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371.
Sotaro Yamasaki Mitsuo Shoji Megumi Kayanuma Vladimir Sladek Daniel Ken Inaoka Yuichi Matsuo Tomoo Shiba Luke Young Anthony L. Moore Kiyoshi Kita Yasuteru Shigeta 《BBA》2021,1862(4):148356
Alternative oxidase (AOX) catalyzes the four-electron reduction of dioxygen to water as an additional terminal oxidase, and the catalytic reaction is critical for the parasite to survive in its bloodstream form. Recently, the X-ray crystal structure of trypanosome alternative oxidase (TAO) complexed with ferulenol was reported and the molecular structure of the non-heme diiron center was determined. The binding of O2 was a unique side-on type compared to other iron proteins. In order to characterize the O2 binding state of TAO, the O2 binding states were searched at a quantum mechanics/molecular mechanics (QM/MM) theoretical level in the present study. We found that the most stable O2 binding state is the end-on type, and the binding states of the side-on type are higher in energy. Based on the binding energies and electronic structure analyses, O2 binds very weakly to the TAO iron center (ΔE =6.7 kcal mol?1) in the electronic state of Fe(II)…OO, not in the suggested charge transferred state such as the superoxide state (Fe(III)OO· –) as seen in hemerythrin. Coordination of other ligands such as water, Cl?, CN?, CO, N3? and H2O2 was also examined, and H2O2 was found to bind most strongly to the Fe(II) site by ΔE = 14.0 kcal mol?1. This was confirmed experimentally through the measurement of ubiquinol oxidase activity of TAO and Cryptosporidium parvum AOX which was found to be inhibited by H2O2 in a dose-dependent and reversible manner. 相似文献
372.
Yamato Miyazawa Kenji Kawaguchi Ryo Katsuta Tomoo Nukada 《Bioscience, biotechnology, and biochemistry》2020,84(8):1560-1569
ABSTRACT DAMASCENOLIDETM [1, 4-(4-methylpent-3-en-1-yl)furan-2(5H)-one], which has a citrus-like odor, is an important aroma component of roses. We have previously reported on the synthesis and odor evaluation of double-bond isomers of 1 and concluded that the position and the geometric isomerism of the double-bond had a significant effect on the odor. For the purpose of deepening knowledge about structure–odor relationships, we synthesized 13 analogs of compound 1 and evaluated their odors. As a result, it was found that the presence of two double-bonds and branched methyl group at the terminal position in the side chain was essential in order to have a citrus-like odor. Substitution of the side chain with appropriate length at the appropriate 4-position of the 2(5H)-furanone ring was also an important factor in determining the quality of the odor. 相似文献
373.
Koji Tomoo Hirofumi Ohishi Toshimasa Ishida Masatoshi Inoue Kiyoshi Ikeda Shigeyuki Sumiya Kunihiro Kitamura 《Proteins》1994,19(4):330-339
The crystal structure of n-dodecylphosphorylcholine (n-C12PC)–bovine pancreas phospholipase A2 (PLA2) complex provided the following structural.characteristics: (1) the dodecyl chain of n-C12PC was located at the PLA2 N -terminal helical region by hydrophobic interactions, which corresponds to the binding pocket of 2-acyl fatty acid chain (β-chain) of the substrate phospholipid, (2) the region from Lys-53 to Lys-56 creates a cholinereceiving pocket of n-C12PC and (3) the N-termillal group of Ala-1 shifts significantly toward the Tyr-52 OH group by the binding of the n-C12PC inhibitor. Since the accuracy of the X-ray analysis (R = 0.275 at 2.3 Å resolution) was insufficient to establish these important X-ray insights, the complex structure was further investigated through the molecular dynamics (M D) simulation, assuming a system in aqueous solution at 310K. The M D simulation covering 176 ps showed that the structural characteristics observed by X-ray analysis are intrinsic and also stable in the dynamic state. Furthermore, the M D simulation made clear that the PLA2 binding pocket is large enough to permit the conformational fluctuation of the n-C12PC hydrocarbon chain. © 1994 Wiley-Liss, Inc. © 1994 Wiley-Liss, Inc. 相似文献
374.
Dense vesicles mediate the final step in the delivery of seedproteins to vacuoles in developing pumpkin (Cucurbita sp.) cotyledons.To explore the vesicle-mediated transport system that is targetedto vacuoles in plant cells, we isolated the dense vesicles andexamined then for the presence of guanine nucleotide-bindingproteins. GTP-binding proteins of 25 kDa and 27 kDa were detectedon the isolated vesicles. The 25-kDa protein had dithiothreitol-dependentGTP-binding activity, but binding of GTP by the 27-kDa proteinshowed no such dependence. Binding of [ 相似文献
375.
K Tomoo H Ohishi M Doi T Ishida M Inoue K Ikeda H Mizuno 《Biochemical and biophysical research communications》1992,187(2):821-827
Three-dimensional structure of a bovine pancreas phospholipase A2 (PLA2) crystal complexed with n-dodecylphosphorylcholine (n-C12PC), a substrate-type inhibitor, has been determined by the X-ray diffraction method. The present conventional R value is 0.275 at 2.3A resolution. The binding mode of n-C12PC to the PLA2 was clearly indicated, where the dodecyl chain was stably held by the hydrophobic contacts with the N-terminal region of PLA2 (Leu-2, Phe-5, and Ile-9), and the choline moiety was contacted with the hydrophobic space created by the side chains of Lys-53 and 56. The present result indicates that remarkable changes from the native PLA2 structure are caused at the N-terminal and middle (residues 60 to 70) regions by the binding of n-C12PC to the enzyme. 相似文献
376.