Biophysical characterization and design of a minimal version of the Hoechst RNA aptamer

RNA aptamers are oligonucleotides, selected through Systematic Evolution of Ligands by EXponential Enrichment (SELEX), that can bind to specific target molecules with high affinity. One such molecule is the RNA aptamer that binds to a blue-fluorescent Hoechst dye that was modified with bulky t-Bu groups to prevent non-specific binding to DNA. This aptamer has potential for biosensor applications; however, limited information is available regarding its conformation, molecular interactions with the ligand, and binding mechanism. The study presented here aims to biophysically characterize the Hoechst RNA aptamer when complexed with the t-Bu Hoechst dye and to further optimize the RNA sequence by designing and synthesizing new sequence variants. Each variant aptamer-t-Bu Hoechst complex was evaluated through a combination of fluorescence emission, native polyacrylamide gel electrophoresis, fluorescence titration, and isothermal titration calorimetry experiments. The results were used to design a minimal version of the aptamer consisting of only 21 nucleotides. The performed study also describes a more efficient method for synthesizing the t-Bu Hoechst dye derivative. Understanding the biophysical properties of the t-Bu Hoechst dye-RNA complex lays the foundation for nuclear magnetic resonance spectroscopy studies and its potential development as a building block for an aptamer-based biosensor that can be used in medical, environmental or laboratory settings.

Isothermal titration calorimetry and surface plasmon resonance methods to probe protein-protein interactions

Isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR) are two commonly used methods to probe biomolecular interactions. ITC can provide information about the binding affinity, stoichiometry, changes in Gibbs free energy, enthalpy, entropy, and heat capacity upon binding. SPR can provide information about the association and dissociation kinetics, binding affinity, and stoichiometry. Both methods can determine the nature of protein-protein interactions and help understand the physicochemical principles underlying complex biochemical pathways and communication networks. This methods article discusses the practical knowledge of how to set up and troubleshoot these two experiments with some examples.

Simulation-guided development of an optical calorimeter for high dose rate dosimetry

Optical Calorimetry (OC) is based on interferometry and provides a direct measurement of spatially resolved absorbed dose to water by measuring refractive index changes induced by radiation. The purpose of this work was to optimize and characterize in software an OC system tailored for ultra-high dose rate applications and to build and test a prototype in a clinical environment. A radiation dosimeter using the principles of OC was designed in optical modelling software. Traditional image quality instruments, fencepost and contrast phantoms, were utilized both in software and experimentally in a lab environment to investigate noise reduction techniques and to test the spatial and dose resolution of the system. Absolute dose uncertainty was assessed by measurements in a clinical 6 MV Flattening Filter Free (FFF) photon beam with dose rates in the range 0.2-6 Gy/s achieved via changing the distance from the source. Design improvements included: equalizing the pathlengths of the interferometer, isolating the system from external vibrations and controlling the system's internal temperature as well as application of mathematical noise reduction techniques. Simulations showed that these improvements should increase the spatial resolution from 22 to 35 lp/mm and achieve a minimum detectable dose of 0.2 Gy, which was confirmed experimentally. In the FFF beam, the absolute dose uncertainty was dose rate dependent and decreased from 2.5 ± 0.8 to 2.5 ± 0.2 Gy for dose rates of 0.2 and 6 Gy/s, respectively. A radiation dosimeter utilizing the principles of OC was developed and constructed. Optical modelling software and image quality phantoms allowed for iterative testing and refinement. The refined OC system proved capable of measuring absorbed dose to water in a linac generated photon beam. Reduced uncertainty at higher dose rates indicates the potential for OC as a dosimetry system for high dose rate techniques such as microbeam and ultra-high dose-rate radiotherapy.

Investigation of steric hindrance effect on the interactions between four alkaloids and HSA by isothermal titration calorimetry and molecular docking

The binding of four alkaloids with human serum albumin (HSA) was investigated by isothermal titration calorimetry (ITC), spectroscopy and molecular docking techniques. The findings demonstrated that theophylline or caffeine can bind to HAS, respectively. The number of binding sites and binding constants are obtained. The binding mode is a static quenching process. The effects of steric hindrance, temperature, salt concentration and buffer solution on the binding indicated that theophylline and HSA have higher binding affinity than caffeine. The fluorescence and ITC results showed that the interaction between HSA and theophylline or caffeine is an entropy-driven spontaneous exothermic process. The hydrophobic force was the primary driving factor. The experimental results were consistent with the molecular docking data. Based on the molecular structures of the four alkaloids, steric hindrance might be a major factor in the binding between HSA and these four alkaloids. This study elucidates the mechanism of interactions between four alkaloids and HSA.

pH-dependent interactions of biologically important metal ions with hen egg white lysozyme based on its hydration properties: Thermodynamic and mechanistic insights

Importance of metal ion selectivity in biomolecules and their key role in proteins are widely explored. However, understanding the thermodynamics of how hydrated metal ions alter the protein hydration and their conformation is also important. In this study, the interaction of some biologically important Ca2+, Mn2+, Co2+, Cu2+, and Zn2+ ions with hen egg white lysozyme at pH 2.1, 3.0, 4.5 and 7.4 has been investigated. Intrinsic fluorescence studies have been employed for metal ion-induced protein conformational changes analysis. Thermostability based on protein hydration has been investigated using differential scanning calorimetry (DSC). Thermodynamic parameters emphasizing on metal ion-protein binding mechanistic insights have been well discussed using isothermal titration calorimetry (ITC). Overall, these experiments have reported that their interactions are pH-dependent and entropically driven. This research also reports the strongly hydrated metal ions as water structure breaker unlike osmolytes based on DSC studies. These experimental results have highlighted higher concentrations of different metal ions effect on the protein hydration and thermostability which might be helpful in understanding their interactions in aqueous solutions.

Addressing the complexities in measuring cyclodextrin-sterol binding constants: A multidimensional study

A class of cyclodextrin (CD) dimers has emerged as a potential new treatment for atherosclerosis; they work by forming strong, soluble inclusion complexes with oxysterols, allowing the body to reduce and heal arterial plaques. However, characterizing the interactions between CD dimers and oxysterols presents formidable challenges due to low sterol solubility, the synthesis of modified CDs resulting in varying number and position of molecular substitutions, and the diversity of interaction mechanisms. To address these challenges and illuminate the nuances of CD-sterol interactions, we have used multiple orthogonal approaches for a comprehensive characterization. Results obtained from three independent techniques - metadynamics simulations, competitive isothermal titration calorimetry, and circular dichroism - to quantify CD-sterol binding are presented. The objective of this study is to obtain the binding constants and gain insights into the intricate nature of the system, while accounting for the advantages and limitations of each method. Notably, our findings demonstrate ∼1000× stronger affinity of the CD dimer for 7-ketocholesterol in comparison to cholesterol for the 1:1 complex in direct binding assays. These methodologies and findings not only enhance our understanding of CD dimer-sterol interactions, but could also be generally applicable to prediction and quantification of other challenging host-guest complex systems.

