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3,257 results on '"Yokoyama, Shigeyuki"'

7. List of contributors

Author

Adderley, Shawn J., primary, Allen, Bruce G., additional, Andersen, Haley, additional, Bagher, Amina M., additional, Bourque, Kyla, additional, Brandt, Asher L., additional, Chatenet, David, additional, Dallagnol, Juliana C.C., additional, Denovan-Wright, Eileen M., additional, Hori, Tetsuya, additional, Hébert, Terence E., additional, Hudson, Brian D., additional, Laprairie, Robert B., additional, Mirka, Victor Michael, additional, Nassour, Hassan, additional, Ramachandran, Rithwik, additional, Yokoyama, Shigeyuki, additional, and Young, Alexander P., additional

Published
2022
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11. Cavity as a source of conformational fluctuation and high-energy state: High-pressure NMR study of a cavity-enlarged mutant of T4 lysozyme

Author

Maeno, Akihiro, Sindhikara, Daniel, Hirata, Fumio, Otten, Renee, Dahlquist, Frederick W., Yokoyama, Shigeyuki, Akasaka, Kazuyuki, Mulder, Frans A. A., and Kitahara, Ryo

Subjects
Physics - Biological Physics, Physics - Chemical Physics, Quantitative Biology - Biomolecules
Abstract

Although the structure, function, conformational dynamics, and controlled thermodynamics of proteins are manifested by their corresponding amino acid sequences, the natural rules for molecular design and their corresponding interplay remain obscure. In this study, we focused on the role of internal cavities of proteins in conformational dynamics. We investigated the pressure-induced responses from the cavity-enlarged L99A mutant of T4 lysozyme, using high-pressure NMR spectroscopy. The signal intensities of the methyl groups in the 1H/13C HSQC spectra, particularly those around the enlarged cavity, decreased with the increasing pressure, and disappeared at 200 MPa, without the appearance of new resonances, thus indicating the presence of heterogeneous conformations around the cavity within the ground state ensemble. Above 200 MPa, the signal intensities of more than 20 methyl groups gradually decreased with the increasing pressure, without the appearance of new resonances. Interestingly, these residues closely matched those sensing a large conformational change between the ground- and high-energy states, at atmospheric pressure. 13C and 1H NMR line-shape simulations showed that the pressure-induced loss in the peak intensity could be explained by the increase in the high-energy state population. In this high-energy state, the aromatic side chain of F114 gets flipped into the enlarged cavity. The accommodation of the phenylalanine ring into the efficiently packed cavity may decrease the partial molar volume of the high-energy state, relative to the ground state. We suggest that the enlarged cavity is involved in the conformational transition to high-energy states and in the volume fluctuation of the ground state., Comment: 46 pages (including 13 pages of supporting materials), 7 figures, 7 supporting figures

Published
2014
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12. 1H, 13C, and 15N resonance assignments and solution structure of the N-terminal divergent calponin homology (NN-CH) domain of human intraflagellar transport protein 54.

Author

Kuwasako, Kanako, Dang, Weirong, He, Fahu, Takahashi, Mari, Tsuda, Kengo, Nagata, Takashi, Tanaka, Akiko, Kobayashi, Naohiro, Kigawa, Takanori, Güntert, Peter, Shirouzu, Mikako, Yokoyama, Shigeyuki, and Muto, Yutaka

Abstract

The intraflagellar transport (IFT) machinery plays a crucial role in the bidirectional trafficking of components necessary for ciliary signaling, such as the Hedgehog, Wnt/PCR, and cAMP/PKA systems. Defects in some components of the IFT machinery cause dysfunction, leading to a wide range of human diseases and developmental disorders termed ciliopathies, such as nephronophthisis. The IFT machinery comprises three sub-complexes: BBsome, IFT-A, and IFT-B. The IFT protein 54 (IFT54) is an important component of the IFT-B sub-complex. In anterograde movement, IFT54 binds to active kinesin-II, walking along the cilia microtubule axoneme and carrying the dynein-2 complex in an inactive state, which works for retrograde movement. Several mutations in IFT54 are known to cause Senior-Loken syndrome, a ciliopathy. IFT54 possesses a divergent Calponin Homology (CH) domain termed as NN-CH domain at its N-terminus. However, several aspects of the function of the NN-CH domain of IFT54 are still obscure. Here, we report the 1H, 15N, and 13C resonance assignments of the NN-CH domain of human IFT54 and its solution structure. The NN-CH domain of human IFT54 adopts essentially the α1–α2–α3–α4–α5 topology as that of mouse IFT54, whose structure was determined by X-ray crystallographic study. The structural information and assignments obtained in this study shed light on the molecular function of the NN-CH domain in IFT54. [ABSTRACT FROM AUTHOR]

