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ATP Driven Pumps II: P-type Pumps01:34

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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.
A typical P-type pump has three cytosolic domains: nucleotide-binding (N), phosphorylation (P), and activator (A) domains. These domains are connected to the membrane-spanning helices by short amino acid segments. ATP hydrolysis and covalent phosphoenzyme intermediate formation are crucial parts of the catalytic cycle. At the highly...
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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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Mechanically-gated ion channels are proteins found in eukaryotic and prokaryotic cell membranes that open in response to mechanical stress. Tension, compression, swelling, and shear stress can alter the conformation of the protein, opening a transmembrane channel that allows the passage of ions for signal transmission. In eukaryotes, mechanically-gated channels are distributed in several regions like the neurons, lungs, skin, bladder, and heart, where they play critical roles in numerous...
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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, 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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Novel Techniques for Observing Structural Dynamics of Photoresponsive Liquid Crystals
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Femtosecond-to-millisecond structural changes in a light-driven sodium pump.

Petr Skopintsev1, David Ehrenberg2, Tobias Weinert1

  • 1Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institut, Villigen, Switzerland.

Nature
|June 6, 2020
PubMed
Summary

Researchers visualized the Krokinobacter eikastus rhodopsin 2 (KR2) sodium pump's photocycle using serial crystallography. This reveals how structural changes enable light-driven sodium transport across membranes.

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Area of Science:

  • Biophysics
  • Structural Biology
  • Optogenetics

Background:

  • Light-driven sodium pumps, like Krokinobacter eikastus rhodopsin 2 (KR2), are crucial for microbial energy conversion and valuable optogenetic tools.
  • Previous studies solved resting-state structures of KR2, but the dynamic structural changes enabling active sodium transport remained unclear.

Purpose of the Study:

  • To elucidate the time-resolved structural dynamics of the KR2 sodium pump during its photocycle.
  • To understand the molecular mechanisms of light-driven sodium translocation across cellular membranes.

Main Methods:

  • Serial X-ray crystallography at the Swiss X-ray Free Electron Laser.
  • Time-resolved data collection across a range of pump-probe delays (femtoseconds to milliseconds).
  • Integration of structural data with spectroscopic methods and quantum chemical calculations.

Main Results:

  • High-resolution snapshots captured KR2 structural changes from femtoseconds to milliseconds.
  • Retinal isomerization and binding pocket rearrangements occurred within nanoseconds.
  • An electrostatic gate opened in microseconds, followed by transient sodium binding near the retinal.
  • A second potential sodium-binding site was identified near the extracellular exit at 20 milliseconds.

Conclusions:

  • The study provides unprecedented molecular insight into the dynamic process of light-driven sodium transport.
  • Identified key structural intermediates and timings governing KR2 function.
  • Advances understanding of active cation transport mechanisms and optogenetic tool operation.