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The ability to exploit energy autonomously is one of the hallmarks of Life. Mastering such processes in artificial nanosystems can open unforeseen technological opportunities. In the last decades, light- and chemically-driven autonomous systems have been developed in relation to conformational motion and self-assembly, mostly in relation to molecular motors. On the contrary, despite electrical energy is an attractive energy source to power nanosystems, its autonomous exploitation remains essentially unexplored. Herein we demonstrate the autonomous exploitation of electrical energy by a self-assembling system. Threading and dethreading motions of a pseudorotaxane take place autonomously in solution, between the electrodes of a scanning electrochemical microscope. This innovative actuation mode allows operating a molecular machine with an energy efficiency of 9%, unprecedented in autonomous systems. The strategy is general and can be applied to any redox-driven system. Ultimately, our study brings molecular nanoscience one step closer to everyday technology.

Current cancer research is limited by the availability of reliable in vivo and in vitro models that are able to reproduce the fundamental hallmarks of cancer. Animal experimentation is of paramount importance in the progress of research, but it is becoming more evident that it has several limitations due to the numerous differences between animal tissues and real, in vivo human tissues. 3D bioprinting techniques have become an attractive tool for many basic and applied research fields. Concerning cancer, this technology has enabled the development of three-dimensional in vitro tumor models that recreate the characteristics of real tissues and look extremely promising for studying cancer cell biology. As 3D bioprinting is a relatively recently developed technique, there is still a lack of characterization of the chemical cellular microenvironment of 3D bioprinted constructs. In this work, we fabricated a cervical tumor model obtained by 3D bioprinting of HeLa cells in an alginate-based matrix. Characterization of the spheroid population obtained as a function of culturing time was performed by phase-contrast and confocal fluorescence microscopies. Scanning electrochemical microscopy and platinum nanoelectrodes were employed to characterize oxygen concentrations—a fundamental characteristic of the cellular microenvironment—with a high spatial resolution within the 3D bioprinted cervical tumor model; we also demonstrated that the diffusion of a molecular model of drugs in the 3D bioprinted construct, in which the spheroids were embedded, could be measured quantitatively over time using scanning electrochemical microscopy.

In memory of the 85th birthday of Yakov S. Lebedev (Moscow), who died in 1996, we start this Review on soft-glass matrix effects in donor–acceptor complexes with an appreciation of his pioneering work on high-field EPR spectroscopy on tribochemically generated donor–acceptor complexes. The mechanochemical activation of polycrystalline mixtures of porphyrins (and other donors) and quinone acceptors was found to produce large concentrations of triplet donor molecules and donor–acceptor radical pairs with unusual stability. The Review is continued with reporting on W-band high-field EPR and fast-laser studies on disaccharide matrix effects on structure and dynamics of donor–acceptor protein complexes related to photosynthesis, including the non-oxygenic bacterial reaction center (RC) and the oxygenic RCs Photosystem I (PS I) and Photosystem II (PS II, preliminary results). Some organisms can survive complete dehydration and high temperatures by adopting an anhydrobiotic state in which the intracellular medium contains large amounts of disaccharides, in particular trehalose and sucrose. Trehalose is most effective in protecting biostructures, both in vivo and in vitro. To clarify the molecular mechanisms of disaccharide bioprotection, structure and dynamics of sucrose and trehalose matrices at different controlled hydration levels were probed by perdeuterated nitroxide spin labels and native cofactor intermediates in their charge-separated states. Trehalose forms a homogeneous amorphous phase in which the hosted molecules are uniformly distributed. Notably, their rotational mobility at room temperature is dramatically impaired by thetrehalose H-bonding network confinement to an extent that in normal protein–matrix systems is only observed at low temperatures around 150K. From the experimental results, formation of an extended H-bonding network of trehalose with protein molecules is inferred, involving both bulk and local water molecules. The H-bond network extends homogeneously over the whole matrix integrating and immobilizing the hosted protein. Taken together, these observations suggest that in photosystems, such as bacterial RCs and PS I complexes, of different size and complexity regarding subunit composition and oligomeric organization, the molecular configuration of the cofactors involved in the primary processes of charge separation is not significantly distorted by incorporation into trehalose glass, even under extensive dehydration. By means of pulsed W-band high-field multiresonance EPR spectroscopies, such as ELDOR-detected NMR and ENDOR, in conjunction with using isotope labeled water (D2O and H217O), the biologically important issue of sensing and quantification of local water in proteins is addressed. The bacterial RC embedded into the trehalose glass matrix is used as model system. The two native radical cofactor ions of the primary electron donor and acceptor as well as an artificial nitroxide spin label site-specifically attached to the protein surface are studied in the experiments. The three paramagnetic reporter groups probe distinctly different local environments. They sense water molecules via their magnetic hyperfine and quadrupole interactions with either deuterons or 17O nuclei. It is shown that by using oxygen-17 labeled water, quantitative conclusions can be drawn differentiating between local and bulk water. It is concluded that dry trehalose operates as anhydrobiotic protein stabilizer by means of selective changes in the first solvation shell of the protein upon trehalose–matrix dehydration with subsequent changes in the hydrogen-bonding network. Such changes usually have an impact on the global function of a biological system. Finally, preliminary results of optical and W-band EPR experiments on the extremolytes ectoine and its derivative hydroxyectoine are reported; these compounds appear to share several stress-protecting properties with trehalose in terms of stabilizing protein matrices. For instance, they display remarkable stabilizing capabilities towards sensitive proteins and enzymes with respect to freeze-thawing, heat-treatment, and freeze-drying procedures. Moreover, hydroxyectoine is a good glass-forming compound and exhibits a remarkable bioprotective effect against desiccation and heat denaturation of functional protein complexes.