Published
2024
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14. Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hsp90 traps and stabilizes an unfolded kinase

Author

Verba, Kliment A, Wang, Ray Yu-Ruei, Arakawa, Akihiko, Liu, Yanxin, Shirouzu, Mikako, Yokoyama, Shigeyuki, and Agard, David A

Subjects
Biochemistry and Cell Biology, Biological Sciences, Animals, Cell Cycle Proteins, Chaperonins, Cyclin-Dependent Kinase 4, Enzyme Stability, HSP90 Heat-Shock Proteins, Humans, Models, Molecular, Multiprotein Complexes, Protein Structure, Secondary, Protein Unfolding, Sf9 Cells, General Science & Technology
Abstract

The Hsp90 molecular chaperone and its Cdc37 cochaperone help stabilize and activate more than half of the human kinome. However, both the mechanism by which these chaperones assist their "client" kinases and the reason why some kinases are addicted to Hsp90 while closely related family members are independent are unknown. Our structural understanding of these interactions is lacking, as no full-length structures of human Hsp90, Cdc37, or either of these proteins with a kinase have been elucidated. Here we report a 3.9 angstrom cryo-electron microscopy structure of the Hsp90-Cdc37-Cdk4 kinase complex. Surprisingly, the two lobes of Cdk4 are completely separated with the β4-β5 sheet unfolded. Cdc37 mimics part of the kinase N lobe, stabilizing an open kinase conformation by wedging itself between the two lobes. Finally, Hsp90 clamps around the unfolded kinase β5 strand and interacts with exposed N- and C-lobe interfaces, protecting the kinase in a trapped unfolded state. On the basis of this structure and an extensive amount of previously collected data, we propose unifying conceptual and mechanistic models of chaperone-kinase interactions.

Published
2016

15. Site‐specific photo‐crosslinking/cleavage for protein–protein interface identification reveals oligomeric assembly of lysosomal‐associated membrane protein type 2A in mammalian cells

Author

Terasawa, Kazue, primary, Seike, Tatsuro, additional, Sakamoto, Kensaku, additional, Ohtake, Kazumasa, additional, Terada, Tohru, additional, Iwata, Takanori, additional, Watabe, Tetsuro, additional, Yokoyama, Shigeyuki, additional, and Hara‐Yokoyama, Miki, additional

Published
2023
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16. Serum anti-DIDO1, anti-CPSF2, and anti-FOXJ2 antibodies as predictive risk markers for acute ischemic stroke

