Low pKa Research Articles

Low pKa Phosphido-Boranes Capture Carbon Dioxide with Exceptional Strength: DFT Predictions Followed by Experimental Validation.

We have developed a class of phosphido-boranes (BoPh's) with formula X+[R2PBH3-] that bind CO2 with exceptional strength (ΔG = -8.2 to -24.0 kcal/mol) at ambient conditions. We use quantum mechanics (QM) to determine how the choice of electron-donating versus electron-withdrawing ligand impacts the CO2 binding strength, in the presence of a donating borane moiety. We also examine the role of the cation in CO2 binding, finding that the ion position relative to the bound CO2 dramatically alters binding strength. We find that the BoPh with two ethyl ligands Li[Et2PBH3] leads to ΔG = -24.0 kcal/mol upon CO2 binding while Li[Ph2PBH3] leads to ΔG = -12.8 kcal/mol. We synthesized the BoPh with two phenyl ligands Li[Ph2PBH3] to validate the QM-predicted stability and predicted pKa.

Photocleavable Protecting Groups Using a Sulfite Self‐Immolative Linker for High Uncaging Quantum Yield and Aqueous Solubility

AbstractUsing light as an external stimulus to control (bio)chemical processes offers many distinct advantages. Most importantly, it allows for spatiotemporal control simply through operating the light source. Photocleavable protecting groups (PPGs) are a cornerstone class of compounds that are used to achieve photocontrol over (bio)chemical processes. PPGs are able to release a payload of interest upon light irradiation. The successful application of PPGs hinges on their efficiency of payload release, captured in the uncaging Quantum Yield (QY). Heterolytic PPGs efficiently release low pKa payloads, but their efficiency drops significantly for payloads with higher pKa values, such as alcohols. For this reason, alcohols are usually attached to PPGs via a carbonate linker. The self‐immolative nature of the carbonate linker results in concurrent release of CO2 with the alcohol payload upon irradiation. We introduce herein novel PPGs containing sulfites as self‐immolative linkers for photocaged alcohol payloads, for which we discovered that the release of the alcohol proceeds with higher uncaging QY than an identical payload released from a carbonate‐linked PPG. Furthermore, we demonstrate that uncaging of the sulfite‐linked PPGs results in the release of SO2 and show that the sulfite linker improves water solubility as compared to the carbonate‐based systems.

Photocleavable Protecting Groups Using a Sulfite Self-Immolative Linker for High Uncaging Quantum Yield and Aqueous Solubility.

Using light as an external stimulus to control (bio)chemical processes offers many distinct advantages. Most importantly, it allows for spatiotemporal control simply through operating the light source. Photocleavable protecting groups (PPGs) are a cornerstone class of compounds that are used to achieve photocontrol over (bio)chemical processes. PPGs are able to release a payload of interest upon light irradiation. The successful application of PPGs hinges on their efficiency of payload release, captured in the uncaging Quantum Yield (QY). Heterolytic PPGs efficiently release low pKa payloads, but their efficiency drops significantly for payloads with higher pKa values, such as alcohols. For this reason, alcohols are usually attached to PPGs via a carbonate linker. The self-immolative nature of the carbonate linker results in concurrent release of CO2 with the alcohol payload upon irradiation. We introduce herein novel PPGs containing sulfites as self-immolative linkers for photocaged alcohol payloads, for which we discovered that the release of the alcohol proceeds with higher uncaging QY than an identical payload released from a carbonate-linked PPG. Furthermore, we demonstrate that uncaging of the sulfite-linked PPGs results in the release of SO2 and show that the sulfite linker improves water solubility as compared to the carbonate-based systems.

