Tryptophan fluorescence quenching by alkaline earth metal cations in deionized bacteriorhodopsin

Decoupling Global and Local Structural Changes in Self-aminoacylating Ribozymes Reveals the Critical Role of Local Structural Dynamics in Ribozyme Activity

Self-aminoacylating ribozymes catalyze the attachment of amino acids to RNA, serving as pivotal models to investigate the catalytic roles of RNA in prebiotic evolution. In this study, we investigated how divalent metal ions (Mg2+ and Ca2+) modulate local and global structures in two such ribozymes, S-1A.1-a and S-2.1-a, using 4-cyanotryptophan (4CNW) fluorescence and native gel electrophoresis. By tracking 4CNW fluorescence changes at varying concentrations of Mg2+ and Ca2+ and temperatures, we determined how these ions influence the catalytic sites and overall conformations of the ribozymes. Our findings reveal that Mg2+ specifically binds to S-1A.1-a at low concentrations, stabilizing the local structure around the aminoacylation site and causing the site to become more buried, which is essential for catalytic activity. Although higher Mg2+ and Ca2+ concentrations induce global structural rearrangements, these shifts have minimal impact on the local environment of the aminoacylation site, underscoring the dominance of local structural stability in sustaining ribozyme function. In contrast, the activity of S-2.1-a effectively adapts to both Mg2+ and Ca2+, and its fluorescence results indicate a more solvent-exposed aminoacylation site. Overall, these data highlight that local structural changes in the ribozyme's catalytic core are more critical for its function than global conformational shifts. Our study highlights the importance of local environmental changes in ion-dependent ribozyme catalysis and provides insights into the molecular mechanisms of self-aminoacylating ribozymes.

Unveiling the Metal-Dependent Aggregation Properties of the C-terminal Region of Amyloidogenic Intrinsically Disordered Protein Isoforms DPF3b and DPF3a

Double-PHD fingers 3 (DPF3) is a BAF-associated human epigenetic regulator, which is increasingly recognised as a major contributor to various pathological contexts, such as cardiac defects, cancer, and neurodegenerative diseases. Recently, we unveiled that its two isoforms (DPF3b and DPF3a) are amyloidogenic intrinsically disordered proteins. DPF3 isoforms differ from their C-terminal region (C-TERb and C-TERa), containing zinc fingers and disordered domains. Herein, we investigated the disorder aggregation properties of C-TER isoforms. In agreement with the predictions, spectroscopy highlighted a lack of a highly ordered structure, especially for C-TERa. Over a few days, both C-TERs were shown to spontaneously assemble into similar antiparallel and parallel β-sheet-rich fibrils. Altered metal homeostasis being a neurodegeneration hallmark, we also assessed the influence of divalent metal cations, namely Cu²⁺, Mg²⁺, Ni²⁺, and Zn²⁺, on the C-TER aggregation pathway. Circular dichroism revealed that metal binding does not impair the formation of β-sheets, though metal-specific tertiary structure modifications were observed. Through intrinsic and extrinsic fluorescence, we found that metal cations differently affect C-TERb and C-TERa. Cu²⁺ and Ni²⁺ have a strong inhibitory effect on the aggregation of both isoforms, whereas Mg²⁺ impedes C-TERb fibrillation and, on the contrary, enhances that of C-TERa. Upon Zn²⁺ binding, C-TERb aggregation is also hindered, and the amyloid autofluorescence of C-TERa is remarkably red-shifted. Using electron microscopy, we confirmed that the metal-induced spectral changes are related to the morphological diversity of the aggregates. While metal-treated C-TERb formed breakable and fragmented filaments, C-TERa fibrils retained their flexibility and packing properties in the presence of Mg²⁺ and Zn²⁺ cations.

Review of Fluorescence Spectroscopy in Environmental Quality Applications

Fluorescence spectroscopy is an optical spectroscopic method that has been applied for the assessment of environmental quality extensively during the last 20 years. Most of the earlier works have used conventional light sources in spectrofluorometers to assess quality. Many recent works have used laser sources of light for the same purpose. The improvement of the energy sources and of the higher resolution spectrometers has led to a tremendous increase in applications. The motivation for the present review study is the increasing use of laser sources in environmental applications. The review is divided in two parts. The fundamental principles of fluorescence spectroscopy are described in the first part. The environmental applications are described in the second part.

Studies on the temperature effect on bacteriorhodopsin of purple and blue membrane by fluorescence and absorption spectroscopy

Fluorescence and absorption spectra were used to study the temperature effect on the conformation of bacteriorhodopsin (bR) in the blue and purple membranes (termed as bRb and bRp respectively). The maximum emission wavelengths of tryptophan fluorescence in both proteins at room temperature are 340 nm, and the fluorescence quantum yield of bRb is about 1.4 fold higher than that of bRp. As temperature increases, the tryptophan fluorescence of bRb decreases, while the tryptophan fluorescence of bRp increases. The binding study of extrinsic fluorescent probe bis-ANS indicated that the probe can bind only to bRb, but not to bRp. These results suggest that significant structural difference existed between bRb and bRp. It was also found that both kinds of bR are highly thermal stable. The maximum wavelength of the protein fluorescence emission only shifted from 340 nm to 346 nm at 100 degrees C. More interestingly, as temperature increased, the characteristic absorption peak of bRb at 605 nm decreased and a new absorption peak at 380 nm formed. The transition occurred at a narrow temperature range (65 degrees C-70 degrees C). These facts indicated that an intermediate can be induced by high temperature. This phenomenon has not been reported before.