scholarly journals Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic "fingerprinting"

2007 ◽  
Vol 104 (31) ◽  
pp. 12634-12639 ◽  
Author(s):  
S. Liu ◽  
G. Bokinsky ◽  
N. G. Walter ◽  
X. Zhuang
Keyword(s):  
Single Molecule ◽  
Reaction Pathway ◽  
Multistep Reaction

scholarly journals Modelling reaction kinetics inside cells

2008 ◽  
Vol 45 ◽  
pp. 41-56 ◽  
Author(s):  
Ramon Grima ◽  
Santiago Schnell
Keyword(s):  
Molecular Biology ◽  
Reaction Kinetics ◽  
Single Molecule ◽  
Predictive Accuracy ◽  
Reaction Pathway ◽  
Imaging Techniques ◽  
Deterministic Models ◽  
Non Invasive ◽  
The Past ◽  
Fundamental Length

In the past decade, advances in molecular biology such as the development of non-invasive single molecule imaging techniques have given us a window into the intricate biochemical activities that occur inside cells. In this chapter we review four distinct theoretical and simulation frameworks: (i) non-spatial and deterministic, (ii) spatial and deterministic, (iii) non-spatial and stochastic and (iv) spatial and stochastic. Each framework can be suited to modelling and interpreting intracellular reaction kinetics. By estimating the fundamental length scales, one can roughly determine which models are best suited for the particular reaction pathway under study. We discuss differences in prediction between the four modelling methodologies. In particular we show that taking into account noise and space does not simply add quantitative predictive accuracy but may also lead to qualitatively different physiological predictions, unaccounted for by classical deterministic models.

Dehalogenation of 5-bromouracil by bisulfite buffers. Kinetic evidence for a multistep reaction pathway

1975 ◽  
Vol 97 (19) ◽  
pp. 5572-5577 ◽  
Author(s):  
Frank A. Sedor ◽  
Dan G. Jacobson ◽  
Eugene G. Sander
Keyword(s):  
Reaction Pathway ◽  
Multistep Reaction

CHLOROGENIC ACID – APPLICATION OF CONTEMPORARY DENSITY FUNCTIONALS TO A SINGLE MOLECULE

2021 ◽  
Author(s):  
Svetlana Marković ◽  
◽  
Jelena Tošović ◽  
Keyword(s):  
Electron Transfer ◽  
Chlorogenic Acid ◽  
Single Molecule ◽  
Reaction Pathway ◽  
Radical Scavenging Activity ◽  
Radical Scavenging ◽  
Hydrogen Atom Transfer ◽  
Density Functionals ◽  
Perfect Agreement ◽  
Stable Conformation

Although chlorogenic acid (5-O-caffeoylquinic acid, 5CQA) is a dietary phenol known for its pharmacological and nutritional properties, its structural features and mechanisms of oxidative action have not been completely elucidated. Clarification of the 5CQA structure was conducted by comparing the experimental and simulated IR, Raman, 1H-NMR, 13C-NMR, and UV spectra. For this purpose, a comprehensive conformational analysis of 5CQA was performed to reveal its most stable conformations in the gas-state and solution. Excellent agreement between all experimental and simulated spectra indicates correct arrangement of the atoms in the 5CQA molecule. In addition, the most stable conformation in solution coincides with that predicted with sophisticated NMR experiments. The quantum mechanics–based test for overall free-radical scavenging activity was applied for the investigation of antioxidative capacity of 5CQA relative to trolox (6-hydroxy-2,5,7,8- tetramethylchroman-2-carboxylic acid, Tx) as a reference compound. Hydrogen atom transfer (HAT), radical adduct formation (RAF), sequential proton loss electron transfer (SPLET), and single electron transfer – proton transfer (SET-PT) reactions of 5CQA and Tx with HO· and CH3OO· radicals were examined in benzene, pentyl ethanoate, and basic aqueous solutions. In non-polar solvents 5CQA reacts with HO· via HAT and RAF mechanisms, whereas HAT is the only reaction pathway with CH3OO·. At physiological conditions 5CQA exists in the form of monoanion and dianion. Both anionic forms undergo only HAT mechanism with CH3OO·. With HO·, the anions conform to the HAT, RAF, SPLET, and SET-PT mechanisms. Because all reactions of dianion are diffusion controlled, its contribution to scavenging HO· is comparable to that of more abundant monoanion. The calculated rate constant for overall reaction of 5CQA with HO· is in perfect agreement with the corresponding experimental value. The order of reactivity toward selected free radicals is the same in nonpolar and polar solutions: in comparison to Tx, 5CQA is more reactive toward HO·, but less reactive toward CH3OO·. Very good agreement between the experimental and calculated results confirms the ability of contemporary density functionals to quantify subtle physico-chemical interactions.