Heterocyclic effect boosted peroxidase-like activity of MIL(Fe) metal-organic framework for colorimetric assay and dye removal

Metal-organic frameworks (MOFs) have emerged as promising candidates for enzyme mimics due to their abundant pore structures and adjustable active sites. The catalytic activity particularly depends on the electronic character of the organic ligand. In this study, we report an iron-based MOF nanozyme FeTDC, created by replacing the 1,4-dicarboxybenzene ligand with five-membered 2,5-thiophenedicarboxylic acid (H2TDC). In comparison with the phenyl analogue, the sulfur-based heterocyclic ligand demonstrates high electron delocalization, and a low pKa value, which are beneficial for enhancing the metal/ligand interactions. Accordingly, FeTDC can facilitate the oxidation of the benzidine substrate in the presence of H2O2, thereby exhibiting remarkable peroxidase-like activity. The generation of hydroxyl radical (•OH) at the Fe active sites contributes to the catalytic process. Furthermore, the smartphone-assisted colorimetric assay of pyrophosphate was developed with high sensitivity, based on its inhibitory effect. When FeTDC was utilized for the removal of benzidine dye under high-salt condition, a 90 % of removal rate was achieved due to the synergistic effect of enzyme catalysis and physical adsorption. This work presents a novel perspective of heterocyclic effect on the design of MOF nanozymes, thereby expanding their applicability in the control of pollutants.

Overcoming Challenges with Biochemical Studies of Selenocysteine and Selenoproteins.

Selenocysteine (Sec) is an essential amino acid that distinguishes itself from cysteine by a selenium atom in place of a sulfur atom. This single change imparts distinct chemical properties to Sec which are crucial for selenoprotein (Sec-containing protein) function. These properties include a lower pKa, enhanced nucleophilicity, and reversible oxidation. However, studying Sec incorporation in proteins is a complex process. While we find Sec in all domains of life, each domain has distinct translation mechanisms. These mechanisms are unique to canonical translation and are composed of Sec-specific enzymes and an mRNA hairpin to drive recoding of the UGA stop codon with Sec. In this review, we highlight the obstacles that arise when investigating Sec insertion, and the role that Sec has in proteins. We discuss the strategic methods implemented in this field to address these challenges. Though the Sec translation system is complex, a remarkable amount of information has been obtained and specialized tools have been developed. Continued studies in this area will provide a deeper understanding on the role of Sec in the context of proteins, and the necessity that we have for maintaining this complex translation machinery to make selenoproteins.

Proton Conduction via Water and Ammonia Coordinated Metal Cationic Species in MOF and MHOF Platforms.

Although metal-organic frameworks (MOFs) and metalo hydrogen-bonded organic frameworks (MHOFs) are designed as promising solid-state proton conductors by incorporating various protonic species intrinsically or extrinsically, design and development of such materials by employing the concept of proton conduction through coordinated polar protic solvent is largely unexplored. Herein, we have constructed two proton-conducting materials having different solvent coordinated metal cationic species: In-H2O-MOF, ({[In(H2O)6][In3(Pzdc)6]·15H2O}n; H2Pzdc: pyrazine-2,3-dicarboxylic acid) with coordinated water molecules from hexaaquaindium cationic species, and MHOF-4, ([{Co(NH3)6}2(2,6-NDS)2(H2O)2]n; 2,6-H2NDS: 2,6-naphthalenedisulfonic acid) with coordinated ammonia from hexaammoniacobalt cationic species. Interestingly, higher proton conductivity was achieved for In-H2O-MOF (1.5 × 10-5 S cm-1) than MHOF-4 (6.3 × 10-6 S cm-1) under the extreme conditions (80 ºC and 95% RH), which could be attributed to enhanced acidity of coordinated water molecules having much lower pKa value than that of coordinated ammonia. Greater charge polarization on hydrogen atoms of In3+-coordinated water molecules than that of Co2+-coordinated ammonia led to the high conductivity of In-H2O-MOF, as evident by quantum chemical studies. Such a comparative study on metal-coordinated protic polar solvents in achieving proton conduction in crystalline solids is yet to be made.

In Situ Generation and High Bioresistance of Trityl-based Semiquinone Methide Radicals Under Anaerobic Conditions in Cellular Systems.

