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

2021 ◽  
Vol 118 (49) ◽  
pp. e2101006118
Author(s):  
Noel Q. Hoffer ◽  
Krishna Neupane ◽  
Michael T. Woodside
Keyword(s):  
Nucleic Acid ◽  
High Resolution ◽  
Optical Tweezers ◽  
Energy Landscape ◽  
Transition States ◽  
Energy Transition ◽  
High Energy ◽  
Sequence Dependence ◽  
High Energy Transition ◽  
Nucleotide Residue

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.

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

2009 ◽  
Vol 08 (supp01) ◽  
pp. 983-1001 ◽  
Author(s):  
YAN-LI DING ◽  
LI-DONG GONG ◽  
DONG-XIA ZHAO ◽  
MING-BO ZHANG ◽  
ZHONG-ZHI YANG
Keyword(s):  
Ab Initio ◽  
Nucleophilic Substitution ◽  
Gas Phase ◽  
Chemical Bond ◽  
Energy Transition ◽  
High Energy ◽  
Ab Initio Method ◽  
Substitution Reactions ◽  
Nucleophilic Substitution Reactions ◽  
High Energy Transition

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]- .

scholarly journals The high‐energy transition state of the glutamate transporter homologue GltPh

2020 ◽  
Vol 40 (1) ◽  
Author(s):  
Gerard H M Huysmans ◽  
Didar Ciftci ◽  
Xiaoyu Wang ◽  
Scott C Blanchard ◽  
Olga Boudker
Keyword(s):  
Transition State ◽  
Glutamate Transporter ◽  
Energy Transition ◽  
High Energy ◽  
High Energy Transition

Road Performance of Common Piezoelectric Transducer for Asphalt Pavement Energy Harvesting

2015 ◽  
Vol 744-746 ◽  
pp. 1491-1494 ◽  
Author(s):  
Cong Li
Keyword(s):  
Piezoelectric Transducer ◽  
Asphalt Pavement ◽  
Energy Transition ◽  
High Energy ◽  
Piezoelectric Transducers ◽  
Traffic Load ◽  
High Energy Transition ◽  
Road Performance ◽  
Stiffness Characteristics ◽  
Better Than

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.

Note on the High Energy Transition in the Ag110m Decay

1964 ◽  
Vol 19 (7) ◽  
pp. 1257-1258 ◽  
Author(s):  
W. H. Brantley ◽  
T. Katoh ◽  
J. H. Hamilton
Keyword(s):  
Energy Transition ◽  
High Energy ◽  
High Energy Transition

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

1970 ◽  
Vol 48 (10) ◽  
pp. 1558-1565 ◽  
Author(s):  
B. J. Fuhr ◽  
B. W. Goodwin ◽  
H. M. Hutton ◽  
T. Schaefer
Keyword(s):  
Magnetic Resonance ◽  
Proton Magnetic Resonance ◽  
Energy Transition ◽  
High Energy ◽  
Methine Proton ◽  
Mirror Image ◽  
Proton Spectrum ◽  
Free Energy Barrier ◽  
Matrix Formalism ◽  
High Energy Transition

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.

scholarly journals The nuclear β -spectra of thorium B→C and C→C', and the intensities of some β -ray lines of thorium (B+C+C")

1948 ◽  
Vol 195 (1042) ◽  
pp. 287-300 ◽  
Keyword(s):  
Internal Conversion ◽  
Conversion Coefficient ◽  
Energy Transition ◽  
Detailed Comparison ◽  
High Energy ◽  
Internal Conversion Coefficient ◽  
Dipole Radiation ◽  
Allowed Transition ◽  
Forbidden Transitions ◽  
High Energy Transition

The β -spectra of Th(C+C") and Th(B+C+C") have been measured using semicircular focusing. The sources were mounted between two thin films to prevent the escape of ThC" by α -recoil. The intensities of seven of the β -ray lines were measured and the continuous spectra of ThB. C and ThC. C' were found by subtraction using the known spectrum of ThC". D. The β -ray end-point of ThC. C' is at 2·250 MeV, and the shape of the β -ray spectrum differs but little from that of an allowed transition for energies above 0·9 MeV. A detailed comparison is made with the shape of the compound spectrum required to account for the known γ -rays of ThC', using the theory of forbidden transitions. A spin change of ∆ I = ± 2 is ruled out, but ∆ I = 0 or ± 1 is possible. The β -spectrum of Th B seems to be composite with its principal end-points at 0·331 and 0·569 MeV. The intensity of the high-energy transition between the ground states is about 0·12 ± 0·02 electrons per disintegration. The K internal conversion coefficient of the F γ -ray was found to be about Q·377, 16% higher than the theoretical value for magnetic dipole radiation.

scholarly journals The high-energy transition state of a membrane transporter

2020 ◽  
Author(s):  
Gerard H. M. Huysmans ◽  
Didar Ciftci ◽  
Xiaoyu Wang ◽  
Scott C. Blanchard ◽  
Olga Boudker
Keyword(s):  
Transition State ◽  
Single Molecule ◽  
Conformational Transition ◽  
Energy Transition ◽  
High Energy ◽  
Structural Features ◽  
Isomerization Reaction ◽  
Linear Free Energy Relationship ◽  
Relationship Analysis ◽  
High Energy Transition

AbstractMembrane 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.

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