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Three-dimensional structure of binase in solution

Reibarkh MYa1, D E Nolde, L I Vasilieva

  • 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, Moscow.

FEBS Letters
|August 26, 1998
PubMed
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We determined the 3D structure of binase, an extracellular ribonuclease, using NMR data. Its structure, featuring alpha-helices and beta-sheets, differs from barnase, explaining their varying thermostability.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Biophysics

Background:

  • Binase is a small extracellular ribonuclease.
  • Understanding its spatial structure is crucial for explaining its biological function and stability.
  • Comparing binase with related proteins like barnase can reveal insights into protein stability and evolution.

Purpose of the Study:

  • To determine the three-dimensional spatial structure of binase in aqueous solution.
  • To elucidate the structural basis for binase's biological activity and thermostability.
  • To compare the structure of binase with barnase to understand differences in their stability.

Main Methods:

  • Nuclear Magnetic Resonance (NMR) spectroscopy (1H-NMR) was used to collect data.
  • Torsion angle dynamics (DYANA program) were employed to calculate structures using NOE, hydrogen bond, and dihedral angle constraints.

Related Experiment Videos

  • Energy minimization was performed using the ECEPP/2 potential (FANTOM program).

    • Main Results:

    • Twenty distinct spatial structures of binase were obtained, revealing a detailed molecular model.
    • Binase comprises three alpha-helices and two beta-sheets (antiparallel and parallel).
    • Flexible loops, significant for biological function, were identified within the binase structure.

    Conclusions:

    • The determined spatial structure of binase provides a foundation for understanding its enzymatic activity.
    • Structural differences between binase and barnase account for their distinct thermostability profiles.
    • This study offers insights into protein structure-function relationships and the evolution of ribonuclease stability.