Unifying features in protein-folding mechanisms

Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13286-91. doi: 10.1073/pnas.1835776100. Epub 2003 Oct 31.

Abstract

We compare the folding of representative members of a protein superfamily by experiment and simulation to investigate common features in folding mechanisms. The homeodomain superfamily of three-helical, single-domain proteins exhibits a spectrum of folding processes that spans the complete transition from concurrent secondary and tertiary structure formation (nucleation-condensation mechanism) to sequential secondary and tertiary formation (framework mechanism). The unifying factor in their mechanisms is that the transition state for (un)folding is expanded and very native-like, with the proportion and degree of formation of secondary and tertiary interactions varying. There is a transition, or slide, from the framework to nucleation-condensation mechanism with decreasing stability of the secondary structure. Thus, framework and nucleation-condensation are different manifestations of an underlying common mechanism.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Dose-Response Relationship, Drug
  • Humans
  • Kinetics
  • Models, Molecular
  • Protein Denaturation
  • Protein Folding*
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Proto-Oncogene Proteins c-myb / chemistry
  • Shelterin Complex
  • Software
  • Telomere-Binding Proteins / chemistry
  • Telomeric Repeat Binding Protein 1 / chemistry
  • Temperature
  • Thermodynamics
  • Urea / pharmacology

Substances

  • Proto-Oncogene Proteins c-myb
  • Shelterin Complex
  • TERF2IP protein, human
  • Telomere-Binding Proteins
  • Telomeric Repeat Binding Protein 1
  • Urea