Nobuyasu Koga

 

Dr. Nobuyasu Koga (古賀信康)


 

 

Reseach Interests:

Proteins fold into unique three-dimensional structures spontaneously according to amino acid sequences, and then exert function based on their folded structures. My research interests are in uncovering the principles for protein folding and functions using computational methods and biochemical experiments, and applying the principles for designing novel proteins for therapeutics and materials. Currently, I'm working on designing ideal protein structures for understanding protein folding.

 

Education:

2003-2006 Ph.D. Department of Molecular Science Graduate School of Science and Technology, Kobe University, Japan

2001-2003 M.Sc. Department of Chemistry Graduate School of Science and Technology, Kobe University, Japan

1997-2001 B.Sc. Faculty of Science, Kobe University, Japan

 

Research and Professional Experience:

2007-Current Senior Fellow at Department of Biochemistry, University of Washington, Seattle WA

2007-2007 Postdoctoral Fellow at Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto Japan

2006-2007 Postdoctoral Fellow at the Faculty of Science, Kobe University, Hyogo Japan

 

Fellowship:

2007-2009 JSPS Postdoctoral Research Fellowship for Research Abroad

2003-2006 JSPS Predoctoral Research Fellowship

 

Peer-reviewed Publication: 

Koga N., Tatsumi-Koga R., Liu G., Xiao R., Acton T. B., Montelione G. T., Baker D., Principles for designing ideal protein structures. Nature, 491, 222-227, 2012

Kenzaki H., Koga N., Hori N., Kanada R., Li W. Okazaki K., Yao X. -Q. Takada S., CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work. Journal of Chemical Theory and Computation7(6), 1979-1989, 2011

Fleishman J. F., Leaver-Fay A., Corn J. E., Stauch E. -M. Khare D. S., Koga N., Ashworth J. Murphy P., Richter F., Lemmon G., Meiler J.. Baker D., RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite. PLoS ONE6(6), 1-10, 2011

Fleishman S. J., Khare S. D., Koga N., Baker D. Restricted sidechain plasticity in the structures of native proteins and complexes. Protein Science, 20(4), 753-757, 2011 

Koga N., Kameda T., Okazaki K., Takada S., Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations. Proc. Natl. Acad. Sci. USA, 106 (43),18237-18242, 2009 

Okazaki K., Koga N., Takada S., Onuchic J. N., Wolynes P. G., Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations. Proc. Natl. Acad. Sci. USA, 103 (32), 11844-11849, 2006

Koga N.Takada S., Folding-based molecular simulations reveal mechanisms of the rotary motor F1-ATPase. Proc. Natl. Acad. Sci. USA, 103 (14), 5367-5372, 2006

Takagi F., Koga N., Takada S., How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: Molecular simulations. Proc. Natl. Acad. Sci. USA, 100 (20), 11367-11372, 2003

Koga N., Takada S., Roles of Native Topology and Chain-length Scaling in Protein Folding:A Simulation Study with a Go-like Model. Journal of Molecular Biology, 313 (1), 171-180, 2001 

 

Artworks from the paper: "Principles for designing ideal protein structures"

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