RESUMEN
Unconventional computing paradigms explore new methods for processing information beyond the capabilities of traditional electronic architectures. In this work, we present our approach to digital computation through enzymatic reactions in chemically buffered environments. A key aspect of this approach is its reliance on pH-sensitive enzymatic reactions, with the direction of the reaction controlled by maintaining pH levels within a specific range. When the pH crosses a defined threshold, the reaction moves forward and vice versa, akin to the switching action of electronic switches in digital circuits. The binary signals (0 and 1) are encoded as different concentrations of strong acids or bases, offering a bio-inspired method for computation. The final readout is done using UV-vis spectroscopy after applying detection reactions to indicate whether the output is 1 (indicated by the presence of the enzymatic reaction's product) or 0 (indicated by the absence of the enzymatic reaction's product). We build and evaluate a set of digital circuits in the lab using our proposed methodology to model the circuits using chemical reactions. In addition, we demonstrate the implementation of a neural network classifier using our framework.
Asunto(s)
Redes Neurales de la Computación , Concentración de Iones de Hidrógeno , Enzimas/metabolismo , Enzimas/químicaRESUMEN
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
Asunto(s)
Hemoproteínas , Óxido Nítrico , Electrónica , Hemo/química , Hierro/química , Óxido Nítrico/química , Óxidos de Nitrógeno/químicaRESUMEN
Loop-mediated isothermal amplification (LAMP) is an outstanding method for molecular diagnostics, as the rapid, specific, and sensitive amplification of target genes is possible. However, it is necessary to measure fluorescence in the quantitative analysis of LAMP products, so a sophisticated optical setup is required. This study tried to develop a novel sensing method that can quantify target analytes with simple equipment, such as nonspectroscopic white light and a CMOS camera. To achieve this, a retroreflective Janus particle (RJP) as a probe and specially designed loop primers, fluorescein isothiocyanate (FITC)- and biotin-modified loop primers, were introduced into the LAMP system. By performing LAMP in the presence of designed primers, double-stranded amplicons possessing FITC and biotin labels at each end are generated in proportion to the quantity of the target pathogen. Using the anti-FITC antibody-modified sensing surface and streptavidin-conjugated RJP probes, the amplicons can be captured in sandwich-configuration and detected under nonspectroscopic conditions composed of white light and a camera. To confirm the feasibility of the sensing system, the invA gene of Salmonella was selected as the target. It was possible to quantitatively analyze the Salmonella concentration from 0 to 106 colony-forming units, sufficiently covering the required detection range. In addition, quantitative analyses of pathogens in contaminated food sources, including milk and chicken meat, were successfully conducted with a limit of detection of 10 CFU.
Asunto(s)
Amplificación de Genes , Técnicas de Amplificación de Ácido Nucleico , Animales , Cartilla de ADN , Leche , Salmonella/genética , Sensibilidad y EspecificidadRESUMEN
MitoNEET, a key regulatory protein in mitochondrial energy metabolism, exhibits a uniquely ligated [2Fe-2S] cluster with one histidine and three cysteines. This unique cluster has been postulated to sense the redox environment and release Fe-S cofactors under acidic pH. Reported herein is a synthetic system that shows how [2Fe-2S] clusters react with protons and rearrange their coordination geometry. The low-temperature stable, site-differentiated clusters [Fe2S2(SPh)3(CF3COO)]2- and [Fe2S2(SPh)3(py)]- have been prepared via controlled protonation below -35 °C and characterized by NMR, UV-vis, and X-ray absorption spectroscopy. Both complexes exhibit anodically shifted redox potentials compared to [Fe2S2(SPh)4]2- and convert to [Fe4S4(SPh)4]2- upon warming to room temperature. The current study provides insight into how mitoNEET releases its [2Fe-2S] in response to highly tuned acidic conditions, the chemistry of which may have further implications in Fe-S biogenesis.