Mapping of the metabolic activity of tumor tissues represents a fundamental approach to better identify the tumor type, elucidate metastatic mechanisms and support the development of targeted cancer therapies. The spatially resolved quantification of Warburg effect key metabolites, such as glucose and lactate, is essential. Miniaturized electrochemical biosensors scanned over cancer cells and tumor tissue to visualize the metabolic characteristics of a tumor is attractive but very challenging due to the limited oxygen availability in the hypoxic environments of tumors that impedes the reliable applicability of glucose oxidase-based glucose micro-biosensors. Herein, the development and application of a new glucose micro-biosensor is presented that can be reliably operated under hypoxic conditions. The micro-biosensor is fabricated in a one-step synthesis by entrapping during the electrochemically driven growth of a polymeric matrix on a platinum microelectrode glucose oxidase and a catalytically active Prussian blue type aggregate and mediator. The as-obtained functionalization improves significantly the sensitivity of the developed micro-biosensor for glucose detection under hypoxic conditions compared to normoxic conditions. By using the micro-biosensor as non-invasive sensing probe in Scanning Electrochemical Microscopy (SECM), the glucose uptake by a breast metastatic adenocarcinoma cell line, with an epithelial morphology, is measured.

The ability to exploit energy autonomously is one of the hallmarks of Life. Mastering such processes in artificial nanosystems can open unforeseen technological opportunities. In the last decades, light- and chemically-driven autonomous systems have been developed in relation to conformational motion and self-assembly. On the contrary, the autonomous exploitation of electrical energy remains essentially unexplored, despite being an attractive energy source. Herein we demonstrate the autonomous operation of an electrochemically-powered self-assembling nanomachine. Threading and dethreading motions of a pseudorotaxane take place autonomously in solution, between the electrodes of a scanning electrochemical microscope. This innovative actuation mode allows operating a molecular machine with an energy efficiency of 9%, unprecedented in autonomous systems. The strategy is general and can be applied to any redox-driven system, including molecular pumps that perform work repetitively. Ultimately, our study brings molecular nanoscience one step closer to everyday technology.

Tardigrades, also known as water bears, make up a phylum of small but extremely hardy animals, renowned for their ability to survive extreme stresses, including desiccation. How tardigrades survive desiccation is one of the enduring mysteries of animal physiology. Here we show that CAHS D, an intrinsically disordered protein belonging to a unique family of proteins possessed only by tardigrades, undergoes a liquid-to-gel phase transition in a concentration dependent manner. Unlike other gelling proteins, such as gelatin, our data support a mechanism in which gel formation of CAHS D is driven by intermolecular β-β interactions. We find that gel formation corresponds with strong coordination of water and slowing of water diffusion. The degree of water coordination correlates with the ability of CAHS D to protect lactate dehydrogenase from unfolding when dried. This implies that the mechanism for unfolding protection can be attributed to a combination of hydration and slowed molecular motion. Conversely, rapid diffusion leading to efficient molecular shielding appears to be the predominant mechanism preventing protein aggregation. Our study demonstrates that distinct mechanisms are required for holistic protection during desiccation, and that protectants, such as CAHS D, can act as molecular ‘Swiss Army Knives’ capable of providing protection through several different mechanisms simultaneously.

The electronic, optical, and redox properties of thiophene-based materials have made them pivotal in nanoscience and nanotechnology. However, the exploitation of oligothiophenes in photodynamic therapy is hindered by their intrinsic hydrophobicity that lowers their biocompatibility and availability in water environments. Here, we developed human serum albumin (HSA)–oligothiophene bioconjugates that afford the use of insoluble oligothiophenes in physiological environments. UV–vis and electrophoresis proved the conjugation of the oligothiophene sensitizers to the protein. The bioconjugate is water-soluble and biocompatible, does not have any “dark toxicity”, and preserves HSA in the physiological monomeric form, as confirmed by dynamic light scattering and circular dichroism measurements. In contrast, upon irradiation with ultralow light doses, the bioconjugate efficiently produces reactive oxygen species (ROS) and leads to the complete eradication of cancer cells. Real-time monitoring of the photokilling activity of the HSA–oligothiophene bioconjugate shows that living cells “explode” upon irradiation. Photodependent and dose-dependent apoptosis is one of the primary mechanisms of cell death activated by bioconjugate irradiation. The bioconjugate is a novel theranostic platform able to generate ROS intracellularly and provide imaging through the fluorescence of the oligothiophene. It is also a real-time self-reporting system able to monitor the apoptotic process. The induced phototoxicity is strongly confined to the irradiated region, showing localized killing of cancer cells by precise light activation of the bioconjugate.

The kinetics of flash-induced re-reduction of the Photosystem II (PS II) primary electron donor P680 was studied in solution and in trehalose glassy matrices at different relative humidity. In solution, and in the re-dissolved glass, kinetics were dominated by two fast components with lifetimes in the range of 2–7 μs, which accounted for >85% of the decay. These components were ascribed to the direct electron transfer from the redox-active tyrosine YZ to P680 +. The minor slower components were due to charge recombination between the primary plastoquinone acceptor QA − and P680 +. Incorporation of the PS II complex into the trehalose glassy matrix and its successive dehydration caused a progressive increase in the lifetime of all kinetic phases, accompanied by an increase of the amplitudes of the slower phases at the expense of the faster phases. At 63% relative humidity the fast components contribution dropped to ~50%. A further dehydration of the trehalose glass did not change the lifetimes and contribution of the kinetic components. This effect was ascribed to the decrease of conformational mobility of the protein domain between YZ and P680, which resulted in the inhibition of YZ → P680 + electron transfer in about half of the PS II population, wherein the recombination between QA − and P680 + occurred. The data indicate that PS II binds a larger number of water molecules as compared to PS I complexes. We conclude that our data disprove the “water replacement” hypothesis of trehalose matrix biopreservation.

