ATP binding to a multisubunit enzyme: statistical thermodynamics analysis

Due to inter-subunit communication, multisubunit enzymes usually hydrolyze ATP in a concerted fashion. However, so far the principle of this process remains poorly understood. In this study, from the viewpoint of statistical thermodynamics, a simple model is presented. In this model, we assume that the binding of ATP will change the potential of the corresponding enzyme subunit, and the degree of this change depends on the state of its adjacent subunits. The probability of enzyme in a given state satisfies the Boltzmann's distribution. Although it looks much simple, this model can fit the recent experimental data of chaperonin TRiC/CCT well. From this model, the dominant state of TRiC/CCT can be obtained. This study provided a new way to understand biophysical processes by statistical thermodynamics analysis

On the efficient numerical solution of lattice systems with low-order couplings

We apply the Quasi Monte Carlo (QMC) and recursive numerical integration methods to evaluate the Euclidean, discretized time path-integral for the quantum mechanical anharmonic oscillator and a topological quantum mechanical rotor model. For the anharmonic oscillator both methods outperform standard Markov Chain Monte Carlo methods and show a significantly improved error scaling. For the quantum mechanical rotor we could, however, not find a successful way employing QMC. On the other hand, the recursive numerical integration method works extremely well for this model and shows an at least exponentially fast error scaling

Synthesis of Low Abundant Vitamin D Metabolites and Assaying Their Distribution in Human Serum by Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) as a New Tool for Diagnosis and Risk Prediction of Vitamin DRelated Diseases

This chapter provides an overview of versatile and efficient chemical syntheses of vitamin D derivatives by application of either linear or convergent synthesis approaches. Synthesis of the most relevant naturally occurring vitamin D metabolites and their deuterated counterparts to use as calibration and reference standards in LC-MS/MS assays is also shown. The chapter then summarizes the most important mass spectrometric approaches to quantify important vitamin D metabolites in human biofluids. In addition, new developments are described that are aimed at the pathobiological interpretation of the measured vitamin D metabolite distributions in various human diseases

Analysis of natural organic matter via fourier transform ion cyclotron resonance mass spectrometry: an overview of recent non‐petroleum applications

Among the different techniques for mass analysis, ultra‐high‐resolution Fourier transform ion cyclotron resonance (FTICR) is the method of choice for highly complex samples, as it offers unrivaled mass accuracy and resolving power, combined with a high degree of flexibility in hybrid instruments as well as for ion activation techniques. FTICR instruments are readily embraced by the biological and biomedical research communities and applied over a wide range of applications for the analysis of biomolecules such as carbohydrates, lipids, nucleic acids, and proteins. In the field of natural organic matter (NOM) analysis, petroleum‐related studies currently dominate FTICR‐MS applications. Recently, however, there is a growing interest in developing high‐performance MS methods for the characterization of NOM samples from natural aquatic and terrestrial environments. Here, we present an overview of FTICR‐MS techniques for complex, non‐petroleum NOM samples, including data analysis and novel tandem mass spectrometry (MS/MS) methods for structural classifications. © 2020 The Authors. Mass Spectrometry Reviews published by John Wiley & Sons Ltd.Peer Reviewe

First insights into chlorhexidine retention in the oral cavity after application of different regimens

Objectives This in situ study aimed to determine and compare the chlorhexidine (CHX) retention in the oral cavity after the application of different CHX pharmaceutical regimens. Methods Five volunteers used different CHX treatment regimens including mouth rinses, dental spray and toothpaste gel. After the application of the different CHX regimens, 2-μl samples were taken from saliva and buccal mucosa pellicle as well as the dental pellicle samples formed on standardized enamel surfaces. Sample collection was conducted at six time points within 12 h. Retention of CHX was measured using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Results CHX retention values in the oral mucosa pellicle were significantly higher than those in saliva. CHX remained in the mucosal pellicle at microgrammes per millilitre levels for 12 h after mouth rinsing, 10 h after spray application and 2 h after using the toothpaste. CHX was detected in the dental pellicle for at least 12 h after application of mouth rinsing and spray. Retention of CHX after mouth rinsing or spray application was significantly higher than the retention after using toothpaste. Conclusions Oral mucosa was the favourable site for CHX retention. Higher mouth rinse concentration and longer rinsing time produced a slight increase in CHX retention. CHX spray provided considerable retention values, whereas toothpaste gel delivered the lowest retention after application. MALDI-TOF was a sensitive method with excellent limits of quantification for CHX detection