Asunto(s)
Proteínas Hierro-AzufreRESUMEN
Iron-sulfur clusters (Fe-S) have been well established as a target for nitric oxide (NO) in biological systems. Complementary to protein-bound studies, synthetic models have provided a platform to study what iron nitrosylated products and byproducts are produced depending on a controlled reaction environment. We have previously shown a model [2Fe-2S] system that produced a dinitrosyl iron complex (DNIC) upon nitrosylation along with hydrogen sulfide (H2S), another important gasotransmitter, in the presence of thiol, and hypothesized a similar reactivity pattern with [4Fe-4S] clusters which have largely produced inconsistent reaction products across biological and synthetic systems. Roussin's black anion (RBA), [Fe4(µ3-S)3(NO)7]-, is a previously established reaction product from synthetic [4Fe-4S] clusters with NO. Here, we present a new reactivity for the nitrosylation of a synthetic [4Fe-4S] cluster in the presence of thiol and thiolate. [Et4N]2[Fe4S4(SPh)4] (1) was nitrosylated in the presence of excess PhSH to generate H2S and an "RBA-like" intermediate that when further reacted with [NEt4][SPh] produced a {Fe(NO)2}9 DNIC, [Et4N][Fe(NO)2(SPh)2] (2). This "RBA-like" intermediate proved difficult to isolate but shares striking similarities to RBA in the presence of thiol based on IR υ(NO) stretching frequencies. Surprisingly, the same reaction products were produced when the reaction started with RBA and thiol. Similar to 1/NO, RBA in the presence of thiol and thiolate generates stoichiometric amounts of DNIC while releasing its bridging sulfides as H2S. These results suggest not only that RBA may not be the final product of [4Fe-4S] + NO but also that RBA has unprecedented reactivity with thiols and thiolates which may explain current challenges around identifying biological nitrosylated Fe-S clusters.
Asunto(s)
Óxido NítricoRESUMEN
The reduction of nitrate (NO3-) to nitrite (NO2-) is of significant biological and environmental importance. While MoIV(O) and MoVI(O)2 complexes that mimic the active site structure of nitrate reducing enzymes are prevalent, few of these model complexes can reduce nitrate to nitrite through oxygen atom transfer (OAT) chemistry. We present a novel strategy to induce nitrate reduction chemistry of a previously known catalyst MoIV(O)(SN)2 (2), where SN = bis(4- tert-butylphenyl)-2-pyridylmethanethiolate, that is otherwise incapable of achieving OAT with nitrate. Addition of nitrate with the Lewis acid Sc(OTf)3 (OTf = trifluoromethanesulfonate) to 2 results in an immediate and clean conversion of 2 to MoVI(O)2(SN)2 (1). The Lewis acid additive further reacts with the OAT product, nitrite, to form N2O and O2. This work highlights the ability of Sc3+ additives to expand the reactivity scope of an existing MoIV(O) complex together with which Sc3+ can convert nitrate to stable gaseous molecules.
Asunto(s)
Materiales Biomiméticos/química , Ácidos de Lewis/química , Molibdeno/química , Nitratos/química , Compuestos Organometálicos/química , Oxidorreductasas/química , Materiales Biomiméticos/metabolismo , Ácidos de Lewis/metabolismo , Estructura Molecular , Molibdeno/metabolismo , Nitratos/metabolismo , Compuestos Organometálicos/metabolismo , Oxidación-Reducción , Oxidorreductasas/metabolismoRESUMEN
A mixed-valent Cu(I)Cu(II) complex, [CuI,II2(UN-O-)]2+ (1), reacts with NO(g) at -80 °C to form [CuI,II2(UN-O-)(NO)]2+ (2), best described as a mixed-valent nitrosyl complex that has a ν(N-O) band at 1670 cm-1 in its infrared (IR) spectrum. Complex 2 undertakes a one-electron oxidation via the addition of O2(g) to generate a new intermediate, best described as a superoxide and nitrosyl adduct, [CuII2(UN-O-)(NO)(O2-)]2+ (3), based on its distinctively blue-shifted ν(N-O) band at 1853 cm-1. Over the course of 20 min at -80 °C, 3 is converted to the peroxynitrite (PN) complex [CuII2(UN-O-)(-OONâO)]2+ (4), which was characterized by low-temperature electrospray ionization mass spectrometry (ESI-MS) and IR spectroscopy; ν(N-O) absorptions at 1520 and 1640 cm-1 have been assigned as cis- and trans-conformers of the PN ligand in 4. Alternatively, the superoxide complex [CuII2(UN-O-)(O2â¢-)]2+ (5) is found to react with NO(g) to generate the same intermediate superoxide and nitrosyl adduct 3 (based on IR criteria), which likewise converts to the same PN complex 4. The O-O bond in 4 undergoes heterolysis in dichloromethane solvent and is postulated to produce nitronium ion, leading to ortho-nitration of 2,4-di-tert-butylphenol (DTBP). However, in 2-methyltetrahydrofuran as solvent, the O-O bond undergoes homolysis to generate â¢NO2 (detected spectrophotometrically) and a putative higher-valent complex, [CuII,III2(UN-O-)(O2-)]2+, that abstracts a H-atom from DTBP to give [CuII2(UN-O-)(OH)]2+ and a phenoxyl radical. The latter may dimerize to form the bis-phenol observed experimentally or couple with the â¢NO2 present, leading to o-phenol nitration.
