Diffusion-based determination of protein homodimerization on reconstituted membrane surfaces

A General Strategy for Enhanced Single-Molecule Imaging Through Intramolecular Energy Transfer

Single-molecule imaging demands fluorophores with exceptional photostability and photon budget. This study presents an intramolecular energy transfer (IMET) strategy to enhance these critical properties. We developed xanthene-based IMET cassettes by covalently linking donor and acceptor, achieving significant improvements in single-molecule imaging performance. While extensive spectral overlap is generally beneficial in bulk systems, single-molecule imaging necessitates careful optimization to minimize direct acceptor excitation at the high excitation powers typically used. Our optimized cassettes, featuring rhodamine as donor and Si-rhodamine as acceptor, exhibit 94.8% energy transfer efficiency. This configuration effectively minimizes direct excitation-induced acceptor bleaching, as 94.9% of molecules exhibit donor photobleaching prior to acceptor photobleaching. This efficient energy management leads to a 670% enhancement in photostability, arising from the competition between IMET and photobleaching pathways, which effectively channels excitation energy away from photo-destructive processes. Time-resolved transient absorption spectroscopy revealed that IMET occurs on a picosecond timescale, significantly faster than both fluorescence relaxation (nanoseconds) and photobleaching (seconds). Notably, these IMET cassettes demonstrated superior performance in single-molecule tracking applications, including on supported lipid bilayers and in live-cell tracking of epidermal growth factor receptor (EGFR) dynamics, highlighting the broad potential of the IMET strategy for advancing single-molecule imaging.

Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane

The oncogene RAS, extensively studied for decades, presents persistent gaps in understanding, hindering the development of effective therapeutic strategies due to a lack of precise details on how RAS initiates MAPK signaling with RAF effector proteins at the plasma membrane. Recent advances in X-ray crystallography, cryo-EM, and super-resolution fluorescence microscopy offer structural and spatial insights, yet the molecular mechanisms involving protein-protein and protein-lipid interactions in RAS-mediated signaling require further characterization. This study utilizes single-molecule experimental techniques, nuclear magnetic resonance spectroscopy, and the computational Machine-Learned Modeling Infrastructure (MuMMI) to examine KRAS4b and RAF1 on a biologically relevant lipid bilayer. MuMMI captures long-timescale events while preserving detailed atomic descriptions, providing testable models for experimental validation. Both in vitro and computational studies reveal that RBDCRD binding alters KRAS lateral diffusion on the lipid bilayer, increasing cluster size and decreasing diffusion. RAS and membrane binding cause hydrophobic residues in the CRD region to penetrate the bilayer, stabilizing complexes through β-strand elongation. These cooperative interactions among lipids, KRAS4b, and RAF1 are proposed as essential for forming nanoclusters, potentially a critical step in MAP kinase signal activation.