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Sequence comparison of single-stranded DNA binding proteins and its structural implications.

B V Prasad, W Chiu

    Journal of Molecular Biology
    |February 5, 1987
    PubMed
    Summary
    This summary is machine-generated.

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    This study reveals that single-stranded DNA binding proteins share conserved aromatic and basic residues, crucial for DNA binding. These findings support a model where stacking and electrostatic interactions stabilize the protein-DNA complex.

    Area of Science:

    • Molecular Biology
    • Biochemistry
    • Structural Biology

    Background:

    • Several proteins, including gene product 5 protein (GP5), PIKE, gene product 32 protein (GP32), RecA, SSB, and SSF, strongly bind single-stranded DNA without sequence specificity.
    • Gene product 5 protein (GP5) from phage M13 is the smallest in this group and possesses a well-characterized three-dimensional structure.

    Purpose of the Study:

    • To identify conserved regions and functional residues within a class of single-stranded DNA binding proteins.
    • To investigate the structural basis for the stabilization of protein-single-stranded DNA complexes.

    Main Methods:

    • Comparative sequence analysis of GP5 with PIKE, GP32, RecA, SSB, and SSF.
    • Utilizing the GP5 sequence as a template to search for aligned aromatic and basic residues in homologous proteins.

    Related Experiment Videos

  • Secondary structure prediction for DNA binding domains.

    • Main Results:

    • Alignment of five aromatic and four charged residues was identified in the DNA binding domains of the studied proteins.
    • Statistically significant sequence homology was observed between the DNA binding domains of PIKE, GP32, and RecA with GP5.
    • The DNA binding domains exhibit a preference for beta-sheet secondary structures, suggesting a common structural motif.

    Conclusions:

    • The interaction between single-stranded DNA and these proteins is stabilized by stacking interactions of aromatic residues with DNA bases and electrostatic interactions of basic residues with DNA phosphates.
    • A triple-stranded beta-sheet may represent a common structural motif in the DNA binding domains of these proteins.