scholarly journals Mechanistic Insights into Water-Catalyzed Formation of Levoglucosenone from Anhydrosugar Intermediates by Means of High-Level Theoretical Procedures

2016 ◽  
Vol 69 (9) ◽  
pp. 943 ◽  
Author(s):  
Wenchao Wan ◽  
Li-Juan Yu ◽  
Amir Karton
Keyword(s):  
Activation Energy ◽  
Reaction Mechanism ◽  
Ring Opening ◽  
Reaction Pathway ◽  
Fast Pyrolysis ◽  
Rate Determining Step ◽  
Dehydration Reactions ◽  
High Level ◽  
Multistep Reaction ◽  
Hydration And Dehydration

Levoglucosenone (LGO) is an important anhydrosugar product of fast pyrolysis of cellulose and biomass. We use the high-level G4(MP2) thermochemical protocol to study the reaction mechanism for the formation of LGO from the 1,4:3,6-dianhydro-α-d-glucopyranose (DGP) pyrolysis intermediate. We find that the DGP-to-LGO conversion proceeds via a multistep reaction mechanism, which involves ring-opening, ring-closing, enol-to-keto tautomerization, hydration, and dehydration reactions. The rate-determining step for the uncatalyzed process is the enol-to-keto tautomerization (ΔG‡298 = 68.6 kcal mol–1). We find that a water molecule can catalyze five of the seven steps in the reaction pathway. In the water-catalyzed process, the barrier for the enol-to-keto tautomerization is reduced by as much as 15.1 kcal mol–1, and the hydration step becomes the rate-determining step with an activation energy of ΔG‡298 = 58.1 kcal mol–1.

scholarly journals Template-Directed Catalysis of a Multistep Reaction Pathway for Nonenzymatic RNA Primer Extension

Biochemistry ◽  
2018 ◽  
Vol 58 (6) ◽  
pp. 755-762 ◽  
Author(s):  
Travis Walton ◽  
Lydia Pazienza ◽  
Jack W. Szostak
Keyword(s):  
Reaction Pathway ◽  
Primer Extension ◽  
Multistep Reaction

Tetraphenylethylene AIEgen bearing thiophenylbipyridine receptor for selective detection of copper(II) ion

2021 ◽  
Author(s):  
Dinesh N Nadimetla ◽  
Sheshanath Bhosale
Keyword(s):  
Reaction Pathway ◽  
Selective Detection ◽  
Multistep Reaction

Highly emissive tetraphenylethylene (TPE) chromophore appended thiophenylbipyridine pendant as a receptor (1) site has been successively synthesized via multistep reaction pathway. The synthesized chromophore 1 was been well characterized by...

scholarly journals Spatiotemporal organization of branched microtubule networks

2019 ◽  
Author(s):  
Akanksha Thawani ◽  
Howard A Stone ◽  
Joshua W Shaevitz ◽  
Sabine Petry
Keyword(s):  
Single Molecule ◽  
Reaction Pathway ◽  
Reaction Model ◽  
Sequential Reaction ◽  
Spatiotemporal Organization ◽  
Nucleation Sites ◽  
Egg Extracts ◽  
Microtubule Networks ◽  
Rate Limiting ◽  
Kinetics Of

