Excess Absorbance as a Novel Approach for Studying the Self-Aggregation of Vital Dyes in Liquid Solution.

In the present paper, a simple method for analyzing the self-aggregation of dyes in a solution by a UV-visible absorption measurements is proposed. The concept of excess absorbance is introduced to determine an equation whose coefficients determine the parameters of the aggregation equilibrium. The computational peculiarities of the model are first discussed theoretically and then applied to sodium fluorescein in polar protic and aprotic solvents, as well as in aqueous solutions of methylene blue, which is a cationic dye. Although the experimental responses are very different, the model appears to work equally well in both cases. The model reveals that the trimer is the most likely configuration in both solvents. Furthermore, aggregation is strongly favored for the protic solvent. Interestingly, the model establishes that in aqueous solutions of methylene blue, the tetramer is the predominant form, which has long been assumed and recently demonstrated with sophisticated computational techniques.

Recommendations for performing measurements of apparent equilibrium constants of enzyme-catalyzed reactions and for reporting the results of these measurements.

The measurement of values of apparent equilibrium constants K' for enzyme-catalyzed reactions involve a substantial number of critical details, neglect of which could lead to systematic errors. Here, interferences, impurities in the substances used, and failure to achieve equilibrium are matters of substantial consequence. Careful reporting of results is of great importance if the results are to have archival value. Thus, attention must be paid to the identification of the substances, specification of the reaction(s), the conditions of reaction, the definition of the equilibrium constant(s) and standard states, the use of standard nomenclature, symbols, and units, and uncertainties. This document contains a general discussion of various aspects of these equilibrium measurements as well as STRENDA (Standards for Reporting Enzymology Data) recommendations regarding the measurements and the reporting of results.

Determination of association equilibrium constant from single molecule fluorescence localization microscopy.

Single molecule fluorescence localization microscopy provides molecular localization with a precision in the tens of nanometer range in the plane perpendicular to the light propagation. This opens the possibility to count molecules and correlate their locations, starting from a map of the actual positions in a single molecule super resolution image. Considering molecular pair correlation as an indication of interaction, and a way to discern them from free molecules, we describe a method to calculate thermodynamic equilibrium constants. In this work, we use as a test system two complementary homo-oligonucleotides, one strand marked with Cyanine 3.5 and the other with Alexa Fluor 647. Hybridization is controlled by the amount of each strand, temperature, and the ionic force, and measured in steady state emission. The same samples are examined in Stochastic Optical Reconstruction Microscopy (STORM) experiments with split-field simultaneous two-colour detection. The effect of multiblinking, labelling-detection efficiency, and determination of the critical distance for association are discussed. We consistently determine values in STORM coincident with those of the bulk experiment.

Determining the domain-level reaction-diffusion properties of an actin-binding protein transgelin-2 within cells.

Proteins in cells undergo repeated binding to other molecules, thereby reducing the apparent extent of their intracellular diffusion. While much effort has been made to analytically decouple these combined effects of pure diffusion and chemical binding, it is difficult with conventional approaches to attribute the measured quantities to the nature of specific domains of the proteins. Motivated by the common goal in cell signaling research aimed at identifying the domains responsible for particular intermolecular interactions, here we describe a framework for determining the local physicochemical properties of cellular proteins associated with immobile scaffolds. To validate this new approach, we apply it to transgelin-2, an actin-binding protein whose intracellular dynamics remains elusive. We develop a fluorescence recovery after photobleaching (FRAP)-based framework, in which comprehensive combinations of domain-deletion mutants are created, and the difference among them in FRAP response is analyzed. We demonstrate that transgelin-2 in actin stress fibers (SFs) interacts with F-actin via two separate domains, and the chemical properties are determined for the individual domains. Its pure diffusion properties independent of the association to F-actin is also obtained. Our approach will thus be useful, as presented here for transgelin-2, in addressing the signaling mechanism of cellular proteins associated with SFs.

Comment on the calculation of equilibrium constant and thermodynamic parameters by the distribution coefficient in Environmental Research 203 (2022) 111814.