Real time detection of pathogenic bacteria in veterinary microbiology using isothermal microcalorimetry - A different approach

With today's challenges regarding antibiotic resistance and the importance of the implementation of prudent use of antibiotics, fast and reliable diagnostic tools for bacterial infections and subsequent antimicrobial susceptibility testing are of utmost relevance. Isothermal microcalorimetry (IMC) is a broadly applicable method, with which metabolic heat flow in reproducing bacteria can be measured in real time. To the best of the authors' knowledge, this is the first report on examination of 124 urine samples from feline and canine urinary tract infection with an IMC-based prototype instrument. A concentration-dependent time of peak heat flow by dilution series with Escherichia coli and Enterococcus faecalis reference strains demonstrated the general good performance of the prototype for detection of these bacteria. With diagnostic culture being set as a gold standard, the diagnostic sensitivity of IMC compared to bacteriological culture was 80 %, the diagnostic specificity was 97 %. With a Cohens' kappa value (κ) of 0.80, the two methods show good concordance. The results from our study demonstrate that the IMC technology is suitable to allow reliable, but much faster detection of bacteria than conventional culture, especially for Escherichia coli. Thus, implementing IMC technology could markedly speed up the bacteriological diagnostic process in veterinary medicine.

NMR-identification of the interaction between BRCA1 and the intrinsically disordered monomer of the Myc-associated factor X

The breast cancer susceptibility 1 (BRCA1) protein plays a pivotal role in modulating the transcriptional activity of the vital intrinsically disordered transcription factor MYC. In this regard, mutations of BRCA1 and interruption of its regulatory activity are related to hereditary breast and ovarian cancer (HBOC). Interestingly, so far, MYC's main dimerization partner MAX (MYC-associated factor X) has not been found to bind BRCA1 despite a high sequence similarity between both oncoproteins. Herein, we show that a potential reason for this discrepancy is the heterogeneous conformational space of MAX, which encloses a well-documented folded coiled-coil homodimer as well as a less common intrinsically disordered monomer state-contrary to MYC, which exists mostly as intrinsically disordered protein in the absence of any binding partner. We show that when the intrinsically disordered state of MAX is artificially overpopulated, the binding of MAX to BRCA1 can readily be observed. We characterize this interaction by nuclear magnetic resonance (NMR) spectroscopy chemical shift and relaxation measurements, complemented with ITC and SAXS data. Our results suggest that BRCA1 directly binds the MAX monomer to form a disordered complex. Though probed herein under biomimetic in-vitro conditions, this finding can potentially stimulate new perspectives on the regulatory network around BRCA1 and its involvement in MYC:MAX regulation.

Bayesian Regression Quantifies Uncertainty of Binding Parameters from Isothermal Titration Calorimetry More Accurately Than Error Propagation

We compare several different methods to quantify the uncertainty of binding parameters estimated from isothermal titration calorimetry data: the asymptotic standard error from maximum likelihood estimation, error propagation based on a first-order Taylor series expansion, and the Bayesian credible interval. When the methods are applied to simulated experiments and to measurements of Mg(II) binding to EDTA, the asymptotic standard error underestimates the uncertainty in the free energy and enthalpy of binding. Error propagation overestimates the uncertainty for both quantities, except in the simulations, where it underestimates the uncertainty of enthalpy for confidence intervals less than 70%. In both datasets, Bayesian credible intervals are much closer to observed confidence intervals.

Computed Protein-Protein Enthalpy Signatures as a Tool for Identifying Conformation Sampling Problems

Understanding the thermodynamic signature of protein-peptide binding events is a major challenge in computational chemistry. The complexity generated by both components possessing many degrees of freedom poses a significant issue for methods that attempt to directly compute the enthalpic contribution to binding. Indeed, the prevailing assumption has been that the errors associated with such approaches would be too large for them to be meaningful. Nevertheless, we currently have no indication of how well the present methods would perform in terms of predicting the enthalpy of binding for protein-peptide complexes. To that end, we carefully assembled and curated a set of 11 protein-peptide complexes where there is structural and isothermal titration calorimetry data available and then computed the absolute enthalpy of binding. The initial "out of the box" calculations were, as expected, very modest in terms of agreement with the experiment. However, careful inspection of the outliers allows for the identification of key sampling problems such as distinct conformations of peptide termini not being sampled or suboptimal cofactor parameters. Additional simulations guided by these aspects can lead to a respectable correlation with isothermal titration calorimetry (ITC) experiments (R2 of 0.88 and an RMSE of 1.48 kcal/mol overall). Although one cannot know prospectively whether computed ITC values will be correct or not, this work shows that if experimental ITC data are available, then this in conjunction with computed ITC, can be used as a tool to know if the ensemble being simulated is representative of the true ensemble or not. That is important for allowing the correct interpretation of the detailed dynamics of the system with respect to the measured enthalpy. The results also suggest that computational calorimetry is becoming increasingly feasible. We provide the data set as a resource for the community, which could be used as a benchmark to help further progress in this area.

Potential Clinically Relevant Effects of Sialylation on Human Serum AAG-Drug Interactions Assessed by Isothermal Titration Calorimetry: Insight into Pharmacoglycomics?

Human serum alpha-1 acid glycoprotein is an acute-phase plasma protein involved in the binding and transport of many drugs, especially basic and lipophilic substances. It has been reported that the sialic acid groups that terminate the N-glycan chains of alpha-1 acid glycoprotein change in response to certain health conditions and may have a major impact on drug binding to alpha-1 acid glycoprotein. The interaction between native or desialylated alpha-1 acid glycoprotein and four representative drugs-clindamycin, diltiazem, lidocaine, and warfarin-was quantitatively evaluated using isothermal titration calorimetry. The calorimetry assay used here is a convenient and widely used approach to directly measure the amount of heat released or absorbed during the association processes of biomolecules in solution and to quantitatively estimate the thermodynamics of the interaction. The results showed that the binding of drugs with alpha-1 acid glycoprotein were enthalpy-driven exothermic interactions, and the binding affinity was in the range of 10-5-10-6 M. Desialylated alpha-1 acid glycoprotein showed significantly different binding with diltiazem, lidocaine, and warfarin compared with native alpha-1 acid glycoprotein, whereas clindamycin showed no significant difference. Therefore, a different degree of sialylation may result in different binding affinities, and the clinical significance of changes in sialylation or glycosylation of alpha-1 acid glycoprotein in general should not be neglected.

Direct Oral FXa Inhibitors Binding to Human Serum Albumin: Spectroscopic, Calorimetric, and Computational Studies

Direct FXa inhibitors are an important class of bioactive molecules (rivaroxaban, apixaban, edoxaban, and betrixaban) applied for thromboprophylaxis in diverse cardiovascular pathologies. The interaction of active compounds with human serum albumin (HSA), the most abundant protein in blood plasma, is a key research area and provides crucial information about drugs' pharmacokinetics and pharmacodynamic properties. This research focuses on the study of the interactions between HSA and four commercially available direct oral FXa inhibitors, applying methodologies including steady-state and time-resolved fluorescence, isothermal titration calorimetry (ITC), and molecular dynamics. The HSA complexation of FXa inhibitors was found to occur via static quenching, and the complex formation in the ground states affects the fluorescence of HSA, with a moderate binding constant of 10⁴ M^-1. However, the ITC studies reported significantly different binding constants (10³ M^-1) compared with the results obtained through spectrophotometric methods. The suspected binding mode is supported by molecular dynamics simulations, where the predominant interactions were hydrogen bonds and hydrophobic interactions (mainly π-π stacking interactions between the phenyl ring of FXa inhibitors and the indole moiety of Trp214). Finally, the possible implications of the obtained results regarding pathologies such as hypoalbuminemia are briefly discussed.

