Time-resolved detection of SDS-induced conformational changes in α-synuclein by a micro-stopped-flow system

Mechanisms of Biomolecular Self-Assembly Investigated Through In Situ Observations of Structures and Dynamics

Biomolecular self-assembly of hierarchical materials is a precise and adaptable bottom-up approach to synthesizing across scales with considerable energy, health, environment, sustainability, and information technology applications. To achieve desired functions in biomaterials, it is essential to directly observe assembly dynamics and structural evolutions that reflect the underlying energy landscape and the assembly mechanism. This review will summarize the current understanding of biomolecular assembly mechanisms based on in situ characterization and discuss the broader significance and achievements of newly gained insights. In addition, we will also introduce how emerging deep learning/machine learning-based approaches, multiparametric characterization, and high-throughput methods can boost the development of biomolecular self-assembly. The objective of this review is to accelerate the development of in situ characterization approaches for biomolecular self-assembly and to inspire the next generation of biomimetic materials.

Intrinsically disordered plant protein PARCL colocalizes with RNA in phase-separated condensates whose formation can be regulated by mutating the PLD

In higher plants, long-distance RNA transport via the phloem is crucial for communication between distant plant tissues to align development with stress responses and reproduction. Several recent studies suggest that specific RNAs are among the potential long-distance information transmitters. However, it is yet not well understood how these RNAs enter the phloem stream, how they are transported, and how they are released at their destination. It was proposed that phloem RNA-binding proteins facilitate RNA translocation. In the present study, we characterized two orthologs of the phloem-associated RNA chaperone-like (PARCL) protein from Arabidopsis thaliana and Brassica napus at functional and structural levels. Microscale thermophoresis showed that these phloem-abundant proteins can bind a broad spectrum of RNAs and show RNA chaperone activity in FRET-based in vitro assays. Our SAXS experiments revealed a high degree of disorder, typical for RNA-binding proteins. In agroinfiltrated tobacco plants, eYFP-PARCL proteins mainly accumulated in nuclei and nucleoli and formed cytosolic and nuclear condensates. We found that formation of these condensates was impaired by tyrosine-to-glutamate mutations in the predicted prion-like domain (PLD), while C-terminal serine-to-glutamate mutations did not affect condensation but reduced RNA binding and chaperone activity. Furthermore, our in vitro experiments confirmed phase separation of PARCL and colocalization of RNA with the condensates, while mutation as well as phosphorylation of the PLD reduced phase separation. Together, our results suggest that RNA binding and condensate formation of PARCL can be regulated independently by modification of the C-terminus and/or the PLD.

Applications of Time-Resolved Thermodynamics for Studies on Protein Reactions

Thermodynamics and kinetics are two important scientific fields when studying chemical reactions. Thermodynamics characterize the nature of the material. Kinetics, mostly based on spectroscopy, have been used to determine reaction schemes and identify intermediate species. They are certainly important fields, but they are almost independent. In this review, our attempts to elucidate protein reaction kinetics and mechanisms by monitoring thermodynamic properties, including diffusion in the time domain, are described. The time resolved measurements are performed mostly using the time resolved transient grating (TG) method. The results demonstrate the usefulness and powerfulness of time resolved studies on protein reactions. The advantages and limitations of this TG method are also discussed.

A Time-Resolved Diffusion Technique for Detection of the Conformational Changes and Molecular Assembly/Disassembly Processes of Biomolecules

Biological liquid-liquid phase separation (LLPS) is driven by dynamic and multivalent interactions, which involves conformational changes and intermolecular assembly/disassembly processes of various biomolecules. To understand the molecular mechanisms of LLPS, kinetic measurements of the intra- and intermolecular reactions are essential. In this review, a time-resolved diffusion technique which has a potential to detect molecular events associated with LLPS is presented. This technique can detect changes in protein conformation and intermolecular interaction (oligomer formation, protein-DNA interaction, and protein-lipid interaction) in time domain, which are difficult to obtain by other methods. After the principle and methods for signal analyses are described in detail, studies on photoreactive molecules (intermolecular interaction between light sensor proteins and its target DNA) and a non-photoreactive molecule (binding and folding reaction of α-synuclein upon mixing with SDS micelle) are presented as typical examples of applications of this unique technique.

Spectrally Silent Protein Reaction Dynamics Revealed by Time-Resolved Thermodynamics and Diffusion Techniques

Biological functions essentially consist of a series of chemical reactions, including intermolecular interactions, and also involve the cooperation of a number of biological molecules performing these reactions. To understand this function at the molecular level, all steps of the reactions must be elucidated. However, since the biosystems including the surrounding environment are notably large, the reactions have to be elucidated from several different approaches. A variety of techniques have been developed to obtain structural information, and the knowledge of the three-dimensional structure of biomolecules has increased dramatically. Contrarily, the current information on reaction dynamics, which is essential for understanding reactions, is still not enough. Although frequently used techniques, such as spectroscopy, have revealed several important processes of reactions, there are various hidden dynamics that are not detected by these methods (silent dynamics). For example, although water molecules are essential for bioreactions, dynamics of the protein-water interaction are very difficult to trace and spectrally silent. Transient association/dissociations of proteins with partner proteins are difficult to observe. Another important property to understand the reaction of proteins is fluctuations, which are random movements that do not change the average structure and energy. The importance of fluctuations has been pointed out in order to explain enzymatic activity; however, it is extremely difficult to detect changes in fluctuation during a reaction. In this Account, unique time-resolved methods, time-resolved thermodynamics, and time-resolved diffusion methods, both of which are able to detect silent dynamics in solution at physiological temperature, are described.Thermodynamic properties are important for characterizing materials, in particular, macromolecules such as biomolecules. Therefore, the data available regarding these properties, for several stable proteins, is abundant. However, it is almost impossible to characterize short-lived intermediate species in irreversible reactions using traditional thermodynamic techniques. Similarly, although the translational diffusion coefficient is a useful property to determine the protein size and intermolecular interactions, there have been no reports revealing reaction dynamics. The transient grating (TG) method enables us to measure these quantities in a time-resolved manner for a variety of irreversible reactions. With this method, it is now possible to study biomolecule reactions from the viewpoint of thermodynamic properties and diffusion, and to elucidate reaction dynamics that cannot be detected by other spectroscopic methods.Here, the principles of the methodologies used, their characteristic advantages, and their applications to protein reactions are described. The TG measurements of octopus rhodopsin revealed a spectrally hidden intermediate and determined an energetic profile along the reaction coordinate. This emphasizes that the measurement in solution, not for trapped intermediates, is important to characterize the reaction intermediates. The application of these methods to a blue light sensor PixD revealed many spectrally silent dynamics as well as the importance of fluctuation for the reaction. As an example of the time-resolved heat capacity change and transient thermal expansion measurements, the reaction of PYP was briefly described. The reaction scheme of another blue light sensor protein, phototropins, and a spectrally silent DNA binding process of EL222 were fully elucidated by the time-resolved diffusion method.