This comment discussed the calculation of equilibrium constant and thermodynamic parameters in the paper of Kayalvizhi et al. (2022). This paper is of high academic value, however, there are some calculation and quotation errrors. The equilibrium constant K evolved from the distribution coefficient has a dimension of L/g, which is not the standard equilibrium constant, therefore, it cannot be used to calculate the thermodynamic parameters. This comment firstly analyzed the calculation errors made by Kayalvizhi et al. (2022), then established the relationship between distribution coefficient and standard equilibirum constant, and recalculated the thermodynamic parameters by using the correct distribution coefficient equation. As a research paper, authors not only provide the originality and novelty, but also give its correct results. This comment can bring to the attention of readers, authors, editors and reviewers about the thermodynamic calculation. At the same time, it is helpful to avoid the misuse and propagation of the incorrect equation in the area of adsorption thermodynamics.

Optimized Biocatalytic Synthesis of 2-Selenopyrimidine Nucleosides by Transglycosylation*.

Selenium-modified nucleosides are powerful tools to study the structure and function of nucleic acids and their protein interactions. The widespread application of 2-selenopyrimidine nucleosides is currently limited by low yields in established synthetic routes. Herein, we describe the optimization of the synthesis of 2-Se-uridine and 2-Se-thymidine derivatives by thermostable nucleoside phosphorylases in transglycosylation reactions using natural uridine or thymidine as sugar donors. Reactions were performed at 60 or 80 °C and at pH 9 under hypoxic conditions to improve the solubility and stability of the 2-Se-nucleobases in aqueous media. To optimize the conversion, the reaction equilibria in analytical transglycosylation reactions were studied. The equilibrium constants of phosphorolysis of the 2-Se-pyrimidines were between 5 and 10, and therefore differ by an order of magnitude from the equilibrium constants of any other known case. Hence, the thermodynamic properties of the target nucleosides are inherently unfavorable, and this complicates their synthesis significantly. A tenfold excess of sugar donor was needed to achieve 40-48 % conversion to the target nucleoside. Scale-up of the optimized conditions provided four Se-containing nucleosides in 6-40 % isolated yield, which compares favorably to established chemical routes.

Two Intercalation Mechanisms of Oxazole Yellow Dimer (YOYO-1) into DNA.

The oxazole yellow dye, YOYO-1 (a symmetric homodimer), is a commonly used molecule for staining DNA. We applied the brightness analysis to study the intercalation of YOYO-1 into the DNA. We distinguished two binding modes of the dye to dsDNA: mono-intercalation and bis-intercalation. Bis-intercalation consists of two consecutive mono-intercalation steps, characterised by two distinct equilibrium constants (with the average number of base pair per binding site equals 3.5): K1=3.36±0.43×107M-1 and K2=1.90±0.61×105M-1, respectively. Mono-intercalation dominates at high concentrations of YOYO-1. Bis-intercalation occurs at low concentrations.

General Principles for Yield Optimization of Nucleoside Phosphorylase-Catalyzed Transglycosylations.

The biocatalytic synthesis of natural and modified nucleosides with nucleoside phosphorylases offers the protecting-group-free direct glycosylation of free nucleobases in transglycosylation reactions. This contribution presents guiding principles for nucleoside phosphorylase-mediated transglycosylations alongside mathematical tools for straightforward yield optimization. We illustrate how product yields in these reactions can easily be estimated and optimized using the equilibrium constants of phosphorolysis of the nucleosides involved. Furthermore, the varying negative effects of phosphate on transglycosylation yields are demonstrated theoretically and experimentally with several examples. Practical considerations for these reactions from a synthetic perspective are presented, as well as freely available tools that serve to facilitate a reliable choice of reaction conditions to achieve maximum product yields in nucleoside transglycosylation reactions.

Measuring the affinity of protein-protein interactions on a single-molecule level by mass photometry.

Measurements of biomolecular interactions are crucial to understand the mechanisms of the biological processes they facilitate. Bulk-based methods such as ITC and SPR provide important information on binding affinities, stoichiometry, and kinetics of interactions. However, the ensemble averaging approaches are not able to probe the intrinsic heterogeneity often displayed by biological systems. Interactions that involve cooperativity or result in the formation of multicomponent complexes pose additional experimental challenges. Single-molecule techniques have previously been applied to solve these problems. However, single-molecule experiments are often technically demanding and require labeling or immobilization of the molecules under study. A recently developed single-molecule method, mass photometry (MP), overcomes these limitations. Here we applied MP to measure the affinities of biomolecular interactions. We have demonstrated how MP allows the user to study multivalent complexes and quantify the affinities of different binding sites in a single measurement. Results obtained from this single-molecule technique have been validated by ITC and BLI. The quality and information content of the MP data, combined with simple and fast measurements and low sample consumption makes MP a new preferred method for measuring strong protein-protein interactions.

