Computational design and experimental testing of the fastest-folding β-sheet protein

Stefano Piana, Krishnarjun Sarkar, Kresten Lindorff-Larsen, Minghao Guo, Martin Gruebele, David E. Shaw

Research output: Contribution to journalArticlepeer-review

Abstract

One of the most important and elusive goals of molecular biology is the formulation of a detailed, atomic-level understanding of the process of protein folding. Fast-folding proteins with low free-energy barriers have proved to be particularly productive objects of investigation in this context, but the design of fast-folding proteins was previously driven largely by experiment. Dramatic advances in the attainable length of molecular dynamics simulations have allowed us to characterize in atomic-level detail the folding mechanism of the fast-folding all-β WW domain FiP35. In the work reported here, we applied the biophysical insights gained from these studies to computationally design an even faster-folding variant of FiP35 containing only naturally occurring amino acids. The increased stability and high folding rate predicted by our simulations were subsequently validated by temperature-jump experiments. The experimentally measured folding time was 4.3 μs at 80 °C-about three times faster than the fastest previously known protein with β-sheet content and in good agreement with our prediction. These results provide a compelling demonstration of the potential utility of very long molecular dynamics simulations in redesigning proteins well beyond their evolved stability and folding speed.

Original languageEnglish (US)
Pages (from-to)43-48
Number of pages6
JournalJournal of Molecular Biology
Volume405
Issue number1
DOIs
StatePublished - Jan 7 2011

Keywords

  • WW domain
  • fluorescence
  • molecular dynamics
  • protein engineering
  • temperature jump

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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