Evaluating beta-turn mimics as beta-sheet folding nucleators

Proc Natl Acad Sci U S A. 2009 Jul 7;106(27):11067-72. doi: 10.1073/pnas.0813012106. Epub 2009 Jun 18.

Abstract

Beta-turns are common conformations that enable proteins to adopt globular structures, and their formation is often rate limiting for folding. Beta-turn mimics, molecules that replace the i + 1 and i + 2 amino acid residues of a beta-turn, are envisioned to act as folding nucleators by preorganizing the pendant polypeptide chains, thereby lowering the activation barrier for beta-sheet formation. However, the crucial kinetic experiments to demonstrate that beta-turn mimics can act as strong nucleators in the context of a cooperatively folding protein have not been reported. We have incorporated 6 beta-turn mimics simulating varied beta-turn types in place of 2 residues in an engineered beta-turn 1 or beta-bulge turn 1 of the Pin 1 WW domain, a three-stranded beta-sheet protein. We present 2 lines of kinetic evidence that the inclusion of beta-turn mimics alters beta-sheet folding rates, enabling us to classify beta-turn mimics into 3 categories: those that are weak nucleators but permit Pin WW folding, native-like nucleators, and strong nucleators. Strong nucleators accelerate folding relative to WW domains incorporating all alpha-amino acid sequences. A solution NMR structure reveals that the native Pin WW beta-sheet structure is retained upon incorporating a strong E-olefin nucleator. These beta-turn mimics can now be used to interrogate protein folding transition state structures and the 2 kinetic analyses presented can be used to assess the nucleation capacity of other beta-turn mimics.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Humans
  • Kinetics
  • Molecular Mimicry*
  • Molecular Sequence Data
  • Mutant Proteins
  • NIMA-Interacting Peptidylprolyl Isomerase
  • Peptidylprolyl Isomerase / chemistry*
  • Protein Stability
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Solutions
  • Thermodynamics

Substances

  • Mutant Proteins
  • NIMA-Interacting Peptidylprolyl Isomerase
  • Solutions
  • PIN1 protein, human
  • Peptidylprolyl Isomerase

Associated data

  • PDB/2KBU