Comment on the thermodynamic calculation using the non-standard equilibrium constant re Jemutai-Kimosop et al. (2020) and Conde-Cid et al. (2019).

This comment discussed the calculation of thermodynamic parameters about the paper of Jemutai-Kimosop et al. (2020) and Conde-Cid et al. (2019). Although these articles are valuable, in these cases, the equilibrium constant (K), which is used for the calculation of thermodynamic parameter is incorrect. The root reason for the errors in both articles is that the non-standard equilibrium constant was used to calculate the thermodynamic parameter, which is contrary to the principle of thermodynamics. This comment provided a correct method for the calculation of the standard equilibrium constant by using the distribution coefficient and Langmuir equation. This note can avoid the misuse and propagation of the incorrect equation in the area of adsorption thermodynamics.

Estimation of the driving force for dioxygen formation in photosynthesis.

Photosynthetic water oxidation to molecular oxygen is carried out by photosystem II (PSII) over a reaction cycle involving four photochemical steps that drive the oxygen-evolving complex through five redox states Si (i = 0,…, 4). For understanding the catalytic strategy of biological water oxidation it is important to elucidate the energetic landscape of PSII and in particular that of the final S4 → S0 transition. In this short-lived chemical step the four oxidizing equivalents accumulated in the preceding photochemical events are used up to form molecular oxygen, two protons are released and at least one substrate water molecule binds to the Mn4CaO5 cluster. In this study we probed the probability to form S4 from S0 and O2 by incubating YD-less PSII in the S0 state for 2­3 days in the presence of (18)O2 and H2(16)O. The absence of any measurable (16,18)O2 formation by water-exchange in the S4 state suggests that the S4 state is hardly ever populated. On the basis of a detailed analysis we determined that the equilibrium constant K of the S4 → S0 transition is larger than 1.0 × 10(7) so that this step is highly exergonic. We argue that this finding is consistent with current knowledge of the energetics of the S0 to S4 reactions, and that the high exergonicity is required for the kinetic efficiency of PSII.

In situ esterification and extractive fermentation for butyl butyrate production with Clostridium tyrobutyricum.

Butyl butyrate (BB) is a valuable chemical that can be used as flavor, fragrance, extractant, and so on in various industries. Meanwhile, BB can also be used as a fuel source with excellent compatibility as gasoline, aviation kerosene, and diesel components. The conventional industrial production of BB is highly energy-consuming and generates various environmental pollutants. Recently, there have been tremendous interests in producing BB from renewable resources through biological routes. In this study, based on the fermentation using the hyper-butyrate producing strain Clostridium tyrobutyricum ATCC 25755, efficient BB production through in situ esterification was achieved by supplementation of lipase and butanol into the fermentation. Three commercially available lipases were assessed and the one from Candida sp. (recombinant, expressed in Aspergillus niger) was identified with highest catalytic activity for BB production. Various conditions that might affect BB production in the fermentation have been further evaluated, including the extractant type, enzyme loading, agitation, pH, and butanol supplementation strategy. Under the optimized conditions (5.0 g L-1 of enzyme loading, pH at 5.5, butanol kept at 10.0 g L-1 ), 34.7 g L-1 BB was obtained with complete consumption of 50 g L-1 glucose as the starting substrate. To our best knowledge, the BB production achieved in this study is the highest among the ever reported from the batch fermentation process. Our results demonstrated an excellent biological platform for renewable BB production from low-value carbon sources. Biotechnol. Bioeng. 2017;114: 1428-1437. © 2017 Wiley Periodicals, Inc.

An Ideal Solid Solution Model for C-S-H.

A model for an ideal solid solution, developed by Nourtier-Mazauric et al. [Oil & Gas Sci. Tech. Rev. IFP, 60 [2] (2005) 401], is applied to calcium-silicate-hydrate (C-S-H). Fitting the model to solubility data reported in the literature for C-S-H yields reasonable values for the compositions of the end-members of the solid solution and for their equilibrium constants. This model will be useful in models of hydration kinetics of tricalcium silicate because it is easier to implement than other solid solution models, it clearly identifies the driving force for growth of the most favorable C-S-H composition, and it still allows the model to accurately capture variations in C-S-H composition as the aqueous solution changes significantly at early hydration times.

[Difference in inclusion behavior of ß-cyclodextrin and hydroxypropyl-ß-cyclodextrin with menthol].