In the present study, we have investigated the effect of hydroxyectoine (Ect-OH), a heterocyclic amino acid, on oxygen evolution in photosystem II (PS II) membrane fragments and on photoinhibition of Mn-depleted PS II (apo-WOC-PS II) preparations. The degree of photoinhibition of apo-WOC-PS II preparations was estimated by the loss of the capability of exogenous electron donor (sodium ascorbate) to restore the amplitude of light-induced changes of chlorophyll fluorescence yield (∆F). It was found that Ect-OH (i) stimulates the oxygen-evolving activity of PS II, (ii) accelerates the electron transfer from exogenous electron donors (K4[Fe(CN)6], DPC, TMPD, Fe2+, and Mn2+) to the reaction center of apo-WOC-PS II, (iii) enhances the protective effect of exogenous electron donors against donor-side photoinhibition of apo-WOC-PS II preparations. It is assumed that Ect-OH can serve as an artificial electron donor for apo-WOC-PS II, which does not directly interact with either the donor or acceptor side of the reaction center. We suggest that the protein conformation in the presence of Ect-OH, which affects the extent of hydration, becomes favorable for accepting electrons from exogenous donors. To our knowledge, this is the first study dealing with redox activity of Ect-OH towards photosynthetic pigment–protein complexes.

Genetic alterations affecting subunits of the mitochondrial respiratory chain complexes often impair their catalytic activities and result in enhanced production of reactive oxygen species (ROS). An electrochemical setup was employed to quantify mitochondrial ROS production in plasma membrane-permeabilized cellular models of two genetic diseases: the Δcytb cell line bearing a microdeletion in the mitochondrial MT-CYB gene causing a severe encephalomyopathy and the RJ206 cell line, harbouring a pathogenic mutation associated with Leber's hereditary optic neuropathy. The responses of black platinum modified microelectrodes to the most common cellular redox buffers, namely, NADH and glutathione, as well as substrates deriving from the oxidative metabolism of glucose, were investigated; a relatively high sensitivity, although lower than that for ROS, was shown for NADH. Time-resolved amperometric measurements of ROS production upon respiratory chain activation at high NADH/NAD+ ratio revealed a 50 % and 100 % increase of ROS in cells bearing defective complex I and complex III, respectively, as compared to wild type cells.

Hybrid nanomaterials are a subject of extensive research in nanomedicine, and their clinical application is reasonably envisaged in the near future. However, the fate of nanomaterials in biological environments poses serious limitations to their application; therefore, schemes to monitor them and gain control on their toxicity could be of great help for the development of the field. Here, we propose a probe for PEGylated nanosurfaces based on hyaluronic acid (HA) functionalized with rhodamine B (RB). We show that the high-affinity interaction of this fluorogenic hyaluronan (HA-RB) with nanoparticles exposing PEGylated surfaces results in their sensing, labeling for super-resolution imaging, and synergistic cellular internalization. HA-RB forms nanogels that interact with high affinity-down to the picomolar range-with silica nanoparticles, selectively when their surface is covered by a soft and amphiphilic layer. This surface-driven interaction triggers the enhancement of the luminescence intensity of the dyes, otherwise self-quenched in HA-RB nanogels. The sensitive labeling of specific nanosurfaces also allowed us to obtain their super-resolution imaging via binding-activated localization microscopy (BALM). Finally, we show how this high-affinity interaction activates a synergistic cellular uptake of silica nanoparticles and HA-RB nanogels, followed by a differential fate of the two partner nanomaterials inside cells.

Summary Protein reduction/oxidation processes trigger and finely regulate a myriad of physiological and pathological cellular functions. Many biochemical and biophysical stimuli have been recently explored to precisely and effectively modulate intracellular redox signaling, due to the considerable therapeutic potential. Here, we propose a first step toward an approach based on visible light excitation of a thiophene-based semiconducting polymer (P3HT), demonstrating the realization of a hybrid interface with the Cytochrome c protein (CytC), in an extracellular environment. By means of scanning electrochemical microscopy and spectro-electrochemistry measurements, we demonstrate that, upon optical stimulation, a functional interaction between P3HT and CytC is established. Polymer optical excitation locally triggers photoelectrochemical reactions, leading to modulation of CytC redox activity, either through an intermediate step, involving reactive oxygen species formation, or via a direct photoreduction process. Both processes are triggered by light, thus allowing excellent spatiotemporal resolution, paving the way to precise modulation of protein redox signaling., Graphical Abstract, Highlights • Conjugated polymers and light modulate the redox state of cytochrome c protein • Phototransduction processes are clarified by electrochemical microscopy • The approach opens the way to selective optical triggering of protein redox state, Interfacial Electrochemistry; Biochemistry Methods; Polymers

Cells of the facultative photosynthetic bacterium Rhodobacter capsulatus exploit the simultaneous presence in the cultural medium of the toxic oxyanion tellurite (TeO32-) and the redox mediator lawsone (2-hydroxy-1,4-naphthoquinone) by reducing tellurite to metal Te0 nanoprecipitates (TeNPs) outside the cells. Here we have studied the mechanism by which lawsone interacts with metabolically active cells and analysed both structure and composition of the TeNPs collected from the growth medium of phototrophycally grown R. capsulatus. High Resolution Transmission Electron Microscopy (HR-TEM) images and Energy-Dispersive X-ray (EDX) microanalysis of TeNPs showed a central core of polycrystalline tellurium interspersed in an organic matrix with a predominant protein-based composition. The main proteins from Te0 nanostructures were identified by Liquid Chromatography tandem-Mass Spectrometry and were all correlated with the cell outer membrane composition. The interaction of reduced lawsone with tellurite and with the bacterial cells was probed by Cyclic Voltammetry and Scanning ElectroChemical Microscopy (SECM). We concluded that lawsone is required for the reduction of tellurite to metal Te0 in a reaction mechanism dependent on reducing equivalents deriving from the cell photosynthetic metabolism. SECM experiments demonstrate that lawsone, by diffusing inside the bacterial cells, is effectively available at the membrane site of the photosynthetic electron transport chain.