Author

Hiwasa, Takaki, Wang, Hao, Goto, Ken-ichiro, Mine, Seiichiro, Machida, Toshio, Kobayashi, Eiichi, Yoshida, Yoichi, Adachi, Akihiko, Matsutani, Tomoo, Sata, Mizuki, Yamagishi, Kazumasa, Iso, Hiroyasu, Sawada, Norie, Tsugane, Shoichiro, Kunimatsu, Mitoshi, Kamitsukasa, Ikuo, Mori, Masahiro, Sugimoto, Kazuo, Uzawa, Akiyuki, Muto, Mayumi, Kuwabara, Satoshi, Kobayashi, Yoshio, Ohno, Mikiko, Nishi, Eiichiro, Hattori, Akiko, Yamamoto, Masashi, Maezawa, Yoshiro, Kobayashi, Kazuki, Ishibashi, Ryoichi, Takemoto, Minoru, Yokote, Koutaro, Takizawa, Hirotaka, Kishimoto, Takashi, Matsushita, Kazuyuki, Kobayashi, Sohei, Nomura, Fumio, Arasawa, Takahiro, Kagaya, Akiko, Maruyama, Tetsuro, Matsubara, Hisahiro, Tomiita, Minako, Hamanaka, Shinsaku, Imai, Yushi, Nakagawa, Tomoo, Kato, Naoya, Terada, Jiro, Matsumura, Takuma, Katsumata, Yusuke, Naito, Akira, Tanabe, Nobuhiro, Sakao, Seiichiro, Tatsumi, Koichiro, Ito, Masaaki, Shiratori, Fumiaki, Sumazaki, Makoto, Yajima, Satoshi, Shimada, Hideaki, Shirouzu, Mikako, Yokoyama, Shigeyuki, Kudo, Takashi, Doi, Hirofumi, Iwase, Katsuro, Ashino, Hiromi, Li, Shu-Yang, Kubota, Masaaki, Tomiyoshi, Go, Shinmen, Natsuko, Nakamura, Rika, Kuroda, Hideyuki, and Iwadate, Yasuo

Published
2021
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18. Cavity as a Source of Conformational Fluctuation and High-Energy State: High-Pressure NMR Study of a Cavity-Enlarged Mutant of T4Lysozyme

Author

Maeno, Akihiro, Sindhikara, Daniel, Hirata, Fumio, Otten, Renee, Dahlquist, Frederick W, Yokoyama, Shigeyuki, Akasaka, Kazuyuki, Mulder, Frans AA, and Kitahara, Ryo

Subjects
Bacteriophage T4, Carbon Isotopes, Computer Simulation, Hydrophobic and Hydrophilic Interactions, Models, Molecular, Muramidase, Mutation, Nuclear Magnetic Resonance, Biomolecular, Pressure, Protein Conformation, Proton Magnetic Resonance Spectroscopy, Recombinant Proteins, Viral Proteins, Water, Physical Sciences, Chemical Sciences, Biological Sciences, Biophysics
Abstract

Although the structure, function, conformational dynamics, and controlled thermodynamics of proteins are manifested by their corresponding amino acid sequences, the natural rules for molecular design and their corresponding interplay remain obscure. In this study, we focused on the role of internal cavities of proteins in conformational dynamics. We investigated the pressure-induced responses from the cavity-enlarged L99A mutant of T4 lysozyme, using high-pressure NMR spectroscopy. The signal intensities of the methyl groups in the (1)H/(13)C heteronuclear single quantum correlation spectra, particularly those around the enlarged cavity, decreased with the increasing pressure, and disappeared at 200 MPa, without the appearance of new resonances, thus indicating the presence of heterogeneous conformations around the cavity within the ground state ensemble. Above 200 MPa, the signal intensities of >20 methyl groups gradually decreased with the increasing pressure, without the appearance of new resonances. Interestingly, these residues closely matched those sensing a large conformational change between the ground- and high-energy states, at atmospheric pressure. (13)C and (1)H NMR line-shape simulations showed that the pressure-induced loss in the peak intensity could be explained by the increase in the high-energy state population. In this high-energy state, the aromatic side chain of F114 gets flipped into the enlarged cavity. The accommodation of the phenylalanine ring into the efficiently packed cavity may decrease the partial molar volume of the high-energy state, relative to the ground state. We suggest that the enlarged cavity is involved in the conformational transition to high-energy states and in the volume fluctuation of the ground state.

Published
2015

19. RNA targeting by the type III-A CRISPR-Cas Csm complex of Thermus thermophilus.

Author

Staals, Raymond HJ, Zhu, Yifan, Taylor, David W, Kornfeld, Jack E, Sharma, Kundan, Barendregt, Arjan, Koehorst, Jasper J, Vlot, Marnix, Neupane, Nirajan, Varossieau, Koen, Sakamoto, Keiko, Suzuki, Takehiro, Dohmae, Naoshi, Yokoyama, Shigeyuki, Schaap, Peter J, Urlaub, Henning, Heck, Albert JR, Nogales, Eva, Doudna, Jennifer A, Shinkai, Akeo, and van der Oost, John