Microcalorimetric growth behavior of E. coli ATCC 25922 in an MCDSC

Isothermal microcalorimetry can provide a general analytical tool for the characterization of bacterial growth. Methodologies and equipment have been studied to expand the application and disseminate the use of the technique. The MCDSC is a microcalorimeter capable of measuring in the range of 0.2 μW that can operate at a temperature range of -20 to 140 °C or under isothermal conditions. Here, we present the first investigation of MCDSC for E. coli growth with the Baranyi and Roberts modeling application. This study presented the calorimetric E. coli fingerprint at MCDSC and compares it with the plate count technique, giving the data more biological meaning. The calorimeter was able to accurately detect growth metabolism and discriminate E. coli at different inoculum densities. Additionally, the MCDSC can offer a new point of view for evaluating microbial growth, such as the significant reduction in error due to dispersed data by the viable counting method.

Isothermal Titration Calorimetry Analysis of a Cooperative Riboswitch Using an Interdependent-Sites Binding Model

Isothermal titration calorimetry (ITC) is a powerful biophysical tool to characterize energetic profiles of biomacromolecular interactions without any alteration of the underlying chemical structures. In this protocol, we describe procedures for performing, analyzing, and interpreting ITC data obtained from a cooperative riboswitch-ligand interaction.

Characterization of ATG8-Family Interactors by Isothermal Titration Calorimetry

Isothermal titration calorimetry (ITC) is the gold standard for providing quantitative and thermodynamic understanding of the interaction mechanisms between core autophagy machinery, autophagy receptors, and ATG8. Here, we used two model peptides and Arabidopsis thaliana ATG8A to characterize ATG8-peptide interactions. We employed ITC using three different methods (direct ligand titration, displacement, and competition assays) to characterize, directly and indirectly, the interaction of the peptides with ATG8. We then analyzed the ITC data by global and statistical methods and discussed advantages, drawbacks, and negative controls for each approach. We finally provide a thorough description of all the steps, including data analysis and presentation, preparation of recombinant ATG8A from E. coli, and troubleshooting notes for technical problems that can be encountered. Although we used ATG8-peptide interactions here, these assays can be applied to any other one-to-one protein-protein and ligand-protein interactions and competitive binders.

Analysis of Aptamer-Small Molecule Binding Interactions Using Isothermal Titration Calorimetry

Isothermal titration calorimetry (ITC) is a technique where the heat given off, or absorbed, during a binding event is measured and used to determine the binding thermodynamics and affinity associated with binding. This protocol focuses on ITC applications for studying aptamer interactions with small molecule ligands where ITC has the advantage of being a label-free solution-based technique. The limitation of ITC using a relatively large amount of material compared to other analytical techniques is not applicable here as large amounts of nucleic acids, especially DNA, can be readily obtained. In this chapter we describe how to use ITC methods to measure the thermodynamics and affinity of binding using the interaction of quinine with a DNA cocaine-binding aptamer as an example.

Complementary Experimental Methods to Obtain Thermodynamic Parameters of Protein Ligand Systems

In recent years, thermophoresis has emerged as a promising tool for quantifying biomolecular interactions. The underlying microscopic physical effect is still not understood, but often attributed to changes in the hydration layer once the binding occurs. To gain deeper insight, we investigate whether non-equilibrium coefficients can be related to equilibrium properties. Therefore, we compare thermophoretic data measured by thermal diffusion forced Rayleigh scattering (TDFRS) (which is a non-equilibrium process) with thermodynamic data obtained by isothermal titration calorimetry (ITC) (which is an equilibrium process). As a reference system, we studied the chelation reaction between ethylenediaminetetraacetic acid (EDTA) and calcium chloride (CaCl2) to relate the thermophoretic behavior quantified by the Soret coefficient ST to the Gibb's free energy ΔG determined in the ITC experiment using an expression proposed by Eastman. Finally, we have studied the binding of the protein Bovine Carbonic Anhydrase I (BCA I) to two different benzenesulfonamide derivatives: 4-fluorobenzenesulfonamide (4FBS) and pentafluorobenzenesulfonamide (PFBS). For all three systems, we find that the Gibb's free energies calculated from ST agree with ΔG from the ITC experiment. In addition, we also investigate the influence of fluorescent labeling, which allows measurements in a thermophoretic microfluidic cell. Re-examination of the fluorescently labeled system using ITC showed a strong influence of the dye on the binding behavior.

Supramolecular Protein-Polyelectrolyte Assembly at Near Physiological Conditions-Water Proton NMR, ITC, and DLS Study

The in vivo potency of polyphosphazene immunoadjuvants is inherently linked to the ability of these ionic macromolecules to assemble with antigenic proteins in aqueous solutions and form physiologically stable supramolecular complexes. Therefore, in-depth knowledge of interactions in this biologically relevant system is a prerequisite for a better understanding of mechanism of immunoadjuvant activity. Present study explores a self-assembly of polyphosphazene immunoadjuvant-PCPP and a model antigen-lysozyme in a physiologically relevant environment-saline solution and neutral pH. Three analytical techniques were employed to characterize reaction thermodynamics, water-solute structural organization, and supramolecular dimensions: isothermal titration calorimetry (ITC), water proton nuclear magnetic resonance (wNMR), and dynamic light scattering (DLS). The formation of lysozyme-PCPP complexes at near physiological conditions was detected by all methods and the avidity was modulated by a physical state and dimensions of the assemblies. Thermodynamic analysis revealed the dissociation constant in micromolar range and the dominance of enthalpy factor in interactions, which is in line with previously suggested model of protein charge anisotropy and small persistence length of the polymer favoring the formation of high affinity complexes. The paper reports advantageous use of wNMR method for studying protein-polymer interactions, especially for low protein-load complexes.

The use of isothermal titration calorimetry for the assay of enzyme activity: Application in higher education practical classes

Determination of enzyme activity is crucial for discovery, research, and development in life sciences. The activity of enzymes is routinely determined using spectrophotometric assays that measure rates of substrate consumption or product formation. Though colorimetric-based detection systems are simple, rapid, and economical to perform, the majority of enzymes are unsuitable for this technique as their substrates/products do not absorb in the UV or visible range. This limitation can be addressed by the use of coupled-enzyme assays or artificial chromogenic substrates; however these approaches have their own drawbacks. Here, we describe a method based on the use of an isothermal titration calorimeter (ITC) to measure the heat produced or absorbed during any enzyme-catalyzed reaction. The concept of calorimetric enzyme assays was demonstrated for the determination of enzyme hexokinase activity, which cannot be monitored colorimetrically without first coupling it to another enzymatic reaction. The assay is suitable for incorporation into undergraduate laboratory classes, providing students with an appreciation for; the versatility and ease of use of ITC assays; ITC as a flexible generic method for exploring the functional characteristics of uncharacterized enzymes; an activity detection parameter suitable for enzymes that either have no straightforward colorimetric methods available or require the use of nonartificial chromogenic substrates.

Membrane Fusion Biophysical Analysis of Fusogenic Liposomes

Liposomes represent important drug carrier vehicles in biological systems. A fusogenic liposomal system composed of equimolar mixtures of the cationic lipid DOTAP and the phospholipid DOPE showed high fusion and delivery efficiencies with cells and lipid vesicles. However, aspects of the thermodynamics involving the interaction of these fusogenic liposomes and biomimetic systems remain unclear. Here, we investigate the fusion of this system with large unilamellar vesicles (LUVs) composed of the zwitterionic lipid POPC and increasing fractions of the anionic lipid POPG and up to 30 mol % cholesterol. The focus here is to concomitantly follow changes in size, zeta-potential, and enthalpy binding upon membrane interaction and fusion. Isothermal titration calorimetry (ITC) data showed that membrane fusion in our system is an exothermic process in the absence of cholesterol, suggesting that electrostatic attraction is the driving force for fusion. An endothermic component appeared and eventually dominated the titration at 30 mol % cholesterol, which we propose is caused by membrane fluidification when cholesterol is diluted upon fusion. The inflection points of the ITC data occurred around 0.5-0.7 POPG/DOTAP for all systems, the same stoichiometry for which zeta-potential and dynamic light scattering measurements showed an increase in size coupled with charge neutralization of the system, which is consistent with the fact that fusion in our system is charge-mediated. Microscopy observations of the final mixtures revealed the presence of giant vesicles, which is a clear indication of fusion, coexisting with intermediate-sized objects that could be the result of both fusion and/or aggregation. The results show that the fusion efficiency of the DOTAP:DOPE fusogenic system is modulated by the charge and membrane packing of the acceptor membrane and explain why the system fuses very efficiently with cells.

