The COVID-19 pandemic, which was caused by SARS-CoV-2, initiated a global health crisis in 2019. SARS-CoV-2 is a single-stranded RNA virus encased in a lipid envelope that houses key structural proteins, including the Spike glycoprotein, which mediates viral entry into host cells. Within the Spike protein, the S2 subunit, and particularly its fusion domain, plays a critical role in merging viral and host membranes. Understanding the fusion domain interactions at the molecular level is important for advancing applications such as the development of novel antiviral therapies. This study investigates the self-assembly of SARS-CoV-2 S2 subunit fusion peptides (FPs) and their interaction with biomimetic plasma membrane (PM) models composed of physiological mixes of phospholipids, sphingomyelin, and cholesterol. Complementary techniques, including atomic force microscopy, neutron reflectometry and grazing incidence X-ray diffraction, provided detailed insights into lipid nano-mechanics and in-plane molecular structure. Our findings reveal several types of FP assemblies at the PM interface, including the formation of rigid fibres, spiral structures, and segregated domains. These behaviours are influenced by FP intrinsic features such as hydrophobicity and molecular structure, and the resultant interactions with lipid headgroups and tail regions. This work enhances our molecular-level understanding of FP-lipid interactions, shedding light on viral entry mechanisms. Furthermore, the ability of these peptides to self-assemble, modulated by the surrounding lipid environment, positions them as promising building blocks for innovative functional biomaterials.

A.M. and E.G. acknowledge the financial support from by MCIN/AEI/10.13039/501100011033 under grants PID2021-129054NA-I00 and PID2023-147156NB-I00, respectively. A.M. also acknowledges the financial support from the Department of Education of the Basque Government under grant PIBA_2023_1_0054 and from the IKUR Strategy under the collaboration agreement between Ikerbasque Foundation and Materials Physics Center. AAF is grateful for support from the Provincial Council of Gipuzkoa under the program Fellow Gipuzkoa. E.G. also acknowledges the financial support by UCM under grant PR12/24-31566 (Ayudas para la financiación de proyectos de investigación UCM 2023).

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