Binding dynamics of linear alkyl-sulfates of different chain lengths on a protein surface

Abstract

Sulfate-based anionic surfactants, such as sodium dodecyl sulfate (SDS), are widely recognized for their ability to deactivate and denature proteins. Despite extensive research, the molecular mechanisms governing the preferential binding of surfactants to protein surfaces remain incompletely understood. This study employs molecular dynamics (MD) simulations to investigate interactions between subtilisin E (SubE) and two anionic surfactants: SDS and sodium hexyl sulfate (SHS), with SHS possessing alkyl chains half the length of SDS. Simulations conducted at a low surfactant concentration (0.5% w/v) reveal distinct binding dynamics and interaction preferences of these surfactants with the SubE protein surface. Results demonstrate that the presence of SDS and SHS does not induce significant alterations in the overall secondary structure of SubE compared to simulations in pure water. The residue-level analysis identifies SDS as having greater contact with surface residues than SHS, particularly in helical and turn regions of SubE. SDS exhibits persistent binding sites in proximity to active site residues, suggesting potential implications for the observed experimental reduction in enzymatic activity. Dynamic interaction analysis indicates rapid and sustained binding of nearly all surfactant molecules to the protein within the initial 10-25 ns, with SDS displaying more transient interactions compared to SHS. Specific interaction patterns are observed between SDS and catalytic triad residues Asp32, His64, and Ser221, as well as Asn155 in the oxyanion hole, contrasting with the minimal interaction observed with SHS. These findings offer insights into the molecular mechanisms underlying surfactant-protein interactions, underscoring opportunities for engineering protein stability and functionality in the presence of surfactants.