Research Theme

De novo Design of Protein Molecule

Keywords

Protein Design, Protein Folding, Structural Biology

Protein molecules spontaneously fold into unique three-dimensional structures specified by their amino acid sequences from random coils to carry out their functions. Many protein studies have been performed by analyzing naturally occurring proteins. However, it is difficult to reach fundamental working principles of protein molecules only by analyzing naturally occurring proteins, since they evolved in their particular environments spending billions of years. In our lab, we explore the principles by computationally designing protein molecules completely from scratch and experimentally assessing how they behave.

Protein design holds promise for applications ranging from catalysis to therapeutics. There has been considerable recent progress in computationally designing proteins with new functions. Many protein design studies have been conducted using naturally occurring protein structures as design scaffolds. However, since naturally occurring proteins have evolutionally optimized their structures for their functions, implementing new functions into the structures of naturally occurring proteins is difficult for most of cases. Rational methods for building any arbitrary protein structures completely from scratch provide us opportunities for creating new functional proteins. In our lab, we tackle to establish theories and technologies for designing any arbitrary protein structures precisely from scratch. The established methods will open up an avenue of rational design for novel functional proteins that will contribute to industry and therapeutics.

Selected Publications

1. Rie Koga, Mami Yamamoto, Takahiro Kosugi, Naohiro Kobayashi, Toshihiko Sugiki, Toshimichi Fujiwara, Nobuyasu Koga, Robust folding of a de novo designed ideal protein even with most of the core mutated to valine. Proc. Natl. Acad. Sci. USA, 117(49), 31149-31156 (2020).
2. Rie Koga and Nobuyasu Koga, Consistency principle for protein design, Biophys. Physicobiol. 16, 304-309 (2019).
3. Nobuyasu Koga, Rie Tatsumi-Koga, Gaohua Liu, Rong Xiao, Thomas B. Acton, Gaetano T. Montelione and David Baker, Principles for designing ideal protein structures, Nature 491(7423), 222-227 (2012).
4. Yu-Ru Lin, Nobuyasu Koga, Rie Tatsumi-Koga, Gaohua Liu, Amanda F. Clouser, Gaetano T. Montelione, David Baker, Control over overall shape and size in de novo designed proteins, Proc. Natl. Acad. Sci. USA 112(40), E5478-5485 (2015).