Protein corona formation on different-shaped CdSe/CdS semiconductor nanocrystals.

Nanoparticles (NPs) have been widely studied and applied in medical and pharmaceutical fields. When NPs enter the environment, they are covered with protein molecules to form the so-called "protein corona". Because NPs and proteins are comparable in size, the shape of NPs has a significant impact on NP-protein interactions.

Concerted primary proton transfer reactions in a thermophilic rhodopsin studied by time-resolved infrared spectroscopy at high temperature.

The primary proton transfer reactions of thermophilic rhodopsin, which was first discovered in an extreme thermophile, Thermus thermophilus JL-18, were investigated using time-resolved Fourier transform infrared spectroscopy at various temperatures ranging from 298 to 343 K (25 to 70 °C) and proton transport activity analysis. The analyses were performed using counterion (D95E, D95N, D229E, and D229N) and proton donor mutants (E106D and E106Q) as well. First, the initial proton transfer from the protonated retinal Schiff base (PRSB) to D95 was identified.

SOD1 gains pro-oxidant activity upon aberrant oligomerization: change in enzymatic activity by intramolecular disulfide bond cleavage.

Copper-zinc superoxide dismutase (SOD1) has been proposed as one of the causative proteins of amyotrophic lateral sclerosis (ALS). The accumulation of non-native conformers, oligomers, and aggregates of SOD1 in motor neurons is considered responsible for this disease. However, it remains unclear which specific feature of these species induces the onset of ALS.

Concentration Quantification of the Low-Complexity Domain of Fused in Sarcoma inside a Single Droplet and Effects of Solution Parameters.

Liquid-liquid phase separation (LLPS) is an important phenomenon in biology, and it is desirable to develop quantitative methods to analyze protein droplets generated by LLPS. This study quantified the change in protein concentration in a droplet in label-free and single-droplet conditions using Raman imaging and the Raman band of water as an intensity standard. Small changes in the protein concentration with variations in pH and salt concentration were observed, and it was shown that the concentration in the droplet decreases as the conditions become less favorable for droplet formation.

FTIR study of the surface-ligand exchange reaction with glutathione on biocompatible rod-shaped CdSe/CdS semiconductor nanocrystals.

Semiconductor nanocrystals (SNCs) are an essential optical tool in life sciences. Application of SNCs to living systems requires that their surfaces be covered with biocompatible molecules. The surface capping of SNCs by glutathione (GSH) is an effective means to prepare biocompatible SNCs and involves replacement of the initial surface ligands with GSH.

Observation of liquid-liquid phase separation of ataxin-3 and quantitative evaluation of its concentration in a single droplet using Raman microscopy.

Liquid-liquid phase separation (LLPS) plays an important role in a variety of biological processes and is also associated with protein aggregation in neurodegenerative diseases. Quantification of LLPS is necessary to elucidate the mechanism of LLPS and the subsequent aggregation process. In this study, we showed that ataxin-3, which is associated with Machado-Joseph disease, exhibits LLPS in an intracellular crowding environment mimicked by biopolymers, and proposed that a single droplet formed in LLPS can be quantified using Raman microscopy in a label-free manner.

Pro-Oxidant Activity of an ALS-Linked SOD1 Mutant in Zn-Deficient Form.

Cu, Zn superoxide dismutase (SOD1) is a representative antioxidant enzyme that catalyzes dismutation of reactive oxygen species in cells. However, (E,E)-SOD1 mutants in which both copper and zinc ions were deleted exhibit pro-oxidant activity, contrary to their antioxidant nature, at physiological temperatures, following denaturation and subsequent recombination of Cu. This oxidative property is likely related to the pathogenesis of amyotrophic lateral sclerosis (ALS); however, the mechanism by which Cu re-binds to the denatured (E,E)-SOD1 has not been elucidated, since the concentration of free copper ions in cells is almost zero.

Enhancement of Oxidative Reaction by the Intramolecular Electron Transfer between the Coordinated Redox-Active Metal Ions in SOD1.