Using isotope labeled water (D2O and H217O) and pulsed W-band (94 GHz) high- field multiresonance EPR spectroscopies, such as ELDOR-detected NMR and ENDOR, the biologically important question of detection and quantification of local water in proteins is addressed. A bacterial reaction center (bRC) from Rhodobacter sphaeroides R26 embedded into a trehalose glass matrix is used as a model system. The bRC hosts the two native radical cofactor ions Image ID:c7cp03942e-t1.gif (primary electron donor) and Image ID:c7cp03942e-t2.gif (primary electron acceptor) as well as an artificial nitroxide spin label site-specifically attached to the surface of the H-protein domain. The three paramagnetic reporter groups have distinctly different local environments. They serve as local probes to detect water molecules via magnetic interactions (electron–nuclear hyperfine and quadrupole) with either deuterons or 17O nuclei. bRCs were equilibrated in an atmosphere of different relative humidities allowing us to control precisely the hydration levels of the protein. We show that by using oxygen-17 labeled water quantitative conclusions can be made in contrast to using D2O which suffers from proton–deuterium exchange processes in the protein. From the experiments we also conclude that dry trehalose operates as an anhydrobiotic protein stabilizer in line with the “anchorage hypothesis” of bio-protection. It predicts selective changes in the first solvation shell of the protein upon trehalose–matrix dehydration with subsequent changes in the hydrogen-bonding network. Changes in hydrogen-bonding patterns usually have an impact on the global function of a biological system.

Disaccharide glasses are increasingly used to immobilize proteins at room temperature for structural/functional studies and long-term preservation. To unravel the molecular basis of protein immobilization, we studied the effect of sugar/protein concentration ratios in trehalose or sucrose matrixes, in which the bacterial photosynthetic reaction center (RC) was embedded as a model protein. The structural, dynamical, and H-bonding characteristics of the sugar-protein systems were probed by high-field W-band EPR of a matrix-dissolved nitroxide radical. We discovered that RC immobilization and thermal stabilization, being independent of the protein concentration in trehalose, occur in sucrose only at sufficiently low sugar/protein ratios. EPR reveals that only under such conditions does sucrose form a microscopically homogeneous matrix that immobilizes, via H-bonds, the nitroxide probe. We conclude that the protein immobilization capability depends critically on the propensity of the glass-forming sugar to create intermolecular H-bond networks, thus establishing long-range, homogeneous connectivity within the matrix.

The ubiquinol:cytochrome (cyt) c oxidoreductase (or cyt bc1) is an important membrane protein complex in photosynthetic and respiratory energy transduction. In bacteria such as Rhodobacter capsulatus it is constituted of three subunits: the iron-sulfur protein, cyt b and cyt c1, which form two catalytic domains, the Qo (hydroquinone (QH2) oxidation) and Qi (quinone (Q) reduction) sites. At the Qo site, the pathways of bifurcated electron transfers emanating from QH2 oxidation are known, but the associated proton release routes are not well defined. In energy transducing complexes, Zn2+ binding amino acid residues often correlate with proton uptake or release pathways. Earlier, using combined EXAFS and structural studies, we identified Zn coordinating residues of mitochondrial and bacterial cyt bc1. In this work, using the genetically tractable bacterial cyt bc1, we substituted each of the proposed Zn binding residues with non-protonatable side chains. Among these mutants, only the His291Leu substitution destroyed almost completely the Qo site catalysis without perturbing significantly the redox properties of the cofactors or the assembly of the complex. In this mutant, which is unable to support photosynthetic growth, the bifurcated electron transfer reactions that result from QH2 oxidation at the Qo site, as well as the associated proton(s) release, were dramatically impaired. Based on these findings, on the putative role of His291 in liganding Zn, and on its solvent exposed and highly conserved position, we propose that His291 of cyt b is critical for proton release associated to QH2 oxidation at the Qo site of cyt bc1.

Levels of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in cells and cell redox balance are of great interest in live cells as they are correlated to several pathological and physiological conditions of living cells. ROS and RNS detection is limited due to their spatially restricted abundance: they are usually located in sub-cellular areas (e.g., in specific organelles) at low concentration. In this work, we will review and highlight the electrochemical approach to this bio-analytical issue. Combining electrochemical methods and miniaturization strategies, specific, highly sensitive, time, and spatially resolved measurements of cellular oxidative stress and redox balance analysis are possible. Graphical abstract In this work, we highlight and review the use of electrochemistry for the highly spatial and temporal resolved detection of ROS/RNS levels and of redox balance in living cells. These levels are central in several pathological and physiological conditions and the electrochemical approach is a vibrant bio-analytical trend in this field.

Protein aggregation is a complex physiological process, primarily determined by stress-related factors revealing the hidden aggregation propensity of proteins that otherwise are fully soluble. Here we report a mechanism by which glycolytic glyceraldehyde-3-phosphate dehydrogenase of Arabidopsis thaliana (AtGAPC1) is primed to form insoluble aggregates by the glutathionylation of its catalytic cysteine (Cys149). Following a lag phase, glutathionylated AtGAPC1 initiates a self-aggregation process resulting in the formation of branched chains of globular particles made of partially misfolded and totally inactive proteins. GSH molecules within AtGAPC1 active sites are suggested to provide the initial destabilizing signal. The following removal of glutathione by the formation of an alternative disulfide bond between Cys149 and Cys153 reinforces the aggregation process. Besides acting as a protective mechanism against overoxidation, S-glutathionylation of AtGAPC1 triggers an unexpected aggregation pathway with completely different and still unexplored physiological implications.

Protein aggregation is a complex physiological process, primarily determined by stress-related factors revealing the hidden aggregation propensity of proteins that otherwise are fully soluble. Here we report a mechanism by which glycolytic glyceraldehyde-3-phosphate dehydrogenase of Arabidopsis thaliana (AtGAPC1) is primed to form insoluble aggregates by the glutathionylation of its catalytic cysteine (Cys149). Following a lag phase, glutathionylated AtGAPC1 initiates a self-aggregation process resulting in the formation of branched chains of globular particles made of partially misfolded and totally inactive proteins. GSH molecules within AtGAPC1 active sites are suggested to provide the initial destabilizing signal. The following removal of glutathione by the formation of an intramolecular disulfide bond between Cys149 and Cys153 reinforces the aggregation process. Physiological reductases, thioredoxins and glutaredoxins, could not dissolve AtGAPC1 aggregates but could efficiently contrast their growth. Besides acting as a protective mechanism against overoxidation, S-glutathionylation of AtGAPC1 triggers an unexpected aggregation pathway with completely different and still unexplored physiological implications.