Unraveling the Binding Mechanism of Alzheimer's Drugs with Irisin: Spectroscopic, Calorimetric, and Computational Approaches

The prevalence of Alzheimer’s disease (AD) has been a major health concern for a long time. Despite recent progress, there is still a strong need to develop effective disease-modifying therapies. Several drugs have already been approved to retard the progression of AD-related symptoms; however, there is a need to develop an effective carrier system for the delivery of drugs to combat such diseases. In recent years, various biological macromolecules, including proteins, have been used as carriers for drug delivery. Irisin is a beneficial hormone in such diseases, including AD and related pathologies. Herein, the interaction mechanism of irisin with AD drugs such as memantine, galantamine, and fluoxetine is investigated. Fluorescence studies revealed that the above drugs bind to irisin with significant affinity, with fluoxetine having the highest binding affinity. Isothermal titration calorimetry (ITC) complemented the spontaneous binding of these drugs with irisin, delineating various associated thermodynamic and binding parameters. Molecular docking further validated the fluorescence and ITC results and unfolded the mechanism that hydrogen bonding governs the binding of fluoxetine to irisin with a significant binding score, i.e., −6.3 kcal/mol. We believe that these findings provide a promising solution to fight against AD as well as a platform for further research to utilize irisin in the drug-delivery system for an effective therapeutic strategy.

Interactions between Hydrolysable Tannins and Lipid Vesicles from Escherichia coli with Isothermal Titration Calorimetry

Isothermal titration calorimetry (ITC) was used to study the interactions between hydrolysable tannins (HTs) and lipid vesicles prepared from a phospholipid extract of Escherichia coli (E. coli). A group of 24 structurally different HTs was selected, and structural differences affecting their affinities to interact with lipid vesicles in aqueous buffered media were identified. In general, the interactions between HTs and lipid vesicles were exothermic in nature, and ITC as a technique functioned well in the screening of HTs for their affinity for lipids. Most notably, the galloyl moiety, the structural flexibility of the entire tannin structure, the hydrophobicity of the tannin, and higher molecular weight were observed to be important for the stronger interactions with the lipids. The strongest interactions with lipids were observed for rugosins D and G. It was also observed that some HTs with moderate hydrophobicities, such as geraniin, chebulagic acid, and chebulinic acid, did not have any detectable interactions with the lipid vesicles, suggesting that a hydrophobic structure alone does not guarantee an affinity for lipids.

Quantitative Analysis of the Interactions of Metal Complexes and Amphiphilic Systems: Calorimetric, Spectroscopic and Theoretical Aspects

Metals and metal-based compounds have many implications in biological systems. They are involved in cellular functions, employed in the formation of metal-based drugs and present as pollutants in aqueous systems, with toxic effects for living organisms. Amphiphilic molecules also play important roles in the above bio-related fields as models of membranes, nanocarriers for drug delivery and bioremediating agents. Despite the interest in complex systems involving both metal species and surfactant aggregates, there is still insufficient knowledge regarding the quantitative aspects at the basis of their binding interactions, which are crucial for extensive comprehension of their behavior in solution. Only a few papers have reported quantitative analyses of the thermodynamic, kinetic, speciation and binding features of metal-based compounds and amphiphilic aggregates, and no literature review has yet addressed the quantitative study of these complexes. Here, we summarize and critically discuss the recent contributions to the quantitative investigation of the interactions of metal-based systems with assemblies made of amphiphilic molecules by calorimetric, spectrophotometric and computational techniques, emphasizing the unique picture and parameters that such an analytical approach may provide, to support a deep understanding and beneficial use of these systems for several applications.

Real time monitoring of Staphylococcus aureus biofilm sensitivity towards antibiotics with isothermal microcalorimetry

Biofilm-associated infections with Staphylococcus aureus are difficult to treat even after administration of antibiotics that according to the standard susceptibility assays are effective. Currently, the assays used in the clinical laboratories to determine the sensitivity of S. aureus towards antibiotics are not representing the behaviour of biofilm-associated S. aureus, since these assays are performed on planktonic bacteria. In research settings, microcalorimetry has been used for antibiotic susceptibility studies. Therefore, in this study we investigated if we can use isothermal microcalorimetry to monitor the response of biofilm towards antibiotic treatment in real-time. We developed a reproducible method to generate biofilm in an isothermal microcalorimeter setup. Using this system, the sensitivity of 5 methicillin-sensitive S. aureus (MSSA) and 5 methicillin-resistant S. aureus (MRSA) strains from different genetic lineages were determined towards: flucloxacillin, cefuroxime, cefotaxime, gentamicin, rifampicin, vancomycin, levofloxacin, clindamycin, erythromycin, linezolid, fusidic acid, co-trimoxazole, and doxycycline. In contrast to conventional assays, our calorimetry-based biofilm susceptibility assay showed that S. aureus biofilms, regardless MSSA or MRSA, can survive the exposure to the maximum serum concentration of all tested antibiotics. The only treatment with a single antibiotic showing a significant reduction in biofilm survival was rifampicin, yet in 20% of the strains, emerging antibiotic resistance was observed. Furthermore, the combination of rifampicin with flucloxacillin, vancomycin or levofloxacin was able to prevent S. aureus biofilm from becoming resistant to rifampicin. Isothermal microcalorimetry allows real-time monitoring of the sensitivity of S. aureus biofilms towards antibiotics in a fast and reliable way.

Mechanism of Mucin Recognition by Lectins: A Thermodynamic Study

Isothermal titration microcalorimetry (ITC) can directly determine the thermodynamic binding parameters of biological molecules including affinity constant, binding stoichiometry, heat of binding (enthalpy) and indirectly the entropy, and free energy of binding. ITC has been extensively used to study the binding of lectins to mono- and oligosaccharides, but limitedly in applications to lectin-glycoprotein interactions. Inherent experimental challenges to ITC include sample precipitation during the experiment and relative high amount of sample required, but careful design of experiments can minimize these problems and allow valuable information to be obtained. For example, the thermodynamics of binding of lectins to multivalent globular and linear glycoproteins (mucins) have been described. The results are consistent with a dynamic binding mechanism in which lectins bind and jump from carbohydrate to carbohydrate epitope in these molecules leading to increased affinity. Importantly, the mechanism of binding of lectins to mucins appears similar to that for a variety of protein ligands binding to DNA. Recent results also show that high-affinity lectin-mucin cross-linking interactions are driven by favorable entropy of binding that is associated with the bind and jump mechanism. The results suggest that the binding of ligands to biopolymers, in general, may involve a common mechanism that involves enhanced entropic effects that facilitate binding interactions.