AbstractTo understand how chromosomes are segregated, it is necessary to explain the precise spatiotemporal organization of microtubules (MTs) in the mitotic spindle. We useXenopusegg extracts to study the nucleation and dynamics of MTs in branched networks, a process that is critical for spindle assembly. Surprisingly, new branched MTs preferentially originate near the minus-ends of pre-existing MTs. A sequential reaction model, consisting of deposition of nucleation sites on an existing MT, followed by rate-limiting nucleation of branches, reproduces the measured spatial profile of nucleation, the distribution of MT plus-ends and tubulin intensity. By regulating the availability of the branching effectors TPX2, augmin and γ-TuRC, combined with single-molecule observations, we show that first TPX2 is deposited on pre-existing MTs, followed by binding of augmin/γ-TuRC to result in the nucleation of branched MTs. In sum, regulating the localization and kinetics of nucleation effectors governs the architecture of branched MT networks.Impact StatementA sequential reaction pathway involving TPX2, augmin and γ-TuRC governs the assembly and architecture of branched microtubule networks.

scholarly journals Dynamic action of the Sec machinery during initiation, protein translocation and termination

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Tomas Fessl ◽  
Daniel Watkins ◽  
Peter Oatley ◽  
William John Allen ◽  
Robin Adam Corey ◽  
...  
Keyword(s):  
Single Molecule ◽  
Atp Hydrolysis ◽  
Protein Translocation ◽  
Reaction Pathway ◽  
Signal Sequence ◽  
Slow Phase ◽  
Protein Insertion ◽  
Membrane Protein Insertion ◽  
Two Phases ◽  
Dependent Transport

Protein translocation across cell membranes is a ubiquitous process required for protein secretion and membrane protein insertion. In bacteria, this is mostly mediated by the conserved SecYEG complex, driven through rounds of ATP hydrolysis by the cytoplasmic SecA, and the trans-membrane proton motive force. We have used single molecule techniques to explore SecY pore dynamics on multiple timescales in order to dissect the complex reaction pathway. The results show that SecA, both the signal sequence and mature components of the pre-protein, and ATP hydrolysis each have important and specific roles in channel unlocking, opening and priming for transport. After channel opening, translocation proceeds in two phases: a slow phase independent of substrate length, and a length-dependent transport phase with an intrinsic translocation rate of ~40 amino acids per second for the proOmpA substrate. Broad translocation rate distributions reflect the stochastic nature of polypeptide transport.

scholarly journals Quantum Interference and Spin Filtering Effects in Photo-responsive Endoperoxide Based Single Molecular Device

2021 ◽  
Author(s):  
Ashima Bajaj ◽  
Rishu Khurana ◽  
Md. Ehesan Ali
Keyword(s):  
Single Molecule ◽  
Quantum Interference ◽  
Density Functional ◽  
Reaction Pathway ◽  
Stimuli Responsive ◽  
Spin Configuration ◽  
De Broglie Waves ◽  
Filtering Efficiency ◽  
External Stimuli ◽  
Spin Filtering

<div>The development of stimuli responsive systems that can switch between two distinct spin states under the application of an external stimuli has always remained an illusory challenge. Here, we report a stimuli-based spin filter by utilizing photo-responsive endoperoxide (EPO) based single molecule device. The photo-irradiation on EPO triggers the homolytic cleavage of the peroxide O-O bond generating diradical intermediate centered on two O-atoms which facilitates high spin filtering efficiency when placed between gold electrodes. The broken conjugated scenario due to peroxide bridge of EPO hinders the propagation of de-Broglie waves across the molecular skeleton. While the diradical intermediate of EPO yields high conductance for one of the spin configuration. The transmission characteristics of various photoproducts along the photochemical reaction pathway of EPO are also investigated using density functional theory in combination with non-equilibrium Green’s function (NEGF-DFT) technique. We demonstrate the key role played by Quantum Interference (QI) effects in dramatic modulation of conductance arising due to different degree of conjugation along the reaction pathway of EPO.</div><div><br></div>

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