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Nakamura Y, Umeki N, Abe M, Sako Y. Mutation-Specific Mechanisms of Hyperactivation of Noonan Syndrome SOS Molecules Detected with Single-molecule Imaging in Living Cells. Sci Rep 2017; 7:14153. [PMID: 29074966 PMCID: PMC5658395 DOI: 10.1038/s41598-017-14190-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 10/04/2017] [Indexed: 11/30/2022] Open
Abstract
Noonan syndrome (NS) is a congenital hereditary disorder associated with developmental and cardiac defects. Some patients with NS carry mutations in SOS, a guanine nucleotide exchange factor (GEF) for the small GTPase RAS. NS mutations have been identified not only in the GEF domain, but also in various domains of SOS, suggesting that multiple mechanisms disrupt SOS function. In this study, we examined three NS mutations in different domains of SOS to clarify the abnormality in its translocation to the plasma membrane, where SOS activates RAS. The association and dissociation kinetics between SOS tagged with a fluorescent protein and the living cell surface were observed in single molecules. All three mutants showed increased affinity for the plasma membrane, inducing excessive RAS signalling. However, the mechanisms by which their affinity was increased were specific to each mutant. Conformational disorder in the resting state, increased probability of a conformational change on the plasma membrane, and an increased association rate constant with the membrane receptor are the suggested mechanisms. These different properties cause the specific phenotypes of the mutants, which should be rescuable with different therapeutic strategies. Therefore, single-molecule kinetic analyses of living cells are useful for the pathological analysis of genetic diseases.
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Affiliation(s)
- Yuki Nakamura
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Japan
| | - Nobuhisa Umeki
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Japan
| | - Mitsuhiro Abe
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Japan.
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Iino R, Iida T, Nakamura A, Saita EI, You H, Sako Y. Single-molecule imaging and manipulation of biomolecular machines and systems. Biochim Biophys Acta Gen Subj 2017; 1862:241-252. [PMID: 28789884 DOI: 10.1016/j.bbagen.2017.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/23/2017] [Accepted: 08/03/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND Biological molecular machines support various activities and behaviors of cells, such as energy production, signal transduction, growth, differentiation, and migration. SCOPE OF REVIEW We provide an overview of single-molecule imaging methods involving both small and large probes used to monitor the dynamic motions of molecular machines in vitro (purified proteins) and in living cells, and single-molecule manipulation methods used to measure the forces, mechanical properties and responses of biomolecules. We also introduce several examples of single-molecule analysis, focusing primarily on motor proteins and signal transduction systems. MAJOR CONCLUSIONS Single-molecule analysis is a powerful approach to unveil the operational mechanisms both of individual molecular machines and of systems consisting of many molecular machines. GENERAL SIGNIFICANCE Quantitative, high-resolution single-molecule analyses of biomolecular systems at the various hierarchies of life will help to answer our fundamental question: "What is life?" This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Ryota Iino
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Japan.
| | - Tatsuya Iida
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Japan
| | - Akihiko Nakamura
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Japan
| | - Ei-Ichiro Saita
- Information Processing Biology Unit, Okinawa Institute of Science and Technology Graduate University, Japan
| | - Huijuan You
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, China.
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Nakamura Y, Hibino K, Yanagida T, Sako Y. Switching of the positive feedback for RAS activation by a concerted function of SOS membrane association domains. Biophys Physicobiol 2016; 13:1-11. [PMID: 27924253 PMCID: PMC5042160 DOI: 10.2142/biophysico.13.0_1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 12/11/2015] [Indexed: 01/12/2023] Open
Abstract
Son of sevenless (SOS) is a guanine nucleotide exchange factor that regulates cell behavior by activating the small GTPase RAS. Recent in vitro studies have suggested that an interaction between SOS and the GTP-bound active form of RAS generates a positive feedback loop that propagates RAS activation. However, it remains unclear how the multiple domains of SOS contribute to the regulation of the feedback loop in living cells. Here, we observed single molecules of SOS in living cells to analyze the kinetics and dynamics of SOS behavior. The results indicate that the histone fold and Grb2-binding domains of SOS concertedly produce an intermediate state of SOS on the cell surface. The fraction of the intermediated state was reduced in positive feedback mutants, suggesting that the feedback loop functions during the intermediate state. Translocation of RAF, recognizing the active form of RAS, to the cell surface was almost abolished in the positive feedback mutants. Thus, the concerted functions of multiple membrane-associating domains of SOS governed the positive feedback loop, which is crucial for cell fate decision regulated by RAS.