Analysis of Protein-DNA Interactions Using Isothermal Titration Calorimetry: Successes and Failures

Isothermal titration calorimetry (ITC) is a golden standard for the characterization of protein-DNA binding affinities and allows direct assessment of the accompanying thermodynamic driving forces. Their interpretation can give insight into role of electrostatics, specificity of the DNA recognition, contribution of protein folding upon DNA binding and help to distinguish between minor and major groove binders. The main advantages of ITC are that the binding is measured in solution, and it requires no labeling of the samples, however, the method is not well suited for high-performance studies. Here we describe the sample preparation, a procedure to perform a typical ITC experiment, data analysis, and lastly discuss how to interpret the obtained thermodynamic parameters. In conclusion, we show examples of several unsuccessful ITC experiments and identify the underlying reasons for failed experiments. In most cases with a proper adjustment of the experimental setup, it was possible to obtain data appropriate for further analysis.

Melatonin Binding to Human NQO2 by Isothermal Titration Calorimetry

To ensure the physical interaction between a protein and its ligand, many techniques can be applied. One of them, isothermal titration calorimetry (ITC), measures the heat exchange between a forming molecular complex and its milieu. From this heat exchange, it is possible to acquire the thermodynamic parameters, the binding stoichiometry and the affinity constant (K_a) between the two interacting binding partners, which can then be used to determine the dissociation constant (K_d). We made use of ITC to determine the true K_d of melatonin for its putative receptor MT3, also known as the enzyme quinone reductase 2 (NQO2). In this chapter, we describe the step-by-step procedure for performing this experiment and extend it to 2-iodomelatonin, a melatonin derivative that was used in the initial identification and characterization of MT3. The dissociation constants of melatonin and 2-iodomelatonin toward NQO2 derived from these experiments are in line with data reported previously, albeit using alternative techniques.

A hybrid strategy combining solution NMR spectroscopy and isothermal titration calorimetry to characterize protein-nanodisc interaction

NMR is a powerful tool for characterizing intermolecular interactions at atomic resolution. However, the nature of the complex interactions of membrane-binding proteins makes it difficult to elucidate the interaction mechanisms. Here, we demonstrated that structural and thermodynamic analyses using solution NMR spectroscopy and isothermal titration calorimetry (ITC) can clearly detect a specific interaction between the pleckstrin homology (PH) domain of ceramide transport protein (CERT) and phosphatidylinositol 4-monophosphate (PI4P) embedded in the lipid nanodisc, and distinguish the specific interaction from nonspecific interactions with the bulk surface of the lipid nanodisc. This NMR-ITC hybrid strategy provides detailed characterization of protein-lipid membrane interactions.

Insulin Analogues with Altered Insulin Receptor Isoform Binding Specificities and Enhanced Aggregation Stabilities

Insulin is a lifesaver for millions of diabetic patients. There is a need for new insulin analogues with more physiological profiles and analogues that will be thermally more stable than human insulin. Here, we describe the chemical engineering of 48 insulin analogues that were designed to have changed binding specificities toward isoforms A and B of the insulin receptor (IR-A and IR-B). We systematically modified insulin at the C-terminus of the B-chain, at the N-terminus of the A-chain, and at A14 and A18 positions. We discovered an insulin analogue that has Cα-carboxyamidated Glu at B31 and Ala at B29 and that has a more than 3-fold-enhanced binding specificity in favor of the "metabolic" IR-B isoform. The analogue is more resistant to the formation of insulin fibrils at 37 °C and is also more efficient in mice than human insulin. Therefore, [AlaB29,GluB31,amideB31]-insulin may be interesting for further clinical evaluation.

Development of biparatopic bispecific antibody possessing tetravalent scFv-Fc capable of binding to ROBO1 expressed in hepatocellular carcinoma cells

There is no standard structural format of the biparatopic bispecific antibody (bbsAb) which is used against the target molecule because of the diversity of biophysical features of bispecific antibodies (bsAbs). It is therefore essential that the interaction between the antibody and antigen is quantitatively analyzed to design antibodies that possess the desired properties. Here, we generated bsAbs, namely, a tandem scFv-Fc, a diabody-Fc, and an immunofusion-scFv-Fc-scFv, that possessed four scFv arms at different positions and were capable of recognizing the extracellular domains of ROBO1. We examined the interactions between these bsAbs and ROBO1 at the biophysical and cellular levels. Of these, immunofusion-B2212A scFv-Fc-B5209B scFv was stably expressed with the highest relative yield. The kinetic and thermodynamic features of the interactions of each bsAb with soluble ROBO1 (sROBO1) were validated using surface plasmon resonance and isothermal titration calorimetry. In all bsAbs, the immunofusion-scFv-Fc-scFv format showed homogeneous interaction with the antigen with higher affinity compared with that of monospecific antibodies. In conclusion, our study presents constructive information to design druggable bbsAbs in drug applications.

Kinetic analysis of microcalorimetric data derived from microbial growth: Basic theoretical, practical and industrial considerations

We report here a mathematical framework for the quantitative interpretation of exponential bacterial growth measured with isothermal microcalorimetry. The method allows determination of many parameters that define the exponential growth phase. To automate the analysis, we also wrote a coding program, so that the approach could be embedded in a commercial setting. As an exemplar, we apply the method to a commercial probiotic product. The outcome was that we could identify characteristic parameters of growth (including rate constant and doubling time), and hence authenticate product quality, within 15 h. This compares favourably with the current 7-10 days required for conventional microbiological assessment (to allow release of product for bottling and marketing) via plating methods. The method would lend itself to growth analysis of single and mixed bacterial cultures.

Durability of Flame-Retarded, Co-Extruded Profiles Based on High-Density Polyethylene and Wheat Straw Residues

At present, little information is available in the scientific literature related to the durability (weathering resistance) of fire-retarded wood and natural fiber-reinforced thermoplastics. In this work, thermoplastic profiles for façade applications based on high-density polyethylene, wheat straw particles, and fire-retardants were extruded and their reaction-to-fire performance before and after artificial weathering evaluated. Profile geometries were either solid or hollow-core profiles, and fire-retardants (FR) were added either in the co-extruded layer or in the bulk. Various FR for inclusion in the co-extruded layer were screened based on UL-94 tests. For profile extrusion, two types of FR were chosen: a coated intumescent combination based on ammonium polyphosphate (APP) and an APP coated with melamine and without formaldehyde. Before weathering, the peak heat release rate (pHRR) and the total heat release (THR), which were determined using cone calorimeter measurements, were reduced by up to 64% and 67% due to the FR. However, even before weathering, pHRR of the profiles was relatively high, with best (lowest) values between 230 and 250 kW/m² under the test conditions. After 28 days of artificial weathering, changes in reaction-to-fire performance and color were evaluated. Use of the APP in the co-extruded layer worsened color change compared to the formulation without APP but the pHRR was not significantly changed. The influence of weathering on the fire behavior was small compared to the difference between fire-retarded and non-fire-retarded materials. Results from the cone calorimeter were analyzed with regard to ETAG 028, which provides requirements related to the durability of fire performance of building products. In many formulations, increase in THR was less than 20% compared to before weathering, which would place some of the profiles in class C or better (EN 13501-1). However, due to the high pHRR, at best, class D was obtained under the conditions of this study. In addition to cone calorimeter measurements, results from the single flame source test, limiting oxygen index determination and thermogravimetric analysis, are shown and discussed. Strength properties, water uptake and swelling of the profiles, thermal conductivity, and energy dispersive X-ray data are also presented.

Microscale Thermophoresis (MST ) as a Tool for Measuring Dynamin Superfamily Protein (DSP)-Lipid Interactions

Microscale thermophoresis (MST ) is a robust new fluorescence-based technology that enables measurement of biomolecular interactions and binding affinities (K_D). MST is an immobilization-free alternative to surface plasmon resonance (SPR ) and is cost-effective relative to isothermal titration calorimetry (ITC ). In this chapter, using Drp1 as an example, we demonstrate for the first time, the application of MST to the determination of DSP-lipid interactions and the accurate measurement of K_D under physiologically relevant solution conditions.

