Analysis of the impact of protein conformational dynamics and intermolecular interactions on water flux through TIP3;1 aquaporins of Zea mays L.

Abstract

The discovery of aquaporins (AQPs) in 1992 had a profound impact on our understanding of the mechanisms underlying the transport of substances across cell membranes. To further understand water mobilization through AQPs, this study focuses on the characterization of water flux through the TIP3;1 aquaporins of Zea mays L. using molecular dynamics. The primary objective is to elucidate how protein–water intermolecular interactions and protein conformational dynamics impact water mobility across the cell membrane. To conduct this analysis, the three-dimensional structure of TIP3;1 was modeled using AlphaFold2, from which the complete system was constructed. This system consisted of a homotetramer of TIP3;1 immersed in a fragment of cell membrane and solvated with water molecules and ions. Subsequently, molecular dynamics simulations were conducted for 90 ns, resulting in the determination of an osmotic permeability coefficient (p_f) of 0.8172 ± 0.146 × 10⁻¹⁴ cm³ s⁻¹. In general, the mobility of water along the single-file water channel is influenced by the complex interplay of protein conformational dynamics and hydrogen bonding. The conformational dynamics of the protein channel modify the pore radius available for the passage of water, which affects the frequency of protein–water interactions and consequently influences the mobility of water in the channel. This study contributes to our understanding of the molecular mechanisms by which AQP activity is modulated without involving changes in protein chemical composition.