Bioreduction of spin labels and polarizing agents (generally stable radicals) has been an obstacle limiting the in-cell applications of pulsed electron paramagnetic resonance (EPR) spectroscopy and dynamic nuclear polarization (DNP). In this work, we have demonstrated that two semiquinone methide radicals (OXQM⋅ and CTQM⋅) can be easily produced from the trityl-based quinone methides (OXQM and CTQM) via reduction by various reducing agents including biothiols and ascorbate under anaerobic conditions. Both radicals have relatively low pKa's and exhibit EPR single line signals at physiological pH. Moreover, the bioreduction of OXQM in three cell lysates enables quantitative generation of OXQM⋅ which was most likely mediated by flavoenzymes. Importantly, the resulting OXQM⋅ exhibited extremely high stability in the E.coli lysate under anaerobic conditions with 76- and 14.3-fold slower decay kinetics as compared to the trityl OX063 and a gem-diethyl pyrrolidine nitroxide, respectively. Intracellular delivery of OXQM into HeLa cells was also achieved by covalent conjugation with a cell-permeable peptide as evidenced by the stable intracellular EPR signal from the OXQM⋅ moiety. Owing to extremely high resistance of OXQM⋅ towards bioreduction, OXQM and its derivatives show great application potential in in-cell EPR and in-cell DNP studies for various cells which can endure short-term anoxic treatments.

Constant-pH MD simulations of the protonation-triggered conformational switching in diphtheria toxin translocation domain

Protonation of key residues in the diphtheria toxin translocation (T)-domain triggered by endosomal acidification is critical for inducing a series of conformational transitions critical for the cellular entry of the toxin. Previous experiments revealed the importance of histidine residues in modulating pH-dependent transitions. They suggested the presence of a “safety latch” preventing premature refolding of the T-domain by a yet poorly understood mechanism. Here, we used constant-pH molecular dynamics simulations to systematically investigate the protonation sequence in the wild-type T-domain and the following mutants: H223Q, H257Q, E259Q, and H223Q/H257Q. Comparison of these computational results with previous experimental data on T-domain stability and activity with the H-to-Q replacements confirms the role of H223 (pKa = 6.5) in delaying the protonation of the main trigger, H257 (pKa = 2.2 in the WT and pKa = 4.9 in H223Q). Our calculations also reveal a very low pKa for a neighboring acidic residue E259, which does not get protonated even during simulations at pH 3. This residue also contributes to the formation of the safety latch, with the pKa of H257 increasing from 2.2 to 5.1 upon E259Q replacement. In contrast, the latter replacement has virtually no effect on the protonation of the H223. Thus, we conclude that the interplay of the protonation in the H223/H257/E259 triad has evolved to prevent triggering the accidental refolding of the T-domain by a fluctuation in the protonation of the main trigger at neutral pH, before the incorporation of the toxin inside the endosome. Subsequent acidification of the endosome overcomes the safety latch and triggers conformational switching via repulsion of H223+ and H257+. This protonation/conformation relationship corroborates experimental findings and offers a detailed stepwise molecular description of the transition mechanism, which can be instrumental in optimizing the potential applications of the T-domain for targeted delivery of therapies to tumors and other diseased acidic tissues.

Comparing thiol and selenol reactivity towards peroxynitrite by computer simulation

Peroxynitrite is a very reactive species implicated in a variety of pathophysiological cellular processes. Particularly, peroxynitrite-mediated oxidation of cellular thiol-containing compounds such as cysteine residues is a key process which has been extensively studied. Cysteine plays roles in many redox biochemistry pathways. In contrast, selenocysteine, the 21st amino acid, is only present in 25 human proteins. Investigating the molecular basis of selenocysteine's reactivity may provide insights into its unique role in these selenocysteine-containing proteins. The two-electron oxidation of thiols or selenols by peroxynitrite is a process that is carried out by the thiolate/selenate forms and peroxynitrous acid.In this work, we shed light on the molecular basis of the differential reactivity of both species towards peroxynitrite by means of state-of-the-art computer simulations. We performed electronic structure calculations of the reaction in the methanethiolate and methaneselenolate model systems with peroxynitrous acid at different levels of theory using an implicit solvent scheme. In addition, we employed a multi-scale quantum mechanics/molecular mechanics approach for obtaining free energy profiles of these chemical reactions in aqueous solution, which enabled the comparison between the simulations and the available experimental data. Our results suggest that the larger reactivity observed in the selenocysteine case at physiological pH is mainly due to the lower pKa, which affords a larger fraction of the reactive anionic species in these conditions, and in a second place to a slightly enhanced intrinsic reactivity of the selenate form due to its larger nucleophilicity.

