Single molecule force spectroscopy reveals the context dependent folding pathway of the C-terminal fragment of Top7

Top7 is a de novo designed protein with atomic level accuracy and shows a folded structure not found in nature. Previous studies showed that the folding of Top7 is not cooperative and involves various folding intermediate states. In addition, various fragments of Top7 were found to fold on their own in isolation. These features displayed by Top7 are distinct from those of naturally occurring proteins of a similar size and suggest a rough folding energy landscape. However, it remains unknown if and how the intra-polypeptide chain interactions among the neighboring sequences of Top7 affect the folding of these Top7 fragments. Here we used single-molecule optical tweezers to investigate the folding–unfolding pathways of full length Top7 as well as its C-terminal fragment (CFr) in different sequence environments. Our results showed that the mechanical folding of Top7 involves an intermediate state that likely involves non-native interactions/structure. More importantly, we found that the folding of CFr is entirely dependent upon its sequence context in which it is located. When in isolation, CFr indeed folds into a cooperative structure showing near-equilibrium unfolding–folding transitions at ∼6.5 pN in OT experiments. However, CFr loses its autonomous cooperative folding ability and displays a folding pathway that is dependent on its interactions with its neighboring sequence/structure. This context-dependent folding dynamics and pathway of CFr are distinct from those of naturally occurring proteins and highlight the critical importance of intra-chain interactions in shaping the overall energy landscape and the folding pathway of Top7. These new insights may have important implications on the de novo design of proteins.

Optical tweezers experiments reveal that the folding of the C-terminal fragment of Top7 (cFr) is context-dependent. Depending on its neighboring sequence, cFr shows very different folding pathways and folding kinetics.      

Synthesis and VUV-UV spectroscopic properties of rare earth borosilicate oxyapatite: RE5Si2BO13:Ln (RE=La, Gd, Y; Ln=Eu, Tb)

Three rare earth borosilicate oxyapatites, RE₅Si₂BO₁₃ (RE=La, Gd, Y), were synthesized via wet chemical method, of which RE₅Si₂BO₁₃ (RE=Gd, Y) were first reported in this work. In the three oxyapatites, [BO₄] and [SiO₄] share the [TO₄] tetrahedral oxyanion site, and RE³⁺ ions occupy all metal sites. The differential scanning calorimetry-thermo gravimetry measurements and high temperature powder X-ray diffraction pattern revealed a vitrification process within 300-1200 °C, which was due to the glass-forming nature of borosilicates. From the VUV excitation spectra of Eu³⁺ and Tb³⁺ in RE₅Si₂BO₁₃, the optical band gaps were found to be 6.31, 6.54 and 6.72 eV for RE₅Si₂BO₁₃ (RE=La, Gd, Y), respectively. The emission and excitation bands of Eu³⁺ and Tb³⁺ are discussed relating with their coordination environments. Among the three hosts, Y₅Si₂BO₁₃ would be the best for Eu³⁺ and Tb³⁺-doped phosphors.     

Stereoselective diversity-oriented solution and solid-phase synthesis of tetrahydroquinoline-based polycyclic derivatives

A diversity-oriented solution and solid-phase synthesis of tetrahydroquinoline-based tricyclic derivatives has been achieved from enantiomerically pure, natural product-like bicyclic scaffold. The solution synthesis of enantiopure bicyclic scaffold was developed by asymmetric hetero Michael reaction. Our approach for the synthesis of polycyclic derivatives utilized regio- and stereoselective hetero Michael reaction and ring-closing metathesis as key steps in solution and on solid phase.     

Zeolite NaY-mediated oxidation of dyes with H2O2: unique heterogeneous non-transition metal center cleavage of H2O2 under visible light irradiation

This study investigated the visible-light catalysis mediated by zeolite NaY on the oxidation of dyes with H₂O₂. The results demonstrated that zeolite NaY acts as a sink for the electron from the photo-excited dye in the heterogeneous catalysis. Furthermore, the electron can effectively activate H₂O₂ to produce ^·OH radical that is a powerful oxidant for the oxidation of dye at room temperature. The effects of the framework topology, Si/Al ratio, and exchangeable cation of the zeolite on the oxidation of various dyes were also shown.     

Palladium-catalyzed amidation of enol triflates: a new synthesis of enamides

[reaction: see text] The palladium-catalyzed coupling of a range of enol triflates with amides, carbamates, and sulfonamides has been developed. This offers a simple and widely applicable synthesis of enamides, which may not be readily available by other means.     