Subjects
Thermus thermophilus, Endoribonucleases, Bacterial Proteins, RNA, Bacterial, Microscopy, Electron, Amino Acid Sequence, Base Sequence, Protein Structure, Quaternary, Protein Binding, Models, Molecular, Molecular Sequence Data, RNA Cleavage, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-Associated Proteins, RNA, Bacterial, Microscopy, Electron, Protein Structure, Quaternary, Models, Molecular, Developmental Biology, Biological Sciences, Medical and Health Sciences
Abstract

CRISPR-Cas is a prokaryotic adaptive immune system that provides sequence-specific defense against foreign nucleic acids. Here we report the structure and function of the effector complex of the Type III-A CRISPR-Cas system of Thermus thermophilus: the Csm complex (TtCsm). TtCsm is composed of five different protein subunits (Csm1-Csm5) with an uneven stoichiometry and a single crRNA of variable size (35-53 nt). The TtCsm crRNA content is similar to the Type III-B Cmr complex, indicating that crRNAs are shared among different subtypes. A negative stain EM structure of the TtCsm complex exhibits the characteristic architecture of Type I and Type III CRISPR-associated ribonucleoprotein complexes. crRNA-protein crosslinking studies show extensive contacts between the Csm3 backbone and the bound crRNA. We show that, like TtCmr, TtCsm cleaves complementary target RNAs at multiple sites. Unlike Type I complexes, interference by TtCsm does not proceed via initial base pairing by a seed sequence.

Published
2014

21. A Potent PDK4 Inhibitor for Treatment of Heart Failure with Reduced Ejection Fraction.

Author

Aizawa, Kenichi, Ikeda, Akari, Tomida, Shota, Hino, Koki, Sugita, Yuuki, Hirose, Tomoyasu, Sunazuka, Toshiaki, Kido, Hiroshi, Yokoyama, Shigeyuki, and Nagai, Ryozo

Subjects
HEART failure, VENTRICULAR ejection fraction, PYRUVATE dehydrogenase kinase, KREBS cycle, TREATMENT failure
Abstract

Heart failure with reduced ejection fraction (HFrEF) is characterized not only by reduced left ventricular ejection fraction (EF) but is also combined with symptoms such as dyspnea, fatigue, and edema. Several pharmacological interventions have been established. However, a treatment targeting a novel pathophysiological mechanism is still needed. Evidence indicating that inhibition of pyruvate dehydrogenase kinase 4 (PDK4) may be cardioprotective has been accumulating. Thus, we focused on vitamin K3 and used its framework as a new PDK4 inhibitor skeleton to synthesize new PDK4 inhibitors that show higher activity than the existing PDK4 inhibitor, dichloroacetic acid, and tested their cardioprotective effects on a mouse heart failure model. Among these inhibitors, PDK4 inhibitor 8 improved EF the most, even though it did not reverse cardiac fibrosis or wall thickness. This novel, potent PDK4 inhibitor may improve EF of failing hearts by regulating bioenergetics via activation of the tricarboxylic acid cycle. [ABSTRACT FROM AUTHOR]

Published
2024
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25. Inhibition of a NEDD8 Cascade Restores Restriction of HIV by APOBEC3G

Author

Stanley, David J, Bartholomeeusen, Koen, Crosby, David C, Kim, Dong Young, Kwon, Eunju, Yen, Linda, Cartozo, Nathalie Caretta, Li, Ming, Jäger, Stefanie, Mason-Herr, Jeremy, Hayashi, Fumiaki, Yokoyama, Shigeyuki, Krogan, Nevan J, Harris, Reuben S, Peterlin, Boris Matija, and Gross, John D

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Immunology, Sexually Transmitted Infections, HIV/AIDS, Infectious Diseases, Infection, APOBEC-3G Deaminase, CD4-Positive T-Lymphocytes, Carrier Proteins, Cell Line, Cullin Proteins, Cyclopentanes, Cytidine Deaminase, HEK293 Cells, HIV, HIV Infections, Humans, Magnetic Resonance Imaging, NEDD8 Protein, Pyrimidines, RNA Interference, RNA, Small Interfering, Ubiquitin-Protein Ligases, Ubiquitins, vif Gene Products, Human Immunodeficiency Virus, Microbiology, Virology, Medical microbiology
Abstract

