Method to extract multiple states in F
            <sub>1</sub>
            -ATPase rotation experiments from jump distributions

Volkan-Kacso, Sandor; Le, Luan Q.; Zhu, Kaicheng; Su, Haibin; Marcus, R. A.

doi:10.1073/pnas.1915314116

Cited by 6 publications

(24 citation statements)

References 32 publications

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“…We estimated G from the rotational fluctuations based on the fluctuation-dissipation theorem as described previously (12). It has been reported that the stepping velocity depends on the angular position using a high resolution method (9,10) and theoretical consideration (29) but in our data, as we could not specify the reason for the angular position dependency in our study and estimated v by fitting a straight line to the averaged curves of 20 trajectories (Fig. 1 B) as described in the Materials and Methods.…”

Section: Resultsmentioning

confidence: 99%

Tight Chemomechanical Coupling of the F1 Motor Relies on Structural Stability

Tanaka

Kawakami

Okaniwa

et al. 2020

Biophysical Journal

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The F 1 motor is a rotating molecular motor that ensures a tight chemomechanical coupling between ATP hydrolysis/synthesis reactions and rotation steps. However, the mechanism underlying this tight coupling remains to be elucidated. In this study, we used electrorotation in single-molecule experiments using an F 1 bE190D mutant to demonstrate that the stall torque was significantly smaller than the wild-type F 1 , indicating a loose coupling of this mutant, despite showing similar stepping torque as the wild-type. Experiments on the ATPase activity after heat treatment and gel filtration of the a 3 b 3 -subcomplex revealed the unstable structure of the bE190D mutant. Our results suggest that the tight chemomechanical coupling of the F 1 motor relies on the structural stability of F 1 . We also discuss the difference between the stepping torque and the stall torque.

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Section: Resultsmentioning

confidence: 99%

Tight Chemomechanical Coupling of the F1 Motor Relies on Structural Stability

Tanaka

Kawakami

Okaniwa

et al. 2020

Biophysical Journal

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“…Recently, the theory was used as a basis for detecting an intermediate state (Volkán-Kacsó et al, 2019). The method relies on the analysis of angular jumps, a measure of the instantaneous velocity of rotation, detected by a nanoscale probe attached to the rotor shaft of the ThF1 motor.…”

Section: Detection Of An Intermediate State Related To Atp Binding An...mentioning

confidence: 99%

F1-ATPase Rotary Mechanism: Interpreting Results of Diverse Experimental Modes With an Elastic Coupling Theory

Volkan-Kacso

Marcus

2022

Front. Microbiol.

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In this chapter, we review single-molecule observations of rotary motors, focusing on the general theme that their mechanical motion proceeds in substeps with each substep described by an angle-dependent rate constant. In the molecular machine F1-ATPase, the stepping rotation is described for individual steps by forward and back reaction rate constants, some of which depend strongly on the rotation angle. The rotation of a central shaft is typically monitored by an optical probe. We review our recent work on the theory for the angle-dependent rate constants built to treat a variety of single-molecule and ensemble experiments on the F1-ATPase, and relating the free energy of activation of a step to the standard free energy of reaction for that step. This theory, an elastic molecular transfer theory, provides a framework for a multistate model and includes the probe used in single-molecule imaging and magnetic manipulation experiments. Several examples of its application are the following: (a) treatment of the angle-dependent rate constants in stalling experiments, (b) use of the model to enhance the time resolution of the single-molecule imaging apparatus and to detect short-lived states with a microsecond lifetime, states hidden by the fluctuations of the imaging probe, (c) treatment of out-of-equilibrium “controlled rotation” experiments, (d) use of the model to predict, without adjustable parameters, the angle-dependent rate constants of nucleotide binding and release, using data from other experiments, and (e) insights obtained from correlation of kinetic and cryo-EM structural data. It is also noted that in the case where the release of ADP would be a bottleneck process, the binding of ATP to another site acts to accelerate the release by 5–6 orders of magnitude. The relation of the present set of studies to previous and current theoretical work in the field is described. An overall goal is to gain mechanistic insight into the biological function in relation to structure.

