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Araki K, Watanabe-Nakayama T, Sasaki D, Sasaki YC, Mio K. Molecular Dynamics Mappings of the CCT/TRiC Complex-Mediated Protein Folding Cycle Using Diffracted X-ray Tracking. Int J Mol Sci 2023; 24:14850. [PMID: 37834298 PMCID: PMC10573753 DOI: 10.3390/ijms241914850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
The CCT/TRiC complex is a type II chaperonin that undergoes ATP-driven conformational changes during its functional cycle. Structural studies have provided valuable insights into the mechanism of this process, but real-time dynamics analyses of mammalian type II chaperonins are still scarce. We used diffracted X-ray tracking (DXT) to investigate the intramolecular dynamics of the CCT complex. We focused on three surface-exposed loop regions of the CCT1 subunit: the loop regions of the equatorial domain (E domain), the E and intermediate domain (I domain) juncture near the ATP-binding region, and the apical domain (A domain). Our results showed that the CCT1 subunit predominantly displayed rotational motion, with larger mean square displacement (MSD) values for twist (χ) angles compared with tilt (θ) angles. Nucleotide binding had a significant impact on the dynamics. In the absence of nucleotides, the region between the E and I domain juncture could act as a pivotal axis, allowing for greater motion of the E domain and A domain. In the presence of nucleotides, the nucleotides could wedge into the ATP-binding region, weakening the role of the region between the E and I domain juncture as the rotational axis and causing the CCT complex to adopt a more compact structure. This led to less expanded MSD curves for the E domain and A domain compared with nucleotide-absent conditions. This change may help to stabilize the functional conformation during substrate binding. This study is the first to use DXT to probe the real-time molecular dynamics of mammalian type II chaperonins at the millisecond level. Our findings provide new insights into the complex dynamics of chaperonins and their role in the functional folding cycle.
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Affiliation(s)
- Kazutaka Araki
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan;
| | - Takahiro Watanabe-Nakayama
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan;
| | - Daisuke Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan (Y.C.S.)
| | - Yuji C. Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan (Y.C.S.)
| | - Kazuhiro Mio
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan;
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Oda M. Analysis of the Structural Dynamics of Proteins in the Ligand-Unbound and -Bound States by Diffracted X-ray Tracking. Int J Mol Sci 2023; 24:13717. [PMID: 37762021 PMCID: PMC10531450 DOI: 10.3390/ijms241813717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Although many protein structures have been determined at atomic resolution, the majority of them are static and represent only the most stable or averaged structures in solution. When a protein binds to its ligand, it usually undergoes fluctuation and changes its conformation. One attractive method for obtaining an accurate view of proteins in solution, which is required for applications such as the rational design of proteins and structure-based drug design, is diffracted X-ray tracking (DXT). DXT can detect the protein structural dynamics on a timeline via gold nanocrystals attached to the protein. Here, the structure dynamics of single-chain Fv antibodies, helix bundle-forming de novo designed proteins, and DNA-binding proteins in both ligand-unbound and ligand-bound states were analyzed using the DXT method. The resultant mean square angular displacements (MSD) curves in both the tilting and twisting directions clearly demonstrated that structural fluctuations were suppressed upon ligand binding, and the binding energies determined using the angular diffusion coefficients from the MSD agreed well with the binding thermodynamics determined using isothermal titration calorimetry. In addition, the size of gold nanocrystals is discussed, which is one of the technical concerns of DXT.
