Publications

Suyong Re, Shigehisa Watabe, Wataru Nishima, Eiro Muneyuki, Yoshiki Yamaguchi, Alexander D. MacKerell Jr. and *Yuji Sugita,
Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase,
Scientific Reports 8, 1644 (2018).

[Summary] Ion mobility mass spectrometry (IM-MS) is a technique capable of investigating structural changesof biomolecules based on their collision cross section (CCS). Recent advances in IM-MS allow us toseparate carbohydrate isomers with subtle conformational differences, but the relationship betweenCCS and atomic structure remains elusive. Here, we characterize conformational ensembles of gasphaseN-glycans under the electrospray ionization condition using molecular dynamics simulations withenhanced sampling. We show that the separation of CCSs between isomers reflects folding features ofN-glycans, which are determined both by chemical compositions and protonation states. Providing aphysicochemical basis of CCS for N-glycans helps not only to interpret IM-MS measurements but also toestimate CCSs of complex glycans.

*Sho Fujii, Ryuta Fukano, Yoshihito Hayami, Hiroaki Ozawa, Eiro Muneyuki, Noboru Kitamura, and *Masa-aki Haga,
Simultaneous Formation and Spatial Patterning of ZnO on ITO Surfaces by Local Laser-Induced Generation of Microbubbles in Aqueous Solutions of [Zn(NH₃)₄]²⁺,
ACS Applied Materials & Interfaces 9, 8413-8419 (2017).

[Summary] We demonstrate the simultaneous formation and spatial patterning of ZnO nanocrystals on an indium−tin oxide (ITO) surface upon local heating using a laser (1064 nm) and subsequent formation of microbubbles. Laser irradiation of an ITO surface in aqueous [Zn(NH3)4]2+solution (1.0×10-2 M at pH 12.0) under an optical microscope produced ZnO nanocrystals, the presence of which was confirmed by X-ray diffraction analysis and Raman microspectroscopy. Scanning the focused laser beam over the ITO surface generated a spatial ZnO pattern (height:∼60 nm,width:∼1μm) in the absence of a template or mask. The Marangoni convection generated in the vicinity of the micro-bubbles resulted in a rapid concentration/accumulation of [Zn(NH3)4]2+ around the microbubbles, which led to the formation of ZnO at the solid−bubble−solution three-phase contact line around the bubbles and thus afforded ZnO nanocrystals on the ITO surface upon local heating with a laser.

Kano Suzuki, Kenji Mizutani, Shintaro Maruyama, Kazumi Shimono, Fabiana L. Imai, Eiro Muneyuki, Yoshimi Kakinuma, Yoshiko Ishizuka-Katsura, Mikako Shirouzu, Shigeyuki Yokoyama, Ichiro Yamato and *Takeshi Murata,
Crystal structures of the ATP-binding and ADP-release dwells of the V₁ rotary motor.,
Nature Communications 7, 13235 (2016).

[Summary] V1-ATPases are highly conserved ATP-driven rotary molecular motors found in various membrane systems. We recently reported the crystal structures for the Enterococcus hirae A3B3DF (V1) complex, corresponding to the catalytic dwell state waiting for ATP hydrolysis. Here we present the crystal structures for two other dwell states obtained by soaking nucleotide-free V1 crystals in ADP. In the presence of 20 μM ADP, two ADP molecules bind to two of three binding sites and cooperatively induce conformational changes of the third site to an ATP-binding mode, corresponding to the ATP-binding dwell. In the presence of 2 mM ADP, all nucleotide-binding sites are occupied by ADP to induce conformational changes corresponding to the ADP-release dwell. Based on these and previous findings, we propose a V1-ATPase rotational mechanism model.

*Jun Tamogami, Keitaro Sato, Sukuna Kurokawa, Takumi Yamada, Toshifumi Nara, Makoto Demura, Seiji Miyauchi, Takashi Kikukawa, Eiro Muneyuki, Naoki Kamo,
Formation of M-Like Intermediates in Proteorhodopsin in Alkali Solutions (pH ≧~8.5) Where the Proton Release Occurs First in Contrast to the Sequence at Lower pH,
Biochemistry 55(7), 1036-48 (2016).

[Summary] Proteorhodopsin (PR) is an outward light-driven proton pump observed in marine eubacteria. Despite many structural and functional similarities to bacteriorhodopsin (BR) in archaea, which also acts as an outward proton pump, the mechanism of the photoinduced proton release and uptake is different between two H+-pumps. In this study, we investigated the pH dependence of the photocycle and proton transfer in PR reconstituted with the phospholipid membrane under alkaline conditions. Under these conditions, as the medium pH increased, a blue-shifted photoproduct (defined as Ma), which is different from M, with a pKa of ca. 9.2 was produced. The sequence of the photoinduced proton uptake and release during the photocycle was inverted with the increase in pH. A pKa value of ca. 9.5 was estimated for this inversion and was in good agreement with the pKa value of the formation of Ma (~9.2). In addition, we measured the photoelectric current generated by PRs attached to a thin polymer film at varying pH. Interestingly, increases in the medium pH evoked bidirectional photocurrents, which may imply a possible reversal of the direction of the proton movement at alkaline pH. Based on these findings, a putative photocycle and proton transfer scheme in PR under alkaline pH conditions was proposed.