Asunto(s)
Complejos de Coordinación/síntesis química , Cobre/química , Óxido Nítrico/química , Oxígeno/química , Ácido Peroxinitroso/química , Complejos de Coordinación/química , Estructura MolecularRESUMEN
Nitric oxide (NO) is an important signaling molecule that is involved in many physiological and pathological functions. Iron-sulfur proteins are one of the main reaction targets for NO, and the [Fe-S] clusters within these proteins are converted to various iron nitrosyl species upon reaction with NO, of which dinitrosyl iron complexes (DNICs) are the most prevalent. Much progress has been made in identifying the origin of cellular DNIC generation. However, it is not well-understood which other products besides DNICs may form during [Fe-S] cluster degradation nor what effects DNICs and other degradation products can have once they are generated in cells. Even more elusive is an understanding of the manner by which cells cope with unwanted [Fe-S] modifications by NO. This Account describes our synthetic modeling efforts to identify cluster degradation products derived from the [2Fe-2S]/NO reaction in order to establish their chemical reactivity and repair chemistry. Our intent is to use the chemical knowledge that we generate to provide insight into the unknown biological consequences of cluster modification. Our recent advances in three different areas are described. First, new reaction conditions that lead to the formation of previously unrecognized products during the reaction of [Fe-S] clusters with NO are identified. Hydrogen sulfide (H2S), a gaseous signaling molecule, can be generated from the reaction between [2Fe-2S] clusters and NO in the presence of acid or formal H⢠(e(-)/H(+)) donors. In the presence of acid, a mononitrosyl iron complex (MNIC) can be produced as the major iron-containing product. Second, cysteine analogues can efficiently convert MNICs back to [2Fe-2S] clusters without the need for any other reagents. This reaction is possible for cysteine analogues because of their ability to labilize NO from MNICs and their capacity to undergo C-S bond cleavage, providing the necessary sulfide for [2Fe-2S] cluster formation. Lastly, unique dioxygen reactivity of various types of DNICs has been established. N-bound neutral {Fe(NO)2}(10) DNICs react with O2 to generate low-temperature stable peroxynitrite (ONOO(-)) species, which then carry out nitration chemistry in the presence of phenolic substrates, relevant to tyrosine nitration chemistry. The reaction between S-bound anionic {Fe(NO)2}(9) DNICs and O2 results in the formation of Roussin's red esters (RREs) and thiol oxidation products, chemistry that may be important in biological cysteine oxidation. The N-bound cationic {Fe(NO)2}(9) DNICs can spontaneously release NO, and this property can be utilized in developing a new class of NO-donating agents with anti-inflammatory activity.