Sequential assembly enhanced selectivity on magnetic imprinted polymers for specific capture of naringin: A combination of synergistic dual sites and imprinted effect

Green and sustainable recovery of high-value natural flavonoids in agricultural wastes could not only improve natural resource utilization, but also could effectively reduce environmental pollution. Recently, great efforts have been made for research on the development of magnetic imprinted composite adsorbent, but the simultaneous promotion of stable selectivity and high adsorption amounts still faces its challenges. Inspired by “Sandwich-like” transport channels with proper steric and specific affinity sites, herein we designed a new kind of surface-imprinted magnetic colloidal nanocrystal clusters (MCNCs) with dual recognition sites (MCNCs@DR-MIPs) via sequential surface imprinted strategy. A two-step sequential surface-initiated atom transfer radical polymerization (SI-ATRP) was employed to construct the double imprinted sites, which can significantly improve the adsorption selectivity and adsorption amounts. In this design, the metal ion Zn(II) and the low pKa boronic acid APBA (1-allylpyridine-3-boronic acid, pKa = 7.4) could effectively tune the appropriate yolk-shell confinement sites, the obtained artificial double imprinted binding sites establishes the promising chemical environment for selective separation. As expected, the adsorption equilibrium experiments exhibited adsorption kinetics (180 min) and the maximum equilibrium binding capacity (34.60 µmol g−1). In virtue of unique advantages of magnetic separation materials, this novel absorbent exhibited a green and environmentally friendly enrichment process for naringin (NRG). Meanwhile, MCNCs@DR-MIPs showed excellent selectivity (imprinted factor 2.15) and regeneration properties (only decreased by 8.22 % after 7 cycles) for NRG. Additionally, the commercially available NRG could be effectively extracted and concentrated to 94.78 %. This study offers a sustainable effective strategy for flavonoids purification of magnetic separation materials and promotes advance the other natural compounds from agricultural wastes.

Critical roles of soil composition and pollutant properties on the degradation of PPCPs during ferrous/persulfate processes

Pharmaceuticals and personal care products (PPCPs) are widely used worldwide and cause potential soil pollution. Fe2+-activated persulfate (PS) processes (Fe-PAPs) are promising techniques for soil remediation. However, a knowledge gap exists in the mechanistic insights into the dominant factors affecting the degradation of different PPCPs in varied soil types. This study systematically investigated the roles of soil components and pollutant properties in the degradation of three PPCPs (triclosan (TCS), triclocarban (TCC), and naproxen (NPS)) in the nine soils in the Fe2+/PS system. The degradation efficiencies of TCS and NPS ranged from 10.92 % to 91.62 % and 46.59 % to 99.81 %, respectively, whereas nearly no degradation was observed for TCC. PPCPs with high water solubility, high energies of the highest occupied molecular orbital (EHOMO), low pKa values, low energy gap (ΔE), or low vertical ionization potential (VIP) were more favorable for degradation. XPS analysis suggested that aliphatic carbon (Ali–C–C(H)), ether or alcohol carbon (C–O), and aldehyde or ketonic carbon (CO) on SOM significantly inhibited TCS degradation. The results of ROS quenching experiments showed that SO4•− and 1O2 played major roles in TCS and NPS degradation in the six soils, with the relative contributions ranged from 24.82 % to 99.14 % and 0.15 % to 73.40 %, respectively. The interaction between soil components, active species, and pollutants resulted in the distinct intermediates of TCS and NPS in different soils. Our findings provide in-depth insights into the role of soil composition and pollutant properties on the remediation of PPCP-contaminated soils in Fe-PAPs.

Photonic Nanochains for Continuous Glucose Monitoring in Physiological Environment.

Diabetes is a common disease that seriously endangers human health. Continuous glucose monitoring (CGM) is important for the prevention and treatment of diabetes. Glucose-sensing photonic nanochains (PNCs) have the advantages of naked-eye colorimetric readouts, short response time and noninvasive detection of diabetes, showing immense potential in CGM systems. However, the developed PNCs cannot disperse in physiological environment at the pH of 7.4 because of their poor hydrophilicity. In this study, we report a new kind of PNCs that can continuously and reversibly detect the concentration of glucose (Cg) in physiological environment at the pH of 7.4. Polyacrylic acid (PAA) added to the preparation of PNCs forms hydrogen bonds with polyvinylpyrrolidone (PVP) in Fe3O4@PVP colloidal nanoparticles and the hydrophilic monomer N-2-hydroxyethyl acrylamide (HEAAm), which increases the content of PHEAAm in the polymer shell of prepared PNCs. Moreover, 4-(2-acrylamidoethylcarbamoyl)-3-fluorophenylboronic acid (AFPBA), with a relatively low pKa value, is used as the glucose-sensing monomer to further improve the hydrophilicity and glucose-sensing performances of PNCs. The obtained Fe3O4@(PVP-PAA)@poly(AFPBA-co-HEAAm) PNCs disperse in artificial serum and change color from yellow-green to red when Cg increases from 3.9 mM to 11.4 mM, showing application potential for straightforward CGM.