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Affiliation(s)
- Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
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Yamamoto YY, Uno Y, Sha E, Ikegami K, Ishii N, Dohmae N, Sekiguchi H, Sasaki YC, Yohda M. Asymmetry in the function and dynamics of the cytosolic group II chaperonin CCT/TRiC. PLoS One 2017; 12:e0176054. [PMID: 28463997 PMCID: PMC5413064 DOI: 10.1371/journal.pone.0176054] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/04/2017] [Indexed: 12/27/2022] Open
Abstract
The eukaryotic group II chaperonin, the chaperonin-containing t-complex polypeptide 1 (CCT), plays an important role in cytosolic proteostasis. It has been estimated that as much as 10% of cytosolic proteins interact with CCT during their folding process. CCT is composed of 8 different paralogous subunits. Due to its complicated structure, molecular and biochemical investigations of CCT have been difficult. In this study, we constructed an expression system for CCT from a thermophilic fungus, Chaetomium thermophilum (CtCCT), by using E. coli as a host. As expected, we obtained recombinant CtCCT with a relatively high yield, and it exhibited fairly high thermal stability. We showed the advantages of the overproduction system by characterizing CtCCT variants containing ATPase-deficient subunits. For diffracted X-ray tracking experiment, we removed all surface exposed cysteine residues, and added cysteine residues at the tip of helical protrusions of selected two subunits. Gold nanocrystals were attached onto CtCCTs via gold-thiol bonds and applied for the analysis by diffracted X-ray tracking. Irrespective of the locations of cysteines, it was shown that ATP binding induces tilting motion followed by rotational motion in the CtCCT molecule, like the archaeal group II chaperonins. When gold nanocrystals were attached onto two subunits in the high ATPase activity hemisphere, the CtCCT complex exhibited a fairly rapid response to the motion. In contrast, the response of CtCCT, which had gold nanocrystals attached to the low-activity hemisphere, was slow. These results clearly support the possibility that ATP-dependent conformational change starts with the high-affinity hemisphere and progresses to the low-affinity hemisphere.
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Affiliation(s)
- Yohei Y. Yamamoto
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Yuko Uno
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Eiryo Sha
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Kentaro Ikegami
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Noriyuki Ishii
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
- The United Graduate School of Agricultural Science, Gifu University, Tsukuba, Ibaraki, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | | | - Yuji C. Sasaki
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Masafumi Yohda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
- * E-mail:
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Yamamoto YY, Tsuchida K, Noguchi K, Ogawa N, Sekiguchi H, Sasaki YC, Yohda M. Characterization of group II chaperonins from an acidothermophilic archaeon Picrophilus torridus. FEBS Open Bio 2016; 6:751-64. [PMID: 27398315 PMCID: PMC4932455 DOI: 10.1002/2211-5463.12090] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 05/14/2016] [Accepted: 05/16/2016] [Indexed: 12/20/2022] Open
Abstract
Chaperonins are a type of molecular chaperone that assist in the folding of proteins. Group II chaperonins play an important role in the proteostasis in the cytosol of archaea and eukarya. In this study, we expressed, purified, and characterized group II chaperonins from an acidothermophilic archaeon Picrophilus torridus. Two genes exist for group II chaperonins, and both of the gene products assemble to form double‐ring complexes similar to other archaeal group II chaperonins. One of the Picrophilus chaperonins, PtoCPNα, was able to refold denatured GFP at 50 °C. As expected, PtoCPNα exhibited an ATP‐dependent conformational change that is observed by the change in fluorescence and diffracted X‐ray tracking (DXT). In contrast, PtoCPNα lost its protein folding ability at moderate temperatures, becoming unable to interact with unfolded proteins. At lower temperatures, the release rate of the captured GFP from PtoCPNα was accelerated, and the affinity of denatured protein to PtoCPNα was weakened at the lower temperatures. Unexpectedly, in the DXT experiment, the fine motions were enhanced at the lower temperatures. Taken together, the results suggest that the fine tilting motions of the apical domain might correlate with the affinity of group II chaperonins for denatured proteins.
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Affiliation(s)
- Yohei Y Yamamoto
- Department of Biotechnology and Life Science Tokyo University of Agriculture and Technology Koganei Japan; Research Fellow of Japan Society for the Promotion of Science Chiyoda, Tokyo Japan
| | - Kanako Tsuchida
- Department of Biotechnology and Life Science Tokyo University of Agriculture and Technology Koganei Japan
| | - Keiichi Noguchi
- Instrumentation Analysis Center Tokyo University of Agriculture and Technology Koganei Japan
| | - Naoki Ogawa
- Department of Integrated Science in Physics and Biology College of Humanities and Sciences Nihon University Setagaya-ku Japan
| | | | - Yuji C Sasaki
- Graduate School of Frontier Sciences University of Tokyo Kashiwa Japan
| | - Masafumi Yohda
- Department of Biotechnology and Life Science Tokyo University of Agriculture and Technology Koganei Japan
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Abstract
Chaperonins are nanomachines that facilitate protein folding by undergoing energy (ATP)-dependent movements that are coordinated in time and space owing to complex allosteric regulation. They consist of two back-to-back stacked oligomeric rings with a cavity at each end where protein substrate folding can take place. Here, we focus on the GroEL/GroES chaperonin system from Escherichia coli and, to a lesser extent, on the more poorly characterized eukaryotic chaperonin CCT/TRiC. We describe their various functional (allosteric) states and how they are affected by substrates and allosteric effectors that include ATP, ADP, nonfolded protein substrates, potassium ions, and GroES (in the case of GroEL). We also discuss the pathways of intra- and inter-ring allosteric communication by which they interconvert and the coupling between allosteric transitions and protein folding reactions.
