Determination of the cis–trans Isomerization Barriers of l-Alanyl-l-proline in Aqueous Solutions and at Water/Hydrophobic Interfaces by On-Line Temperature-Jump Relaxation HPLC and Dynamic On-Column Reaction HPLC

Temperature-Dependent Fold-Switching Mechanism of the Circadian Clock Protein KaiB

The oscillator of the cyanobacterial circadian clock relies on the ability of the KaiB protein to switch reversibly between a stable ground-state fold (gsKaiB) and an unstable fold-switched fold (fsKaiB). Rare fold-switching events by KaiB provide a critical delay in the negative feedback loop of this post-translational oscillator. In this study, we experimentally and computationally investigate the temperature dependence of fold switching and its mechanism. We demonstrate that the stability of gsKaiB increases with temperature compared to fsKaiB and that the Q10 value for the gsKaiB → fsKaiB transition is nearly three times smaller than that for the reverse transition. Simulations and native-state hydrogen-deuterium exchange NMR experiments suggest that fold switching can involve both subglobally and near-globally unfolded intermediates. The simulations predict that the transition state for fold switching coincides with isomerization of conserved prolines in the most rapidly exchanging region, and we confirm experimentally that proline isomerization is a rate-limiting step for fold switching. We explore the implications of our results for temperature compensation, a hallmark of circadian clocks, through a kinetic model.

Staphylococcus aureus Exfoliative Toxin E, Oligomeric State and Flip of P186: Implications for Its Action Mechanism

Staphylococcal exfoliative toxins (ETs) are glutamyl endopeptidases that specifically cleave the Glu381-Gly382 bond in the ectodomains of desmoglein 1 (Dsg1) via complex action mechanisms. To date, four ETs have been identified in different Staphylococcus aureus strains and ETE is the most recently characterized. The unusual properties of ETs have been attributed to a unique structural feature, i.e., the 180° flip of the carbonyl oxygen (O) of the nonconserved residue 192/186 (ETA/ETE numbering), not conducive to the oxyanion hole formation. We report the crystal structure of ETE determined at 1.61 Å resolution, in which P186(O) adopts two conformations displaying a 180° rotation. This finding, together with free energy calculations, supports the existence of a dynamic transition between the conformations under the tested conditions. Moreover, enzymatic assays showed no significant differences in the esterolytic efficiency of ETE and ETE/P186G, a mutant predicted to possess a functional oxyanion hole, thus downplaying the influence of the flip on the activity. Finally, we observed the formation of ETE homodimers in solution and the predicted homodimeric structure revealed the participation of a characteristic nonconserved loop in the interface and the partial occlusion of the protein active site, suggesting that monomerization is required for enzymatic activity.

Dual-tautomerism separation method based on asymmetric transformation: Gram-scale preparation of high-purity punicalagin from pomegranate peel wastes

In this study, a special orthogonal separation method, named as dual-tautomerism separation (DTS), was developed for the purification of tautomeric compounds from complex matrixes. In DTS, isomers of these compounds are individually collected and asymmetrically transformed to the mixtures of isomers. After separating the mixture with an identical method, high-purity compounds can be prepared from the newly generated isomers but impurities remain in another one. To validate the effectiveness, a DTS was developed to prepare punicalagin in gram-scale from pomegranate peel waste. Isomerization kinetic and thermodynamic of punicalagin were accurately assayed by dynamic HPLC built on low-temperature or/and loop-based stop-flow two-dimensional liquid chromatography. After the isomerization based on it, 9.3 g of pomegranate peel extract was firstly separated on C18 column, and F_α and F_β around α-punicalagin and β-punicalagin were obtained. Then, the proportion of α-punicalagin in F_α and F_β was optimized to 52.7% and 32.0% based on isomerization kinetics and thermodynamic. With the aid of low-temperature injection, F_α and F_β were loaded and secondly purified. After waste recycling, totally 3.0 g of punicalagin with the purify of 99.5% was obtained within two days, which would strongly support the resource utilization of pomegranate peel waste. Because only an individual method was employed in the two-step purification, the separation in DTS was fully compatible.

Intrinsic difference between phenyl hexyl- and octadecyl-bonded silicas in the solute retention selectivity in reversed-phase liquid chromatography with aqueous mobile phase

For choosing an optimal column for a particular separation by reversed-phase liquid chromatography (RPLC), it is essential to quantitatively understand the effects of the chemical structure of hydrophobic bonded layer derived onto silica particles on the distribution equilibrium of a solute compound at the interface between the aqueous mobile phase and the packing material. However, there is still a lack of understanding of the solute distribution equilibrium in RPLC separation due to the complexities of the chemistry at the interface between the mobile phase and the bonded layer. We successfully determined the distribution coefficients of various organic compounds concerning to their accumulation onto the water/bonded layer interface and into the bonded layer from bulk water using surface-bubble-modulated liquid chromatography with octadecyl- and phenyl hexyl-bonded silica columns. The water/phenyl hexyl-bonded layer interface accumulates organic compounds much less than the water/octadecyl-bonded layer interface due to its lower interfacial tension, and this result suggests that phenyl hexyl group orient their benzene ring facing toward water. On the other hand, aromatic moiety of phenyl hexyl group enhances partitioning of the organic compounds into the bonded layer. Experimental findings in the present work demonstrated that the water/bonded layer interface and the bonded layer itself have independent contributions to the solute distribution and the water/phenyl hexyl-bonded layer interface shows quite different solute retention selectivity from the water/octadecyl-bonded layer interface.

Synthesis and conformational analysis of an expanded cyclic ketoxime-hexapeptide

In this work the synthesis of a linear hexapeptide with a hydroxylamine functionality at the N-terminus and a ketone instead of the carboxylic acid at the C-terminus is described. Cyclization by ketoxime formation yields the 19-membered ring-expanded cyclic hexapeptide cyclo[Goly-Val-Ala-Pro-Leu-Kly] which adopts a main conformer with two intramolecular hydrogen bonds. The hydrolytic stability of a ketoxime lies between the inert amide and the labile imine. The substitution of an amide bond for an iminium bond transforms the irreversible macrocyclization into a reversible process, but macrocyclic imines are difficult to isolate because they are prone to hydrolysis. The enhanced chemical stability of the ketoxime justifies its application in ligation protocols. The detailed NMR analysis of a ketoxime linkage presented here identifies its local conformational preferences in a constrained peptide environment.

Micro- and Nano-Liquid Phases Coexistent with Ice as Separation and Reaction Media

Ice has a variety of scientifically interesting features, some of which have not been reasonably interpreted despite substantial efforts by researchers. Most chemical studies of ice have focused on the elucidation of its physicochemical nature and its roles in the natural environment. Ice often contains impurities, such as salts, and in such cases, a liquid phase coexists with solid ice over a wide temperature range. This impure ice also acts as a cryoreactor, governing the circulation of chemical species of environmental importance. Reactions and phenomena occurring in this liquid phase show features different from those seen in normal bulk aqueous solutions. In the present account, we discuss the chemical characteristics of the liquid phase that develops in a frozen aqueous phase and show how novel analytical systems can be designed based on he features of the liquid phase which are predictable in some cases but unpredictable in others.