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Related Experiment Videos

Conformational deformation in deoxymyoglobin by hydrostatic pressure

T Yamato1, J Higo, Y Seno

  • 1Department of Chemistry, Faculty of Science, Kyoto University, Japan.

Proteins
|August 1, 1993
PubMed
Summary

High pressure significantly alters sperm whale deoxymyoglobin structure, compressing interhelix regions more than others. Volume fluctuations are dominated by low-frequency normal modes, revealing pressure

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Area of Science:

  • Biophysics
  • Structural Biology
  • Protein Dynamics

Background:

  • Sperm whale deoxymyoglobin is a crucial protein for oxygen transport.
  • Understanding protein behavior under pressure is vital for various biological and medical applications.

Purpose of the Study:

  • To investigate the effects of hydrostatic pressure on the equilibrium conformation and volume fluctuations of sperm whale deoxymyoglobin.
  • To analyze the compressibility of different regions within the deoxymyoglobin molecule.

Main Methods:

  • Normal mode analysis
  • Strain tensor analysis
  • Calculation of linear compressibility between C-alpha atoms

Main Results:

  • Pressure-induced deformation is heterogeneous, with interhelix regions compressing more than other parts.

Related Experiment Videos

  • Hydrophobic clusters show varying compressibility, decreasing from bottom to distal to proximal sides.
  • Atomic displacement under 1,000 atm is small (0.12 Å) compared to room temperature fluctuations.
  • Protein excluded volume decreases by 0.9% at 1,000 atm.
  • Volume fluctuations are dominated by low-frequency normal modes.

    • Conclusions:

    • Deoxymyoglobin exhibits significant pressure-dependent structural changes, particularly in interhelix regions.
    • The compressibility of hydrophobic clusters is lower than interhelix regions, despite internal cavities.
    • Low-frequency modes play a critical role in protein volume fluctuations under pressure.