Do Intrinsically Disordered Proteins Possess High Specificity in Protein–Protein Interactions?

Specific protein–protein interactions are critical to cellular function. Structural flexibility and disorder‐to‐order transitions upon binding enable intrinsically disordered proteins (IDPs) to overcome steric restrictions and form complementary binding interfaces, and thus, IDPs are widely considered to have high specificity and low affinity for molecular recognition. However, flexibility may also enable IDPs to form complementary binding interfaces with misbinding partners, resulting in a great number of nonspecific interactions. Consequently, it is questionable whether IDPs really possess high specificity. In this work, we investigated this question from a thermodynamic viewpoint. We collected mutant thermodynamic data for 35 ordered protein complexes and 43 disordered protein complexes. We found that the enthalpy–entropy compensation for disordered protein complexes was more complete than that for ordered protein complexes. We further simulated the binding processes of ordered and disordered protein complexes under mutations. Simulation data confirmed the observation of experimental data analyses and further revealed that disordered protein complexes possessed smaller changes in binding free energy than ordered protein complexes under the same mutation perturbations. Therefore, interactions of IDPs are more malleable than those of ordered proteins due to their structural flexibility in the complex. Our results provide new clues for exploring the relationship between protein flexibility, adaptability, and specificity.     

Frontispiece: What Are We Missing by Not Measuring the Net Charge of Proteins?

The net electrostatic charge (Z) of a folded protein in solution represents a bird's eye view of its surface potentials—including contributions from tightly bound metal, solvent, buffer, and cosolvent ions—and remains one of its most enigmatic properties. Few tools are available to the average biochemist to rapidly and accurately measure Z at pH≠pI. Tools that have been developed more recently seem to go unnoticed. Most scientists are content with this void and estimate the net charge of a protein from its amino acid sequence, using textbook values of pK_a. Thus, Z remains unmeasured for nearly all folded proteins at pH≠pI. When marveling at all that has been learned from accurately measuring the other fundamental property of a protein—its mass—one wonders: what are we missing by not measuring the net charge of folded, solvated proteins? A few big questions immediately emerge in bioinorganic chemistry. When a single electron is transferred to a metalloprotein, does the net charge of the protein change by approximately one elementary unit of charge or does charge regulation dominate, that is, do the pK_a values of most ionizable residues (or just a few residues) adjust in response to (or in concert with) electron transfer? Would the free energy of charge regulation (ΔΔG_z) account for most of the outer sphere reorganization energy associated with electron transfer? Or would ΔΔG_z contribute more to the redox potential? And what about metal binding itself? When an apo-metalloprotein, bearing minimal net negative charge (e.g., Z=−2.0) binds one or more metal cations, is the net charge abolished or inverted to positive? Or do metalloproteins regulate net charge when coordinating metal ions? The author's group has recently dusted off a relatively obscure tool—the “protein charge ladder”—and used it to begin to answer these basic questions.     

Extraction of Reliable Molecular Information from Diffusion NMR Spectroscopy: Hydrodynamic Volume or Molecular Mass?

Measuring accurate translational self-diffusion coefficients (D_t) by NMR techniques with modern spectrometers has become rather routine. In contrast, the derivation of reliable molecular information therefrom still remains a nontrivial task. In this paper, two established approaches to estimating molecular size in terms of hydrodynamic volume (V_H) or molecular weight (M) are compared. Ad hoc designed experiments allowed the critical aspects of their application to be explored by translating relatively complex theoretical principles into practical take-home messages. For instance, comparing the D_t values of three isosteric Cp₂MCl₂ complexes (Cp=cyclopentadienyl, M=Ti, Zr, Hf), having significantly different molecular mass, provided an empirical demonstration that V_H is the critical molecular property affecting D_t. This central concept served to clarify the assumptions behind the derivation of D_t=ƒ(M) power laws from the Stokes–Einstein equation. Some pitfalls in establishing log (D_t) versus log (M) linear correlations for a set of species have been highlighted by further investigations of selected examples. The effectiveness of the Stokes–Einstein equation itself in describing the aggregation or polymerization of differently shaped species has been explored by comparing, for example, a ball-shaped silsesquioxane cage with its cigar-like dimeric form, or styrene with polystyrene macromolecules.     