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“…Finite dwell time is responsible for slower time scale while the fast time scale corresponds to the bead's relaxation time. Adapted with journal permission for reference [23].…”

Section: Extraction Of Physical Quantities From Dwellsmentioning

confidence: 99%

“…(b) Reaction scheme in four state model with the additional metastable state (2*) in green box. Adapted with journal permission for reference [23].…”

Section: Boundary Conditionsmentioning

confidence: 99%

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Kinetic modelling of 70S ribosome and F1-ATPase

Le¹

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Theoretical models have been developed to understand kinetics of ribosomes and F 1 -ATPase which are important enzymes responsible for protein synthesis and ATP production in cells respectively. One important aspects of protein synthesis is accuracytranslation speed relation and how it is related to overall cell growth. For F 1 -ATPase , it is important to understand how F 1 -ATPase hydrolyzes ATP molecules based on which the mechanism of ATP synthesis is deduced due to the assumption that synthesis is just the reverse of hydrolysis.A novel pseudo-GTPase activated state, which was discovered recently, may play a role in selection of cognate during initial selection phase of protein synthesis. By assuming the state to exist after codon recognition and prior GTPase activation, kinetic analysis shows that rates between codon recognition and pseudo-GTPase activation are comparable for cognates (7 s −1 ) and near cognates (3 s −1 ). However, cognate in pseudo-GTPase activated state can proceed at significantly faster rate (138 s −1 ) to GTPase activated compared to near cognate (0.3 s −1 ). The effective rate from codon recognition to GTPase activated is slowed down, thus requiring less intrinsic selectivity between two states for selection while maintain good accuracy and fast speed.The effect of free [M g 2+ ] on translation kinetics and accuracy has been investigated based on a coarse-grained model of detailed translation scheme. Ribosomes can be broady categorized into three states: free, initial selection and proofreading. Increasing [M g 2+ ] will accelerate association speed between ternary complexes (both cognates and near cognates) and free ribosomes, resulting in decrease in accuracy. Increasing [M g 2+ ] from 1 mM to 3 mM results in faster translation speed due to increasing association speed of cognates with sufficient free ribosomes. Despite the drop in accuracy, it is still sufficient for selection and with faster speed, ribosomes seem to operate in "effizienter" regime. Further increase of [M g 2+ ] to 7 mM leads to plummet of translation speed. This is attributed to more sluggish ribosomes occupied with near cognates, causing less ribosomes for cognates. The regime is termed "competition" highlighting the effect of near cognates on translation. The translation model is incorporated into a growth model in an attempt to study the effect of accuracy on cellular proteome and growth during exponential phase. The proteome consists of free amino acids, metabolic proteins and ribosomes. The assumption i It may not be rare but interesting enough to have two main supervisors during PhD. I would like to thank my current supervisor Dr. Dong Zhili and former supervisor Dr. Su Haibin for this four year journey. Dr. Zhili has shown kind support after my supervisor Dr. Haibin left Singapore for Hong Kong. Despite his departure, Dr. Haibin still helps me with projects by giving me an opportunity to stay in Hong Kong for 5 months funded by his research grant and Matching-Fund scheme for International Visiting Internship...

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Method to extract multiple states in F ₁ -ATPase rotation experiments from jump distributions

Cited by 6 publications

References 32 publications

Tight Chemomechanical Coupling of the F1 Motor Relies on Structural Stability

Tight Chemomechanical Coupling of the F1 Motor Relies on Structural Stability

F1-ATPase Rotary Mechanism: Interpreting Results of Diverse Experimental Modes With an Elastic Coupling Theory

Kinetic modelling of 70S ribosome and F1-ATPase

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Method to extract multiple states in F 1 -ATPase rotation experiments from jump distributions

Cited by 6 publications

References 32 publications

Tight Chemomechanical Coupling of the F1 Motor Relies on Structural Stability

Tight Chemomechanical Coupling of the F1 Motor Relies on Structural Stability

F1-ATPase Rotary Mechanism: Interpreting Results of Diverse Experimental Modes With an Elastic Coupling Theory

Kinetic modelling of 70S ribosome and F1-ATPase

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Product

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Method to extract multiple states in F ₁ -ATPase rotation experiments from jump distributions