Volatile oils are important active components in traditional Chinese medicine, but their components are complicated and unstable. It is common to use cyclodextrin inclusion technique to improve the stability of volatile oils and make them easier to be prepared. At present, ß-cyclodextrin (ß-CD) is the most common inclusion material. The evaluation indicators for inclusion technique usually contain the inclusion rate and the oil content in the inclusion compound. However, the articles about the study on selecting inclusion materials for volatile oils were few. In this paper, menthol, the main active ingredient of mint volatile oil, was used as model drug, while ß-CD and hydroxypropyl-ß-cyclodextrin (HP-ß-CD) were used as the inclusion materials. Inclusion equilibrium constant (K), solubilization ratio were investigated, and the results were combined with IR, DSC and TG to verify the formation of inclusion complexes. It turned out that in the range of 0-15 mmol•L⁻¹, the solubility of menthol was increased linearly with the increase of HP-ß-CD concentration, with AL-type phase solubility diagram, K=3 188.62 L•mol⁻¹; in the range of 0-12.5 mmol•L⁻¹, the solubility of menthol was increased linearly with the increase of ß-CD concentration, K=818.73 L•mol⁻¹. When the concentration was over 12.5 mmol•L⁻¹, the solubility of menthol appeared to be a negative deviation with the increase of ß-CD concentration, with AN-type solubility diagram. The above results showed that the inclusion behavior was different between ß-CD and HP-ß-CD, laying a foundation for further study on inclusion complexes of volatile oil.

EmrE dimerization depends on membrane environment.

The small multi-drug resistant (SMR) transporter EmrE functions as a homodimer. Although the small size of EmrE would seem to make it an ideal model system, it can also make it challenging to work with. As a result, a great deal of controversy has surrounded even such basic questions as the oligomeric state. Here we show that the purified protein is a homodimer in isotropic bicelles with a monomer-dimer equilibrium constant (KMD(2D)) of 0.002-0.009mol% for both the substrate-free and substrate-bound states. Thus, the dimer is stabilized in bicelles relative to detergent micelles where the KMD(2D) is only 0.8-0.95mol% (Butler et al. 2004). In dilauroylphosphatidylcholine (DLPC) liposomes KMD(2D) is 0.0005-0.0008mol% based on Förster resonance energy transfer (FRET) measurements, slightly tighter than bicelles. These results emphasize the importance of the lipid membrane in influencing dimer affinity.

Formaldehyde and methylene glycol equivalence: critical assessment of chemical and toxicological aspects.

Due largely to the controversy concerning the potential human health effects from exposure to formaldehyde gas in conjunction with the misunderstanding of the well-established equilibrium relationship with its hydrated reaction product, methylene glycol, the concept of chemical equivalence between these two distinctly different chemicals has been adopted by regulatory authorities. Chemical equivalence implies not only that any concentration of methylene glycol under some condition of use would be nearly or completely converted into formaldehyde gas, but also that these two substances would be toxicologically equivalent as well. A relatively simple worst case experiment using 37% formalin (i.e., concentrated methylene glycol) dispels the concept of chemical equivalence and a review of relevant literature demonstrates that methylene glycol has no inherent toxicity apart from whatever concentration of formaldehyde that might be present in equilibrium with such solutions.

Investigating the influence of solvent type and pH on protein adsorption onto silica surface by evanescent-wave cavity ring-down spectroscopy.

Several studies have explored the adsorption of various proteins onto solid-liquid interfaces, revealing the crucial role of buffer solutions in biological processes. However, a comprehensive evaluation of the buffer's influence on protein absorption onto fused silica is still lacking. This study employs evanescent-wave cavity ring-down spectroscopy (EW-CRDS) to assess the influence of buffer solutions and pH on the adsorption kinetics of three globular proteins: hemoglobin (Hb), myoglobin (Mb), and cytochrome c (Cyt-C) onto fused silica. The EW-CRDS tool, with a ring-down time of 1.4 µ s and a minimum detectable absorbance of 1 × 10 - 6 , enabled precise optical measurements at solid-liquid interfaces. The three heme proteins' adsorption behavior was investigated at pH 7 in three different solvents: deionized (DI) water, tris(hydroxymethyl)-aminomethane hydrochloride (Tris-HCl), and phosphate buffered saline (PBS). For each protein, the surface coverage, the adsorption and desorption constants, and the surface equilibrium constant were optically measured by our EW-CRDS tool. Depending on the nature of each solvent, the proteins showed a completely different adsorption trend on the silica surface. The adsorption of Mb on the silica surface was depressed in the presence of both Tris-HCl and PBS buffers compared with unbuffered (DI water) solutions. In contrast, Cyt-C adsorption appears to be relatively unaffected by the choice of buffer, as it involves strong electrostatic interactions with the surface. Notably, Hb exhibits an opposite trend, with enhanced protein adsorption in the presence of Tris-HCl and PBS buffer. The pH investigations demonstrated that the electrostatic interactions between the proteins and the surface had a major influence on protein adsorption on the silica surface, with adsorption being greatest when the pH values were around the protein's isoelectric point. This study demonstrated the ability of the highly sensitive EW-CRDS tool to study the adsorption events of the evanescent-field-confined protein species in real-time at low surface coverages with fast resolution, making it a valuable tool for studying biomolecule kinetics at solid-liquid interfaces.

