Extraction and application of structural and functional elements of proteins.

2013 Fiscal Year Final Research Report

• Project/Area Number: 23370074
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Biophysics
• Research Institution: Nara Institute of Science and Technology
• Principal Investigator: KAMIKUBO Hironari 奈良先端科学技術大学院大学, 物質創成科学研究科, 准教授 (20311128)
• Co-Investigator(Kenkyū-buntansha): KATAOKA Mikio 奈良先端科学技術大学院大学, 物質創成科学研究科, 教授 (30150254) ; YAMAZAKI Yoichi 奈良先端科学技術大学院大学, 物質創成科学研究科, 助教 (40332770)
• Project Period (FY): 2011-11-18 – 2014-03-31
• Keywords: 蛋白質工学 / 分子設計 / フォールディング / 酵素

Research Abstract

Nowadays, artificially engineered proteins are utilized in various life science areas. In addition, engineered proteins are known to be one of promised candidates for next generation drugs. However, effective methods for rational design of artificial proteins have not been developed. Using comprehensive alanine insertion mutation analysis, we have revealed that regions of several subsequent amino acid residues in a protein, named as "Element", are responsible for the function and structure. In this work, we established a working hypothesis that those elements act as building blocks in the proteins, and verified it. In the result, by implanting the elements from a protein into another protein with a different function, we successfully modified the protein function as we wish. This success implies that the elements act as a kind of building-block to mediate a particular protein function, and will enable us to design an artificial protein rationally.

Research Products

• [Journal Article] Excited-State Proton Transfer in Fluorescent Photoactive Yellow Protein Containing 7-Hydroxycoumarin (2014)
  • Author(s): D. Novitasari, H. Kamikubo, Y. Yamazaki, M. Yamaguchi, M. Kataoka
  • Journal Title: Advanced Materials Research Volume: 896 Pages: 85-88
  • Peer Reviewed
• [Journal Article] Theoretical analysis of the geometrical isotope effect on the hydrogen bonds in photoactive yellow protein with multi-component density functional theory (2013)
  • Author(s): Y. Kita, H. Kamikubo, M. Kataoka, M. Tachikawa
  • Journal Title: Chem. Phys Volume: 419 Pages: 50-53
  • Peer Reviewed
• [Journal Article] (1)H, (13)C, and (15)N resonance assignment of photoactive yellow protein (2013)
  • Author(s): Pool TJ, Oktaviani NA, Kamikubo H, Kataoka M, Mulder FA
  • Journal Title: Biomol NMR Assign Volume: 7(1) Pages: 97-100
  • Peer Reviewed
• [Journal Article] Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography (2012)
  • Author(s): Schotte F, Cho HS, Kaila VR, Kamikubo H, Dashdorj N, Henry ER, Graber TJ, Henning R, Wulff M, Hummer G, Kataoka M, Anfinrud PA
  • Journal Title: Proc Natl Acad Sci USA Volume: 109(47) Pages: 19256-61
  • Peer Reviewed
• [Journal Article] Comprehensive determination of protein tyrosine pKa values for photoactive yellow protein using indirect 13C NMR spectroscopy (2012)
  • Author(s): Oktaviani NA, Pool TJ, Kamikubo H, Slager J, Scheek RM, Kataoka M, Mulder FA
  • Journal Title: Biophys J. 2012 Feb Volume: 8 Pages: 579-86
  • Peer Reviewed
• [Journal Article] Changes in the hydrogen-bond network around the chromophore of photoactive yellow protein in the ground and excited states (2011)
  • Author(s): Mizuno M, Kamikubo H, Kataoka M, Mizutani Y
  • Journal Title: J Phys Chem B Volume: 115(29) Pages: 9306-10
  • Peer Reviewed
• [Presentation] Functional modification of a protein by using element implantaion (2013)
  • Author(s): H. Kamikubo
  • Organizer: Sixth Korea-Japan Seminars on Biomolecular Sciences : Experiments and Simulations
  • Place of Presentation: Okazaki, Japan
  • Year and Date: 20131125-27
• [Presentation] The mechanism of induced folding of Staphylococcal nuclease (2013)
  • Author(s): M. Kataoka
  • Organizer: Telluride Conference on Protein Dynamics 2013
  • Place of Presentation: Telluride, USA
  • Year and Date: 20130805-09
• [Presentation] Is tertiary structure required for a specific function? (2013)
  • Author(s): M. Kataoka
  • Organizer: 8th Asian Biophysics Association Symposium
  • Place of Presentation: Jeju, Korea
  • Year and Date: 20130526-29
• [Remarks]
  • URL: http://mswebs.naist.jp/LABs/kataoka/