Calorimetric Analysis of the Interplay between Synthetic Tn Antigen-Presenting MUC1 Glycopeptides and Human Macrophage Galactose-Type Lectin

Human macrophage galactose-type lectin (hMGL, HML, CD301, CLEC10A), a C-type lectin expressed by dendritic cells and macrophages, is a receptor for N-acetylgalactosamine α-linked to serine/threonine residues (Tn antigen, CD175) and its α2,6-sialylated derivative (sTn, CD175s). Because these two epitopes are among malignant cell glycan displays, particularly when presented by mucin-1 (MUC1), assessing the influence of the site and frequency of glycosylation on lectin recognition will identify determinants governing this interplay. Thus, chemical synthesis of the tandem-repeat O-glycan acceptor region of MUC1 and site-specific threonine glycosylation in all permutations were carried out. Isothermal titration calorimetry (ITC) analysis of the binding of hMGL to this library of MUC1 glycopeptides revealed an enthalpy-driven process and an affinity enhancement of an order of magnitude with an increasing glycan count from 6-8 μM for monoglycosylated peptides to 0.6 μM for triglycosylated peptide. ITC measurements performed in D2O permitted further exploration of the solvation dynamics during binding. A shift in enthalpy-entropy compensation and contact position-specific effects with the likely involvement of the peptide surroundings were detected. KinITC analysis revealed a prolonged lifetime of the lectin-glycan complex with increasing glycan valency and with a change in the solvent to D2O.

Silver(I)-mediated base pairing in DNA involving the artificial nucleobase 7,8-dihydro-8-oxo-1,N6-ethenoadenine

The artificial nucleobase 7,8-dihydro-8-oxo-1,N⁶-ethenoadenine (X) was investigated with respect to its ability to engage in Ag(I)-mediated base pairing in DNA. Spectroscopic data indicate the formation of dinuclear X-Ag(I)₂-X homo base pairs and mononuclear X-Ag(I)-C base pairs (C, cytosine). Density functional theory calculations and molecular dynamics simulations indicate that the nucleobase changes from its lactam tautomeric form prior to the formation of the Ag(I)-mediated base pair to the lactim form after the incorporation of the Ag(I) ions. Fluorescence spectroscopy indicates that the two Ag(I) ions of the homo base pair are incorporated sequentially. Isothermal titration calorimetry confirms that the affinity of one of the Ag(I) ions is about tenfold higher than that of the other Ag(I) ion. The computational analysis by means of density functional theory confirms a much larger reaction energy for the incorporation of the first Ag(I) ion. The thermal stabilization upon the formation of the dinuclear Ag(I)-mediated homo base pair exceeds the one previously observed for the closely related nucleobase 1,N⁶-ethenoadenine by far, despite very similar structures. This additional stabilization may stem from the presence of water molecules engaged in hydrogen bonding with the additional oxygen atom of the artificial nucleobase X. The highly stabilizing Ag(I)-mediated base pair is a valuable addition to established dinuclear metal-mediated base pairs.

Investigations of Lipid Binding to Acyl-CoA-Binding Proteins (ACBP) Using Isothermal Titration Calorimetry (ITC)

Isothermal titration calorimetry (ITC) is a quantitative, biophysical method to investigate intermolecular binding between biomolecules by directly measuring the heat exchange in the binding reaction. The assay is carried out in solution when the molecules interact in vitro. This allows to determine values for binding affinity (K_d), binding stoichiometry (n), as well as changes in Gibbs free energy (ΔG), entropy (ΔS), and enthalpy (ΔH). This method also addresses the kinetics of enzymatic reactions for a substrate during conversion to a product. ITC has been used to study the interactions between proteins and ligands such as those of acyl-CoA-binding proteins (ACBPs) and acyl-CoA thioesters or ACBPs with protein partners. ITC has also been used in investigating interactions between antiserum and antigen, as well as those involving RNA and DNA and other macromolecules. We describe the methods used to isolate and purify a recombinant rice ACBP (OsACBP) for ITC. To study OsACBP binding to long-chain acyl-CoA thioesters, a microcalorimeter was used at 30 °C, and the ligand (acyl-CoA thioesters or a protein partner in the first cell), was mixed with the ACBP protein solution in a second cell, for more than 40 min comprising 20 injections. Subsequently, the binding parameters including the heat-release data were analyzed and various thermodynamic parameters were calculated.

Isothermal Titration Calorimetry

Calorimetry is a classical biophysical method that by definition measures heat. In isothermal titration calorimetry (ITC), the heat is the result of titrating interacting components together and allows direct determination of the thermodynamics for this process. The measured heat reflects the enthalpy change (ΔH), and the prospect of determining this in biological systems where high-resolution structural information is available has led to the possibility of rational thermodynamics-guided design of ligands. Although there are limitations to this approach due to the participation of solvent in the thermodynamics, ITC has become an established technique in many labs providing a valuable tool with which to quantify protein-protein interactions. With careful use, ITC can also provide additional insights into the binding process or be used in increasingly complex systems and where interaction is coupled to other molecular events.

Studying Lipid-Protein Interactions Using Protein-Lipid Overlay and Protein-Liposome Association Assays

The study of lipid-protein interactions is crucial for understanding reactions of proteins involved in lipid metabolism, lipid transport, and lipid signaling. Different detection methods can be employed for the identification of lipid-binding interactions. Isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR) spectroscopy enable real-time monitoring of lipid protein interactions and provide thermodynamic parameters of the interacting partners. However, these technologies depend on the availability of the large equipment, limiting the practicability in many laboratories. Protein-lipid overlay assays are a simple first approach to screen for protein interactions with different lipids or lipid intermediates and are independent of large equipment. Subsequently, specific interactions can be analyzed in detail using protein-liposome association assays.

Estimation of non-constant variance in isothermal titration calorimetry using an ITC measurement model

Isothermal titration calorimetry (ITC) is the gold standard for accurate measurement of thermodynamic parameters in solution reactions. In the data processing of ITC, the non-constant variance of the heat requires special consideration. The variance function approach has been successfully applied in previous studies, but is found to fail under certain conditions in this work. Here, an explicit ITC measurement model consisting of main thermal effects and error components has been proposed to quantitatively evaluate and predict the non-constant variance of the heat data under various conditions. Monte Carlo simulation shows that the ITC measurement model provides higher accuracy and flexibility than variance function in high c-value reactions or with additional error components, for example, originated from the fluctuation of the concentrations or other properties of the solutions. The experimental design of basic error evaluation is optimized accordingly and verified by both Monte Carlo simulation and experiments. An easy-to-run Python source code is provided to illustrate the establishment of the ITC measurement model and the estimation of heat variances. The accurate and reliable non-constant variance of heat is helpful to the application of weighted least squares regression, the proper evaluation or selection of the reaction model.

Procedures for Measuring Excreted and Ingested Calories to Assess Nutrient Absorption Using Bomb Calorimetry

OBJECTIVE

With the upsurge in interest in the gut microbiome, complete and accurate measurement of ingested calories and calories lost through excreted stool is crucial for assessing the effect of the microbiota on nutrient absorption.

METHODS

Measurement of ingested and excreted calories was conducted over 3 days. Meals were made in duplicate: one was given to the participant, and one was used for the measurement of calories. Stool was marked by nonabsorbable dye ingested prior to and at the end of each 3-day diet period and was collected for caloric assessment from the appearance of the first dye marker until the appearance of the second dye marker.

