Computational Design and Experimental Testing of the Fastest-Folding beta-Sheet Protein

作者：Piana Stefano; Sarkar Krishnarjun; Lindorff Larsen Kresten; Guo Minghao; Gruebele Martin^*; Shaw David E

来源：Journal of Molecular Biology, 2011, 405(1): 43-48.

DOI：10.1016/j.jmb.2010.10.023

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

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-beta 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 mu s at 80 degrees C about three times faster than the fastest previously known protein with beta-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.

• 出版日期2011-1-7