Why Are Proteins Charged? Networks of Charge–Charge Interactions in Proteins Measured by Charge Ladders and Capillary Electrophoresis

Almost all proteins contain charged amino acids. While the function in catalysis or binding of individual charges in the active site can often be identified, it is less clear how to assign function to charges beyond this region. Are they necessary for solubility? For reasons other than solubility? Can manipulating these charges change the properties of proteins? A combination of capillary electrophoresis (CE) and protein charge ladders makes it possible to study the roles of charged residues on the surface of proteins outside the active site. This method involves chemical modification of those residues to generate a large number of derivatives of the protein that differ in charge. CE separates those derivatives into groups with the same number of modified charged groups. By studying the influence of charge on the properties of proteins using charge ladders, it is possible to estimate the net charge and hydrodynamic radius and to infer the role of charged residues in ligand binding and protein folding.     

Reliable Determinations of Protein–Ligand Interactions by Direct ESI-MS Measurements. Are We There Yet?

The association-dissociation of noncovalent interactions between protein and ligands, such as other proteins, carbohydrates, lipids, DNA, or small molecules, are critical events in many biological processes. The discovery and characterization of these interactions is essential to a complete understanding of biochemical reactions and pathways and to the design of novel therapeutic agents that may be used to treat a variety of diseases and infections. Over the last 20 y, electrospray ionization mass spectrometry (ESI-MS) has emerged as a versatile tool for the identification and quantification of protein–ligand interactions in vitro. Here, we describe the implementation of the direct ESI-MS assay for the determination of protein–ligand binding stoichiometry and affinity. Additionally, we outline common sources of error encountered with these measurements and various strategies to overcome them. Finally, we comment on some of the outstanding challenges associated with the implementation of the assay and highlight new areas where direct ESI-MS measurements are expected to make significant contributions in the future.     

Real-Time Analysis of Folding upon Binding of a Disordered Protein by Using Dissolution DNP NMR Spectroscopy

The kinase inhibitory domain of the cell cycle regulatory protein p27^Kip1 (p27) was nuclear spin hyperpolarized using dissolution dynamic nuclear polarization (D-DNP). While intrinsically disordered in isolation, p27 adopts secondary structural motifs, including an α-helical structure, upon binding to cyclin-dependent kinase 2 (Cdk2)/cyclin A. The sensitivity gains obtained with hyperpolarization enable the real-time observation of ¹³C NMR signals during p27 folding upon binding to Cdk2/cyclin A on a time scale of several seconds. Time-dependent intensity changes are dependent on the extent of folding and binding, as manifested in differential spin relaxation. The analysis of signal decay rates suggests the existence of a partially folded p27 intermediate during the timescale of the D-DNP NMR experiment.     

Determination of lesinurad in rat plasma by a UHPLC–MS/MS assay

Lesinurad is an oral inhibitor of urate-anion exchanger transporter 1 and has been approved by the US Food and Drug Administration for combination therapy with a xanthine oxidase inhibitor for the treatment of hyperuricemia associated with refractory gout. In the present study, a sensitive and specific ultra high-performance liquid chromatography with tandem mass spectrometry assay was established and verified for the determination of lesinurad in rat plasma and was described in details for the first time. Chromatographic separation of lesinurad and diazepam (internal standard, IS) was performed on a Rapid Resolution HT C18 column (3.0 × 100 mm, 1.8 µm) using methanol–water (70:30, v/v) as the mobile phase at a flow rate of 0.3 mL/min. Lesinurad and IS were extracted from plasma by liquid–liquid extraction using ethyl acetate. The mass spectrometric detection was carried out using an electrospray ionization source in positive mode. Multiple reaction monitoring was used for quantification of the precursor to product ion at m/z 405.6 → 220.9 for lesinurad and m/z 285.1 → 192.8 for IS. The assay was well validated for selectivity, accuracy, precision, recovery, linearity, matrix effects, and stability. The verified method was applied to obtain the pharmacokinetic parameters and concentration–time profiles for lesinurad after oral/intravenous administration in rats. The study might provide an important reference and a necessary complement for the qualitative and quantitative evaluation of lesinurad.     