The denatured Cu, Zn superoxide dismutase (SOD1) has the pro-oxidant activity that is suggested to be related with the pathogenesis of amyotrophic lateral sclerosis (ALS). We showed from the changes in the coordinated metal ions that the Cu ion in the Cu-binding site is the catalytic site of the pro-oxidant activity, and a redox-active metal ion in the Zn-binding site has the auxiliary function to enhance the pro-oxidant activity. The auxiliary function is suggested to arise from the intramolecular electron transfer between the coordinated metal ions in the denatured SOD1.

Time-resolved FTIR study on the structural switching of human galectin-1 by light-induced disulfide bond formation.

Disulfide bonds play a fundamental role in controlling the tertiary structure of proteins; the formation or cleavage of some disulfide bonds can switch the structures and/or functions of proteins. Human galectin-1 (hGal-1), which is a lectin protein, exemplifies how both structure and function are changed by disulfide bonds; the structure and sugar-binding ability of hGal-1 are altered by the formation and cleavage of its three intra-molecular disulfide bonds. In the present study, the dynamics of the structural change of hGal-1 by the formation of disulfide bonds were investigated by time-resolved FTIR spectroscopy combined with a modification in which its thiol groups (-SH) were replaced with S-nitrosylated groups (SNO).

Examination of the association states of dehydroergosterol towards understanding the association structures of sterols in a membrane.

Cholesterol plays a number of roles in cell membranes, and dehydroergosterol (DHE) is a fluorescent derivative of cholesterol, which is used to investigate the association structure of cholesterol. Although the fluorescent property of DHE depends on its association state, it is insufficient to distinguish the association state of DHE only by its fluorescence. Circular dichroism (CD) spectroscopy is an effective way to investigate the molecular geometry of DHE.

Anomalous pressure effects on the photoreaction of a light-sensor protein from Synechocystis, PixD (Slr1694), and the compressibility change of its intermediates.

SyPixD (Slr1694) is a blue-light receptor that contains a BLUF (blue-light sensor using a flavin chromophore) domain for the function of phototaxis. The key reaction of this protein is a light-induced conformational change and subsequent dissociation reaction from the decamer to the dimer. In this study, anomalous effects of pressure on this reaction were discovered, and changes in the compressibility of its short-lived intermediates were investigated.

Time-resolved fluctuation during the photochemical reaction of a photoreceptor protein: phototropin1LOV2-linker.

Although the relationship between structural fluctuations and reactions is important for elucidating reaction mechanisms, experimental data describing such fluctuations of reaction intermediates are sparse. In order to investigate structural fluctuations during a protein reaction, the compressibilities of intermediate species after photoexcitation of a phot1LOV2-linker, which is a typical LOV domain protein with the C-terminal linker including the J-α helix and used recently for optogenetics, were measured in the time-domain by the transient grating and transient lens methods with a high pressure optical cell. The yield of covalent bond formation between the chromophore and a Cys residue (S state formation) relative to that at 0.

Pressure-sensitive reaction yield of the TePixD blue-light sensor protein.

The effect of pressure on the dissociation reaction of the TePixD decamer was investigated by high-pressure transient grating (TG). The TG signal intensity representing the dissociation reaction of the TePixD decamer significantly decreased by applying a relatively small pressure. On the other hand, the reaction rate increased with increasing pressure.

Transient conformational fluctuation of TePixD during a reaction.

Knowledge of the dynamical behavior of proteins, and in particular their conformational fluctuations, is essential to understanding the mechanisms underlying their reactions. Here, transient enhancement of the isothermal partial molar compressibility, which is directly related to the conformational fluctuation, during a chemical reaction of a blue light sensor protein from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (TePixD, Tll0078) was investigated in a time-resolved manner. The UV-Vis absorption spectrum of TePixD did not change with the application of high pressure.

Anomalous diffusion of TePixD and identification of the photoreaction product.

TePixD is a blue-light sensor protein from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (TePixD Tll0078). Although the photochemistry has been examined, so far the photoproduct remains unknown. We have measured the diffusion coefficient (D) of TePixD in the dark by dynamic light scattering and have discovered a very peculiar diffusion property; the decamer oligomer has a larger D than that of the pentamer.