Precise Charge Density Study of CYTOCHROME c-553 By Maximum Entropy Method

Masaki Takata^a,b, Kenichi Kato^b, Hiroshi Tanaka^c, Atsushi Nakagawa^d

and Makoto Sakata^a

^aDepartment of Applied Physics, Nagoya University, Nagoya 464-8603, Japan.

^bJapan Synchrotron Radiation Research Institute, Hyogo 679-5198, Japan

^cDepartment of Material Science, Shimane University, Mtasue 690-8504, Japan.

^dThe Institute for Protein Research, Osaka University, Suita 565-0871, Japan.

(takatama@spring8.or.jp)

Structures of various protein molecules are now studied extensively to explore the structural basis of the protein function. Therefore, the several experimental and analytical techniques have been developed in order to get a high-resolution crystallographic structure of protein crystal. However, most of the studies have been carried out for the atomic arrangement. In order to have a better and deeper understanding for functions and properties of the protein molecule, a precise charge density study is required to reveal bonding nature of molecule especially for an active segment. Recently, we have developed a new program of the Maximum Entropy Method, ENIGMA(Electron and Nuclear Image Generator by Max-ent Analysis)[1], for the charge density study of huge systems, such as proteins and polymers. By ENIGMA, we tackled charge density study of cytochrome c-553, and revealed precise charge density showing characteristic bonding nature of Heme group.

In the present study, we have employed synchrotron radiation single crystal data of cytochrome c-553, of which structure was solved by the multiplewavelength anomalous diffraction method[2]. The reliability factor of the obtained charge density is 2.4%, which is far beyond the value, 19.6%, of the previous conventional structure determination. The obtained charge density clearly exhibits the covalent bonding networks of atoms and the characteristic anisotropy of the Fe-N coordinate bonds in the heme group. Furthermore, the ability of the structure prediction by MEM revealed the solvent water molecule image in the crystal without assuming the existence of water molecule. The present result shall open the door to an accurate charge density study for the structure-function relationship of proteins.

Referneces

1. H.Tanaka, et al., J.Appl. Cryst.,35,282-286(2002)

2. A.Nakagawa, et al., J.Biochem, 108,701-703(1990)