Asunto(s)
Hierro/química , Óxido Nítrico/metabolismo , Óxidos de Nitrógeno/química , Animales , Antiinflamatorios/química , Antiinflamatorios/farmacología , Línea Celular , Cristalografía por Rayos X , Cisteína/química , Citocinas/metabolismo , Sulfuro de Hidrógeno/metabolismo , Proteínas Hierro-Azufre/química , Proteínas Hierro-Azufre/metabolismo , Macrófagos/citología , Macrófagos/efectos de los fármacos , Macrófagos/metabolismo , Ratones , Conformación Molecular , Óxidos de Nitrógeno/síntesis química , Oxidación-Reducción , Oxígeno/química , Ácido Peroxinitroso/química , Transducción de Señal , Espectrometría de FluorescenciaRESUMEN
Dinitrosyl iron complexes (DNICs) are among the most abundant NO-derived cellular species. Monomeric DNICs can exist in the {Fe(NO)2}(9) or {Fe(NO)2}(10) oxidation state (in the Enemark-Feltham notation). However, experimental studies of analogous DNICs in both oxidation states are rare, which prevents a thorough understanding of the differences in the electronic structures of these species. Here, the {Fe(NO)2}(9) DNIC [Fe(dmp)(NO)2](OTf) (1; dmp = 2,9-dimethyl-1,10-phenanthroline) is synthesized from a ferrous precursor via an unusual pathway, involving disproportionation of an {FeNO}(7) complex to yield the {Fe(NO)2}(9) DNIC and a ferric species, which is subsequently reduced by NO gas to generate a ferrous complex that re-enters the reaction cycle. In contrast to most {Fe(NO)2}(9) DNICs with neutral N-donor ligands, 1 exhibits high solution stability and can be characterized structurally and spectroscopically. Reduction of 1 yields the corresponding {Fe(NO)2}(10) DNIC [Fe(dmp)(NO)2] (2). The Mössbauer isomer shift of 2 is 0.08 mm/s smaller than that of 1, which indicates that the iron center is slightly more oxidized in the reduced complex. The nuclear resonance vibrational spectra (NRVS) of 1 and 2 are distinct and provide direct experimental insight into differences in bonding in these complexes. In particular, the symmetric out-of-plane Fe-N-O bending mode is shifted to higher energy by 188 cm(-1) in 2 in comparison to 1. Using quantum chemistry centered normal coordinate analysis (QCC-NCA), this is shown to arise from an increase in Fe-NO bond order and a stiffening of the Fe(NO)2 unit upon reduction of 1 to 2. DFT calculations demonstrate that the changes in bonding arise from an iron-centered reduction which leads to a distinct increase in Fe-NO π-back-bonding in {Fe(NO)2}(10) DNICs in comparison to the corresponding {Fe(NO)2}(9) complexes, in agreement with all experimental findings. Finally, the implications of the electronic structure of DNICs for their reactivity are discussed, especially with respect to N-N bond formation in NO reductases.
RESUMEN
The nitrosylation of inorganic protein cofactors, specifically that of [Fe-S] clusters to form iron nitrosyls, plays a number of important roles in biological systems. In some of these cases, it is expected that a repair process reverts the nitrosylated iron species to intact [Fe-S] clusters. The repair of nitrosylated [2Fe-2S] cluster, primarily in the form of protein-bound dinitrosyl iron complexes (DNICs), has been observed in vitro and in vivo, but the mechanism of this process remains uncertain. The present work expands upon a previous observation (Fitzpatrick et al. J. Am. Chem. Soc. 2014, 136, 7229) of the ability of mononitrosyl iron complexes (MNICs) to be converted into [2Fe-2S] clusters by the addition of nothing other than a cysteine analogue. Herein, each of the critical elementary steps in the cluster repair has been dissected to elucidate the roles of the cysteine analogue. Systematic variations of a cysteine analogue employed in the repair reaction suggest that (i) the bidentate coordination of a cysteine analogue to MNIC promotes NO release from iron, and (ii) deprotonation of the α carbon of the ferric-bound cysteine analogue leads to the C-S cleavage en route to the formation of [2Fe-2S] cluster. The [2Fe-2S] cluster bearing a cysteine analogue has also been synthesized from thiolate-bridged iron dimers of the form [Fe2(µ-SR)2(SR)4](0/2-), which implies that such species may be present as intermediates in the cluster repair. In addition to MNICs, mononuclear tetrathiolate ferric or ferrous species have been established as another form of iron from which [2Fe-2S] clusters can be generated without need for any other reagent but a cysteine analogue. The results of these experiments bring to light new chemistry of classic coordination complexes and provides further insight into the repair of NO-modified [2Fe-2S] clusters.