Ionic liquids (ILs) are promising materials exploited as solvents and media in many innovative applications, some already used at the industrial scale. The chemical structure and physicochemical properties of ILs can differ significantly according to the specific applications for which they have been synthesized. As a consequence, their interaction with biological entities and toxicity can vary substantially. To select highly effective and minimally harmful ILs, these properties need to be investigated. Here we use the so called chromatophores - protein-phospholipid membrane vesicles obtained from the photosynthetic bacterium Rhodobacter sphaeroides- to assess the effects of imidazolinium and pyrrolidinium ILs, with chloride or dicyanamide as counter anions, on the ionic permeability of a native biological membrane. The extent and modalities by which these ILs affect the ionic conductivity can be studied in chromatophores by analyzing the electrochromic response of endogenous carotenoids, acting as an intramembrane voltmeter at the molecular level. We show that chromatophores represent an in vitro experimental model suitable to probe permeability changes induced in cell membranes by ILs differing in chemical nature, degree of oxygenation of the cationic moiety and counter anion. (C) 2015 Elsevier B.V. All rights reserved.

Cell shape is a valuable indicator of cell health status and interactions with the extracellular materials. With the aim to investigate how individual cells respond to chemical microenvironments, we employed 2D monomolecular layers of small organic molecules, characterized by very low roughness. MCF10A cells were grown on these surfaces and characterized by using scanning electrochemical microscopy. The single cell morphologies were analyzed to define a "figure of merit" for the different cell-surface interactions. Such "figure of merit" quantifies the interaction with the microenvironment. This method is applicable to any cell state (metastatic, physiological or pathological) and any surface.

The structural and dynamical interaction of proteins with their microenvironment in disordered matrices plays a decisive role for their function; EPR spectroscopy is a powerful tool for shading light onto the molecular mechanisms of this protein–matrix interplay. To clarify the molecular mechanisms of disaccharide bioprotection, we studied the structure and dynamics of spin-labeled systems and photosynthetic reaction centers (RCs) in sucrose and trehalose matrices at different hydration levels by means of cw and pulse high-field 95 GHz (W-band) EPR as well as by FTIR. In this minireview, we summarize and discuss EPR and FTIR experiments showing that the anhydrobiotic state of the RC–trehalose system (1) is not the result of matrix-induced changes of the local structure of the charge-separated radical-pair cofactors, $${\text{P}}_{865}^{ \cdot + }$$ and $${\text{Q}}_{\text{A}}^{ \cdot - }$$ , and (2) is not the result of changes of local dynamics and local hydrogen bonding of QA in its binding pocket. Rather, the extreme impairment of RC dynamics caused by incorporation into the dehydrated trehalose matrix, which also protects it against thermal denaturation, originates in the high rigidity, already at room temperature, of the dry trehalose glass matrix coating the RC protein surface. This surface hydrogen-bonding scaffold shifts the correlation time of thermal conformational fluctuations into the non-biological time domain. Another intriguing aspect of disaccharide bioprotection is the superior efficiency of trehalose versus sucrose matrices in stabilizing the anhydrobiotic state of proteins. To clarify the molecular basis of this specificity, glassy trehalose–water and sucrose–water binary systems, incorporating a nitroxide radical as spin probe, have been studied by high-field W-band EPR spectroscopy at different water contents. Analysis of the EPR spectra revealed a different structural and dynamical organization in the sucrose and trehalose matrix, only the trehalose being homogeneous in terms of residual water and nitroxide distribution.

The bone marrow (BM) microenvironment plays a pivotal role in the survival and chemoresistance of leukemia stem cells (LSC) in acute myeloid leukemia (AML). However, conventional culture approaches do not reflect physiological conditions of crucial anatomical districts and signals of incubation-induced dysregulation may confound leukemic transcriptome results. In vivo mimetic cultures of the LSC districts will significantly aid in the disentanglement of LSC mechanisms and in the assessment of the therapy. We engineered Petri dishes able to mimic the “hypoxic” conditions found in the stem cell niches and in BM district. Our approach is based on a patented method which controls the physiological concentrations of oxygen, glucose and pH in the culture environment. Cell proliferation and hypoxia-induced apoptosis in the engineered device were investigated for OCI-AML3 and KG1 AML cell lines. We observed a slight but significant reduction in cell proliferation compared with control cells for OCI AML-3, which is in line with a more quiescent cell condition. No significant differences were obtained by culturing KG-1 cells, which are more resistant to low oxygen concentrations. We have analyzed the effects of cell culturing in the hypoxic dishes on the expression of MYC and p21. Immunofluorescence analysis of HIF-1α levels and HIF-1α nuclear localization as a function of oxygen concentration were determined. Time-lapse experiments of AML cell lines and primary BM cells were performed in the in vivo mimetic device to elucidate the response of CD34+ AML cells to different oxygen concentrations. We tested an innovative cell culturing device able to mimic the dynamical conditions of oxygen content, which are found in vivo. Our results shed light on AML cells and progenitor-stem cells behavior in response to oxygen conditions in the BM niche and allow to disentangle the LSCs complex biology. This ”in vivo mimetic” approach will generate crucial information on the molecular mechanisms preserving LSC in AML, thus providing novel potential therapeutic targets to eradicate leukemia initiating cells in their own microenvironment, contrasting therapy resistance. Supported by: Associazione Italiana per la Ricerca sul Cancro, MFAG id. 19044. Citation Format: Giorgia Simonetti, Marco Malferrari, Maila Becconi, Samantha Bruno, Giovanni Martinelli, Stefania Rapino. Acute myeloid leukemia cell and stem-progenitor cell behavior studied in mimetic bone marrow microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1914.

