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Related Concept Videos

ATP Synthase: Structure01:18

ATP Synthase: Structure

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ATP synthase or ATPase is among the most conserved proteins found in bacteria, mammals, and plants. This enzyme can catalyze a forward reaction in response to the electrochemical gradient, producing ATP from ADP and inorganic phosphate. ATP synthase can also work in a reverse direction by hydrolyzing ATP and generating an electrochemical gradient. Different forms of ATP synthases have evolved special features to meet the specific demands of the cell. Based on their specific feature, ATP...
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ATP Synthase: Mechanism01:48

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In animals, the mitochondrial F1F0 ATP synthase is the key protein that synthesizes ATP molecules through a complex catalytic mechanism. While the nuclear genome encodes the majority of ATP synthase subunits, the mitochondrial genome encodes some of the enzyme's most critical components. The formation of this multi-subunit enzyme is a complex multi-step process regulated at the level of transcription, translation, and assembly. Defects in one or more of these steps can result in decreased...
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ATP Driven Pumps II: P-type Pumps01:34

ATP Driven Pumps II: P-type Pumps

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The P-type pumps are a large family of integral membrane transporter ATPases. They are divided into five major types based on substrate specificity, from I to V.
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The ADP/ATP Carrier Protein01:42

The ADP/ATP Carrier Protein

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ADP/ATP carrier or AAC protein is the most abundant carrier protein in the inner mitochondrial membrane. It transports large quantities of ADP and ATP, equivalent to the average human body weight, every day. Among other transporters, ACC protein is one of the best-studied members of the mitochondrial carrier protein family. The ADP/ATP carrier protein comprises two transmembrane helices connected to a loop and a single alpha-helix on the matrix side. It switches between two conformational...
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ATP Driven Pumps I: An Overview01:27

ATP Driven Pumps I: An Overview

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ATP-driven pumps, also known as transport ATPases, are integral membrane proteins. They have binding sites for ATP located on the membrane's cytosolic side and the ion-conducting domain in the transmembrane region. These pumps use the free energy released from ATP hydrolysis to move the solutes across cell membranes against an electrochemical gradient.
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Actin Treadmilling01:18

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Actin filaments undergo polymerization and depolymerization from either end. The polymerization and depolymerization rates depend on the cytosolic concentration of free G-actins. The polymerization rate is generally higher at the plus or barbed end, while the depolymerization rate is higher at the minus or pointed end. At a steady state, critical concentration describes the concentration of free G-actin monomers at which the polymerization rate at the plus end is equal to that of the...
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Nucleotide Exchange Mechanism Involving Angle-Dependent Rate Constants Extracted from F1-ATPase Single-Molecule Rotation Trajectories.

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F<sub>1</sub>-ATPase Rotary Mechanism: Interpreting Results of Diverse Experimental Modes With an Elastic Coupling Theory.

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Dissecting Mechanoenzymatic Properties of Processive Myosins with Ultrafast Force-Clamp Spectroscopy
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Angle-dependent rotation velocity consistent with ADP release in bacterial F-ATPase.

Nathan Suiter1,2, Sándor Volkán-Kacsó1,2

  • 1Department of Mathematics, Physics and Statistics, Azusa Pacific University, Azusa, CA, United States.

Frontiers in Molecular Biosciences
|August 21, 2023
PubMed
Summary

Researchers identified a short-lived state in bacterial F1-ATPase rotation using a model-based method. This finding reveals a common mechanism for nucleotide release bottlenecks in rotary ATPases.

Keywords:
ADP releaseATPATP synthasesingle-molecule theorysingle-molecule tracking

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Biophysics

Background:

  • The F1-ATPase enzyme facilitates cellular energy production through rotation.
  • Understanding the rotation kinetics of Paracoccus denitrificans F1-ATPase (PdF1) is crucial for elucidating its mechano-chemical coupling.
  • Previous studies noted large rotational steps in PdF1, unlike other F-ATPases, hindering kinetic scheme establishment.

Purpose of the Study:

  • To investigate the rotation kinetics of single-molecule PdF1.
  • To identify and characterize short-lived states within the PdF1 rotation cycle.
  • To compare experimental findings with theoretical models to establish a mechano-chemical kinetic scheme.

Main Methods:

  • A model-based method was employed to analyze single-molecule trajectories of PdF1.
  • Angular velocity was extracted from experimental data and compared with theoretical calculations.
  • Kinetic analysis was performed to identify intermediate states and their lifetimes.

Main Results:

  • A short-lived state with a 20 μs lifetime was detected 40° after ATP binding.
  • This state corresponds to a three-nucleotide occupancy preceding ADP release.
  • A similar state was observed in Thermophilic bacillus F1-ATPase, suggesting a conserved mechanism.

Conclusions:

  • The identified short-lived state is a conserved intermediate in F1-ATPase rotary mechanism.
  • This state plays a role in overcoming nucleotide release bottlenecks.
  • The findings provide insights into the mechano-chemical coupling of rotary ATPases.