Symmetry and secondary structure of the replication terminator protein of Bacillus subtilis: sedimentation equilibrium and circular dichroic, infrared, and NMR spectroscopic studies

Biochemistry. 1993 Sep 28;32(38):10216-23. doi: 10.1021/bi00089a043.

Abstract

We have used analytical ultracentrifugation in combination with a number of spectroscopic techniques to analyze the symmetry and secondary structure of the DNA-binding replication terminator protein (RTP) of Bacillus subtilis. Sedimentation equilibrium studies confirm that RTP is a dimer in solution under the conditions used for spectroscopic analysis, whereas the number of cross peaks displayed in 1H-15N HSQC NMR spectra of uniformly 15N-labeled RTP are consistent with the primary structure of the monomer. These two results in combination lead to the conclusion that RTP is a symmetric dimer in solution. Circular dichroic and Fourier-transform infrared spectra reveal, in contrast to the results obtained from a number of commonly used secondary structure prediction algorithms, that RTP contains 20-30% alpha-helical and 40-50% beta-sheet/beta-turn secondary structure and that the conformation of the protein remains unchanged over the pH range 5-8. It is proposed on the basis of protein folding-class prediction algorithms, in combination with various physical properties of RTP, that it belongs to the alpha + beta protein-folding class.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Bacillus subtilis / metabolism*
  • Bacterial Proteins / chemistry
  • Base Sequence
  • Binding Sites
  • Circular Dichroism
  • Cloning, Molecular
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / metabolism
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / isolation & purification
  • Escherichia coli
  • Magnetic Resonance Spectroscopy / methods
  • Molecular Sequence Data
  • Protein Conformation
  • Protein Folding
  • Protein Structure, Secondary*
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / isolation & purification
  • Spectroscopy, Fourier Transform Infrared

Substances

  • Bacterial Proteins
  • DNA, Bacterial
  • DNA-Binding Proteins
  • Recombinant Proteins
  • rtP protein, Bacillus subtilis