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ATP Synthase: Structure01:18

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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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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
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The difference between the calculated and experimentally measured masses is known as the mass defect of the atom. In the case of helium-4, the mass defect indicates a “loss” in mass of 4.0331 amu – 4.0026 amu = 0.0305 amu. The loss in mass accompanying the formation of an atom from protons, neutrons, and electrons is due to the conversion of that mass into energy that is evolved as the atom forms. The nuclear binding energy is the energy produced when the atoms’ nucleons are bound...
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An Oxetane-Based Polyketide Surrogate To Probe Substrate Binding in a Polyketide Synthase.

Bryan D Ellis1, Jacob C Milligan2, Alexander R White1

  • 1Department of Chemistry , University of California Irvine , 1102 Natural Sciences II , Irvine , California 92697 , United States.

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Researchers developed novel oxetane-based mimics to study polyketide synthases (PKSs). This breakthrough allowed the first structural analysis of a ketosynthase intermediate, revealing insights into polyketide biosynthesis.

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Area of Science:

  • Biochemistry
  • Natural Product Biosynthesis
  • Enzymology

Background:

  • Polyketides are diverse bioactive natural products synthesized by polyketide synthases (PKSs).
  • Studying PKSs is challenging due to the high reactivity of poly-β-ketone substrates, hindering structural and mechanistic characterization.
  • Understanding how PKSs handle unstable substrates with high specificity is crucial but poorly understood.

Purpose of the Study:

  • To develop and apply an oxetane-based mimic for interrogating polyketide synthase (PKS) chemistry.
  • To overcome challenges associated with the reactivity of polyketide substrates.
  • To enable structural and mechanistic studies of PKS-polyketide interactions.

Main Methods:

  • Development of an oxetane-based mimic for PKS substrates.
  • Structural determination of a ketosynthase (KS) acyl-enzyme intermediate using the mimic.
  • Molecular dynamics simulations to analyze enzyme-substrate interactions.
  • Investigation of DpsC, the priming KS for daunorubicin biosynthesis.

Main Results:

  • First structural determination of a ketosynthase (KS) acyl-enzyme intermediate with an inert extender unit mimic.
  • Crystal structure and molecular dynamics simulations provided mechanistic insights into DpsC activity.
  • Demonstrated the utility of oxetane-based mimics in studying PKSs.

Conclusions:

  • Oxetane-based polyketide mimics are effective tools for studying PKS mechanistic enzymology.
  • This approach facilitates structural determination of enzyme-intermediate complexes.
  • The developed probes have broad applications for the biosynthetic community studying iterative PKSs.