miniaturization and automation have been utilized to rapidly decrease the time to result for microbiology testing in the clinic. These advances have been made due to the limitations of conventional culture-based microbiology methods, including agar plate and microbroth dilution, which have long turnaround times and require physicians to treat patients empirically with antibiotics before test results are available. Currently, there exist similar limitations in pharmaceutical sterility and bioburden testing, where the long turnaround times associated with standard microbiology testing drive costly inefficiencies in workflows. These include the time lag associated with sterility screening within drug production lines and the warehousing cost and time delays within supply chains during product testing. Herein, we demonstrate a proof-of-concept combination of a rapid microfluidic assay and an efficient cell filtration process that enables a path toward integrating rapid tests directly into pharmaceutical microbiological screening workflows. We demonstrate separation and detection of Escherichia coli directly captured and analyzed from a mammalian (i.e., CHO) cell culture with a 3.0 h incubation. The demonstration is performed using a membrane filtration module that is compatible with sampling from bioreactors, enabling in-line sampling and process monitoring.
Topics: Animals; Bacteria; Bioreactors; CHO Cells; Coloring Agents; Cricetinae; Cricetulus; Filtration; Indicators and Reagents; Microbiological Techniques; Microfluidics; Photochemistry; Technology, Pharmaceutical
PubMed: 30027813
DOI: 10.1177/2472630318779758