Improved Protein Model in SPICA Force Field.

The previous version of the SPICA coarse-grained (CG) force field (FF) protein model focused primarily on membrane proteins and successfully reproduced the dimerization free energies of several transmembrane helices and the stable structures of various membrane protein assemblies. However, that model had limited accuracy when applied to other proteins, such as intrinsically disordered proteins (IDPs) and peripheral proteins, because the dimensions of the IDPs in an aqueous solution were too compact, and protein binding on the lipid membrane surface was overstabilized. To improve the accuracy of the SPICA FF model for the simulation of such systems, in this study, we introduce protein secondary structure-dependent nonbonded interaction parameters to the backbone segments and reoptimize almost all nonbonded parameters for amino acids.

Fluorescence Turn-on of Tetraphenylethylene Derivative by Transfer from Cyclodextrin to Liposomes, HeLa Cells, and E. coli.

Herein, trimethyl-β-cyclodextrin (TMe-β-CDx) and γ-cyclodextrin (γ-CDx) could dissolve a tetraphenylethylene derivative (TPE-OH ) in water through high-speed vibration milling. The fluorescence intensity of the TMe-β-CDx-TPE-OH complex was much higher than that of the γ-CDx-TPE-OH complex, as the rotation of the central C=C double bond of TPE-OH after photoactivation was inhibited in a smaller TMe-β-CDx cavity in comparison with the γ-CDx cavity. In contrast, the fluorescence intensity of the γ-CDx-TPE-OH complex was very weak; nevertheless, it increased after the addition of liposomes due to the transfer of TPE-OH from the γ-CDx cavity to the lipid membrane as a "turn-on" phenomenon.