Comparing the folding landscapes of evolutionarily divergent procaspase-3

All caspases evolved from a common ancestor and subsequently developed into two general classes, inflammatory or apoptotic caspases. The caspase-hemoglobinase fold has been conserved throughout nearly one billion years of evolution and is utilized for both the monomeric and dimeric subfamilies of apoptotic caspases, called initiator and effector caspases, respectively. We compared the folding and assembly of procaspase-3b from zebrafish to that of human effector procaspases in order to examine the conservation of the folding landscape. Urea-induced equilibrium folding/unfolding of procaspase-3b showed a minimum three-state folding pathway, where the native dimer isomerizes to a partially folded dimeric intermediate, which then unfolds. A partially folded monomeric intermediate observed in the folding landscape of human procaspase-3 is not well-populated in zebrafish procaspase-3b. By comparing effector caspases from different species, we show that the effector procaspase dimer undergoes a pH-dependent conformational change, and that the conformational species in the folding landscape exhibit similar free energies. Together, the data show that the landscape for the caspase-hemoglobinase fold is conserved, yet it provides flexibility for species-specific stabilization or destabilization of folding intermediates resulting in changes in stability. The common pH-dependent conformational change in the native dimer, which yields an enzymatically inactive species, may provide an additional, albeit reversible, mechanism for controlling caspase activity in the cell.

pH-dependent formation of three porous In(III)-MOFs: framework diversity and selective gas adsorption

pH-dependent self-assembly and structural transformation have been observed in a series of porous In(III)-MOFs, H3O[In3(pta)4(OH)2]·10H2O (NXU-1), [In(pta)2]·C3H10N (NXU-2) and [In(pta)2]·C3H10N (NXU-3) (H2pta = 2-(4-pyridyl)-terephthalic acid). The structural diversities of NXU-1–3...

pH-dependent 11° F1FO ATP synthase sub-steps reveal insight into the FO torque generating mechanism

Most cellular ATP is made by rotary F1FO ATP synthases using proton translocation-generated clockwise torque on the FO c-ring rotor, while F1-ATP hydrolysis can force counterclockwise rotation and proton pumping. The FO torque-generating mechanism remains elusive even though the FO interface of stator subunit-a, which contains the transmembrane proton half-channels, and the c-ring is known from recent F1FO structures. Here, single-molecule F1FO rotation studies determined that the pKa values of the half-channels differ, show that mutations of residues in these channels change the pKa values of both half-channels, and reveal the ability of FO to undergo single c-subunit rotational stepping. These experiments provide evidence to support the hypothesis that proton translocation through FO operates via a Grotthuss mechanism involving a column of single water molecules in each half-channel linked by proton translocation-dependent c-ring rotation. We also observed pH-dependent 11° ATP synthase-direction sub-steps of the E. coli c10-ring of F1FO against the torque of F1-ATPase-dependent rotation that result from H+ transfer events from FO subunit-a groups with a low pKa to one c-subunit in the c-ring, and from an adjacent c-subunit to stator groups with a high pKa. These results support a mechanism in which alternating proton translocation-dependent 11° and 25° synthase-direction rotational sub-steps of the c10-ring occur to sustain F1FO ATP synthesis.

Development of Efficient One-Pot Methods for the Synthesis of Luminescent Dyes and Sol–Gel Hybrid Materials

This paper presents a comparison of the simultaneous preparation of di-O-alkylated and ether–ester derivatives of fluorescein using different methods (conventional or microwave heating). Shortening of the reaction time and increased efficiency were observed when using a microwave reactor. Moreover, described here for the first time is the application of a fast, simple, and eco-friendly ball-assisted method to exclusively obtain ether–ester derivatives. We also demonstrate that fluorescein can be effectively functionalized by O-alkylation carried out under microwave or ball-milling conditions, saving time and energy and affording the desired products with good yields and minimal byproduct formation. All the synthesized products as well as pH-dependent (prototropic) forms trapped in the SiO2 matrix were examined using UV–Vis and fluorescence spectroscopy.

Efficient transport and biotransformation of dipeptide-like tyrosine/phenylalanine-conjugated phenolic amide esters in THP-1 cells and PBMCs: A potential means for transporting compounds inside monocytes/macrophages

Background: Recent studies suggest that dipeptide-like tyrosine/phenylalanine-conjugated phenolic amide compounds may contain several biological activities including anti-inflammatory activity. However, there is currently no information about their transport and biotransformation in monocytes/macrophages involved in inflammation process. Objective: The objective of this study was to investigate cell transport and biotransformation of the phenolic amides and esters in monocyte/macrophage-like cells. Methods: Cell transport and biotransformation of the phenolic amides and esters (N-coumaroylphenylalanine, N-caffeoylphenylalanine, N-feruloylphenylalanine, N-coumaroyltyrosine, N-caffeoyltyrosine, N-feruloyltyrosine and their O-methyl esters) were investigated in THP-1 cells and PBMCs using HPLC, cellular and kinetics methods Results: In THP-1 cells, the phenolic amides were not transported significantly, but their O-methyl esters were transported significantly (P < 0.02). Also, the transport of the esters was found to be sodium-independent and pH-dependent. Among the tested esters, N-feruloylphenylalanine-O-methyl ester showed the highest uptake (Km of 25 µM), and the uptake was inhibited by PepT1/2 substrate and blocker (GlySar and enalapril) in THP-1 cells. Particularly, enalapril competitively inhibited the uptake with Ki of 560 µM. The data also showed that N-feruloylphenylalanine-O-methyl ester and N-feruloyltyrosine-O-methyl ester could be biotransformed into parent phenolic amides in THP-1 cells. Similarly, the ester compounds were also found to be transported and biotransformed in PBMCs. Conclusion: The data suggest that dipeptide-like tyrosine/phenylalanine-conjugated phenolic amide esters may be transported and biotransformed in THP-1 cells and PBMCs.