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Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

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Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
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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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It is vital to regulate the activity of enzymatic as well as non-enzymatic proteins inside the cell. This can be achieved either through creating a balance between their rate of synthesis and degradation or regulating the intrinsic activity of the protein. Both these regulation mechanisms play an essential role in the normal functioning of cells.
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The Proteasome01:13

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Eukaryotic cells can degrade proteins through several pathways. One of the most important among these is the ubiquitin-proteasome pathway. It helps the cell eliminate the misfolded, damaged, or unwarranted cytoplasmic proteins in a highly specific manner.
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The ubiquitin-proteasome pathway is a well-known mechanism utilized by eukaryotic cells to remove cytoplasmic proteins that are misfolded, damaged, or no longer needed. In this pathway, the protein that needs to be eliminated undergoes a process called ubiquitination, where a chain of ubiquitin molecules is attached to the 48th lysine residue of the target protein. This ubiquitin modification helps the proteasome distinguish between a target protein and a healthy protein.
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In Vitro Ubiquitination and Deubiquitination Assays of Nucleosomal Histones
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Phosphorylation at Ser65 modulates ubiquitin conformational dynamics.

Remy A Yovanno1, Alvin Yu2, Tyler J Wied1

  • 1Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, WBSB 706, Baltimore, MD 21205, USA.

Structure (London, England : 1993)
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Phosphorylation of ubiquitin at Ser65 drives mitochondrial degradation by enabling a rare C-terminally retracted conformation. A novel Bent intermediate was identified, revealing the molecular mechanism of ubiquitin conformational changes.

Keywords:
molecular dynamicsphosphorylationstring methodubiquitin

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Background:

  • Ubiquitin phosphorylation at Ser65 is crucial for mitochondrial degradation.
  • The transition between Major and C-terminally retracted (CR) ubiquitin conformations is key to this process.
  • The precise mechanisms governing this conformational interconversion remain unclear.

Purpose of the Study:

  • To elucidate the molecular mechanisms underlying the interconversion between Major and CR ubiquitin conformations.
  • To identify intermediate states and pathways involved in ubiquitin conformational changes.

Main Methods:

  • All-atom molecular dynamics simulations using the string method with swarms of trajectories.
  • Calculation of the lowest free-energy path between Major and CR conformers.
  • Well-tempered metadynamics calculations and dynamical network modeling.

Main Results:

  • A stable 'Bent' intermediate conformation was identified during the Major to CR transition.
  • This Bent intermediate features C-terminal shifts towards the CR state while Ser65 phosphorylation contacts remain Major-like.
  • A Gln2Ala mutation destabilized the intermediate, and dynamical network analysis showed decoupling of pSer65-proximal residues from the β1 strand during the transition.

Conclusions:

  • The study reveals a novel Bent intermediate in ubiquitin conformational dynamics.
  • This finding clarifies the mechanism of Major to CR ubiquitin transition, critical for mitochondrial degradation.
  • The results highlight the role of specific residue interactions and network dynamics in regulating ubiquitin conformation.