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CSJ Journals

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2021, Vol.50, No.1

162-165

The Folding of Trp-cage is Regulated by Stochastic Flip of the Side Chain of Tryptophan

Takunori Yasuda ,1Yasuteru Shigeta ,2 and Ryuhei Harada *2
1College of Biological Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-0821, Japan
2Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-0821, Japan
https://doi.org/10.1246/cl.200699

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Abstract

Trp-cage is an artificial 20-residue protein and forms a hydrophobic core at its central cage upon folding. In the present study, the folding of Trp-cage was addressed by parallel cascade selection molecular dynamics (PaCS-MD). Our results of PaCS-MD indicate that flip of the side chain of tryptophan (W6) was correlated with the overall folding. In conclusion, flip of stochastic side chain of W6 regulates the folding into the native or mis-folded states of Trp-cage.

figure

Trp-cage is an artificial protein and forms a hydrophobic core upon its folding. In the present study, the folding process was addressed by a rare event sampling method (PaCS-MD). Our computational results showed that stochastic flip of the side chain of W6 in the hydrophobic core regulates folding into the native or mis-folded states of Trp-cage.

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