In this paper, we describe a new method to obtain D2O/H2O exchange in photosynthetic reaction centres fromRhodobacter sphaeroides. The method is characterized by: (i) a very high efficiency of the isotopic replacement; (ii) an extremely low amount of D2O needed; (iii) the short time required for dehydration and D2O rehydration; (iv) the possibility of controlling concomitantly the hydration state of the sample. The proposed method can be applied to other proteins.

We report on the relationship between electron transfer, conformational dynamics, and hydration in photosynthetic reaction centers (RCs) from Rhodobacter sphaeroides. The kinetics of electron transfer from the photoreduced quinone acceptor (Q(A)(-)) to the photo-oxidized primary donor (P(+)), a charge recombination process sensitive to the conformational dynamics of the RC, has been analyzed at room temperature in dehydrated RC-detergent films as a function of the residual water content under controlled relative humidity (r). The hydration level was evaluated by FTIR spectroscopy from the area of the combination band of water (5155 cm(-1)). Sorption isotherms fit the Hailwood and Horrobin model and indicate a significant contribution to hydration of the detergent belt surrounding the RC. Spectral analysis of the water combination and association (2130 cm(-1)) bands suggests strong rearrangements in the hydrogen-bonding organization upon depletion of the hydration shell of the complex. In parallel with these changes, following dehydration below a critical threshold (r approximately equal 40%), the kinetics of P(+)Q(A)(-) recombination become progressively faster and distributed in rate. When r is decreased from 40% to 10% the average rate constant (k) increases from 15 to 40 s(-1), mimicking the behavior of the hydrated system at cryogenic temperatures. We infer that extensive dehydration inhibits dramatically the relaxation from the dark- to the light-adapted conformation of the RC as well as interconversion among lower tier conformational substates. The RC dynamics probed by P(+)Q(A)(-) recombination appear therefore controlled by the thermal fluctuations of the hydration shell. At r < 10% an additional, much faster ((k) approximately equal 3000 s(-1)) kinetic phase of P(+)Q(A)(-) recombination is observed. We suggest such a fast recombination arises from removal of a pool of RC-bound water molecules which are essential to stabilize the primary charge-separated state at physiological conditions.

The coupling between electron transfer and protein dynamics has been investigated in reaction centers (RCs) from the wild type (wt) and the carotenoid-less strain R26 of the photosynthetic bacterium Rhodobacter sphaeroides. Recombination kinetics between the primary photoreduced quinone acceptor (QA-) and photoxidized donor (P+) have been analyzed at room temperature in RCs incorporated into glassy trehalose matrices of different water/sugar ratios. As previously found in R26 RCs, also in the wt RC, upon matrix dehydration, P+QA- recombination accelerates and becomes broadly distributed, reflecting the inhibition of protein relaxation from the dark-adapted to the light-adapted conformation and the hindrance of interconversion between conformational substates. While in wet trehalose matrices (down to approximately one water per trehalose molecule) P+QA- recombination kinetics are essentially coincident in wt and R26 RCs, more extensive dehydration leads to two-times faster and more distributed kinetics in the carotenoid-containing RC, indicating a stronger inhibition of the internal protein dynamics in the wt RC. Coarse-grained Brownian dynamics simulations performed on the two RC structures reveal a markedly larger flexibility of the R26 RC, showing that a rigid core of residues, close to the quinone acceptors, is specifically softened in the absence of the carotenoid. These experimental and computational results concur to indicate that removal of the carotenoid molecule has long-range effects on protein dynamics and that the structural/dynamical coupling between the protein and the glassy matrix depends strongly upon the local mechanical properties of the protein interior. The data also suggest that the conformational change stabilizing P+QA- is localized around the QA binding pocket.

Matrix effects on long-range electron transfer were studied in cyanobacterial Photosystem I (PS I) complexes, embedded into trehalose glasses at different hydration levels. W-band EPR studies demonstrated, via nitroxide spin probes, structural homogeneity of the dry PS I-trehalose matrix and no alteration of cofactors' distance and relative orientation under temperature and matrix variation. In dry trehalose glasses at room temperature (RT), PS I was stable for months. Flash-induced charge recombination kinetics were examined by high-field time-resolved EPR and optical spectroscopies. The kinetics in hydrated PS I-trehalose glasses mostly reflected the reduction of the photooxidized primary donor P700•+ by the reduced terminal iron-sulfur clusters. Upon dehydration, the P700•+ decay accelerated and became more distributed. Continuous distributions of lifetimes τ were extracted from the kinetics by two numerical approaches: a maximum entropy method (MemExp program) and a constrained regularization method (CONTIN program). Both analyses revealed that upon dehydration the contribution of the two slowest components (lifetimes τ ~ 300 ms and ~ 60 ms), attributed to P700•+[FA/FB] − recombination, decreased in parallel with the increase of the fastest component (τ ~ 150 μs), and of additional distributed phases with intermediate lifetimes. Dehydration at RT mimicked the effects of freezing water-glycerol PS I systems, suggesting an impairment of PS I protein dynamics in the dry trehalose glass. Similar effects were observed previously in bacterial reaction centers. The work presented for PS I provides new insights into the crucial issue of protein-matrix interactions for protein functionality as controlled by hydrogen-bond networks of the hydration shell.

