Distribution and Structure Analysis of Fibril-Forming Peptides Focusing on Concentration Dependency

Yoshitake Sakae; Takeshi Kawasaki; Yuko Okamoto

doi:10.1021/acsomega.1c04960

Distribution and Structure Analysis of Fibril-Forming Peptides Focusing on Concentration Dependency

ACS Omega. 2022 Mar 14;7(12):10012-10021. doi: 10.1021/acsomega.1c04960. eCollection 2022 Mar 29.

Authors

Yoshitake Sakae^{1

2}, Takeshi Kawasaki², Yuko Okamoto^{2

3}

Affiliations

¹ Research Organization for Information Science and Technology, Tokyo 105-0013, Japan.
² Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.
³ Information Technology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan.

Abstract

We focus on the concentration dependency of fibril-forming peptides, which have the potential of aggregation by themselves. In this study, we performed replica-exchange molecular dynamics simulations of Lys-Phe-Phe-Glu (KFFE) fragments, which are known to form fibrils in experiments under different concentration environments. The analysis by static structure factors suggested that the density fluctuation of the KFFE fragments becomes large as the concentration increases. It was also found that the number of β-structures and oligomers also increases under a high concentration environment. Hence, a high concentration environment of fibril-forming peptides is likely to cause protein aggregation.