Asunto(s)
Cisteína/análogos & derivados , Cisteína/síntesis química , Compuestos Ferrosos/síntesis química , Óxidos de Nitrógeno/química , Propionatos/química , Compuestos de Azufre/síntesis química , Ligandos , Modelos Químicos , Imitación Molecular , Oxidación-ReducciónRESUMEN
Pumilio and FBF (PUF) proteins are conserved stem cell regulators that maintain germline stem cells (GSCs) in worms and flies. Moreover, they are also present in vertebrate stem cells. The nematode Caenorhabditis elegans has multiple PUF proteins with specialized roles. Among them, PUF-8 protein controls multiple cellular processes, including proliferation, differentiation, sperm-oocyte decision, and cell fate reprogramming, depending on the genetic context in the C. elegans germline. In this review, we describe the possible mechanisms of how PUF-8 protein systematically controls multiple cellular processes in the C. elegans germline. Since PUF proteins are evolutionarily conserved, we suggest that a similar mechanism may be involved in controlling stem cell regulation and differentiation in other organisms, including humans.
Asunto(s)
Proteínas de Caenorhabditis elegans/metabolismo , Caenorhabditis elegans/metabolismo , Diferenciación Celular , Linaje de la Célula , Reprogramación Celular , Oocitos/metabolismo , Proteínas de Unión al ARN/metabolismo , Espermatozoides/metabolismo , Células Madre/metabolismo , Animales , Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/genética , Proliferación Celular , Femenino , Regulación del Desarrollo de la Expresión Génica , Humanos , Masculino , Proteínas de Unión al ARN/genética , Transducción de SeñalRESUMEN
The crosstalk between two biologically important signaling molecules, nitric oxide (NO) and hydrogen sulfide (H2S), proceeds via elusive mechanism(s). Herein we report the formation of H2S by the action of NO on synthetic [2Fe-2S] clusters when the reaction environment is capable of providing a formal H(â¢) (e(-)/H(+)). Nitrosylation of (NEt4)2[Fe2S2(SPh)4] (1) in the presence of PhSH or (t)Bu3PhOH results in the formation of (NEt4)[Fe(NO)2(SPh)2] (2) and H2S with the concomitant generation of PhSSPh or (t)Bu3PhO(â¢). The amount of H2S generated is dependent on the electronic environment of the [2Fe-2S] cluster as well as the type of H(â¢) donor. Employment of clusters with electron-donating groups or H(â¢) donors from thiols leads to a larger amount of H2S evolution. The 1/NO reaction in the presence of PhSH exhibits biphasic decay kinetics with no deuterium kinetic isotope effect upon PhSD substitution. However, the rates of decay increase significantly with the use of 4-MeO-PhSH or 4-Me-PhSH in place of PhSH. These results provide the first chemical evidence to suggest that [Fe-S] clusters are likely to be a site for the crosstalk between NO and H2S in biology.
