Site-Specific Identification of Protein S-Acylation by IodoTMT0 Labeling and Immobilized Anti-TMT Antibody Resin Enrichment

Protein S-acylation is a reversible post-translational modification (PTM). It is present on diverse proteins and has important roles in regulating protein function. Aminolysis with hydroxylamine is widely used in the global identification of the PTM. However, the identification is indirect. Distinct criteria have been used for identification, and the false discovery rate has not been addressed. Here, we report a site-specific method for S-acylation identification based on tagging of S-acylation sites with iodoTMT0. Efforts to improve the performance of the method and confidence of identification are discussed, highlighting the importance of reducing contaminant peptides and keeping the recovery rate consistent between aliquots with or without hydroxylamine treatment. With very stringent criteria, presumptive S-acylation sites of 269, 684, 695, and 780 were identified from HK2 cells, HK11 cells, mouse brain, and mouse liver samples, respectively. Among them, the newly identified protein S-acylation sites are equivalent to 34% of human and 24% of mouse S-acylation sites reported previously. In addition, false-positive rates for S-acylation identification and S-acylation abundances were estimated. Significant differences in S-acylation abundance were found from different samples (from 0.08% in HK2 cells to 0.76% in mouse brain), and the false-positive rates were significantly higher for samples with a low abundance of S-acylation.

Tracking Optical Welding through Groove Modes in Plasmonic Nanocavities

We report the light-induced formation of conductive links across nanometer-wide insulating gaps. These are realized by incorporating spacers of molecules or 2D monolayers inside a gold plasmonic nanoparticle-on-mirror (NPoM) geometry. Laser irradiation of individual NPoMs controllably reshapes and tunes the plasmonic system, in some cases forming conductive bridges between particle and substrate, which shorts the nanometer-wide plasmonic gaps geometrically and electronically. Dark-field spectroscopy monitors the bridge formation in situ, revealing strong plasmonic mode mixing dominated by clear anticrossings. Finite difference time domain simulations confirm this spectral evolution, which gives insights into the metal filament formation. A simple analytic cavity model describes the observed plasmonic mode hybridization between tightly confined plasmonic cavity modes and a radiative antenna mode sustained in the NPoM. Our results show how optics can reveal the properties of electrical transport across well-defined metallic nanogaps to study and develop technologies such as resistive memory devices (memristors).