Systematic Circular Permutation of an Entire Protein Reveals Essential Folding Elements

Nat Struct Biol. 2000 Jul;7(7):580-5. doi: 10.1038/76811.

Abstract

The importance of chain connectivity in determining protein function and stability can be examined by breaking the peptide backbone using a technique such as circular permutation. Cleavage at certain positions results in a complete loss of the ability of the protein to fold. When such cleavage sites occur sequentially in the primary structure, we call the region a 'folding element', a new concept that could assist in our understanding of the protein folding problem. The folding elements of dihydrofolate reductase have been assigned by conducting a systematic circular permutation analysis in which the peptide backbone was sequentially broken between every pair of residues in the protein. The positions of folding elements do not appear to correspond to secondary structure motifs, substrate or coenzyme binding sites, or accessible surface area. However, almost all of the amino acid residues known to be involved in early folding events are located within the folding elements.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Circular Dichroism
  • Escherichia coli / enzymology*
  • Kinetics
  • Models, Molecular
  • Molecular Sequence Data
  • Mutation / genetics
  • NADP / metabolism
  • Peptide Fragments / chemistry*
  • Peptide Fragments / genetics
  • Peptide Fragments / metabolism*
  • Protein Binding
  • Protein Denaturation / drug effects
  • Protein Folding*
  • Protein Structure, Secondary / drug effects
  • Protein Structure, Tertiary / drug effects
  • Spectrometry, Fluorescence
  • Tetrahydrofolate Dehydrogenase / chemistry*
  • Tetrahydrofolate Dehydrogenase / genetics
  • Tetrahydrofolate Dehydrogenase / metabolism*
  • Thermodynamics
  • Titrimetry
  • Tryptophan / metabolism
  • Urea / pharmacology

Substances

  • Peptide Fragments
  • NADP
  • Tryptophan
  • Urea
  • Tetrahydrofolate Dehydrogenase

Associated data

  • PDB/1RX4