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.      

Remote substituent effects on bond dissociation energies of para-substituted aromatic silanes

UB3LYP/6-31G(d) and ROMP2/6-311++G(d,2p) methods were used to calculate the Si-X bond dissociation energies (BDEs) of a number of para-substituted aromatic silanes (4-Y-C(6)H(4)-SiH(2)X, where X = H, F, Cl, or Li). It was found that the substituent effect on the Si-H BDE of 4-Y-C(6)H(4)-SiH(3) was small, as the slope (rho(+)()) of the BDE- regression was only 0.09 kJ/mol. In comparison, the substituent effect on the Si-F BDE of 4-Y-C(6)H(4)-SiH(2)F was much stronger, whose rho(+ )()value was -2.34 kJ/mol. The substituent effect on the Si-Cl BDE of 4-Y-C(6)H(4)-SiH(2)Cl was also found to be strong with a rho(+)() value of -1.70 kJ/mol. However, the substituent effect on the Si-Li BDE of 4-Y-C(6)H(4)-SiH(2)Li was found to have a large and positive slope (+9.12 kJ/mol) against. The origin of the above remarkably different substituent effects on the Si-X BDEs was found to be associated with the ability of the substituent to stabilize or destabilize the starting material (4-Y-C(6)H(4)-SiH(2)X) as well as the product (4-Y-C(6)H(4)-SiH(2)* radical) of the homolysis. Therefore, the direction and magnitude of the effects of Y-substituents on the Z-X BDEs in compounds such as 4-YC(6)H(4)Z-X should have some important dependence on the polarity of the Z-X bond undergoing homolysis. This conclusion was in agreement with that from earlier studies (for example, J. Am. Chem. Soc. 1991, 113, 9363). However, it indicated that the proposal from a recent work (J. Am. Chem. Soc. 2001, 123, 5518) was unfortunately not justified.     

Liquid chromatography/electrospray ionization mass spectrometry for the characterization of twenty-three flavonoids in the extract of Dalbergia odorifera

A method incorporating high-performance liquid chromatography (HPLC) with electrospray ionization and tandem mass spectrometry, with parallel analysis by HPLC with UV detection using a diode-array detector, was developed for the qualitative characterization of flavonoids in D. odorifera. Twenty-three flavonoids, including six isoflavones, six neoflavones, four isoflavanones, three flavanones, two chalcones, one isoflavanonol and one pterocarpan, were unambiguously identified by comparing their retention times, UV and MS spectra with those of authentic compounds. Furthermore, the collision-induced dissociations of the [M-H]- ions were studied to clarify the MS behavior of the different types of flavonoids. In negative ion ESI-MS all the flavonoids yielded prominent [M-H]- ions in the first order mass spectra. Fragments involving losses of CH3*, H2O, CO, C2H2O, and CO2 were observed in the MS/MS spectra. Each of the seven types of flavonoid showed characteristic MS/MS fragmentation patterns. The isoflavanones, flavanones and chalcones were observed to undergo retro-Diels-Alder fragmentations. The spectra of almost all the neoflavonoids unexpectedly exhibited only [M-H-CH3]-* radical anions as base peaks without any further fragmentation. Substitution positions also remarkably influenced the fragmentation behavior, which could assist in distinction among the flavonoid isomers. The fragmentation rules deduced here could aid in the characterization of other flavonoids of these types.     

Photochemical Reaction of Decacarbonyldirhenium with Thiophene and Crystal Structure of Tetradecacarbonylhydridotrirhenium

The photochemical reaction of Re₂(CO)₁₀ with thiophene in hexane solution was investigated under vacuum. Three rhenium clusters: H₂Re₃(CO)₁₂, HRe₃(CO)₁₄ and Re₃(CO)₁₄(OH)₄, were isolated. The structure of Fellmann-Kaesz cluster Complex HRe₃(CO)₁₄ was determined by use of the X-ray diffraction method. The three rhenium atoms form a plane of symmetry and L: Re₁Re₂Re₃ is 107°. The ten carbonyl groups bonded to the two terminal rhenium atoms Re₁ and Re₃, are staggered with respect to the central rhenium atoms. The bond lengths are 3.10 Å for Re₂-Re₃ and 3.34 Å for Re₁-Re₂. The bridging hydride is between Re₁ and Re₂.     

Adiabatic cooling of ions in the penning trap

An ion cloud in a Penning trap can be cooled by adiabatic expansion by reducing the trap's magnetic and electric fields. We treat the ion cloud as a classical gas and obtain the relations between the temperature and the trapping fields. This cooling method may be useful in trapping and cooling of antiprotons with the aim of measuring the gravitational accleration of anti-protons and other experiments on heavy ions.     

Electrostatic layer-by-layer assembled carbon nanotube multilayer film and its electrocatalytic activity for O2 reduction

Multilayer films of shortened multiwalled carbon nanotubes (MWNTs) are homogeneously and stably assembled on glassy carbon electrodes with the layer-by-layer (LBL) method, based on electrostatic interaction of positively charged poly(diallyldimethylammonium chloride) and negatively charged and shortened MWNTs. The film assembly and electrochemical property as well as the electrocatalytic activity toward O2 reduction of the MWNT multilayer film are studied. Scanning electron microscopy, the quartz crystal microbalance technique, ultraviolet-visible-near-infrared spectroscopy, and cyclic voltammetry are used for characterization of film assembly. Experimental results revealed that film growth is uniform, almost with the same coverage of the MWNTs in each layer, and that the assembled MWNTs are mainly in the form of small bundles or single tubes on the electrodes. Electrochemical studies indicate that the LBL assembled MWNT films possess a remarkable electrocatalytic activity toward O2 reduction in alkaline media. This property, combined with the well-dispersed, porous and conductive features of the MWNT film illustrated with the LBL method, suggests the potential application of the MWNT film for constructing an efficient alkaline air electrode for energy conversions.