On the Quantitative Click Conjugation of Molecular Weight Distributions: What Can Theoretically Be Expected?

The assessment of the success of a click conjugation for block copolymer formation often occurs via ill‐defined criteria based on the qualitative shape of the size exclusion chromatography (SEC) distribution as well as unsuitable characteristics of these molecular weight distribution such as the peak molecular weight, M_p. The data presented herein illustrate that from the shape of the SEC distribution, w(log M) versus log M, of the click product—under the assumption of a 100% efficient conjugation reaction—a conclusion about the effectiveness of the click conjugation cannot be derived. It is demonstrated that under certain conditions multi‐modal molecular weight distributions are obtained from two well‐defined monomodal initial distributions. Similarly, the comparison of peak maxima between the conjugate and the initial SEC distributions is a poorly defined criterion to assess the success of a conjugation. The only reliable assessment for the success of the click coupling reaction is the true number average molecular weight, , of the SEC distribution of the click product, as well as a plot of the concentration or number distributions, c versus M, of the precursors and product polymer.

     

Digestion of Enolase and Carbonic Anhydrase as Model Proteins for Therapeutic Proteins in Blood Plasma with Immobilized Thermolysin and Quantification of Some of the Peptides by LC/LC–MS/MS

There is a need for fast method development in the early drug discovery phase of therapeutic proteins. Thermolysin has not been used for quantification of proteins in blood plasma earlier. It is a thermostable protease which permits the use of high temperatures for fast hydrolysis of proteins. Model proteins were digested with immobilized thermolysin on agarose gel. Protein-specific peptides were selected for quantitation and quantified based on stable isotope dilution. Protein digests of blood plasma were cleaned and separated using an automated LC/LC–MS/MS system. Essential digestion parameters that influence thermolysin hydrolytic activity were optimized for high peptide yield. The validated methods were selective, linear, precise and accurate with a limit of detection of 2 nM for both proteins. The proposed strategy for method development could be valuable for quantification of proteins in blood plasma samples. The study underscores and discusses important features of the enzymatic digestion and chromatographic separation.     

Revisiting Thin-Layer Chromatography as a Lipophilicity Determination Tool. Part II — Is Silica Gel a Reliable Adsorbent for Lipophilicity Estimation?

JPC – Journal of Planar Chromatography – Modern TLC - Lipophilicity is often estimated by thin-layer chromatography (TLC) as a fundamental property related to biological and...     

Detection of β-methylphenethylamine,a novel doping substance,by means of UPLC/MS/MS

Novel substances of expected doping activity are constantly introduced to the market. β-Methylphenethylamine (BMPEA) is classified as a doping agent by the World Anti-Doping Agency as it is a positional isomer of amphetamine. In this work, the development and application of a simple and rapid analytical procedure that enables discrimination between both isomers is described. The analytes of interest were extracted from urine by a two-step liquid–liquid extraction and then analyzed by UPLC/MS/MS under isocratic conditions. The entire analytical procedure was validated by evaluating its selectivity, discrimination capabilities, carry-over, sensitivity, and influence of matrix effects on its performance. Application of the method resulted in detection of BMPEA in eight anti-doping samples, including the first report of adverse analytical finding regarding its use. Further analysis showed that BMPEA may be eliminated unchanged along with its phase II conjugates, the hydrolysis of which may considerably improve detection capabilities of the method. Omission of the hydrolysis step may therefore, produce false-negative results. Testing laboratories should also carefully examine their LC/MS/MS-based amphetamine and BMPEA findings as both isomers fragment yielding comparable collision-induced dissociation spectra and their insufficient chromatographic separation may result in misidentification. This is of great importance in case of forensic analyses as BMPEA is not controlled by the public law, and its manufacturing, distribution, and use are legal.     

Native MS and ECD Characterization of a Fab–Antigen Complex May Facilitate Crystallization for X-ray Diffraction

Native mass spectrometry (MS) and top-down electron-capture dissociation (ECD) combine as a powerful approach for characterizing large proteins and protein assemblies. Here, we report their use to study an antibody Fab (Fab-1)–VEGF complex in its near-native state. Native ESI with analysis by FTICR mass spectrometry confirms that VEGF is a dimer in solution and that its complex with Fab-1 has a binding stoichiometry of 2:2. Applying combinations of collisionally activated dissociation (CAD), ECD, and infrared multiphoton dissociation (IRMPD) allows identification of flexible regions of the complex, potentially serving as a guide for crystallization and X-ray diffraction analysis.