Hard sphere crystallization gets rarer with increasing dimension

We recently found that crystallization of monodisperse hard spheres from the bulk fluid faces a much higher free energy barrier in four than in three dimensions at equivalent supersaturation, due to the increased geometrical frustration between the simplex-based fluid order and the crystal [J.A. van Meel, D. Frenkel, and P. Charbonneau, Phys. Rev. E 79, 030201(R) (2009)]. Here, we analyze the microscopic contributions to the fluid-crystal interfacial free energy to understand how the barrier to crystallization changes with dimension. We find the barrier to grow with dimension and we identify the role of polydispersity in preventing crystal formation. The increased fluid stability allows us to study the jamming behavior in four, five, and six dimensions and compare our observations with two recent theories [C. Song, P. Wang, and H. A. Makse, Nature 453, 629 (2008); G. Parisi and F. Zamponi, Rev. Mod. Phys, in press (2009)].Comment: 15 pages, 5 figure

Sustainable Electrochemical Depolymerization of Lignin in Reusable Ionic Liquids

Lignin’s aromatic building blocks provide a chemical resource that is, in theory, ideal for substitution of aromatic petrochemicals. Moreover, degradation and valorization of lignin has the potential to generate many high-value chemicals for technical applications. In this study, electrochemical degradation of alkali and Organosolv lignin was performed using the ionic liquids 1-ethyl-3-methylimidazolium trifluoromethanesulfonate and triethylammonium methanesulfonate. The extensive degradation of the investigated lignins with simultaneous almost full recovery of the electrolyte materials provided a sustainable alternative to more common lignin degradation processes. We demonstrate here that both the presence (and the absence) of water during electrolysis and proton transport reactions had significant impact on the degradation efficiency. Hydrogen peroxide radical formation promoted certain electrochemical mechanisms in electrolyte systems “contaminated” with water and increased yields of low molecular weight products significantly. The proposed mechanisms were tentatively confirmed by determining product distributions using a combination of liquid chromatography-mass spectrometry and gas-chromatography-mass spectrometry, allowing measurement of both polar versus non-polar as well as volatile versus non-volatile components in the mixtures

Growth and microcystin production of a Brazilian Microcystis aeruginosa strain (LTPNA 02) under different nutrient conditions

Cyanobacteria are prokaryotic and photosynthetic organisms, which can produce a wide range of bioactive compounds with different properties; including a variety of toxic compounds, also known as cyanotoxins. In this work, we describe the isolation of seven cyanobacterial strains from two reservoirs in São Paulo State, Brazil. Seven different chemical variants of microcystins (MC-RR, MC-LR, MC-YR, MC-LF, MC-LW, and two demethylated variants, dm-MC-RR and dm-MC-LR) were detected in three of the ten isolated strains. One particular Microcystis aeruginosa strain (LTPNA 02) was chosen to evaluate its growth by cell count, and its toxin production under seven different nutritional regimes. We observed different growth behaviors in the logarithmic growth period for only three experiments (p < 0.05). The total growth analysis identified four experiments as different from the control (p < 0.01). Three microcystin variants (MC-RR, MC-LR and MC-YR) were quantified by liquid chromatography-tandem mass spectrometry. At the experimental end, the toxin content was unchanged when comparing cell growth in ASM-1 (N:P = 1), MLA and BG-11 (N:P = 10) medium. In all other experiments, the lowest microcystin production was observed from cells grown in Bold 3N medium during the exponential growth phase. The highest microcystin content was observed in cultures using BG-11(N:P = 100) medium.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Alfried Krupp von Bohlen und Halbach-StiftungUniversidade de São Paulo Departamento de Análises Clínicas e ToxicológicasSaarland University Institute of Bioanalytical ChemistryUniversidade Federal de São Paulo (UNIFESP) Instituto de Ciências Ambientais, Químicas e FarmacêuticasFriedrich-Schiller University of Jena Institute of NutritionHans Knöll Institute Leibniz Institute for Natural Product Research and Infection BiologyUniversidade de São Paulo Instituto de Química Departamento de BioquímicaUNIFESP, Instituto de Ciências Ambientais, Químicas e FarmacêuticasCNPq: 201609/2012-6SciEL