Estimating RNA Secondary Structure Folding Free Energy Changes with efn2.

A number of analyses require estimates of the folding free energy changes of specific RNA secondary structures. These predictions are often based on a set of nearest neighbor parameters that models the folding stability of a RNA secondary structure as the sum of folding stabilities of the structural elements that comprise the secondary structure. In the software suite RNAstructure, the free energy change calculation is implemented in the program efn2. The efn2 program estimates the folding free energy change and the experimental uncertainty in the folding free energy change. It can be run through the graphical user interface for RNAstructure, from the command line, or a web server. This chapter provides detailed protocols for using efn2.

Structure and Stability of Ago2 MID-Nucleotide Complexes: All-in-One (Drop) His6-SUMO Tag Removal, Nucleotide Binding, and Crystal Growth.

The middle (MID) domain of eukaryotic Argonaute (Ago) proteins and archaeal and bacterial homologues mediates the interaction with the 5'-terminal nucleotide of miRNA and siRNA guide strands. The MID domain of human Ago2 (hAgo2) is comprised of 139 amino acids with a molecular weight of 15.56 kDa. MID adopts a Rossman-like beta1-alpha1-beta2-alpha2-beta3-alpha3-beta4-alpha4 fold with a nucleotide specificity loop between beta3 and alpha3. Multiple crystal structures of nucleotides bound to hAgo2 MID have been reported, whereby complexes were obtained by soaking ligands into crystals of MID domain alone. This protocol describes a simplified one-step approach to grow well-diffracting crystals of hAgo2 MID-nucleotide complexes by mixing purified His6-SUMO-MID fusion protein, Ulp1 protease, and excess nucleotide in the presence of buffer and precipitant. The crystal structures of MID complexes with UMP, UTP and 2'-3' linked α-L-threofuranosyl thymidine-3'-triphosphate (tTTP) are presented. This article also describes fluorescence-based assays to measure dissociation constants (Kd) of MID-nucleotide interactions for nucleoside 5'-monophosphates and nucleoside 3',5'-bisphosphates. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Crystallization of Ago2 MID-nucleotide complexes Basic Protocol 2: Measurement of dissociation constant Kd between Ago2 MID and nucleotides.

Discussion on the thermodynamic calculation and adsorption spontaneity re Ofudje et al. (2023).

Accurate calculations and precise results are very important for the dissemination of scientific knowledge, whereas the errors of calculation will diminish the academic value of the paper. This discussion focuses on the calculation of thermodynamics and the determination of the spontaneity of adsorption processes in the paper of Ofudje et al. (2023). Ofudje et al. found that the apatite synthesized by chemical method (CHAp) has excellent adsorption properties for cadmium ions, which is an important contribution to the remediation of cadmium pollution. However, the calculation results of standard Gibbs free energy change (ΔGo), standard enthalpy change (ΔHo) and standard entropy change (ΔSo) of the adsorption of Cd2+ onto CHAp surface need to be corrected due to an incorrect calculation. Firstly, the partition coefficient (KD) with a dimension cannot be used for thermodynamic calculation. Secondly, the adsorbent mass (m) described by Ofudje et al. in different Sections is inconsistent, leading to incorrect results of Ko and ΔGo. When the appropriate value of the adsorbent mass is selected and the partition coefficient is converted to the standard adsorption equilibrium constant Ko, the calculated ΔGo is less than zero, which means that the adsorption is spontaneous. This discussion provides the correct calculation method of standard adsorption equilibrium constants and thermodynamic parameters, which can improve the reader's judgment and understanding of adsorption spontaneity.