SPring-8, the large synchrotron radiation facility

A joint research team consisting of six different groups clarified, for the first time, how cytochrome c (cyt c), a protein indispensable for respiration in living organisms, loses its function by changing its steric molecular structure and forming a polymer in which many multiple monomers are joined in chains (polymerization^*1) (Figs. 1 and 2). The joint research team consists of scientists from the following: Laboratory for Supramolecular Science (Shun Hirota, Professor) and Laboratory of Bioenergetics and Biophysics at the Graduate School of Materials Science of Nara Institute of Science and Technology (Akira Isogai, President); Graduate School of Life Science (Yoshiki Higuchi, Professor, also a visiting scientist at RIKEN) of the University of Hyogo (Masayoshi Kiyohara, President); RIKEN SPring-8 Center (Tetsuya Ishikawa, Director) of RIKEN (Ryoji Noyori, President); Faculty of Pharmaceutical Sciences of Doshisha Women's College of Liberal Arts; and China West Normal University. Serpinopathies,^*2 which may induce premature senility, hepatic cirrhosis, pulmonary emphysema, and thrombosis, are considered to be caused by the accumulation of chain-shaped unnecessary polymerized proteins in living tissues. This achievement is expected to clarify the causes and prevention of diseases induced by mutation in protein structure.

Protein cyt c is present in mitochondria, which are organelles involved in cell respiration. For nearly half a century, it has been known that cyt c is an indispensable protein for respiration and forms polymers by extending its structure in a chain shape upon denaturation. However, the denaturation mechanism remains unknown. Professor Hirota and his colleagues synthesized cyt c polymers, specifically succeeded in synthesizing pure uniform polymers with crystal structures of dimeric, trimeric, and tetrameric cyt c, and analyzed these molecular structures their characteristics. Meanwhile, Professor Higuchi and his colleagues succeeded in crystallizing each structure and analyzed these molecular structures using synchrotron radiation X-rays at SPring-8. As a result, they found that domain swapping,^*3 in which corresponding domains are swapped when two molecules come into contact, occurs during polymerization of cyt c, assuming that one molecule (monomer) is a structural unit consisting of several domains. The mechanism by which cyt c forms polymer chains by successive domain swapping in multiple molecules was clarified. The results of this research were published online in the American scientific journal Proceedings of the National Academy of Sciences (PNAS) on 6 July 2010.

In proteins, various types of amino acid are sequenced in a long chain, and they form a specific steric structure depending on the sequence of the amino acids and exhibit particular functions. However, when proteins are structurally denatured, i.e., when the long chain of amino acids is not properly refolded or proteins are not properly decomposed to be removed from the cell, the proteins that lost their original functions due to the structure denaturation accumulate in living tissues, inducing diseases. The denaturation mechanism of cyt c clarified in this study is very similar to that proposed for serpinopathies. This achievement is expected to clarify the denaturation mechanism of protein, which is closely related to diseases.

Publication:
"Cytochrome c polymerization by successive domain swapping at the C-terminal helix"
Shun Hirota, Yoko Hattori, Satoshi Nagao, Midori Taketa, Hirofumi Komori, Hironari Kamikubo, Zhonghua Wang, Isao Takahashi, Shigeru Negi, Yukio Sugiura, Mikio Kataoka, and Yoshiki Higuchi
Proceedings of the National Academy of Sciences (PNAS), Published online before print July 6, 2010