Single-Molecule Kinetic Theory of Heterogeneous and Enzyme Catalysis

2009 ◽  
Vol 113 (6) ◽  
pp. 2393-2404 ◽  
Author(s):  
Weilin Xu ◽  
Jason S. Kong ◽  
Peng Chen
Keyword(s):  
Kinetic Theory ◽  
Single Molecule ◽  
Enzyme Catalysis

scholarly journals Single Molecule Enzyme Catalysis: Steps towards Accurate Kinetic Schemes

2013 ◽  
Vol 104 (2) ◽  
pp. 372a
Author(s):  
Tatyana Terentyeva ◽  
Johan Hofkens ◽  
Chun-Biu Li ◽  
Kerstin Blank
Keyword(s):  
Single Molecule ◽  
Enzyme Catalysis ◽  
Kinetic Schemes

An Exactly Solvable Stochastic Kinetic Theory of Single-Molecule Force Experiments

2020 ◽  
Vol 124 (36) ◽  
pp. 7735-7744 ◽  
Author(s):  
Prasanta Kundu ◽  
Soma Saha ◽  
Gautam Gangopadhyay
Keyword(s):  
Kinetic Theory ◽  
Single Molecule ◽  
Exactly Solvable

Conformation Coupled Enzyme Catalysis:  Single-Molecule and Transient Kinetics Investigation of Dihydrofolate Reductase†

Biochemistry ◽  
2005 ◽  
Vol 44 (51) ◽  
pp. 16835-16843 ◽  
Author(s):  
Nina M. Antikainen ◽  
R. Derike Smiley ◽  
Stephen J. Benkovic ◽  
Gordon G. Hammes
Keyword(s):  
Dihydrofolate Reductase ◽  
Single Molecule ◽  
Enzyme Catalysis ◽  
Transient Kinetics

scholarly journals External mechanical force as an inhibition process in kinesin's motion

2005 ◽  
Vol 390 (1) ◽  
pp. 345-349 ◽  
Author(s):  
Aleix Ciudad ◽  
José María Sancho
Keyword(s):  
Kinetic Theory ◽  
Single Molecule ◽  
Turnover Rate ◽  
Mechanical Force ◽  
Velocity Data ◽  
Atp Turnover ◽  
Force Velocity ◽  
Inhibition Process ◽  
Menten Kinetic ◽  
Inhibition Theory

We analysed published force–velocity data for kinesin using classical Michaelis–Menten kinetic theory and found that the effect of force on the stepping rate of kinesin is analogous to the effect of a mixed inhibitor in classical inhibition theory. We derived an analytical expression for the velocity of kinesin (the stepping rate, equal to the ATP turnover rate) as a function of ATP concentration and force, and showed that it accurately predicts the observed single molecule stepping rate of kinesin under a variety of conditions.

Enzyme Catalysis at the Single-Molecule Level

2012 ◽  
pp. 149-168
Author(s):  
Raul Perez-Jimenez ◽  
Jorge Alegre-Cebollada
Keyword(s):  
Single Molecule ◽  
Enzyme Catalysis ◽  
Single Molecule Level

Enzyme Catalysis and Gene Expression Studies at Single Molecule Level

2010 ◽  
Vol 26 (07) ◽  
pp. 1976-1987
Author(s):  
SU Xiao-Dong ◽  
◽  
◽  
JIN Jian-Shi ◽  
XIE Sunney Xiaoliang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Molecule ◽  
Enzyme Catalysis ◽  
Single Molecule Level ◽  
Expression Studies ◽  
Gene Expression Studies

scholarly journals Structural conditions on complex networks for the Michaelis–Menten input–output response

2018 ◽  
Vol 115 (39) ◽  
pp. 9738-9743 ◽  
Author(s):  
Felix Wong ◽  
Annwesha Dutta ◽  
Debashish Chowdhury ◽  
Jeremy Gunawardena
Keyword(s):  
Single Molecule ◽  
Thermodynamic Equilibrium ◽  
Enzyme Catalysis ◽  
Regular Structure ◽  
Coarse Graining ◽  
Necessary And Sufficient Condition ◽  
Input Output ◽  
Linear Framework ◽  
Necessary And Sufficient ◽  
Fundamental Formula

The Michaelis–Menten (MM) fundamental formula describes how the rate of enzyme catalysis depends on substrate concentration. The familiar hyperbolic relationship was derived by timescale separation for a network of three reactions. The same formula has subsequently been found to describe steady-state input–output responses in many biological contexts, including single-molecule enzyme kinetics, gene regulation, transcription, translation, and force generation. Previous attempts to explain its ubiquity have been limited to networks with regular structure or simplifying parametric assumptions. Here, we exploit the graph-based linear framework for timescale separation to derive general structural conditions under which the MM formula arises. The conditions require a partition of the graph into two parts, akin to a “coarse graining” into the original MM graph, and constraints on where and how the input variable occurs. Other features of the graph, including the numerical values of parameters, can remain arbitrary, thereby explaining the formula’s ubiquity. For systems at thermodynamic equilibrium, we derive a necessary and sufficient condition. For systems away from thermodynamic equilibrium, especially those with irreversible reactions, distinct structural conditions arise and a general characterization remains open. Nevertheless, our results accommodate, in much greater generality, all examples known to us in the literature.

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