Preparation and Characteristics of Porous Silica Films by a Modified Base-Catalyzed Sol-Gel Process Containing PVA: II. Film Preparation

Porous SiO₂ films were successfully deposited on silicon substrates by a modified base-catalyzed Sol-Gel process (MBCP) containing polyvinyl alcohol (PVA). The process conditions, such as the gelation time, the synthesis temperature, the stabilizing agent of the precursor solution and the spin coating speed, the heat-treatment, the annealing temperature of the film on the microstructure and porosity of porous SiO₂ films were systematically investigated by SEM, XRD and ellipsometry techniques. This study provides a novel preparation technique for the porous SiO₂ film. Using this process, the resultant film can reach a thickness of 3.6 m for one layer, a porosity of 25–50%, a low thermal conductivity of 0.11 W/m·K. This film will be used as a low dielectric layer, an thermal-insulating layer and a low refractive index layer.     

Kinetics of polyesterification: Adipic acid with ethylene glycol, 1,4-butanediol,and 1,6-hexanediol

Polyesterifications of adipic acid with ethylene glycol, 1,4-butanediol, and 1,6-hexanediol in the absence and presence of the foreign acid (p-toluene sulfonic acid) as catalyst were carried out under constant reaction temperatures of 140–180°C (rather than at constant oil-bath temperatures) and at ratios of diol to diacid of 0.9867–3.5880. The experimental data fit the rate equations proposed by Chen and Wu: d(RCOOR′)/dt = k_ae^αp(RCOOH)²(R′OH) – k_h(H₂O)(RCOOR′) and d(RCOOR′)/dt = k_ac(AH)e^αp(RCOOH)(RO′H) – k_h(H₂O)(RCOOR′) for self-catalyzed and acid-catalyzed reactions, respectively; the data did not fit the other equations appearing in the literature. Here p is the conversion of acid, and α is the constant related to dielectric constants. The reaction rate constants and activation energies for self-catalyzed and acid-catalyzed reactions are calculated. The activation energy is found to decrease with chain length of the alkyl group of the diol. This result is consistent with that observed by Brauman and Blair using ion cyclotron resonance spectroscopy for the variation of acidity of alcohols with chain length of the alkyl group.     

Theoretical formalism and experimental verification of line shapes of NMR intermolecular multiple-quantum coherence spectra

Although the theories and potential applications of intermolecular multiple-quantum coherences (iMQCs) have been under active investigations for over a decade, discussion of iMQC NMR signal formation was mainly confined in the time domain. In this paper, a full line-shape theory was developed to describe iMQC signals in the frequency domain. Relevant features of the line shape, such as peak height, linewidth, and phase, were investigated in detail. Predictions based on the theory agree well with experimental and simulated results. Since radiation-damping effects always couple with iMQCs in highly polarized liquid-state NMR systems, and strongly radiation-damped signals have many spectral characteristics similar to those of iMQCs, a detailed comparison was also made between them from different spectral aspects. With detailed comparison of peak height, linewidth, and phase, this work demonstrates that the iMQC and radiation-damping phenomena result from two completely different physical mechanisms despite that both present similar signal features and coexist in highly polarized liquid-state NMR systems.     

Classification of Cm I energy levels using PCA-BPN and PCA-NLM

Two pattern recognition (PR) techniques, principal component analysis-back propagation networks (PCA-BPN) and principal component analysis-nonlinear mapping (PCA-NLM), have been applied to the problem of classifying unknown energy levels of the first spectrum of curium (Cm I) according to their configurations. In comparison, with those reported by early PR techniques and counter propagation neural networks (CPN's), PCA-BPN has been demonstrated to possess much more prediction accuracy as to its performance on test sets. Obtained results further confirm the most previous assignments with these energy levels given by some early PR techniques and CPN. Moreover, the obtained results definitely reassign some energy levels' electronic configurations which were ambiguously conjectured in previous work.     

Theoretical prediction of noble gas containing anions FNgO- (Ng = He, Ar, and Kr)

The structures and energies of the noble gas containing anions FNgO- (Ng = He, Ar, and Kr) have been calculated by high-level ab initio calculations. The FNgO- anions were found to be deep-energy minima at the singlet electronic state, and their energies are significantly lower than those at the triplet state. High dissociation energy barriers to Ng + OF- were also predicted. The unexpected stability of the FNgO- was due to the dramatic ion-induced O=Ng bond formation. The calculated results suggested possible experimental identification of the anionic species and even some related "ionic compounds" under cryogenic conditions.