scholarly journals Can active hydrodynamic fluctuations affect barrier crossing during enzymatic catalysis?

2021 ◽  
Author(s):  
Ashwani Kr. Tripathi ◽  
Tamoghna Das ◽  
Govind Paneru ◽  
Hyuk Kyu Pak ◽  
Tsvi Tlusty

The cellular milieu is teeming with biochemical nano-machines whose activity is a strong source of correlated non-thermal fluctuations termed “active noise”. Essential elements of this circuitry are enzymes, catalysts that speed up the rate of metabolic reactions by orders of magnitude, thereby making life possible. Here, we examine the possibility that active noise in the cell, or in vitro, affects enzymatic catalytic rate by accelerating or decelerating the crossing of energy barriers during reaction. Considering hydrodynamic perturbations induced by biochemical activity as a source of active noise, we attempt to evaluate their plausible impact on the enzymatic cycle using a combination of analytic and numerical methods. Our estimate shows that the fast component of the active noise spectrum may enhance the rate of enzymes, by up to 50%, while reactions remain practically unaffected by the slow noise spectrum and are mostly governed by thermal fluctuations. Revisiting the physics of barrier crossing under the influence of active hydrodynamic fluctuations suggests that the biochemical activity of macromolecules such as enzymes is coupled to active noise, with potential impact on metabolic networks in living and artificial systems alike.

Biomolecules ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 804
Author(s):  
Andrea Ariano ◽  
Nadia Musco ◽  
Lorella Severino ◽  
Anna De Maio ◽  
Annabella Tramice ◽  
...  

The use of seaweeds as additives in animal nutrition may be a valid option to traditional feed as they represent a rich source of minerals, carbohydrates and antioxidants. The aim of this study was to analyze the chemical composition and in vitro antioxidant capacity of two tropical eucheumatoids, Kappaphycus alvarezii and Kappaphycus striatus, in Malaysian wild offshore waters. The chemical analysis was performed via inductively coupled plasma–optical emission spectroscopy for evaluating the concentration of toxic (Cd, Pb, Hg, As) and essential elements (Mn, Fe, Cu, Ni, Zn, Se); NMR spectroscopy was used for carrageenans investigation. Furthermore, the soluble and fat-soluble antioxidant capacities were determined by FRAP, DPPH and ABTS assays. The chemical analysis revealed a higher content of trace elements in K. alvarezii as compared to K. striatus, and both exhibited a high mineral content. No significant differences in metal concentrations were found between the two species. Both samples showed a mixture of prevailing κ- and t-carrageenans. Finally, the levels of soluble and fat-soluble antioxidants in K. alvarezii were significantly higher than in K. striatus. Our findings suggest that K. alvarezii could be used as a potential feed additive because of its favorable chemical and nutritional features.


mBio ◽  
2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Felipe H. Santiago-Tirado ◽  
Michael D. Onken ◽  
John A. Cooper ◽  
Robyn S. Klein ◽  
Tamara L. Doering

ABSTRACT The blood-brain barrier (BBB) protects the central nervous system (CNS) by restricting the passage of molecules and microorganisms. Despite this barrier, however, the fungal pathogen Cryptococcus neoformans invades the brain, causing a meningoencephalitis that is estimated to kill over 600,000 people annually. Cryptococcal infection begins in the lung, and experimental evidence suggests that host phagocytes play a role in subsequent dissemination, although this role remains ill defined. Additionally, the disparate experimental approaches that have been used to probe various potential routes of BBB transit make it impossible to assess their relative contributions, confounding any integrated understanding of cryptococcal brain entry. Here we used an in vitro model BBB to show that a “Trojan horse” mechanism contributes significantly to fungal barrier crossing and that host factors regulate this process independently of free fungal transit. We also, for the first time, directly imaged C. neoformans-containing phagocytes crossing the BBB, showing that they do so via transendothelial pores. Finally, we found that Trojan horse crossing enables CNS entry of fungal mutants that cannot otherwise traverse the BBB, and we demonstrate additional intercellular interactions that may contribute to brain entry. Our work elucidates the mechanism of cryptococcal brain invasion and offers approaches to study other neuropathogens. IMPORTANCE The fungal pathogen Cryptococcus neoformans invades the brain, causing a meningoencephalitis that kills hundreds of thousands of people each year. One route that has been proposed for this brain entry is a Trojan horse mechanism, whereby the fungus crosses the blood-brain barrier (BBB) as a passenger inside host phagocytes. Although indirect experimental evidence supports this intriguing mechanism, it has never been directly visualized. Here we directly image Trojan horse transit and show that it is regulated independently of free fungal entry, contributes to cryptococcal BBB crossing, and allows mutant fungi that cannot enter alone to invade the brain. IMPORTANCE The fungal pathogen Cryptococcus neoformans invades the brain, causing a meningoencephalitis that kills hundreds of thousands of people each year. One route that has been proposed for this brain entry is a Trojan horse mechanism, whereby the fungus crosses the blood-brain barrier (BBB) as a passenger inside host phagocytes. Although indirect experimental evidence supports this intriguing mechanism, it has never been directly visualized. Here we directly image Trojan horse transit and show that it is regulated independently of free fungal entry, contributes to cryptococcal BBB crossing, and allows mutant fungi that cannot enter alone to invade the brain.