RESULTS

Stool calories per gram for pellets were 4.91 ± 0.06 kcal/g. The mean stool calorie loss as a percentage of ingested calories was 7.3% ± 1.6% (range, 6.6%-8.5%). The stool measurement of kilocalories per gram was not associated with the total measured stool calories or with stool weight (P = 0.2 and P = 0.2, respectively) over the 3-day period. However, the weight of stool samples during each dietary intervention was positively associated with the calorie loss in stool (r = 0.58, P < 0.0001).

CONCLUSIONS

Our methods provide a direct measure of ingested calories and stool calories needed to accurately assess relative stool calorie loss as a measure of nutrient absorption. The weight of stool samples across the marked diet period is crucial to determining total stool calories.

Thermodynamics and Kinetics of Glycolytic Reactions. Part I: Kinetic Modeling Based on Irreversible Thermodynamics and Validation by Calorimetry

In systems biology, material balances, kinetic models, and thermodynamic boundary conditions are increasingly used for metabolic network analysis. It is remarkable that the reversibility of enzyme-catalyzed reactions and the influence of cytosolic conditions are often neglected in kinetic models. In fact, enzyme-catalyzed reactions in numerous metabolic pathways such as in glycolysis are often reversible, i.e., they only proceed until an equilibrium state is reached and not until the substrate is completely consumed. Here, we propose the use of irreversible thermodynamics to describe the kinetic approximation to the equilibrium state in a consistent way with very few adjustable parameters. Using a flux-force approach allowed describing the influence of cytosolic conditions on the kinetics by only one single parameter. The approach was applied to reaction steps 2 and 9 of glycolysis (i.e., the phosphoglucose isomerase reaction from glucose 6-phosphate to fructose 6-phosphate and the enolase-catalyzed reaction from 2-phosphoglycerate to phosphoenolpyruvate and water). The temperature dependence of the kinetic parameter fulfills the Arrhenius relation and the derived activation energies are plausible. All the data obtained in this work were measured efficiently and accurately by means of isothermal titration calorimetry (ITC). The combination of calorimetric monitoring with simple flux-force relations has the potential for adequate consideration of cytosolic conditions in a simple manner.

A Novel Approach to Assess Metabolic Flexibility Overnight in a Whole-Body Room Calorimeter

OBJECTIVE

This study aimed to investigate a novel approach for determining the effects of energy-standardized dinner meals (high-fat and low-fat) on respiratory exchange ratio (RER) dynamics and metabolic flexibility.

METHODS

Using a randomized crossover study design, energy expenditure, RER, and macronutrient oxidation rates were assessed in response to a single dinner meal during an overnight stay in a whole-body room calorimeter. Eight healthy adults completed two overnight chamber stays while fed either a high-fat (60% fat, 20% carbohydrate [CHO], 20% protein; food quotient [FQ] = 0.784) or low-fat (20% fat, 60% CHO, 20% protein; FQ = 0.899) dinner containing 40% of daily energy requirements.

RESULTS

Following the low-fat meal, CHO oxidation first increased before decreasing, resulting in a 12-hour RER:FQ ratio close to 1.0 (0.986 ± 0.019, P = 0.06) and therefore resulting in a 12-hour equilibrated fat balance (29 ± 76 kcal/12 hours). Following the high-fat meal, participants had a RER:FQ ratio above 1.0 (1.061 ± 0.017, P < 0.01), resulting in a significant positive 12-hour fat balance of 376 ± 142 kcal/12 hours. Various RER trajectory parameters were significantly different following the high-fat and low-fat meals.

CONCLUSIONS

This proof-of-concept study provides an alternative approach to quantify metabolic flexibility in response to a high-fat dinner and it can be used to derive indexes of metabolic flexibility, such as the 12-hour RER:FQ ratio or the 12-hour fat balance.

Basal Energy Expenditure of Chinese Healthy Adults: Comparison of Measured and Predicted Values

OBJECTIVE

This study aimed to measure the basal energy expenditure (BEE) of Chinese healthy adults and establish an accurate predictive equation for this population.

METHODS

In total, 470 Chinese healthy adults had their BEE measured using the Cosmed K4b ² portable metabolic system. Multiple linear regression analysis was applied to develop new optimal equations for predicting BEE. The bias, accuracy rate, concordance correlation coefficient (CCC), and root mean square error (RMSE) were used to evaluate the accuracy of the predictive equations.

RESULTS

There was a significant difference in BEE between males and females, with 5,954 kJ/d and 5,089 kJ/d, respectively. People living in rural areas expended significantly higher BEE (5,885 kJ/d) than those in urban areas (5,279 kJ/d). Previous equations developed by Henry, Schofield, Harris-Benedict (H-B), and Liu overestimated the BEE of Chinese healthy adults. The new equations derived from the present study displayed the smallest average bias and RMSE from the measured basal energy expenditure (mBEE). The CCC of the new equations was higher than other predictive equations, but it was lower than 0.8. There was no significant difference in the accuracy rate among all predictive equations.

CONCLUSIONS

Sex and regional differences in BEE were observed in Chinese healthy adults. Neither the widely used previous predictive equations nor the one derived in the present study were accurate enough for estimating the BEE of Chinese healthy adults. Further study is required to develop more accurate equations for predicting the BEE of Chinese healthy adults aged between 20-45 years.

The day-to-day reliability of peak fat oxidation and FATMAX

PURPOSE

Prior studies exploring the reliability of peak fat oxidation (PFO) and the intensity that elicits PFO (FATMAX) are often limited by small samples. This study characterised the reliability of PFO and FATMAX in a large cohort of healthy men and women.

METHODS

Ninety-nine adults [49 women; age: 35 (11) years; [Formula: see text]O2peak: 42.2 (10.3) mL·kg BM-1·min-1; mean (SD)] completed two identical exercise tests (7-28 days apart) to determine PFO (g·min-1) and FATMAX (%[Formula: see text]O2peak) by indirect calorimetry. Systematic bias and the absolute and relative reliability of PFO and FATMAX were explored in the whole sample and sub-categories of: cardiorespiratory fitness, biological sex, objectively measured physical activity levels, fat mass index (derived by dual-energy X-ray absorptiometry) and menstrual cycle status.

RESULTS

No systematic bias in PFO or FATMAX was found between exercise tests in the entire sample (- 0.01 g·min-1 and 0%[Formula: see text]O2peak, respectively; p > 0.05). Absolute reliability was poor [within-subject coefficient of variation: 21% and 26%; typical errors: ± 0.06 g·min-1 and × / ÷ 1.26%[Formula: see text]O2peak; 95% limits of agreement: ± 0.17 g·min-1 and × / ÷ 1.90%[Formula: see text]O2peak, respectively), despite high (r = 0.75) and moderate (r = 0.45) relative reliability for PFO and FATMAX, respectively. These findings were consistent across all sub-groups.

CONCLUSION

Repeated assessments are required to more accurately determine PFO and FATMAX.

