top of page

~Protein Design and Engineering toward the Creation of Bionanobot~

Proteins are biomolecules that are involved in all kinds of biological phenomena and have a wide variety of structures and functions. If it becomes possible for chemists to design and control the structure and function of these proteins as they wish, it will be possible to create "bionanobots" that spontaneously activate the necessary functions when needed in the pharmaceutical and biotechnological fields. However, current protein design is limited to the construction of protein assembly structures, despite the elaborate and complicated techniques required to artificially control proteins, which are rich in complexity and diversity. Therefore, our laboratory aims to establish "new protein design" that maximizes the inherent advantages of individual proteins rather than forcibly controlling their characteristics, and we are promoting research that will lead to the creation of bionanobots in the future.

Screen Shot 2021-12-16 at 19.12.11.png

Protein Design

Harnessing the "forces of evolution" to create the enzyme you wanted! The 2018 Nobel Prize in Chemistry spotlighted the evolutionary molecular engineering of proteins. Among them, the work of one of the laureates, Professor Frances H. Arnold (Prize Share: 1/2), is a groundbreaking study that realized "directed evolution" of proteins. Directed evolution is one of the leading methods in protein design, but there are also "computational design" and "intuitive design," each of which has been developing at a dizzying pace. In our laboratory, we are working on protein design by "intuitive design".

Protein Higher-Order Structure Formation Design
(Reference:Nature 2016, 533, 369-373

In recent years, there has been an upsurge in protein design research aimed at the creation of bionanorobots as described above. However, most of the designs to date have required advanced techniques to artificially control extremely complex and diverse protein structures. As a result, the probability of success is low and involves a lot of trial and error. On the other hand, in Suzuki's previous research, based on the original idea of "using the characteristics of individual proteins rather than forcibly controlling them," we achieved the previously considered difficult task of "producing a uniform protein 2D sheet structure without defects." The design is very simple: Cysteine, a type of amino acid, is attached to the four corners of a square protein as a "connector" and the connectors are linked to each other (disulfide bond formation by oxidation). Furthermore, by changing the connector to histidine, a type of amino acid that enables metal-mediated binding, and by modifying the base protein from a tetramer to an octamer, we were able to create two-dimensional sheets with different structures. We have discovered the potential development and application of this design.

Screen Shot 2021-12-22 at 21.06.34.png

"Artificial Control of Structural Change Ability" + "Addition of Functionality"
=Development into a New and Unique Design

(References:Nature 2016, 533, 369-373, Nature Chemistry 2018, 10, 732-739, Biochemistry 2021, 60, 1050-1062

Detailed examination of the 2D sheet structure obtained in the above design revealed that it takes on a variety of conformational states. This is due to the "open/closed state change" of the 2D sheet structure, reflecting the flexibility of the bonding between cysteine, and this flexible state change can be controlled by the mechanical operation of "stirring (open) ⇄ sedimentation (closed)". Furthermore, it is noteworthy that this open/closed structural change exhibits a property called "auxetic," as shown in the figure below, which is expected to be applied as a nanomaterial that effectively absorbs external shock (in fact, a material based on auxetic properties was used in the sole of Nike shoes released in 2016). In addition, by adding further design to the base protein, we have succeeded in creating variations in the drive control of the open/closed state, and in adding functionality to the 2D sheet.

Screen Shot 2021-12-22 at 21.09.30.png

Design for the Fusion of "Structure" and "Function"

Most current protein designs remain focused on either "structure" or "function. The above-mentioned design was originally aimed at "structure creation," and only after detailed analysis of the sample "function was discovered," leading to the subsequent design. On the other hand, many proteins in nature play the roles of both "construction of structure" and "expression of function. If chemists can freely control both of these roles, protein design is expected to make great strides. Therefore, our laboratory aims to establish "new protein design" that encompasses both structure and function by evolving and developing the method that "bringing out the inherent attractiveness of proteins by utilizing their features, rather than forcibly controlling them." Furthermore, based on the knowledge obtained, we will promote research aimed at the creation of "bionanobots" that are expected to play an active role in many fields in the future. The following projects are currently underway to realize these goals.

Ongoing Projects

  •  Establishment of a simple method for higher-order structure formation by multiple proteins

  • ​ Establishment of a method for the formation of ordered protein assemblies

  •  Creation of functional protein assemblies that incorporate the functions of natural proteins

  •  "Structure Formation Design" × "Artificial Enzyme Design" × "Evolutionary Molecular Engineering"

=Creation of Next Generation Protein Design

(KAKENHI Transformative Research Areas B)

   → Transformative Research Areas (B) 『SPEED』 website

  •  Creation of fusion designs with other biomacromolecules

(collaborative research with Professor Hirohide Saito, Kyoto University)

bottom of page