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Determination of methylisothiocyanate in soil and water by HS-SPME followed by GC–MS–MS with a triple quadrupole

Methylisothiocyanate (MITC) is the main degradation product of metam sodium, a soil disinfectant widely used in agriculture, and is responsible for its disinfectant properties. Because MITC is highly toxic and volatile, metam sodium has to be applied in a manner that tries to reduce atmospheric emissions but still maintains adequate concentration of MITC in soil to ensure its disinfectant effect. Thus, monitoring of MITC concentrations in soil is required, and to this end sensitive, fast, and reliable analytical methods must be developed. In this work, a headspace solid-phase microextraction (HS-SPME) method was developed for MITC determination in water and soil samples using gas chromatography-tandem mass spectrometry (GC–MS–MS) with a triple-quadrupole analyzer. Two MS–MS transitions were acquired to ensure the reliable quantification and confirmation of the analyte. The method had linear behavior in the range tested (0.026–2.6 ng mL^?1 in water, 1–100 ng g^?1 in soil) with r ² over 0.999. Detection limits were 0.017 ng mL^?1 and 0.1 ng g^?1 in water and soil, respectively. Recoveries for five replicates were in the range 76–92 %, and RSD was below 7 % at the two spiking levels tested for each matrix (0.1 and 1 ng mL^?1 for water, 4 and 40 ng g^?1 for soil). The potential of using multiple HS-SPME for analyzing soil samples was also investigated, and its feasibility for quantification of MITC evaluated. The developed HS-SPME method was applied to soil samples from experimental plots treated with metam sodium following good agriculture practices. Figure

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Are the enolates of amides and esters stabilized by electrostatics?

The fact that amides and esters form less stable enolates than ketones might be seen as evidence that electrostatic stabilization is unimportant in these anions. However, ab initio molecular orbital calculations show that electrostatic stabilization does in fact lie beneath the competing resonance effect that causes the decrease in acidity. The electrostatic contribution is revealed by examining torsionally twisted amide and ester structures in which the pi resonance interactions are largely inhibited. These twisted amides and esters have greater enolate acidity than the corresponding ketones. Qualitatively similar behavior is observed with respect to protonation, such that twisted amides and esters are generally less basic than the reference ketones, in striking contrast to their behavior in the normal geometries.     

Simultaneous quantification of ten cytotoxic drugs by a validated LC–ESI–MS/MS method

A liquid chromatography separation with electrospray ionisation and tandem mass spectrometry detection method was developed for the simultaneous quantification of ten commonly handled cytotoxic drugs in a hospital pharmacy. These cytotoxic drugs are cytarabine, gemcitabine, methotrexate, etoposide phosphate, cyclophosphamide, ifosfamide, irinotecan, doxorubicin, epirubicin and vincristine. The chromatographic separation was carried out by RPLC in less than 21 min, applying a gradient elution of water and acetonitrile in the presence of 0.1% formic acid. MS/MS was performed on a triple quadrupole in selected reaction monitoring mode. The analytical method was validated to determine the limit of quantification (LOQ) and quantitative performance: lowest LOQs were between 0.25 and 2 ng mL(-1) for the ten investigated cytotoxic drugs; trueness values (i.e. recovery) were between 85% and 110%, and relative standard deviations for both repeatability and intermediate precision were always inferior to 15%. The multi-compound method was successfully applied for the quality control of pharmaceutical formulations and for analyses of spiked samples on potentially contaminated surfaces.     