2017 ◽  
Vol 37 (3) ◽  
pp. 342-344
Author(s):  
Roberta M. Katzap ◽  
Vany Elisa Pagnussatti ◽  
Ana Elizabeth Figueiredo ◽  
Julia Gabriela Motta ◽  
Domingos O. d'Avila ◽  
...  

Patients with chronic kidney disease on peritoneal dialysis (PD) are susceptible to infections, with peritonitis being the primary cause of dropout. Peritoneal fluid culture is one of the essential elements for proper diagnosis and peritonitis treatment. The aim of this study was to compare the time required to obtain a positive culture using different laboratory methods. An in vitro cross-sectional study was conducted comparing different techniques for preparation and culture of bacteria in peritoneal fluid. The research was carried out with 21 sterile dialysis bags and 21 PD bags containing peritoneal fluid drained from patients without peritonitis. Fluids from the 42 PD bags were contaminated by injecting a coagulase-negative Staphylococcus suspension and then prepared for culture using 4 distinct techniques: A - direct culture; B - post-centrifugation culture; C - direct culture after 4 h sedimentation; and D - culture after 4 h sedimentation and centrifugation. This was followed by seeding. In the 21 contaminated sterile bags, mean times to obtain a positive culture with techniques D (19.6 h ± 2.6) and C (19.1 h ± 2.3) were longer than with technique A (15.8 h ± 3.0; p < 0.01), but not statistically different from group B (19.0 h ± 3.2). The same occurred in the 21 bags drained from patients, with mean times for techniques D (14.0 h ± 1.9) and C (14.5 h ± 1.7) being longer than technique A (12.22 h ± 1.94; p < 0.05) but not statistically different from technique B (13.2 h ± 1.3). The sedimentation and centrifugation steps seem to be unnecessary and may delay antibiotic sensitivity test results by approximately 8 hours.


Genetics ◽  
2003 ◽  
Vol 164 (1) ◽  
pp. 23-29
Author(s):  
Miriam Barlow ◽  
Barry G Hall

Abstract Understanding of the evolutionary histories of many genes has not yet allowed us to predict the evolutionary potential of those genes. Intuition suggests that current biochemical activity of gene products should be a good predictor of the potential to evolve related activities; however, we have little evidence to support that intuition. Here we use our in vitro evolution method to evaluate biochemical activity as a predictor of future evolutionary potential. Neither the class C Citrobacter freundii CMY-2 AmpC β-lactamase nor the class A TEM-1 β-lactamase confer resistance to the β-lactam antibiotic cefepime, nor do any of the naturally occurring alleles descended from them. However, the CMY-2 AmpC enzyme and some alleles descended from TEM-1 confer high-level resistance to the structurally similar ceftazidime. On the basis of the comparison of TEM-1 and CMY-2, we asked whether biochemical activity is a good predictor of the evolutionary potential of an enzyme. If it is, then CMY-2 should be more able than the TEMs to evolve the ability to confer higher levels of cefepime resistance. Although we generated CMY-2 evolvants that conferred increased cefepime resistance, we did not recover any CMY-2 evolvants that conferred resistance levels as high as the best cefepime-resistant TEM alleles.


