PAS-Domain Protein Orientation at a Polyelectrolyte Surface Revealed by Infrared Nanospectroscopy, Chiral Vibrational Spectroscopy, and Molecular Dynamics Simulations
Year: 2026
Type: article
Abstract: is a model PAS-domain protein involved in negative phototaxis, yet its signaling partner remains unidentified. Here, we present a method to resolve protein orientations in PAS-domain signaling by combining nano-FTIR and chiral vibrational sum-frequency generation (VSFG) spectroscopy with molecular dynamics simulations and VSFG spectral calculations. As a demonstration, we used a charged homopolypeptide, poly-l-lysine (PLL), as a surrogate binding surface to probe PYP docking. We found that PYP adopts a preferred interfacial orientation driven primarily by dipole-dipole interactions, despite its water-soluble, i.e., cytoplasmic nature. Remarkably, the inferred interaction surface and orientation closely match those observed in PYP homodimers and in a CNBh-PAS heterodimer. This methodology enables in situ determination of protein orientational preferences during protein-protein interactions and may facilitate identification of binding partners in PAS-domain signaling pathways.
Source: Biomacromolecules
Language: English
Subfield: Atomic and Molecular Physics, and Optics
Field: Physics and Astronomy
Domain: Physical Sciences
Open Access status: hybrid
Estimated APC paid: $4,500
Funders: Laserlab-Europe, European Commission, Deutscher Akademischer Austauschdienst, Deutsche Forschungsgemeinschaft, Freie Universität Berlin, Nemzeti Kutatási Fejlesztési és Innovációs Hivatal, Tempus Közalapítvány, Magyarország Kormánya, Helmholtz-Zentrum Berlin für Materialien und Energie, Horizon 2020, Nemzeti Kutatási, Fejlesztési és Innovaciós Alap, National Research, Development and Innovation Office, German Academic Exchange Service
OpenAlex ID: W7159592568