The molecular crowding effect on ligand-protein interactions, which plays several crucial roles in life processes, has been investigated using various models by adding crowding agents to mimic the intracellular environment. Several studies evaluating this effect have focused on the ligand-protein binding reaction of well-structured binding sites with rigid conformations. However, the crowding effect on flexible binding sites is not well-understood, especially in terms of the conformations. In this work, to elucidate the detailed molecular mechanism underlying the ligand-protein interactions with flexible binding sites on a protein surface, we studied the interaction between the basic protrusion of Escherichia coli ribonuclease HI (RNase HI) and 8-anilinonaphthalene-1-sulfonic acid (ANS). The RNase HI concentration-dependent measurement of ANS fluorescence combined with the multivariate analysis and the fluorescence vibronic structure analysis revealed an increase in the heterogeneous species with an increase in the protein concentration, which is a different behavior from that of proteins with rigid binding sites. This result indicates that ANS molecules bind to the additional binding sites because of the destabilization of the main sites by the excluded volume effect in a crowded environment. The fluorescence vibronic structure analysis yields a detailed molecular picture, indicating that the main species of ANS can have a distorted structure. On the other hand, some ANS molecules move to the minor binding sites of a different microenvironment to secure a stabilized structure. These spectroscopic analyses may show a hypothesis, suggesting that the decrease in the ΔG difference between the main and minor sites due to destabilization of the main binding site could lower the potential barrier between them, inducing the dispersion of binding pathways.
Protein-ligand interactions in crowded cellular environments play a crucial role in biological functions. The crowded environment can perturb the overall protein structure and local conformation, thereby influencing the binding pathway of protein-ligand reactions within the cellular milieu. Therefore, a detailed understanding of the local conformation is crucial for elucidating the intricacies of protein-ligand interactions in crowded cellular environments. In this study, we investigated the feasibility of induced circular dichroism (ICD) using 8-anilinonaphthalene-1-sulfonic acid (ANS) for local conformational analysis at the binding site in a crowding environment. Bovine serum albumin (BSA) concentration-dependent measurements were performed to assess the feasibility of ANS-ICD for analyzing protein interior binding sites. The results showed distinct changes in the ANS-ICD spectra of BSA solutions, indicating their potential for analyzing the internal conformation of proteins. Moreover, temperature-dependent measurements were performed in dilute and crowding environments, revealing distinct denaturation pathways of BSA binding sites. Principal component analysis of ANS-ICD spectral changes revealed lower temperature pre-denaturation in the crowded solution than that in the diluted solution, suggesting destabilization of binding sites owing to self-crowding repulsive interactions. The established ANS-ICD method can provide valuable conformational insights into protein-ligand interactions in crowded cellular environments.
Femtosecond time-resolved transient absorption spectroscopy was performed for a nonfluorescent solvatochromic dye, phenol blue, N-(4-dimethylaminophenyl)-1,4-benzoquinoneimine, which exhibits ultrafast nonradiative decay due to its flexible molecular structure. By exciting the molecule in ethanol (EtOH) solution with two excitation wavelengths located at shorter- and longer-wavelength sides of the visible absorption band, we observed ultrafast nonradiative decay from the excited state, followed by spectral evolution in the ground state. The nonradiative decay in the subpicosecond range creates a vibrationally hot ground state with the lifetime in the picosecond range. Subsequently, a tautomer that absorbs at shorter wavelengths is produced from the hot state, which causes a red shift of the ground-state bleach (GSB). The tautomerization presumably involves twisting of the benzoquinoneimine moiety induced by the breaking of the hydrogen bond (H-bond) between the solute and the solvent molecules. The recombination of the H-bond occurs with a time constant of ∼30 ps, and the system returns to its original state. We also observed low-frequency coherent wavepacket oscillations that modulate the GSB with dephasing times similar to the excited-state lifetime.
We used Raman spectroscopy to investigate the structure and interactions of lysozyme molecules in solution over a wide range of concentrations (2.5-300 mg ml(-1)). No changes in the amide-I band were observed as the concentration was increased, but the width of the Trp band at 1555 cm(-1) and the ratios of the intensities of the Tyr bands at 856 and 837 cm(-1), the Trp bands at 870 and 877 cm(-1), and the bands at 2940 (CH stretching) and 3420 cm(-1) (OH stretching) changed as the concentration was changed. These results reveal that although the distance between lysozyme molecules changed by more than an order of magnitude over the tested concentration range, the secondary structure of the protein did not change. The changes in the molecular interactions occurred in a stepwise process as the order of magnitude of the distance between molecules changed. These results suggest that Raman bands can be used as markers to investigate the behavior of high-concentration solutions of proteins and that the use of Raman spectroscopy will lead to progress in our understanding not only of the basic science of protein behavior under concentrated (i.e., crowded) conditions but also of practical processes involving proteins, such as in the field of biopharmaceuticals.
Raman spectroscopy can be used for analysis of objects by detecting the vibrational spectrum using label-free methods. This imaging method was applied to analysis of peripheral nerve regeneration by examining the sciatic nerve in vitro and in vivo. Raman spectra of intact nerve tissue had three particularly important peaks in the range 2800−3000 cm −1 . Spectra of injured sciatic nerves showed significant changes in the ratio of these peaks. Analysis of cellular spectra suggested that the spectrum for sciatic nerve tissue reflects the axon and myelin components of this tissue. Immunohistochemical analysis showed that the number of axons and the myelinated area were reduced at 7 days after injury and then increased by 28 days. The relative change in the axon to myelin ratio showed a similar initial increase, followed by a decrease at 28 days after injury. These changes correlated with the band intensity ratio and the changes in distribution of axon and myelin in Raman spectral analysis. Thus, our results suggest that label-free biochemical imaging with Raman spectroscopy can be used to detect turnover of axon and myelin in peripheral nerve regeneration.
