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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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In contrast to passive transport, active transport involves a substance being moved through membranes in a direction against its concentration or electrochemical gradient. There are two types of active transport: primary active transport and secondary active transport. Primary active transport utilizes chemical energy from ATP to drive protein pumps embedded in the cell membrane. With energy from ATP, the pumps transport ions against their electrochemical gradients—a direction they would...
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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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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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Kinetic network modeling with molecular simulation inputs: A proton-coupled phosphate symporter.

Yu Liu1, Chenghan Li1, Meghna Gupta2

  • 1Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois.

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This study reveals the reaction pathways of proton-driven phosphate transporters (PiPT) using kinetic modeling and molecular dynamics. It uncovers how pH and phosphate levels influence transporter function and identifies the molecular basis for optimal pH.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Computational Biology

Background:

  • Phosphate is vital for cellular functions and transported by proton-coupled transporters.
  • Similar transporters are found in diverse organisms, including pathogens and cancer cells.
  • Understanding the kinetic framework of proton-driven phosphate transporters (PiPT) is crucial.

Purpose of the Study:

  • To characterize the proton-phosphate co-transport behavior of PiPT.
  • To reveal prevailing reaction pathways under varying conditions.
  • To uncover the molecular origin of optimal pH for PiPT.

Main Methods:

  • Kinetic network modeling.
  • "Bottom-up" molecular dynamics simulations.
  • Analysis of transporter behavior under different pH and phosphate concentrations.

Main Results:

  • Detailed characterization of proton-phosphate co-transport in PiPT.
  • Identification of dominant reaction pathways based on experimental conditions.
  • Elucidation of molecular factors contributing to PiPT's optimal pH.

Conclusions:

  • Kinetic network modeling and molecular dynamics provide a robust framework for studying PiPT.
  • The study elucidates the mechanistic basis of PiPT function and its pH dependency.
  • Findings offer insights into phosphate transport in various biological systems.