X-ray fluorescence holography of biological metal sites: Application to myoglobin

Ayana Sato-Tomita; Artoni Kevin R Ang; Koji Kimura; Riho Marumi; Naohisa Happo; Tomohiro Matsushita; Sam-Yong Park; Naoya Shibayama; Yuji C Sasaki; Kouichi Hayashi

doi:10.1016/j.bbrc.2022.10.003

X-ray fluorescence holography of biological metal sites: Application to myoglobin

Biochem Biophys Res Commun. 2022 Dec 20:635:277-282. doi: 10.1016/j.bbrc.2022.10.003. Epub 2022 Oct 13.

Authors

Affiliations

¹ Division of Biophysics, Department of Physiology, Jichi Medical University, Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan. Electronic address: [email protected].
² Department of Physical Science and Engineering, Nagoya Institute of Technology, Gokiso, Showa, Nagoya, 466-8555, Japan.
³ Department of Computer and Network Engineering, Graduate School of Information Sciences, Hiroshima City University, Asa-Minami-Ku, Hiroshima, 731-3194, Japan.
⁴ Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma, Nara, 630-0192, Japan.
⁵ Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, 230-0045, Japan.
⁶ Division of Biophysics, Department of Physiology, Jichi Medical University, Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan.
⁷ Department of Advanced Material Science, Graduate School of Frontier Science, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.
⁸ Department of Physical Science and Engineering, Nagoya Institute of Technology, Gokiso, Showa, Nagoya, 466-8555, Japan; Japan Synchrotron Radiation Research Institute, SPring-8, Kouto, Sayo, 679-5198, Japan. Electronic address: [email protected].

PMID: 36308907
DOI: 10.1016/j.bbrc.2022.10.003

Abstract

X-ray fluorescence holography (XFH) is a relatively new technique capable of providing unique three-dimensional structural information around specific atoms that act as a light source in crystalline samples. So far, XFH has typically been applied to inorganic materials such as dopants in metals and semiconductors. Here, we investigate the possibility of using XFH to visualize the metal active site in sperm whale myoglobin (Mb), a monomeric oxygen storage heme protein. We demonstrate that the atomic images reconstructed from the hologram data of crystals of carbonmonoxy myoglobin (MbCO) are moderately consistent with the crystal structure, which is also determined in this study by X-ray crystallography in the near-atomic resolution, as well as simulation results. These results open up a new avenue for the application of XFH to local atomic and electronic structure imaging of metal-sites in biomolecules.

Keywords: Atomic imaging; Crystallography; Metalloproteins; X-ray fluorescence holography.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Crystallography, X-Ray
Heme / chemistry
Holography* / methods
Metals
Myoglobin* / chemistry
Protein Conformation
X-Rays

Substances

Myoglobin
Heme
Metals