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Exploring Compactness and Dynamics of Apomyoglobin.

Anna V Glyakina1,2, Mariya Y Suvorina2, Nikita V Dovidchenko2,3

  • 1Institute of Mathematical Problems of Biology, Russian Academy of Sciences, the Branch of Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Moscow, Russia.

Proteins
|December 23, 2024
PubMed
Summary
This summary is machine-generated.

Mutations in whale apomyoglobin (apoMb) alter protein structure and compactness. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) revealed how specific amino acid substitutions impact apoMb

Keywords:
accessible surfaceamyloidogenic regionscompactnessfolding nucleushydrogen‐deuterium exchange

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Analytical Chemistry

Background:

  • Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a powerful technique for studying protein dynamics.
  • Protein structure and compactness influence biological function.
  • Apomyoglobin (apoMb) serves as a model system for investigating protein folding and stability.

Purpose of the Study:

  • To investigate the impact of specific mutations on the structural compactness of whale apomyoglobin (apoMb).
  • To correlate changes in amino acid sequence with alterations in the number of exchangeable hydrogen atoms using HDX-MS.
  • To understand how mutations affect protein dynamics and the stability of key structural elements.

Main Methods:

  • Utilized hydrogen-deuterium exchange mass spectrometry (HDX-MS) to analyze protein structure.
  • Introduced various point mutations into the amino acid sequence of whale apomyoglobin.
  • Compared the deuterium exchange levels and structural compactness of mutant apoMb forms to the wild-type.

Main Results:

  • Mutations V10A, A15S, P120G, and M131A increased the number of exchangeable hydrogen atoms, indicating decreased compactness.
  • Mutant A144S showed a decrease in exchangeable hydrogen atoms, suggesting increased compactness.
  • Mutations L9F and L9E did not significantly alter apoMb compactness.
  • Substitutions V10A and M131A resulted in the largest increase in exchangeable hydrogens due to disrupted contacts between helices A, G, and H.

Conclusions:

  • Amino acid substitutions can significantly alter the structural compactness and dynamics of apomyoglobin.
  • HDX-MS is effective in quantifying these structural changes and identifying key regions affected by mutations.
  • The findings provide insights into protein folding pathways and the role of specific amino acid residues in maintaining protein structure.