1. Design of Supramolecular Protein Assemblies for Nano and Biomedical Applications:

: Design of supramolecular protein assemblies for nano and biomedical applications

- Coiled coil

- Helical barrel

- Channel protein

- 2D/3D templated protein assemblies

- Bio-inspired cathod material in fuel cell

- Biomimetic solar cell

Nature evolves protein sequences for a great variety of structural and functional tasks. This programmability makes proteins ideal for engineering of structural assemblies. We have developed computational protein designs that generate hybrid aseemblies between carbon-based materials and proteins. In particular, we set out to apply principles of protein to engineer peptides that form well-ordered structures on the surface of single-walled carbon nanotubes. The main significance is that we were able to design peptides that specifically recognize surface lattices. We solved the crystal structure of a representative peptide and found that it possessed the intended unit of assembly. Our success demonstrates the potential of protein design in engineering assemblies of functions or materials that are quite unprecedented in nature.

My second project in this field was geared towards designing pepides that associate with fullerene. By searching and testing various fullerene derivatives

and designed peptides, we succeeded in solving the first example of protein crystal structure in the presence of fullerenes. The crystal structure revealed that the association of fullerene with de novo designed peptides could be achieved using computational protein design.

The simulation-guided design principle enables us to engineer a peptide assembly formed only in the presence of a pristine graphene surface. In particular, a rationally designed peptide sequence resulting in the formation of peptide assembly on the surface of a pristine graphene was supported from atomistic simulations in the viewpoint of both thermodynamic stability and energetics. It is shown that for a rationally designed peptide sequence, the structure of peptide self-assembly is thermodynamically stable and is energetically optimized such that both peptide-peptide interactions and peptide-graphene interactions are maximized.

2. Fundamental studies of Protein Folding for diseases such as Diabetes and Brain diseases

: Elucidating the structure of pro-human Islet amyloid peptide (pro-hIAPP) in human type diabetes.

- Analysis the structural and dynamic properties using X-ray crystallography and femto-second FT-IR

- Predict possible structure by homological sequence-dependent modeling and simulate the dynamics of protein in aqueous solution or cytoplasm-like environment

3. Functional Protein Material Design for Brain imaging, Stem Cell, Angiogenesis, Antibacterial and Cosmetics.

Our biomaterial design lab focuses on design and structural characterization of protein-based biomaterials that can be toward to make cellular and molecular therapies effective and practical approaches eventually to treat disease. New biomaterials are now designed rationally or computationally with controlled assembly structure and dynamic functionality to integrate with biological complexity and perform tailored, high-level functions in the body. These biomaterials designs are used to study the mechanisms by which chemical or mechanical signals are sensed by cells, alter cell function and further brain function in vivo.

4. Surface Chemistry for biosensor

- Super-hydrophobic

- Protein assemblies on 2D-materials

- Conducting bio-surfaces

- Simulation of protein behavior on solid surfaces

ex) Single-Molecule Protein Arrays on Sub-10-nm Lithographic Surfaces

Templating assembly of biomolecules can create complex nano-structured devices with precisely tailored chemical or biological responses, with applications in, for example, biomedical or environmental sensors. In this research project, we have focused on developing methods for creating complex molecular top-down templating of assembled structures of proteins or DNAs that is relevant to a range of devices. The main goal is therefore to guide the self-assembly process using engineered templates which control the spatial location and orientation for the self-assembling biomolecules. Especially, we have developed the method to fabricate protein array and assembly that will be directed by lithographic templates in sub-10-nm resolution with arbitrary nano-pattern. The templating of protein assembly could be evaluated in common electron microscopes (SEM, AFM, and TEM) and a variety of imaging techniques.