Tuning Molecular Electron Affinities against Atomic Electronegativities by Spatial Expansion of a π-System

2,1,3-Benzochalcogenadiazoles C₆R₄N₂E ( E / R ; E=S, Se, Te; R=H, F, Cl, Br, I) and C₆H₂R₂N₂E ( E / R’ ; E=S, Se, Te; R=Br, I) are 10π-electron hetarenes. By CV/EPR measurements, DFT calculations, and QTAIM and ELI-D analyses, it is shown that their molecular electron affinities (EAs) increase with decreasing Allen electronegativities and electron affinities of the E and non-hydrogen R (except Cl) atoms. DFT calculations for E / R +e⋅⁻→[E/R]⋅⁻ electron capture reveal negative ΔG values numerically increasing with increasing atomic numbers of the E and R atoms; positive ΔS has a minor influence. It is suggested that the EA increase is caused by more effective charge/spin delocalization in the radical anions of heavier derivatives due to contributions from diffuse (a real-space expanded) p-AOs of the heavier E and R atoms; and that this counterintuitive effect might be of the general character.     

Quantitation by GC–MS of Methylglyoxal as a Marker in Anxiety-Related Studies

Methylglyoxal (MG) is present in the human system. In the cell, MG is degraded by glyoxalase 1 (Glo 1), an enzyme differentially expressed in several mouse models of anxiety-related behavior. It has also been associated with the formation of advanced glycation and lipoxidation end products, contributing to diabetes-related complications. Approaches developed for accurate quantitation of MG in this study include the synthesis of a deuterated MG analog to serve as an internal standard; skillful application of the standard addition protocol (with “reiteration”) to quantitate MG in “blank” samples, allowing the preparation of calibration standards using the same test specimen matrix system; and various pretreatment methods, including extraction and derivatization, to prepare complex brain tissue specimens for gas chromatography–mass spectrometry analysis. Using our method, brain MG levels in high- and low-anxiety-related behavior (HAB and LAB) mice were determined as 5.11 ± 0.89 and 13.05 ± 0.89 μg g^?1, respectively. These data supported the conclusion that MG level in brain is negatively correlated with anxiety in mouse models of anxiety-related studies, contributing to better understanding of the molecular mechanisms underlying reported observations.     

Pharmacokinetic studies of a novel tubulin inhibitor SK1326 in rat plasma by UPLC–MS/MS

A sensitive method for quantitation of SK1326 in rat plasma has been established using ultra-performance liquid chromatography–electrospray ionization tandem mass spectrometry (UPLC–ESI/MS/MS). SK1326 and the internal standard (tramadol) in plasma sample were extracted using acetonitrile. A centrifuged upper layer was then evaporated and reconstituted with a mobile phase of 0.5% formic acid–acetonitrile (35:65, v/v). The reconstituted samples were injected into a C₁₈ reversed-phase column. Using MS/MS in the multiple reaction monitoring mode, SK1326 and tramadol were detected without severe interference from the rat plasma matrix. SK1326 produced a protonated precursor ion ([M + H]⁺) at m/z 432.3 and a corresponding product ion at m/z 114.4. The internal standard produced a protonated precursor ion ([M + H]⁺) at m/z 264.4 and a corresponding product ion at m/z 58.1. Detection of SK1326 in rat plasma by the UPLC–ESI/MS/MS method was accurate and precise with a quantitation limit of 1.0 ng/mL. The validation, reproducibility, stability and recovery of the method were evaluated. The method has been successfully applied to pharmacokinetic studies of SK1326 in rat plasma. The pharmacokinetic parameters of SK1326 were evaluated after intravenous (at a dose of 10 mg/kg) and oral (at a dose of 20 mg/kg) administration of SK1326 in rats. After oral administration (20 mg/kg) of SK1326, the F (fraction absorbed) value was ~77.1%.     

Determination of Nicotine in Dried Mushrooms by Using a Modified QuEChERS Approach and GC–MS–MS

Levels of nicotine higher than the maximum residue level were detected in edible mushrooms. Analyses of self-collected and purchased dried mushrooms were performed with a QuEChERS approach. A small amount (2.5 g) of dried sample matrix was mixed with 5 mL sodium hydroxide solution, 2.5 g of sodium sulfate/sodium chloride mixture (4:1) and 5 mL ethyl acetate. The organic phase was cleaned by using dispersive solid-phase extraction and analysed by GC–MS–MS. The linear range of the method was 0.01–10.00 mg kg^?1 and the limit of detection 0.006 mg kg^?1 on dry weight basis by using EURACHEM method.