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Affiliation(s)
- Ranit Gruber
- Department of Structural Biology, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Amnon Horovitz
- Department of Structural Biology, Weizmann Institute of Science , Rehovot 76100, Israel
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Sekiguchi H, Suzuki Y, Nishino Y, Kobayashi S, Shimoyama Y, Cai W, Nagata K, Okada M, Ichiyanagi K, Ohta N, Yagi N, Miyazawa A, Kubo T, Sasaki YC. Real time ligand-induced motion mappings of AChBP and nAChR using X-ray single molecule tracking. Sci Rep 2014; 4:6384. [PMID: 25223459 PMCID: PMC4165275 DOI: 10.1038/srep06384] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 08/29/2014] [Indexed: 11/12/2022] Open
Abstract
We observed the dynamic three-dimensional (3D) single molecule behaviour of acetylcholine-binding protein (AChBP) and nicotinic acetylcholine receptor (nAChR) using a single molecule tracking technique, diffracted X-ray tracking (DXT) with atomic scale and 100 μs time resolution. We found that the combined tilting and twisting motions of the proteins were enhanced upon acetylcholine (ACh) binding. We present the internal motion maps of AChBP and nAChR in the presence of either ACh or α-bungarotoxin (αBtx), with views from two rotational axes. Our findings indicate that specific motion patterns represented as biaxial angular motion maps are associated with channel function in real time and on an atomic scale.
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Affiliation(s)
- Hiroshi Sekiguchi
- 1] CREST Sasaki Team, Japan Science and Technology Agency, The University of Tokyo, #609 Kiban Bldg., 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8561, Japan [2] Research &Utilization Division, Japan Synchrotron Radiation Research Institute, SPring-8 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yasuhito Suzuki
- 1] CREST Sasaki Team, Japan Science and Technology Agency, The University of Tokyo, #609 Kiban Bldg., 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8561, Japan [2] Graduate School of Frontier Sciences, The University of Tokyo, Kiban Bldg., 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8561, Japan
| | - Yuri Nishino
- 1] Graduate School of Life Sciences, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo, 679-1297, Japan [2] RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Suzuko Kobayashi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Yoshiko Shimoyama
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Weiyan Cai
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Kenji Nagata
- Graduate School of Frontier Sciences, The University of Tokyo, Kiban Bldg., 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8561, Japan
| | - Masato Okada
- Graduate School of Frontier Sciences, The University of Tokyo, Kiban Bldg., 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8561, Japan
| | - Kouhei Ichiyanagi
- 1] CREST Sasaki Team, Japan Science and Technology Agency, The University of Tokyo, #609 Kiban Bldg., 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8561, Japan [2] Graduate School of Frontier Sciences, The University of Tokyo, Kiban Bldg., 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8561, Japan
| | - Noboru Ohta
- Research &Utilization Division, Japan Synchrotron Radiation Research Institute, SPring-8 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Naoto Yagi
- 1] CREST Sasaki Team, Japan Science and Technology Agency, The University of Tokyo, #609 Kiban Bldg., 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8561, Japan [2] Research &Utilization Division, Japan Synchrotron Radiation Research Institute, SPring-8 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Atsuo Miyazawa
- 1] Graduate School of Life Sciences, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo, 679-1297, Japan [2] RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Tai Kubo
- 1] CREST Sasaki Team, Japan Science and Technology Agency, The University of Tokyo, #609 Kiban Bldg., 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8561, Japan [2] Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan [3] Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Yuji C Sasaki
- 1] CREST Sasaki Team, Japan Science and Technology Agency, The University of Tokyo, #609 Kiban Bldg., 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8561, Japan [2] Research &Utilization Division, Japan Synchrotron Radiation Research Institute, SPring-8 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan [3] Graduate School of Frontier Sciences, The University of Tokyo, Kiban Bldg., 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8561, Japan
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