Assessment of the antinociceptive, respiratory-depressant, and reinforcing effects of the low pKa fluorinated fentanyl analogs, FF3 and NFEPP

RationaleRecent studies report that fentanyl analogs with relatively low pKa values produce antinociception in rodents without other mu opioid-typical side effects due to the restriction of their activity to injured tissue with relatively low pH values. However, it is unclear if and to what degree these compounds may produce mu opioid-typical side effects (respiratory depression, reinforcing effects) at doses higher than those required to produce antinociception. ObjectivesThe present study compared the inflammatory antinociceptive, respiratory-depressant, and reinforcing effects of fentanyl and two analogs of intermediate (FF3) and low (NFEPP) pKa values in terms of potency and efficacy in male and female Sprague-Dawley rats. MethodsNociception was produced by administration of Complete Freund's Adjuvant into the hind paw of subjects, and antinociception was measured using an electronic Von Frey test. Respiratory depression was measured using whole-body plethysmography. Reinforcing effects were measured in self-administration using a progressive-ratio schedule of reinforcement. The dose ranges tested for each drug encompassed no effect to maximal effects. ResultsAll compounds produced full effects in all measures but varied in potency. FF3 and fentanyl were equipotent in antinociception and self-administration, but FF3 was less potent than fentanyl in respiratory depression. NFEPP was less potent than fentanyl in every measure. The magnitude of potency difference between antinociception and other effects was greater for FF3 than for NFEPP or fentanyl, indicating that FF3 had the widest margin of safety when relating antinociception to respiratory-depressant and reinforcing effects. ConclusionsLow pKa fentanyl analogs possess potential as safer analgesics, but determining the optimal degree of difference for pKa relative to fentanyl will require further study due to some differences between the current results and findings from prior work with these analogs.

Exploring the pH dependence of an improved PETase

Enzymatic recycling of plastic and especially of polyethylene terephthalate (PET) has shown great potential to reduce its negative impact on our society. PET hydrolases (PETases) have been optimized using rational design and machine learning, but the mechanistic details of the PET depolymerization process remain unclear. Belonging to the carboxylic-ester hydrolase family with a canonical Ser-His-Asp catalytic triad, their observed alkaline pH optimum is generally thought to be related to the protonation state of the catalytic His. Here, we explore this aspect in the context of LCCICCG, an optimized PETase, derived from the leaf-branch compost cutinase enzyme. We use NMR to identify the dominant tautomeric structure of the six histidines. Five show surprisingly low pKa values below 4.0, whereas the catalytic H242 in the active enzyme displays a pKa value that varies from 4.9 to 4.7 when temperatures increase from 30°C to 50°C. Whereas the hydrolytic activity of the enzyme toward a soluble substrate can be modeled by the corresponding protonation/deprotonation curve, an important discrepancy is found when the substrate is the solid plastic. This opens the way to further mechanistic understanding of the PETase activity and underscores the importance of studying the enzyme at the liquid-solid interface.