Materials ◽  
2021 ◽  
Vol 14 (18) ◽  
pp. 5340
Author(s):  
Alicja Tymoszuk

The interactions between nanoparticles and plant cells are still not sufficiently understood, and studies related to this subject are of scientific and practical importance. Silver nanoparticles (AgNPs) are one of the most commonly produced and used nanomaterials. This study aimed to investigate the influence of AgNPs applied at the concentrations of 0, 50, and 100 mg·L−1 during the process of in vitro germination as well as the biometric and biochemical parameters of developed seedlings in three vegetable species: Solanum lycopersicum L. ‘Poranek’, Raphanus sativus L. var. sativus ‘Ramona’, and Brassica oleracea var. sabellica ‘Nero di Toscana’. The application of AgNPs did not affect the germination efficiency; however, diverse results were reported for the growth and biochemical activity of the seedlings, depending on the species tested and the AgNPs concentration. Tomato seedlings treated with nanoparticles, particularly at 100 mg·L−1, had shorter shoots with lower fresh and dry weights and produced roots with lower fresh weight. Simultaneously, at the biochemical level, a decrease in the content of chlorophylls and carotenoids and an increase in the anthocyanins content and guaiacol peroxidase (GPOX) activity were reported. AgNPs-treated radish plants had shorter shoots of higher fresh and dry weight and longer roots with lower fresh weight. Treatment with 50 mg·L−1 and 100 mg·L−1 resulted in the highest and lowest accumulation of chlorophylls and carotenoids in the leaves, respectively; however, seedlings treated with 100 mg·L−1 produced less anthocyanins and polyphenols and exhibited lower GPOX activity. In kale, AgNPs-derived seedlings had a lower content of chlorophylls, carotenoids, and anthocyanins but higher GPOX activity of and were characterized by higher fresh and dry shoot weights and higher heterogeneous biometric parameters of the roots. The results of these experiments may be of great significance for broadening the scope of knowledge on the influence of AgNPs on plant cells and the micropropagation of the vegetable species. Future studies should be aimed at testing lower or even higher concentrations of AgNPs and other NPs and to evaluate the genetic stability of NPs-treated vegetable crops and their yielding efficiency.


2019 ◽  
Vol 11 (10) ◽  
pp. 277 ◽  
Author(s):  
Meire Pereira de Souza Ferrari ◽  
Mayara dos Santos Queiroz ◽  
Matheus Marquezini de Andrade ◽  
Jessica Rezende Trettel ◽  
Hélida Mara Magalhães

This study aimed to evaluate the in vitro growth and biochemical activity of Curcuma longa explants using different MS medium formulations and growth regulators. In all the experiments, plants were grown in MS medium supplemented with agar (6.5 g L-1) and pH adjusted to 5.8. In the first assay, the MS culture medium at 70% strength, supplemented with 30 g L-1 of sucrose, and without the addition of activated carbon, resulted in the highest number of shoots. The sucrose concentration of 60 g L-1, combined with the addition of actived charcoalin half-strength MS medium, resulted in the increased root dry mass, root collar diameter, and relative chlorophyll index. In the second assay, the highest root collar diameter and dry matter of shoots and roots were found in the MS medium supplemented with 4.44 BAP, 0.46 KIN, and 1.08 NAA. The MS medium with 8.88 BAP, 0.92 KIN, and 2.16 &mu;M NAA resulted in the highest number of shoots (7.75), number of leaves (35), and shoot length (88.57 mm). The antioxidant activity was significantly higher in the treatments that resulted in better plantlets growth performance, demonstrating that the antioxidant activity is related to other factors such as a possible role of growth regulators on the elicitation of compounds in plants. Superoxide dismutase had a high enzymatic activity in both assays, whereas the enzymatic activity of catalase and ascorbate peroxidase was dependent on the culture media used.


2021 ◽  
Author(s):  
Nathan Ennist ◽  
Zhenyu Zhao ◽  
Steven Stayrook ◽  
Bohdana Discher ◽  
P Leslie 'Les' Dutton ◽  
...  

Abstract Natural photosynthetic protein complexes capture sunlight to power the energetic catalysis that supports life on Earth. Yet these natural protein structures carry an evolutionary legacy of complexity and fragility that encumbers protein reengineering efforts and obfuscates the underlying design rules for light-driven charge separation. De novo development of a simplified photosynthetic reaction center protein can clarify practical engineering principles needed to build new enzymes for efficient solar-to-fuel energy conversion. Here we report the rational design, X-ray crystal structure, and electron transfer activity of a multi-cofactor protein that incorporates essential elements of photosynthetic reaction centers. This highly stable, modular artificial protein framework can be reconstituted in vitro with interchangeable redox centers for nanometer-scale photochemical charge separation. Transient absorption spectroscopy demonstrates Photosystem II-like tyrosine and metal cluster oxidation, and we measure charge separation lifetimes exceeding 100 ms, ideal for light-activated catalysis. This de novo-designed reaction center builds upon engineering guidelines established for charge separation in earlier synthetic photochemical triads and modified natural proteins, and it shows how synthetic biology may lead to a new generation of genetically encoded, light-powered catalysts for solar fuel production.


