Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent

作者：Nakane Takanori; Hanashima Shinya; Suzuki Mamoru; Saiki Haruka; Hayashi Taichi; Kakinouchi Keisuke; Sugiyama Shigeru; Kawatake Satoshi; Matsuoka Shigeru; Matsumori Nobuaki; Nango Eriko; Kobayashi Jun; Shimamura Tatsuro; Kimura Kanako; Mori Chihiro; Kunishima Naoki; Sugahara Michihiro; Takakyu Yoko; Inoue Shigeyuki; Masuda Tetsuya; Hosaka Toshiaki; Tono Kensuke; Joti Yasumasa; Kameshima Takashi; Hatsui Takaki; Yabashi Makina; Inoue Tsuyoshi; Nureki Osamu; Iwata So

来源：Proceedings of the National Academy of Sciences of the United States of America, 2016, 113(46): 13039-13044.

DOI：10.1073/pnas.1602531113

• phase problem
• de novo phasing
• heavy atom
• detergent
• G protein-coupled receptor

The 3D structure determination of biological macromolecules by X-ray crystallography suffers from a phase problem: to perform Fourier transformation to calculate real space density maps, both intensities and phases of structure factors are necessary; however, measured diffraction patterns give only intensities. Although serial femtosecond crystallography (SFX) using X-ray free electron lasers (XFELs) has been steadily developed since 2009, experimental phasing still remains challenging. Here, using 7.0-keV (1.771 angstrom)X-ray pulses from the SPring-8 Angstrom Compact Free Electron Laser (SACLA), iodine single-wavelength anomalous diffraction (SAD), single isomorphous replacement (SIR), and single isomorphous replacement with anomalous scattering (SIRAS) phasing were performed in an SFX regime for a model membrane protein bacteriorhodopsin (bR). The crystals grown in bicelles were derivatized with an iodine-labeled detergent heavy-atom additive 13a (HAD13a), which contains the magic triangle, I3C head group with three iodine atoms. The alkyl tail was essential for binding of the detergent to the surface of bR. Strong anomalous and isomorphous difference signals from HAD13a enabled successful phasing using reflections up to 2.1- resolution from on 3,000 and 4,000 indexed images from native and derivative crystals, respectively. When more images were merged, structure solution was possible with data truncated at 3.3-angstrom resoluti, which is the lowest resolution among the reported cases of SFX phasing. Moreover, preliminary SFX experiment showed that HAD13a successfully derivatized the G protein-coupled A2a adenosine receptor crystallized in lipidic cubic phases. These results pave the way for de novo structure determination of membrane proteins, which often diffract poorly, even with the brightest XFEL beams.

• 出版日期2016-11-15
• 单位RIKEN