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

TY - JOUR

T1 - Computational design and experimental testing of the fastest-folding ß-sheet protein

AU - Piana, Stefano

AU - Sarkar, Krishnarjun

AU - Lindorff-Larsen, Kresten

AU - Guo, Minghao

AU - Gruebele, Martin

AU - Shaw, David E

N1 - Copyright © 2010 Elsevier Ltd. All rights reserved.

PY - 2011/1/7

Y1 - 2011/1/7

N2 - 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.

AB - 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.

U2 - 10.1016/j.jmb.2010.10.023

DO - 10.1016/j.jmb.2010.10.023

M3 - Journal article

C2 - 20974152

SN - 0022-2836

VL - 405

SP - 43

EP - 48

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

IS - 1

ER -