Theory of the statistics of kinetic transitions with application to single-molecule enzyme catalysis

2006 ◽  
Vol 124 (15) ◽  
pp. 154712 ◽  
Author(s):  
Irina V. Gopich ◽  
Attila Szabo
Keyword(s):  
Single Molecule ◽  
Enzyme Catalysis ◽  
Kinetic Transitions

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

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

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

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 The fast and superprocessive KIF1A predominately resides in a vulnerable one-head-bound state during its chemomechanical cycle

2020 ◽  
Author(s):  
Taylor M. Zaniewski ◽  
Allison M. Gicking ◽  
John Fricks ◽  
William O. Hancock
Keyword(s):  
Single Molecule ◽  
Atp Hydrolysis ◽  
Coiled Coil ◽  
Bound State ◽  
Weakly Bound ◽  
Strong Electrostatic Interaction ◽  
Order Of Magnitude ◽  
Neuronal Transport ◽  
Kinetic Transitions ◽  
Rate Limiting

ABSTRACTKinesin-3 are the fastest and most processive motors of the three neuronal transport kinesin families, yet the sequence of states and rates of kinetic transitions that comprise the chemomechanical cycle are poorly understood. We used stopped-flow fluorescence spectroscopy and single-molecule motility assays to delineate the chemomechanical cycle of the kinesin-3, KIF1A. Our bacterially expressed KIF1A construct, dimerized via a kinesin-1 coiled-coil, exhibits fast velocity and superprocessivity behavior similar to wild-type KIF1A. We established that the KIF1A forward step is triggered by hydrolysis of ATP and not by ATP binding, meaning that KIF1A follows the same chemomechanical cycle as established for kinesin-1 and-2. The ATP-triggered half-site release rate of KIF1A was similar to the stepping rate, indicating that during stepping, rear-head detachment is an order of magnitude faster than in kinesin-1 and kinesin-2. Thus, KIF1A spends the majority of its hydrolysis cycle in a one-head-bound state. Both the ADP off-rate and the ATP on-rate at physiological ATP concentration were fast, eliminating these steps as possible rate limiting transitions. Based on the measured run length and the relatively slow off-rate in ADP, we conclude that attachment of the tethered head is the rate limiting transition in the KIF1A stepping cycle. The fast speed, superprocessivity and load sensitivity of KIF1A can be explained by a fast rear head detachment rate, a rate-limiting step of tethered head attachment that follows ATP hydrolysis, and a relatively strong electrostatic interaction with the microtubule in the weakly-bound post-hydrolysis state.

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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