Observing the base-by-base search for native structure along transition paths during the folding of single nucleic acid hairpins

Biomolecular folding involves searching among myriad possibilities for the native conformation, but the elementary steps expected from theory for this search have never been detected directly. We probed the dynamics of folding at high resolution using optical tweezers, measuring individual trajectories as nucleic acid hairpins passed through the high-energy transition states that dominate kinetics and define folding mechanisms. We observed brief but ubiquitous pauses in the transition states, with a dwell time distribution that matched microscopic theories of folding quantitatively. The sequence dependence suggested that pauses were dominated by microbarriers from nonnative conformations during the search by each nucleotide residue for the native base-pairing conformation. Furthermore, the pauses were position dependent, revealing subtle local variations in energy–landscape roughness and allowing the diffusion coefficient describing the microscopic dynamics within the barrier to be found without reconstructing the shape of the energy landscape. These results show how high-resolution measurements can elucidate key microscopic events during folding to test fundamental theories of folding.

The high-energy transition state of a membrane transporter

Membrane transporters mediate cellular uptake of nutrients, signaling molecules and drugs. Their overall mechanisms are often well understood, but the structural features setting their rates are mostly unknown. Earlier single-molecule fluorescence imaging of a model glutamate transporter homologue suggested that the slow conformational transition from the outward- to the inward-facing state, when the bound substrate is translocated from the extracellular to the cytoplasmic side of the membrane, is rate-limiting to transport. Here, we aim to gain insight into the structure of the high-energy transition state that limits the rate of this critical isomerization reaction. Using bioinformatics, we identify gain-of-function mutants of the transporter and apply linear free energy relationship analysis to infer that the transition state structurally resembles the inward-facing conformation. Based on these analyses, we propose an approach for allosteric modulation of these transporters.

Road Performance of Common Piezoelectric Transducer for Asphalt Pavement Energy Harvesting

The discussion in the paper is focused on energy transition efficiency, stiffness and intensity of common piezoelectric transducers in the following aspects. Firstly, we have found out that bridge piezoelectric transducers possess high energy transition efficiency and the similar stiffness to asphalt pavement through comparing and analyzing road performance of several common piezoelectric transducers. Thus, we hold the view that it is applicable for energy collection of asphalt pavement and will be analyzed subsequently. Secondly, we have analyzed energy transition efficiency and stiffness characteristics of arc bridge piezoelectric transducer and rectangular bridge piezoelectric transducer in laboratory test. The results show that, under the same load stress, arc transducers are better than rectangular transducers in terms of energy transition efficiency; but comparing with rectangular transducers, arc transducers are more prone to be destroyed, which is not helpful for bearing traffic load.

STUDIES ON NUCLEOPHILIC SUBSTITUTION REACTIONS AT CARBON (SN2(C)) AND SILICON (SN2(Si)) IN TERMS OF AB INITIO, POTENTIAL, ACTING ON AN ELECTRON IN A MOLECULE AND MOLECULAR FACE THEORY

The gas-phase identity bimolecular nucleophilic substitution reactions, Cl- + CH3 Cl → ClCH3 + Cl- and Cl- + SiH3Cl → ClSiH3 + Cl- , are investigated in terms of the ab initio method, potential acting on an electron in a molecule (PAEM) and molecular face (MF) theory. The computations have been performed at the CCSD(T)/aug-cc-pVTZ//MP2/6-311+G(3df,3pd) and CISD/aug-cc-pVDZ level. Based on the ab initio calculation, according to the PAEM theory, the strength of a chemical bond during forming or rupturing may be characterized by the D pb , which is a new physical quantity relating to the barrier height of the PAEM along a chemical bond. According to the MF theory, the interesting pictures of electron transfer and interpolarization effect between the reactants are clearly demonstrated to provide visualized spatial changing features of the MF for the title reactions along the IRC routes. The reason why [ Cl⋯CH3⋯Cl]- is a high-energy transition state is also analyzed in comparison with the stable low-energy intermediate [ Cl⋯SiH3⋯Cl]- .

Application of proton magnetic resonance to rotational isomerism in halotoluene derivatives. II. α,α,2,4,6-Pentachlorotoluene

At temperatures below −40 °C the proton magnetic resonance of α,α,2,4,6-pentachlorotoluene in toluene-d8 or methylcyclohexane is an ABX spectrum where X is the methine proton. The C—H bond of the dichloromethyl group lies in the plane of the ring and its proton couples to one ring proton only. As the temperature increases the mean lifetime before interconversion of the "mirror image" isomers decreases and at 70 °C the proton spectrum is A2X. A density matrix formalism is used to calculate the line shape as a function of the lifetime before exchange. The free energy barrier to rotation of the dichloromethyl group is 15.0 ± 0.1 kcal/mole in both solvents. In toluene-d8 the entropy of activation is near zero. The high energy transition state is very likely one in which the C—Cl bonds of the ring and the dichloromethyl groups are eclipsed.