Asunto(s)
Ferredoxinas/química , Sulfuro de Hidrógeno/química , Óxido Nítrico/química , Deuterio/química , Ligandos , Estructura Molecular , Oxidación-Reducción , Espectrometría de Fluorescencia , Espectrofotometría UltravioletaRESUMEN
Reversible modification of iron-sulfur clusters by nitric oxide acts as a genetic switch in a group of regulatory proteins. While the conversion of [Fe-S] clusters to iron-nitrosyls has been widely studied in the past, little is known about the reverse process, the repair of [Fe-S] clusters. Reported here is a system in which a mononitrosyl iron complex (MNIC), (PPN)[Fe(S(t)Bu)3(NO)] (1), is converted to a [2Fe-2S] cluster, (PPN)2[Fe2S2(SCH2CH2C(O)OMe)4] (2). This conversion requires only the addition of a cysteine analogue, 3-mercaptomethylpropionate (MMP), at room temperature without the need for any other reagents. The identity of 2 was confirmed spectroscopically, chemically, crystallographically, and analytically. Mass spectrometry and (34)S labeling studies support that the bridging sulfides in 2 derive from the added MMP, the cysteine analogue. The NO lost during the conversion of 1 to 2 is trapped in a dinitrosyl iron side product, (PPN)[Fe(SCH2CH2C(O)OMe)2(NO)2] (4). The present system implies that MNICs are likely intermediates in the repair of NO-damaged [2Fe-2S] clusters and that cysteine is a viable molecule responsible for the destabilization of MINCs and the formation of [2Fe-2S] clusters.
Asunto(s)
Cisteína/química , Proteínas Hierro-Azufre/química , Hierro/química , Óxidos de Nitrógeno/química , Cisteína/análogos & derivados , Modelos Moleculares , Conformación MolecularRESUMEN
The cross-shelf distributions of total mercury (THg), methylmercury (MeHg) and organic and inorganic matter, as well as the presence of the hgcA gene were investigated on the East Siberian Shelf (ESS) to understand the processes underlying the speciation of sedimentary Hg. Samples were collected from 12 stations grouped into four zones based on water depth: inner shelf (5 stations), mid-shelf (3 stations), outer shelf (2 stations), and slope (2 stations). The THg concentration in the surface sediment increased from the inner shelf (0.25 ± 0.023 nmol g-1) toward the slope (0.52 nmol g-1), and, when normalized to total organic carbon content, the THg showed a positive correlation with the clay-to-sand ratio (r2 = 0.48, p = 0.012) and degree of chemical weathering (r2 = 0.79, p = 0.0001). The highest MeHg concentrations (3.0 ± 1.8 pmol g-1), as well as peaks in the S/C ratio (0.012 ± 0.002) of sediment-leached organic matter, were found on the mid-shelf, suggesting that the activities of sulfate reducers control the net Hg(II) methylation rates in the sediment. This was supported by results from a principal component analysis (PCA) performed with Hg species concentrations and sediment-leached organic matter compositions. The site-specific variation in MeHg showed the highest similarity with that of CHONS compounds in the PCA, where Deltaproteobacteria were projected to be putative Hg(II) methylators in the gene analysis. In summary, the hydrodynamic sorting of lithogenic particles appears to govern the cross-shelf distribution of THg, and in situ methylation is considered a major source of MeHg in the ESS sediment.
Asunto(s)
Mercurio , Compuestos de Metilmercurio , Contaminantes Químicos del Agua , Mercurio/análisis , Sedimentos Geológicos/química , Contaminantes Químicos del Agua/análisis , Monitoreo del Ambiente/métodos , Compuestos de Metilmercurio/análisis , Océanos y MaresRESUMEN
Protonation-assisted deoxygenation of a mono-oxo molybdenum center has been observed in many oxotransferases when the enzyme removes an oxo group to regenerate a substrate binding site. Such a reaction is reported here with discrete synthetic mono-oxo bis(dithiolene) molybdenum and tungsten complexes, the chemistry of which had been rarely studied because of the instability of the resulting deoxygenated products. An addition of tosylic acid to an acetonitrile solution of [Mo(IV)O(S2C2Ph2)2](2-) (1) and [W(IV)O(S2C2Ph2)2](2-) (2) results in the loss of oxide with a concomitant formation of novel deoxygenated complexes, [M(MeCN)2(S2C2Ph2)2] (M = Mo (3), W (4)), that have been isolated and characterized. Whereas protonation of 1 exclusively produces 3, two different reaction products can be generated from 2; an oxidized product, [WO(S2C2Ph2)2](-), is produced with 1 equiv of acid while a deoxygenated product, [W(MeCN)2(S2C2Ph2)2] (4), is generated with an excess amount of proton. Alternatively, complexes 3 and 4 can be obtained from photolysis of [Mo(CO)2(S2C2Ph2)2] (5) and [W(CO)2(S2C2Ph2)2] (6) in acetonitrile. A di- and a monosubstituted adducts of 3, [Mo(CO)2(S2C2Ph2)2] (5) and [Mo(PPh3)(MeCN)(S2C2Ph2)2] (7) are also reported.