Variations in proton transfer pathways and energetics on pristine and defect-rich quartz surfaces in water: Insights into the bimodal acidities of quartz

HypothesisUnderstanding the mechanisms of proton transfer on quartz surfaces in water is critical for a range of processes in geochemical, environmental, and materials sciences. The wide range of surface acidities (>9 pKa units) found on the ubiquitous mineral quartz is caused by the structural variations of surface silanol groups. Molecular scale simulations provide essential tools for elucidating the origin of site-specific surface acidities. SimulationsWe used density-functional tight-binding-based molecular dynamics combined with rare-event metadynamics simulations to probe the mechanisms of deprotonation reactions from ten representative surface silanol groups found on both pristine and defect-rich quartz (101) surfaces with Si vacancies. FindingsThe results show that deprotonation is a highly dynamic process where both the surface hydroxyls and bridging oxygen atoms serve as the proton acceptors, in addition to water. Deprotonation of embedded silanols through intrasurface proton transfer exhibited lower pKa values with less H-bond participation and higher energy barriers, suggesting a new mechanism to explain the bimodal acidity observed on quartz surface. Defect sites, recently shown to comprise a significant portion of the quartz (101) surface, diversify the coordination and local H-bonding environments of the surface silanols, changing both the deprotonation pathways and energetics, leading to a wider range of pKa values (2.4 to 11.5) than that observed on pristine quartz surface (10.4 and 12.1).

β-Dicarbonyls Facilitate Engineered Microbial Bromoform Biosynthesis.

Ruminant livestock produce around 24% of global anthropogenic methane emissions. Methanogenesis in the animal rumen is significantly inhibited by bromoform, which is abundant in seaweeds of the genus Asparagopsis. This has prompted the development of livestock feed additives based on Asparagopsis to mitigate methane emissions, although this approach alone is unlikely to satisfy global demand. Here we engineer a non-native biosynthesis pathway to produce bromoform in vivo with yeast as an alternative biological source that may enable sustainable, scalable production of bromoform by fermentation. β-dicarbonyl compounds with low pKa values were identified as essential substrates for bromoform production and enabled bromoform synthesis in engineered Saccharomyces cerevisiae expressing a vanadate-dependent haloperoxidase gene. In addition to providing a potential route to the sustainable biological production of bromoform at scale, this work advances the development of novel microbial biosynthetic pathways for halogenation.

CO2 desorption using ultrasound at low temperature from CO2-loaded amine solution under pressure conditions

Ultrasound can effectively desorb CO2 from dissolved CO2 gas [CO2 (aq)] in solution at low temperatures. In this study, three various classes (primary, secondary, and tertiary) of amine solutions were used as a CO2 absorbent for loading CO2 under 0.1 and 0.5 MPa. The effectiveness of ultrasound irradiation and stirring to desorb CO2 from CO2-loaded amine solution was evaluated at around 25 °C. The ultrasound had better desorption results than stirring for all three amines. Among the three classes of amine, tertiary amine triethanolamine with low pKa achieved the highest CO2 desorption ratio of 43.2% and 61.8% after CO2 loaded under 0.1 and 0.5 MPa by ultrasound. It was considered that amine with low pKa and strong sterically hindered structure can promote the balance of the rate-determining reaction of H+ transferred from amine cation to HCO3 − and form CO2 (aq) after initial CO2 (aq) was desorbed by ultrasound.

Comparing ATPase activity of ATP-binding cassette subfamily C member 4, lamprey CFTR, and human CFTR using an antimony-phosphomolybdate assay.

Introduction: ATP-binding cassette (ABC) transporters use the hydrolysis of ATP to power the active transport of molecules, but paradoxically the cystic fibrosis transmembrane regulator (CFTR, ABCC7) forms an ion channel. We previously showed that ATP-binding cassette subfamily C member 4 (ABCC4) is the closest mammalian paralog to CFTR, compared to other ABC transporters. In addition, Lamprey CFTR (Lp-CFTR) is the oldest known CFTR ortholog and has unique structural and functional features compared to human CFTR (hCFTR). The availability of these evolutionarily distant orthologs gives us the opportunity to study the changes in ATPase activity that may be related to their disparate functions. Methods: We utilized the baculovirus expression system with Sf9 insect cells and made use of the highly sensitive antimony-phosphomolybdate assay for testing the ATPase activity of human ABCC4 (hABCC4), Lp-CFTR, and hCFTR under similar experimental conditions. This assay measures the production of inorganic phosphate (Pi) in the nanomolar range. Results: Crude plasma membranes were purified, and protein concentration, determined semi-quantitatively, of hABCC4, Lp-CFTR, and hCFTR ranged from 0.01 to 0.36μg/μL. No significant difference in expression level was found although hABCC4 trended toward the highest level. hABCC4 was activated by ATP with the equilibrium constant (Kd) 0.55 ± 0.28mM (n = 8). Estimated maximum ATPase rate (Vmax) for hABCC4 was about 0.2nmol/μg/min when the protein was activated with 1mM ATP at 37°C (n = 7). Estimated maximum ATPase rate for PKA-phosphorylated Lp-CFTR reached about half of hCFTR levels in the same conditions. Vmax for both Lp-CFTR and hCFTR were significantly increased in high PKA conditions compared to low PKA conditions. Maximum intrinsic ATPase rate of hABCC4 in the absence of substrate was twice that of hCFTR when activated in 1mM ATP. Conclusion: The findings here suggest that while both ABCC4 and hCFTR bear one consensus and one degenerate ATPase site, the hCFTR exhibited a reduced intrinsic ATPase activity. In addition, ATPase activity in the CFTR lineage increased from Lp-CFTR to hCFTR. Finally, the studies pave the way to purify hABCC4, Lp-CFTR, and hCFTR from Sf9 cells for their structural investigation, including by cryo-EM, and for studies of evolution in the ABC transporter superfamily.