2021 ◽  
Author(s):  
Caterina Bartolacci ◽  
Cristina Andreani ◽  
Goncalo Dias do Vale ◽  
Stefano Berto ◽  
Margherita Melegari ◽  
...  

Mutant KRAS (KM) is the most common oncogene in lung cancer (LC). KM regulates several metabolic networks, but their role in tumorigenesis is still not sufficiently characterized to be exploited in cancer therapy. To identify metabolic networks specifically deregulated in KMLC, we characterized the lipidome of genetically engineered LC mice, cell lines, patient derived xenografts and primary human samples. We also determined that KMLC, but not EGFR-mutant (EGFR-MUT) LC, is enriched in triacylglycerides (TAG) and phosphatidylcholines (PC). We also found that KM upregulates fatty acid synthase (FASN), a rate-limiting enzyme in fatty acid (FA) synthesis promoting the synthesis of palmitate and PC. We determined that FASN is specifically required for the viability of KMLC, but not of LC harboring EGFR-MUT or wild type KRAS. Functional experiments revealed that FASN inhibition leads to ferroptosis, a reactive oxygen species (ROS)-and iron-dependent cell death. Consistently, lipidomic analysis demonstrated that FASN inhibition in KMLC leads to accumulation of PC with polyunsaturated FA (PUFA) chains, which are the substrate of ferroptosis. Integrating lipidomic, transcriptome and functional analyses, we demonstrated that FASN provides saturated (SFA) and monounsaturated FA (MUFA) that feed the Lands cycle, the main process remodeling oxidized phospholipids (PL), such as PC. Accordingly, either inhibition of FASN or suppression of the Lands cycle enzymes PLA2 and LPCAT3, promotes the intracellular accumulation of lipid peroxides and ferroptosis in KMLC both in vitro and in vivo. Our work supports a model whereby the high oxidative stress caused by KM dictates a dependency on newly synthesized FA to repair oxidated phospholipids, establishing a targetable vulnerability. These results connect KM oncogenic signaling, FASN induction and ferroptosis, indicating that FASN inhibitors already in clinical trial in KMLC patients (NCT03808558) may be rapidly deployed as therapy for KMLC.


2022 ◽  
Vol 10 (1) ◽  
pp. 13
Author(s):  
Tomas Vilde ◽  
Cameron A. Stewart ◽  
Yoav Finer

Despite their popularity, resin composite restorations fail earlier and at higher rates than comparable amalgam restorations. One of the reasons for these rates of failure are the properties of current dental bonding agents. Modern bonding agents are vulnerable to gradual chemical and mechanical degradation from a number of avenues such as daily use in chewing, catalytic hydrolysis facilitated by salivary or bacterial enzymes, and thermal fluctuations. These stressors have been found to work synergistically, all contributing to the deterioration and eventual failure of the hybrid layer. Due to the expense and difficulty in conducting in vivo experiments, in vitro protocols meant to accurately simulate the oral environment’s stressors are important in the development of bonding agents and materials that are more resistant to these processes of degradation. This narrative review serves to summarize the currently employed methods of aging dental materials and critically appraise them in the context of our knowledge of the oral environment’s parameters.


2021 ◽  
Author(s):  
Masaki Sasai

When the mixture solution of cyanobacterial proteins, KaiA, KaiB, and KaiC, is incubated with ATP in vitro, the phosphorylation level of KaiC shows stable oscillations with the temperature-compensated circadian period. We analyzed this temperature compensation by developing a theoretical model describing the feedback relations among reactions and structural transitions in the KaiC molecule. The model showed that the reduced structural cooperativity should weaken the negative feedback coupling among reactions and structural transitions, which enlarges the oscillation amplitude and period, explaining the observed significant period extension upon single amino-acid residue substitution. We propose that an increase in thermal fluctuations similarly attenuates the reaction-structure feedback, explaining the temperature compensation in the KaiABC clock. The model suggests that the ATPase reactions in the CI domain of KaiC affect the period depending on how the reaction rates are modulated. The KaiABC clock provides a unique opportunity to analyze how the reaction-structure coupling regulates the system-level synchronized oscillations of molecules.


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