Basis for metabolite-dependent Cullin-RING ligase deneddylation by the COP9 signalosome

The Cullin-RING ligases (CRLs) are the largest family of ubiquitin E3s activated by neddylation and regulated by the deneddylase COP9 signalosome (CSN). The inositol polyphosphate metabolites promote the formation of CRL-CSN complexes, but with unclear mechanism of action. Here, we provide structural and genetic evidence supporting inositol hexakisphosphate (IP6) as a general CSN cofactor recruiting CRLs. We determined the crystal structure of IP6 in complex with CSN subunit 2 (CSN2), based on which we identified the IP6-corresponding electron density in the cryoelectron microscopy map of a CRL4A-CSN complex. IP6 binds to a cognate pocket formed by conserved lysine residues from CSN2 and Rbx1/Roc1, thereby strengthening CRL-CSN interactions to dislodge the E2 CDC34/UBE2R from CRL and to promote CRL deneddylation. IP6 binding-deficient Csn2K70E/K70E knockin mice are embryonic lethal. The same mutation disabled Schizosaccharomyces pombe Csn2 from rescuing UV-hypersensitivity of csn2-null yeast. These data suggest that CRL transition from the E2-bound active state to the CSN-bound sequestered state is critically assisted by an interfacial IP6 small molecule, whose metabolism may be coupled to CRL-CSN complex dynamics.

Analysis of Multivalent IDP Interactions: Stoichiometry, Affinity, and Local Concentration Effect Measurements

Nuclear magnetic resonance (NMR) titration and isothermal titration calorimetry can be combined to provide an assessment of how multivalent intrinsically disordered protein (IDP) interactions can involve enthalpy-entropy balance. Here, we describe the underlying technical details and additional methods, such as dynamic light scattering analysis, needed to assess these reactions. We apply this to a central interaction involving the disordered regions of phe-gly nucleoporins (FG-Nups) that contain multiple phenylalanine-glycine repeats which are of particular interest, as their interactions with nuclear transport factors (NTRs) underlie the paradoxically rapid yet also highly selective transport of macromolecules mediated by the nuclear pore complex (NPC). These analyses revealed that a combination of low per-FG motif affinity and the enthalpy-entropy balance prevents high-avidity interaction between FG-Nups and NTRs while the large number of FG motifs promotes frequent FG-NTR contacts, resulting in enhanced selectivity.

Accuracy of the Cosmed K5 portable calorimeter

PURPOSE

The purpose of this study was to assess the accuracy of the Cosmed K5 portable metabolic system dynamic mixing chamber (MC) and breath-by-breath (BxB) modes against the criterion Douglas bag (DB) method.

METHODS

Fifteen participants (mean age±SD, 30.6±7.4 yrs) had their metabolic variables measured at rest and during cycling at 50, 100, 150, 200, and 250W. During each stage, participants were connected to the first respiratory gas collection method (randomized) for the first four minutes to reach steady state, followed by 3-min (or 5-min for DB) collection periods for the resting condition, and 2-min collection periods for all cycling intensities. Collection periods for the second and third methods were preceded by a washout of 1-3 min. Repeated measures ANOVAs were used to compare metabolic variables measured by each method, for seated rest and each cycling work rate.

RESULTS

For ventilation (VE) and oxygen uptake (VO2), the K5 MC and BxB modes were within 2.1 l/min (VE) and 0.08 l/min (VO2) of the DB (p≥0.05). Compared to DB values, carbon dioxide production (VCO2) was significantly underestimated by the K5 BxB mode at work rates ≥150W by 0.12-0.31 l/min (p<0.05). K5 MC and BxB respiratory exchange ratio values were significantly lower than DB at cycling work rates ≥100W by 0.03-0.08 (p<0.05).

CONCLUSION

Compared to the DB method, the K5 MC and BxB modes are acceptable for measuring VE and VO2 across a wide range of cycling intensities. Both K5 modes provided comparable values to each other.

Obtaining precise and accurate results by ITC

Acquisition of precise and accurate results by isothermal titration calorimetry (ITC) can be achieved through thoughtful experimental design and modeling and careful experimental operations. Large reported errors in ITC results in determinations of stoichiometries, equilibrium constants and enthalpy changes for ligand binding to proteins are the consequence of poor experiment design, failure to properly calibrate and test instruments and protocols, lack of controls, errors in solution preparation, and incorrect data analyses. Analysis of a recent report that claimed to have determined the "repeatability, precision, and accuracy of the enthalpies and Gibbs energies of a protein-ligand binding reaction" by ITC is used to illustrate how to improve ITC operations and results. The analysis shows that the reported results are misleading because calorimeters were not calibrated, operating parameters were not optimized, errors were made in solution preparations, and data analysis was not optimized. As a consequence, the results do not provide a valid comparison of the capabilities of the calorimeters included in the study. A proposal that reaction of acetazolamide with carbonic anhydrase II be used as a comparison standard for testing ITCs and procedures is problematic because the binding constant is too large and for several other reasons discussed in the paper. Requirements for obtaining precise and accurate results by ITC are discussed and experimental results are presented to illustrate the precision and accuracy attainable with low volume ITCs. The problem of the blank correction is identified as the limiting factor in obtaining accurate results by ITC.

New Biosourced Flame Retardant Agents Based on Gallic and Ellagic Acids for Epoxy Resins

The aim of this work was an investigation of the ability of gallic (GA) and ellagic (EA) acids, which are phenolic compounds encountered in various plants, to act as flame retardants (FRs) for epoxy resins. In order to improve their fireproofing properties, GA and EA were treated with boric acid (to obtain gallic acid derivatives (GAD) and ellagic acid derivatives (EAD)) to introduce borate ester moieties. Thermogravimetric analysis (TGA) highlighted the good charring ability of GA and EA, which was enhanced by boration. The grafting of borate groups was also shown to increase the thermal stability of GA and EA that goes up respectively from 269 to 528 °C and from 496 to 628 °C. The phenolic-based components were then incorporated into an epoxy resin formulated from diglycidyl ether of bisphenol A (DGEBA) and isophorone diamine (IPDA) (72, 18, and 10 wt.% of DGEBA, IPDA, and GA or EA, respectively). According to differential scanning calorimetry (DSC), the glass transition temperature (T_g) of the thermosets was decreased. Its values ranged from 137 up to 108 °C after adding the phenolic-based components. A cone calorimeter was used to evaluate the burning behavior of the formulated thermosets. A significant reduction of the peak of heat release rate (pHRR) for combustion was detected. Indeed, with 10 wt.% of GA and EA, pHRR was reduced by 12 and 44%, respectively, compared to that for neat epoxy resin. GAD and EAD also induced the decrease of pHRR values by 65 and 33%, respectively. In addition, a barrier effect was observed for the resin containing GAD. These results show the important influence of the biobased phenolic compounds and their boron derivatives on the fire behavior of a partially biobased epoxy resin.

Isothermal titration calorimetry as a complementary method for investigating nanoparticle-protein interactions

Isothermal titration calorimetry (ITC) is a complementary technique that can be used for investigations of protein adsorption on nanomaterials, as it quantifies the thermodynamic parameters of intermolecular interactions in situ. As soon as nanomaterials enter biological media, a corona of proteins forms around the nanomaterials, which influences the surface properties and therefore the behavior of nanomaterials tremendously. ITC enhances our understanding of nanoparticle-protein interactions, as it provides information on binding affinity (in form of association constant K_a), interaction mechanism (in form of binding enthalpy ΔH, binding entropy ΔS and Gibbs free energy ΔG) and binding stoichiometry n. Therefore, as a complementary method, ITC enhances our mechanistic understanding of the protein corona. In this minireview, the information obtained from a multitude of ITC studies regarding different nanomaterials and proteins are gathered and relations between nanomaterials' properties and their resulting interactions undergone with proteins are deduced. Nanomaterials formed of a hydrophilic material without strongly charged surface and steric stabilization experience the weakest interactions with proteins. As a result, such nanomaterials undergo the least unspecific protein-interactions and are most promising for allowing an engineering of the protein corona.