NMR measurements of transient low-populated tautomeric and anionic Watson-Crick-like G·T/U in RNA:DNA hybrids: implications for the fidelity of transcription and CRISPR/Cas9 gene editing.

Many biochemical processes use the Watson-Crick geometry to distinguish correct from incorrect base pairing. However, on rare occasions, mismatches such as G·T/U can transiently adopt Watson-Crick-like conformations through tautomerization or ionization of the bases, giving rise to replicative and translational errors. The propensities to form Watson-Crick-like mismatches in RNA:DNA hybrids remain unknown, making it unclear whether they can also contribute to errors during processes such as transcription and CRISPR/Cas editing. Here, using NMR R1ρ experiments, we show that dG·rU and dT·rG mismatches in two RNA:DNA hybrids transiently form tautomeric (Genol·T/U $ \mathbin{\lower.3ex\hbox{$\buildrel\textstyle\rightarrow\over {\smash{\leftarrow}\vphantom{_{\vbox to.5ex{\vss}}}}$}}$ G·Tenol/Uenol) and anionic (G·T-/U-) Watson-Crick-like conformations. The tautomerization dynamics were like those measured in A-RNA and B-DNA duplexes. However, anionic dG·rU- formed with a ten-fold higher propensity relative to dT-·rG and dG·dT- and this could be attributed to the lower pKa (ΔpKa ∼0.4-0.9) of U versus T. Our findings suggest plausible roles for Watson-Crick-like G·T/U mismatches in transcriptional errors and CRISPR/Cas9 off-target gene editing, uncover a crucial difference between the chemical dynamics of G·U versus G·T, and indicate that anionic Watson-Crick-like G·U- could play a significant role evading Watson-Crick fidelity checkpoints in RNA:DNA hybrids and RNA duplexes.

Gold-Promoted Biocompatible Selenium Arylation of Small Molecules, Peptides and Proteins.

A low pKa (5.2), high polarizable volume (3.8 Å), and proneness to oxidation under ambient conditions make selenocysteine (Sec, U) a unique, natural reactive handle present in most organisms across all domains of life. Sec modification still has untapped potential for site-selective protein modification and probing. Herein we demonstrate the use of a cyclometalated gold(III) compound, [Au(bnpy)Cl2 ], in the arylation of diselenides of biological significance, with a scope covering small molecule models, peptides, and proteins using a combination of multinuclear NMR (including 77 Se NMR), and LC-MS. Diphenyl diselenide (Ph-Se)2 and selenocystine, (Sec)2 , were used for reaction optimization. This approach allowed us to demonstrate that an excess of diselenide (Au/Se-Se) and an increasing water percentage in the reaction media enhance both the conversion and kinetics of the C-Se coupling reaction, a combination that makes the reaction biocompatible. The C-Se coupling reaction was also shown to happen for the diselenide analogue of the cyclic peptide vasopressin ((Se-Se)-AVP), and the Bos taurus glutathione peroxidase (GPx1) enzyme in ammonium acetate (2 mM, pH=7.0). The reaction mechanism, studied by DFT revealed a redox-based mechanism where the C-Se coupling is enabled by the reductive elimination of the cyclometalated Au(III) species into Au(I).