Conformational protein dynamics is known to be hampered in amorphous matrixes upon dehydration, both in the absence and in the presence of glass forming disaccharides, like trehalose, resulting in enhanced protein thermal stability. To shed light on such matrix effects, we have compared the retardation of protein dynamics in photo-synthetic bacterial reaction centers (RC) dehydrated at controlled relative humidity in the absence (RC films) or in the presence of trehalose (RC-trehalose glasses). Small scale RC dynamics, associated with the relaxation from the dark-adapted to the light-adapted conformation, have been probed up to the second time scale by analyzing the kinetics of electron transfer from the photoreduced quinone acceptor (Q(A)(-)) to the photoxidized primary donor (P+) as a function of the duration of photoexcitation from 7 ns (laser pulse) to 20 s. A more severe inhibition of dynamics is found in RC trehalose glasses than in RC films: only in the latter system does a complete relaxation to the light-adapted conformation occur even at extreme dehydration, although strongly retarded. To gain insight into the large scale RC dynamics up to the time scale of days, the kinetics of thermal denaturation have been studied at 44 degrees C by spectral analysis of the Q(x) and Q(y) bands of the RC bacteriochlorin cofactors, as a function of the sugar/protein molar ratio, m, varied between 0 and 10(4). Upon increasing m, denaturation is slowed progressively, and above m similar to 500 the RC is stable at least for several days. The stronger retardation of RC relaxation and dynamics induced by trehalose is discussed in the light of a recent molecular dynamics simulation study performed in matrixes of the model protein lysozyme with and without trehalose. We suggest that the efficiency of trehalose in retarding RC dynamics and preventing thermal denaturation stems mainly from its propensity to form and stabilize extended networks of hydrogen bonds involving sugar, residual water, and surface residues of the RC complex and from its ability of reducing the free volume fraction of protein alone matrixes.

We report a method for the purification of plastoquinone-9 (PQ), a prenylquinone cofactor involved in the photosynthetic electron transport chain. The described procedures relies on spinach-chloroplast isolation followed by PQ extraction and chromatographic fractionation. Extraction of PQ was achieved using partition of chloroplast suspension with methanol:petroleum ether. This procedure removed large amounts of green pigments from the extract and thus facilitates the subsequent chromatographic isolation of PQ. To obtain pure PQ, the developed extraction was combined with a two-step chromatographic approach using orthogonal stationary phases, i.e. alumina and octadecylsilane (C18). A small scale protocol for analytical reverse-phase high performance liquid chromatography (RP-HPLC), which may be implemented in most laboratories equipped with conventional systems, is described. The reported methodology represents a valuable tool for the fast production of small amounts of PQ, for which there are no commercial standards available.

Some organisms can survive complete dehydration and high temperatures by adopting an anhydrobiotic state in which the intracellular medium contains large amounts of disaccharides, particularly trehalose and sucrose. Trehalose is most effective also in protecting isolated in vitro biostructures. In an attempt to clarify the molecular mechanisms of disaccharide bioprotection, we compared the structure and dynamics of sucrose and trehalose matrices at different hydration levels by means of high-field W-band EPR and FTIR spectroscopy. The hydration state of the samples was characterized by FTIR spectroscopy and the structural organization was probed by EPR using a nitroxide radical dissolved in the respective matrices. Analysis of the EPR spectra showed that the structure and dynamics of the dehydrated matrices as well as their evolution upon re-hydration differ substantially between trehalose and sucrose. The dehydrated trehalose matrix is homogeneous in terms of distribution of the residual water and spin-probe molecules. In contrast, dehydrated sucrose forms a heterogeneous matrix. It is comprised of sucrose polycrystalline clusters and several bulk water domains. The amorphous form was found only in 30% (volume) of the sucrose matrix. Re-hydration leads to a structural homogenization of the sucrose matrix, whilst in the trehalose matrix several domains develop differing in the local water/radical content and radical mobility. The molecular model of the matrices provides an explanation for the different protein–matrix dynamical coupling observed in dried ternary sucrose and trehalose matrices, and accounts for the superior efficacy of trehalose as a bioprotectant. Furthermore, for bacterial photosynthetic reaction centers it is shown that at low water content the protein–matrix coupling is modulated by the sugar/protein molar ratio in sucrose matrices only. This effect is suggested to be related to the preference for sucrose, rather than trehalose, as a bioprotective disaccharide in some anhydrobiotic organisms.

Following light-induced electron transfer between the primary donor (P) and quinone acceptor (QA) the bacterial photosynthetic reaction center (RC) undergoes conformational relaxations which stabilize the primary charge separated state P+QA− . Dehydration of RCs from Rhodobacter sphaeroides hinders these conformational dynamics, leading to acceleration of P+QA− recombination kinetics [Malferrari et al., J. Phys. Chem. B 115 (2011) 14732-14750]. To clarify the structural basis of the conformational relaxations and the involvement of bound water molecules, we analyzed light-induced P+QA− /PQA difference FTIR spectra of RC films at two hydration levels (relative humidity r = 76% and r = 11%). Dehydration reduced the amplitude of bands in the 3700-3550 cm−1 region, attributed to water molecules hydrogen bonded to the RC, previously proposed to stabilize the charge separation by dielectric screening [Iwata et al., Biochemistry 48 (2009) 1220-1229]. Other features of the FTIR difference spectrum were affected by partial depletion of the hydration shell (r = 11%), including contributions from modes of P (9-keto groups), and from NH or OH stretching modes of amino acidic residues, absorbing in the 3550-3150 cm−1 range, a region so far not examined in detail for bacterial RCs. To probe in parallel the effects of dehydration on the RC conformational relaxations, we analyzed by optical absorption spectroscopy the kinetics of P+QA− recombination following the same photoexcitation used in FTIR measurements (20 s continuous illumination). The results suggest a correlation between the observed FTIR spectral changes and the conformational rearrangements which, in the hydrated system, strongly stabilize the P+QA− charge separated state over the second time scale.

An increasing number of publications report on the efficacy of trehalose in preserving organisms, cells, and macromolecules from adverse environmental conditions such as extreme temperatures and dryness. Although the mechanism by which this disaccharide exerts its protection is still debated, the implementation of trehalose as stabilizer is becoming a praxis in several preparative protocols from the pharmaceutical industry. We tested the ability of trehalose in protecting R-Phycoerythrin (R-PE), a pigment-protein complex widely used as fluorescent marker, from thermal denaturation. Once embedded into a dried trehalose matrix, R-PE retains its optical absorption-emission characteristics even when exposed to 70°C for h or when subjected to freeze-drying. We subsequently examined the protection exerted by trehalose on freeze-dried antihuman CD8-RPE (CD8-RPE) conjugated antibodies. Flow cytometric analysis showed that colyophilized trehalose-CD8-RPE preparations can be exposed for 4 weeks at 45°C without significant loss of functionality. Remarkably, even following 4 weeks incubation at 70°C, the preparations are still able to specifically recognize CD8(+) lymphocyte populations. These results show that colyophilization with trehalose makes possible the preparation of antibody-based diagnostic kits which can withstand breaks in the "cold chain" distribution, particularly suited for use in less-developed countries of the tropical areas.

