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The bonds of adenosine triphosphate (ATP) can be broken through the addition of water, releasing one or two phosphate groups in an exergonic process called hydrolysis. This reaction liberates the energy in the bonds for use in the cell—for instance, to synthesize proteins from amino acids.
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RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
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The addition or removal of phosphate groups from proteins is the most common chemical modification that regulates cellular processes. These modifications can affect the structure, activity, stability, and localization of proteins within cells as well as their interactions with other proteins.
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ATP is a highly unstable molecule. Unless quickly used to perform work, ATP spontaneously dissociates into ADP and inorganic phosphate (Pi), and the free energy released during this process is lost as heat. The energy released by ATP hydrolysis is used to perform work inside the cell and depends on a strategy called energy coupling. Cells couple the exergonic reaction of ATP hydrolysis with endergonic reactions, allowing them to proceed.
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DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart,...
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Pyrophosphate Release in the Protein HIV Reverse Transcriptase.

Murat Atis1, Kenneth A Johnson2, Ron Elber1,3

  • 1Institute for Computational Engineering and Sciences, The University of Texas at Austin , Austin, Texas 78712, United States.

The Journal of Physical Chemistry. B
|September 20, 2017
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Computational analysis reveals how inorganic phosphate (PPi) is released from HIV reverse transcriptase. The study elucidates the molecular mechanisms and free energy profiles governing PPi escape, crucial for understanding enzyme function.

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Enzymology

Background:

  • Enzymatic reactions involve substrate binding, protein reorganization, chemical reactions, and product release.
  • Understanding the product release step is critical for enzyme kinetics and drug development.

Purpose of the Study:

  • To computationally investigate the release of inorganic phosphate (PPi) from HIV reverse transcriptase.
  • To determine the free energy profile, mean first passage time, and molecular mechanisms of PPi escape.

Main Methods:

  • Atomically detailed simulations with explicit solvent.
  • Milestoning algorithm along a reaction coordinate to bridge time scale gaps.
  • Locally enhanced sampling and steered molecular dynamics to define reaction coordinates.

Main Results:

  • The molecular mechanism involves coupling PPi transfer to positively charged lysine residues and a magnesium ion on the exit pathway.
  • The computed PPi release rate is comparable to the chemical reaction step.
  • This suggests that PPi release can become rate-determining depending on the substrate (DNA or RNA template).

Conclusions:

  • The study provides detailed molecular insights into the PPi release mechanism from HIV reverse transcriptase.
  • Computational methods successfully addressed the significant time scale gap between simulations and experiments.
  • Findings contribute to a deeper understanding of enzyme kinetics and potential drug design targeting HIV replication.