Asunto(s)
Molibdeno/química , Compuestos Organometálicos/química , Oxígeno/química , Protones , Tungsteno/química , Fosfinas/química , FotólisisRESUMEN
[This corrects the article DOI: 10.3389/fmicb.2022.1093670.].
RESUMEN
Acid-base reactions are ubiquitous, easy to prepare, and execute without sophisticated equipment. Acids and bases are also inherently complementary and naturally map to a universal representation of "0" and "1." Here, we propose how to leverage acids, bases, and their reactions to encode binary information and perform information processing based upon the majority and negation operations. These operations form a functionally complete set that we use to implement more complex computations such as digital circuits and neural networks. We present the building blocks needed to build complete digital circuits using acids and bases for dual-rail encoding data values as complementary pairs, including a set of primitive logic functions that are widely applicable to molecular computation. We demonstrate how to implement neural network classifiers and some classes of digital circuits with acid-base reactions orchestrated by a robotic fluid handling device. We validate the neural network experimentally on a number of images with different formats, resulting in a perfect match to the in-silico classifier. Additionally, the simulation of our acid-base classifier matches the results of the in-silico classifier with approximately 99% similarity.
RESUMEN
DNA-based nanomechanical devices can be used to characterize the action of DNA-distorting proteins. Here, we have constructed a device wherein two DNA triple-crossover (TX) molecules are connected by a shaft, similar to a previous device that measured the binding free energy of integration host factor. In our case, the binding site on the shaft contains the sequence recognized by SoxR protein, the apo form of which is a transcriptional activator. Another active form is oxidized [2Fe-2S] SoxR formed during redox sensing, and previous data suggest that activated Fe-SoxR distorts its binding site by localized DNA untwisting by an amount that corresponds to ~2 bp. A pair of dyes report the fluorescence resonance energy transfer (FRET) signal between the two TX domains, reflecting changes in the shape of the device upon binding of the protein. The TX domains are used to amplify the signal expected from a relatively small distortion of the DNA binding site. From FRET analysis of apo-SoxR binding, the effect of apo-SoxR on the original TX device is similar to the effect of shortening the TX device by 2 bp. We estimate that the binding free energy of apo-SoxR on the DNA target site is 3.2-6.1 kcal/mol.
Asunto(s)
Apoproteínas/química , Proteínas Bacterianas/química , ADN Bacteriano/química , Nanotecnología/instrumentación , Conformación de Ácido Nucleico , Factores de Transcripción/química , Secuencia de Bases , Proteínas de Unión al ADN/química , Ensayo de Cambio de Movilidad Electroforética , Transferencia Resonante de Energía de Fluorescencia , Modelos Moleculares , Datos de Secuencia MolecularRESUMEN
Inspired by the CO(2)-reductatse activity of tungsten-dependent formate dehydrogenases (W-FDHs), a reduced W-FDH model, [W(IV)(OH)(S(2)C(2)Ph(2))(2)](-), was prepared in situ through hydrolysis of [W(IV)(OPh)(S(2)C(2)Ph(2))(2)](-) (1) and its reactivity with CO(2) was investigated. The reaction between [W(IV)(OH)(S(2)C(2)Ph(2))(2)](-) and CO(2) at room temperature leads to the formation of [W(IV)(O)(S(2)C(2)Ph(2))(2)](2-) (2), which slowly oxidizes to [W(V)(O)(S(2)C(2)Ph(2))(2)](-) (3). Isotopic labeling experiments reveal that the O atom in CO(2) incorporates into 3. This implies that there is carbonic anhydrase like activity, in which carbonation and decarboxylation are mediated by a bis(dithiolene)tungsten complex.