Research
Overview
Proteins are intrinsically dynamic. Many proteins, if not all, present multifaceted behaviors, significant portion of which cannot be explained without its structural plasticity. Nonetheless, protein structures were often studied at a specific state or condition, failing to reveal their potential structural versatility. In numerous cases, proteins accommodate structurally-distinctive conformations upon being exposed to different conditions or interacting with different molecules, and understanding to these structural transitions can be a key to elucidate the mechanistic details of the protein functions and activities (Figure 1).
Figure 1. Structural flexibility of the human tau protein. This protein by itself does not have defined structure, rather adopts multiple conformations (thus, called intrinsically disordered protein; IDP). This structural plasticity is closely correlated with its biological functions and pathological properties (Mukrasch, M. D. et al. PLoS Biol, 2009).
Notably, the native equilibrium states over diverse structural conformations of proteins are maintained with delicate balance, perturbation of which could shift the original structural equilibrium. Diseases of proteinaceous origins are often caused by this disruption of protein dynamics. Among various factors, ‘protein aging’ is one of the major culprits that break the dynamic balance and compromise the structural integrity of proteins (Figure 2). This is particularly true for many proteins showing amyloidogenic properties, such as tau protein, amyloid-β, transthyretin, and a certain class of chaperones.
Figure 2. Structural aging of proteins. Accumulation of stresses and damages causes protein structures to be deformed from its healthy 'native' state to harmful 'intermediate' states. Luckily, most intermediate species are detoxified by proteostasis mechanisms (e.g. recruitment of chaperones), while uncontrolled accumulation of intermediate species results in formation of aggregates and amyloids.
Amyloidogenic diseases, which are occurred by abnormal protein aggregation and amyloid formation, are one of the most old-aged, yet still-elusive challenges for us to appreciate and overcome. It is now believed that the aggregation-prone characters of proteins are rather intrinsic; the well-folded tertiary structures of proteins are necessary not only for their functionalities but also for prevention of their aggregation-prone states from being presented. Indeed, the amyloidogenic properties of proteins are often manifested by disruption of its native tertiary or quaternary structures, and again one of the major factors causing this structural disruption is the structural ‘aging’ (the representative example is shown in Figure 3). In order to appreciate this in detail, we eager to investigate atomic-scale structural features of the amyloidogenic proteins not only in its native ‘healthy’ states but also in the ‘aged’ states. We believe that our approaches will provide 1) unprecedented details to understand the pathogenic mechanisms of amyloidogenic proteins, 2) novel insights to reveal protein aging and protein homeostasis mechanisms, and 3) essential ideas to develop 'different' therapeutic approaches that have never been tried before.
Figure 3. The structural aging and pathogenic mechanism of transthyretin (TTR). In its native and functional state, TTR stabilizes the tetrameric state. However, mutagenesis or stress accumulation (i.e. aging) facilitates dissociation of monomeric species, which is responsible for formation of aggregates and amyloids (Johnson, S. M. et al. J Mol Biol, 2012). TTR is a well-known cause of a few severe amyloidosis diseases.
Research Summary
The long-term goal of our laboratory is to reveal the mechanism of the protein amyloidosis on the basis of complete characterization of the tertiary and quaternary structural features in static and dynamic states. In particular, we are interested in elucidating age-dependent structural transitions of proteins; determination of the ‘4-dimensional atomic-resolution structure’ of a protein would provide unprecedented insights regarding protein aging and aggregation mechanisms. In order to accomplish this goal, we target structural characterization of amyloidogenic proteins and chaperones, structural features of which are known to be affected by aging and to eventually cause various human diseases. Notably, we aim to conduct simultaneous and interactive studies regarding amyloidosis and its protection mechanisms, because we believe that this bilateral approach would provide novel and relevant information regarding the disease-related pathogenesis of amyloidogenic proteins. The specific aims of our laboratory include the following.
1. Characterization of the dynamic structural features of proteins
The intrinsic dynamic features of proteins are highly related not only to their physiological functions but also to the pathological mechanisms. We, therefore, would like to pursue appreciating dynamic features of amyloidogenic proteins in order to elucidate its amyloidosis mechanism. In addition, we are interested in investigating structural plasticity of chaperones. Structural dynamics of chaperones is directly correlated with the cellular protection mechanisms against aggregation-prone proteins, and the structural studies regarding this interplay between amyloidosis and its chaperoning mechanisms will be crucial to understand their actual physiology.
Figure 4. The atomic-resolution structure of Fyn SH3 domain determined by NMR spectroscopy (Neudecker et al. Science, 2012). Fyn SH3 domain is a well-folded and non-amyloidogenic protein in its native state (orange). However, it was shown with NMR that this protein has an alternative low-populated amyloidogenic conformation (green) even in its non-amyloidogenic condition. And, it turned out that once a certain stress (such as aging) perturbs the equilibrium of this protein, population of the amyloidogenic conformation increases, and the protein starts to aggregate. We believe that the case of Fyn SH3 domain represents the rather general pathogenic mechanism of protein amyloidosis.
2. Elucidation of the pathogenesis mechanisms of amyloidogenic proteins
We are eager to appreciate the actual aggregation mechanisms of proteins, which is directly correlated with its pathogenesis. In particular, we are interested in (1) identifying the causes perturbing the native structural state of proteins, (2) revealing the mechanism facilitating aggregation/amyloid formation, and (3) determining the structural model of oligomers/aggregates/amyloids and appreciating its structural architecture.
3. Elucidation of the interactions between chaperones and pathogenic aggregation-prone proteins
We are also highly interested in understanding the mechanisms of chaperones to suppress the pathogenic pathway of aggregation-prone proteins. Notably, the working mechanisms of chaperones are fairly complex; chaperones use various structural features to interact with misfolded and aggregation-prone proteins, and the resultant behaviors of misfolded proteins are also diverse. We aim to understand how chaperones interact with and perturb toxic structural features of the substrate proteins.
Figure 5. Structure of the ACD domain from αB-crystallin (left), and the highly dynamic oligomeric states of αB-crystallin (right). Despite its physiological importance as an essential small heat-shock protein, structural plasticity of this protein is still elusive. This heterogeneous oligomeric feature is closely related with its physiological working mechanisms as an essential small heat-shock proteins (Bakthisaran, R. et al. BBA, 2015).
4. Development of novel therapeutic strategy based on structural understanding to amyloidosis mechanisms of proteins
Many amyloidosis mechanisms of pathogenic proteins are still not appreciated to the atomic scale. We expect that acquisition of structural details for the toxic and aggregation-prone species would enable us to design novel therapeutic molecules to suppress aggregation or even restore structural aging of proteins. In particular, we believe that our study to the amyloidosis mechanism will help us to develop 'different' strategies to overcome many neurodegenerative diseases and amyloidosis pathology.