Structure and Dynamics of Confined Water Inside Diphenylalanine Peptide Nanotubes

Jinfeng Chen; Zongyang Qiu; Jing Huang

doi:10.1021/acsomega.3c06071

Structure and Dynamics of Confined Water Inside Diphenylalanine Peptide Nanotubes

ACS Omega. 2023 Oct 31;8(45):42936-42950. doi: 10.1021/acsomega.3c06071. eCollection 2023 Nov 14.

Authors

Jinfeng Chen^{1

2

3}, Zongyang Qiu^{2

3}, Jing Huang^{2

3}

Affiliations

¹ College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China.
² Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China.
³ Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China.

Abstract

Diphenylalanine (FF) peptides exhibit a unique ability to self-assemble into nanotubes with confined water molecules playing pivotal roles in their structure and function. This study investigates the structure and dynamics of diphenylalanine peptide nanotubes (FFPNTs) using all-atom molecular dynamics (MD) and grand canonical Monte Carlo combined with MD (GCMC/MD) simulations with both the CHARMM additive and Drude polarizable force fields. The occupancy and dynamics of confined water molecules were also examined. It was found that less than 2 confined water molecules per FF help stabilize the FFPNTs on the x-y plane. Analyses of the kinetics of confined water molecules revealed distinctive transport behaviors for bound and free water, and their respective diffusion coefficients were compared. Our results validate the importance of polarizable force field models in studying peptide nanotubes and provide insights into our understanding of nanoconfined water.