Cellular restriction factors help to defend humans against human immunodeficiency virus (HIV). HIV accessory proteins hijack at least three different Cullin-RING ubiquitin ligases, which must be activated by the small ubiquitin-like protein NEDD8, in order to counteract host cellular restriction factors. We found that conjugation of NEDD8 to Cullin-5 by the NEDD8-conjugating enzyme UBE2F is required for HIV Vif-mediated degradation of the host restriction factor APOBEC3G (A3G). Pharmacological inhibition of the NEDD8 E1 by MLN4924 or knockdown of either UBE2F or its RING-protein binding partner RBX2 bypasses the effect of Vif, restoring the restriction of HIV by A3G. NMR mapping and mutational analyses define specificity determinants of the UBE2F NEDD8 cascade. These studies demonstrate that disrupting host NEDD8 cascades presents a novel antiretroviral therapeutic approach enhancing the ability of the immune system to combat HIV.

Published
2012

26. Human adiponectin receptor AdipoR1 assumes closed and open structures

Author

Tanabe, Hiroaki, Fujii, Yoshifumi, Okada-Iwabu, Miki, Iwabu, Masato, Kano, Kuniyuki, Kawana, Hiroki, Hato, Masakatsu, Nakamura, Yoshihiro, Terada, Takaho, Kimura-Someya, Tomomi, Shirouzu, Mikako, Kawano, Yoshiaki, Yamamoto, Masaki, Aoki, Junken, Yamauchi, Toshimasa, Kadowaki, Takashi, and Yokoyama, Shigeyuki

Published
2020
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27. Solution Structure of an Arabidopsis WRKY DNA Binding Domain

Author

Yamasaki, Kazuhiko, Kigawa, Takanori, Inoue, Makoto, Tateno, Masaru, Yamasaki, Tomoko, Yabuki, Takashi, Aoki, Masaaki, Seki, Eiko, Matsuda, Takayoshi, Tomo, Yasuko, Hayami, Nobuhiro, Terada, Takaho, Shirouzu, Mikako, Tanaka, Akiko, Seki, Motoaki, Shinozaki, Kazuo, and Yokoyama, Shigeyuki

Published
2005

34. NMR and X-ray structures of the putative sterol carrier protein 2 from Thermus thermophilus HB8 show conformational changes

Author

Goroncy, Alexander, Murayama, Kazutaka, Shirouzu, Mikako, Kuramitsu, Seiki, Kigawa, Takanori, and Yokoyama, Shigeyuki

Abstract

Abstract: Sterol carrier protein 2 (SCP-2), also known as nonspecific lipid transfer protein, is a ubiquitous intracellular ~13 kDa protein found in mammals, insects, plants, archaea, and bacteria. Vertebrate SCP-2 has been implicated in a wide range of lipid-related functions in vitro, although its actual physiological role is still unknown. Tunnels in the protein serve as fatty acid binding vehicles. Here we report the first putative SCP-2 structure from a bacterium: specifically, the NMR and X-ray structures of the TTHA0401 protein (also designated as TT1886) from the extremely thermophilic bacterium Thermus thermophilus. The NMR structure and the two chain structures (chain A and chain B) of the asymmetric crystallographic unit (space group (P212121)) revealed an internal cavity. However, this cavity is open to the outside, forming a tunnel, in only one of those structures (chain A, X-ray). The location of this tunnel is different from the one found in other SCP-2 proteins, and inaccessible cavities have not been seen before in SCP structures. We present evidence that at physiological concentrations, TTHA0401 likely exists as a monomer in equilibrium between open and closed conformations. This equilibrium is influenced by temperature-dependent dynamics, and is likely to be very different at the high temperatures preferred by this hyperthermophilic bacterium. Alternatively, another protein binding to TTHA0401 may induce a conformational change, which would constitute an intriguing metabolic regulation method in bacteria.

Published
2024
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