The coupling between electron transfer (ET) and the conformational dynamics of the cofactor−protein complex in photosynthetic reaction centers (RCs) from Rhodobacter sphaeroides in water/glycerol solutions or embedded in dehydrated poly(vinyl alcohol) (PVA) films or trehalose glasses is reported. Matrix effects were studied by time-resolved 95 GHz high-field electron paramagnetic resonance (EPR) spectroscopy at room (290 K) and low (150 K) temperature. ET from the photoreduced quinone acceptor (QA•−) to the photo-oxidized donor (P865•+) is strongly matrix-dependent at room temperature: In the trehalose glasses, the recombination kinetics of P865•+QA•−, probed by EPR and optical spectroscopies, is faster and broadly distributed as compared to that of RCs in solution, reflecting the inhibition of the RC relaxation from the dark- to the light-adapted conformational substate and the hindrance of substate interconversion. Similarly accelerated kinetics was observed also in PVA at a water-to-RC molar ratio 10-fold lower than in trehalose. Despite the matrix dependence of the ET kinetics, continuous-wave (cw) EPR and electron spin echo (ESE) analyses of the photogenerated P865•+ and QA•− radical ions and P865•+QA•− radical pairs do not reveal significant matrix effects, at either 290 or 150 K, indicating no change in the molecular radical-pair configuration of the P865•+ and QA•− cofactors. Furthermore, the field dependences of the transverse relaxation times T2 of QA•− essentially coincide in trehalose and PVA at 290 K. T2 is similar in these two matrixes and in the glycerol/water system at 150 K, implying that the librational dynamics of QA•− are also unaffected by the matrix. We infer that the relative geometry of the primary donor and acceptor, as well as the local dynamics and hydrogen bonding of QA in its binding pocket, are not involved in the stabilization of P865•+QA•−. We suggest that the RC relaxation occurs rather by changes throughout the protein/solvent system. The control of the RC dynamics and ET by the environment is discussed, particularly with respect to the extraordinary efficacy of trehalose matrixes in restricting the RC motional degrees of freedom at elevated temperatures.

The photosynthetic reaction center (RC) of Rb. sphaeroides catalyzes light-induced electron transfer events which are connected to the conformational dynamics of the protein. The light-induced charge separation between the primary donor (P) and the quinone acceptor (QA) is stabilized by solvent/protein conformational rearrangements. After a laser pulse P+QA recombination, which occurs with a lifetime t~100 ms in room temperature solutions, is accelerated (t~20 ms) at cryogenic temperatures [1] and in dehydrated glassy matrices at room temperature [2]. After prolonged photoexcitation, a slow phase of recombination (t~250 s) is observed, attributed to additional conformational changes [3]. Differential FTIR bands of water associated with the QA/QA transition have been observed upon continuous illumination, leading to propose that weakly bound water molecules plays a role in P+QA stabilization [4]. By controlling the hydration level of RC-detergent films, through equilibration at given relative humidities (r), a strong inhibition of the P+QA conformational stabilization has been observed at low hydration [5]. We compared FTIR light-minus-dark (P+QA/ PQA) differential spectra in hydrated (r=76%) and dehydrated (r=11%) RC films over the 4000- 1000 cm-1. The spectra differ significantly in the 3750-3550 cm-1 range, the band attributed to weakly hydrogen bonded water molecules [5] being strongly reduced in the dried film. Dehydration also affects the 1800-1200 cm-1 range, which includes contributions from P, the quinones and the peptide. Optical absorption measurements performed under the same photoexcitation regime reveal a slow (t~5 s) kinetic component of P+QA recombination which disappears in the dehydrated sample, indicating at low r a destabilization of the charge separated state. As a whole the data suggest a correlation between the hydration shell dynamics and the conformational RC dynamics which stabilize the charge separated state.

The interplay between protein dynamics and electron transfer (ET) has been extensively investigated in the bacterial photosynthetic reaction center (RC) from Rhodobacter sphaeroides by hampering RC internal motions at low temperatures [1]. Alternatively, the RC dynamics can be inhibited at room temperature by incorporating the RC into dehydrated trehalose matrices [2]. In the glasses the recombination kinetics of the charge separated state P+QA are accelerated and distributed in rate as compared to solution, mimicking at room temperature the effects observed at 10 K in water-glycerol. This is taken to indicate inhibition of the RC relaxation from the dark- to the light-adapted conformation, as well as of the RC thermal fluctuations [1,2]. We proposed that the inhibition is mediated by residual water molecules of the RC hydration shell which bridge protein surface groups with trehalose molecules of the matrix by forming a network of multiple hydrogen bonds [3]. Consistently, similar effects have been observed also in RC films dehydrated in the absence of sugar [4]. However, striking differences are found between RC-trehalose glasses and RC-films: (a) The thermal stability of the RC is tremendously enhanced in the trehalose matrix. (b) In RC-trehalose matrices, the P+QA recombination after a few seconds of continuous photoexcitation is only partially decelerated as compared to the one recorded after a laser flash, whereas in dried RC films a comparable period of continuous illumination leads to a total recovery of the kinetics observed in the hydrated system. These data indicate that in films the protein dynamics can be easily regained, in contrast to trehalose glasses, which reveal much stronger structural constraints. We are extending these studies to a series of RC mutants characterized by a widely altered P+/P midpoint potential relative to wild-type [5]. In these mutants, the acceleration of P+QA recombination induced by cooling to 10 K in the dark decreased with increasing midpoint potential [6]. Interestingly, incorporation into dehydrated trehalose matrices causes instead acceleration of the kinetics by the same factor for all P+/P midpoint potential values.