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Affiliation(s)
- Yuki Nakamura
- Cellular Informatics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan; Nanobiology Laboratories, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kayo Hibino
- Laboratory for Cell Signaling Dynamics, RIKEN QBiC, Suita, Osaka 565-0874, Japan
| | - Toshio Yanagida
- Nanobiology Laboratories, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan; Nanobiology Laboratories, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
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Zhou Y, Mao H, Joddar B, Umeki N, Sako Y, Wada KI, Nishioka C, Takahashi E, Wang Y, Ito Y. The significance of membrane fluidity of feeder cell-derived substrates for maintenance of iPS cell stemness. Sci Rep 2015; 5:11386. [PMID: 26065582 PMCID: PMC4464345 DOI: 10.1038/srep11386] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 04/22/2015] [Indexed: 11/09/2022] Open
Abstract
The biological activity of cell-derived substrates to maintain undifferentiated murine-induced pluripotent stem (iPS) cells was correlated to membrane fluidity as a new parameter of cell culture substrates. Murine embryonic fibroblasts (MEFs) were employed as feeder cells and their membrane fluidity was tuned by chemical fixation using formaldehyde (FA). Membrane fluidity was evaluated by real-time single-molecule observations of green fluorescent protein-labeled epidermal growth factor receptors on chemically fixed MEFs. Biological activity was monitored by colony formation of iPS cells. Treatment with a low concentration of FA sustained the membrane fluidity and biological activity, which were comparable to those of mitomycin C-treated MEFs. The biological activity was further confirmed by sustained expression of alkaline phosphatase, SSEA-1, and other pluripotency markers in iPS cells after 3-5 days of culture on FA-fixed MEFs. Chemical fixation of feeder cells has several advantages such as providing ready-to-use culture substrates without contamination by proliferating feeder cells. Therefore, our results provide an important basis for the development of chemically fixed culture substrates for pluripotent stem cell culture as an alternative to conventional treatment by mitomycin C or x-ray irradiation.
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Affiliation(s)
- Yue Zhou
- Nano Medical Engineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- School of Nursing, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing, Jiangsu Province 210023, China
- Department of Regenerative Medicine, School of Pharmaceutical Science, Jilin University, No.1266 Fujin Road, Changchun 130021, China
| | - Hongli Mao
- Nano Medical Engineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Binata Joddar
- Nano Medical Engineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Nobuhisa Umeki
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ken-Ichi Wada
- Nano Medical Engineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Chieko Nishioka
- Support Unit for Animal Experiment, Research Resources Center, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Eiki Takahashi
- Support Unit for Animal Experiment, Research Resources Center, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yi Wang
- Department of Regenerative Medicine, School of Pharmaceutical Science, Jilin University, No.1266 Fujin Road, Changchun 130021, China
| | - Yoshihiro Ito
- Nano Medical Engineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1Hirosawa, Wako, Saitama 351-0198, Japan
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Marchetti L, Luin S, Bonsignore F, de Nadai T, Beltram F, Cattaneo A. Ligand-induced dynamics of neurotrophin receptors investigated by single-molecule imaging approaches. Int J Mol Sci 2015; 16:1949-79. [PMID: 25603178 PMCID: PMC4307343 DOI: 10.3390/ijms16011949] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 01/05/2015] [Indexed: 01/14/2023] Open
Abstract
Neurotrophins are secreted proteins that regulate neuronal development and survival, as well as maintenance and plasticity of the adult nervous system. The biological activity of neurotrophins stems from their binding to two membrane receptor types, the tropomyosin receptor kinase and the p75 neurotrophin receptors (NRs). The intracellular signalling cascades thereby activated have been extensively investigated. Nevertheless, a comprehensive description of the ligand-induced nanoscale details of NRs dynamics and interactions spanning from the initial lateral movements triggered at the plasma membrane to the internalization and transport processes is still missing. Recent advances in high spatio-temporal resolution imaging techniques have yielded new insight on the dynamics of NRs upon ligand binding. Here we discuss requirements, potential and practical implementation of these novel approaches for the study of neurotrophin trafficking and signalling, in the framework of current knowledge available also for other ligand-receptor systems. We shall especially highlight the correlation between the receptor dynamics activated by different neurotrophins and the respective signalling outcome, as recently revealed by single-molecule tracking of NRs in living neuronal cells.
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Affiliation(s)
- Laura Marchetti
- National Enterprise for nanoScience and nanoTechnology (NEST) Laboratory, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, Pisa I-56127, Italy.
| | - Stefano Luin
- National Enterprise for nanoScience and nanoTechnology (NEST) Laboratory, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, Pisa I-56127, Italy.
| | - Fulvio Bonsignore
- National Enterprise for nanoScience and nanoTechnology (NEST) Laboratory, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, Pisa I-56127, Italy.
| | - Teresa de Nadai
- Biology Laboratory (BioSNS), Scuola Normale Superiore and Istituto di Neuroscienze-CNR, via Moruzzi 1, Pisa I-56100, Italy.
| | - Fabio Beltram
- National Enterprise for nanoScience and nanoTechnology (NEST) Laboratory, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, Pisa I-56127, Italy.
| | - Antonino Cattaneo
- Biology Laboratory (BioSNS), Scuola Normale Superiore and Istituto di Neuroscienze-CNR, via Moruzzi 1, Pisa I-56100, Italy.
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Motegi T, Nabika H, Fu Y, Chen L, Sun Y, Zhao J, Murakoshi K. Effective Brownian ratchet separation by a combination of molecular filtering and a self-spreading lipid bilayer system. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:7496-7501. [PMID: 24913260 DOI: 10.1021/la500943k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A new molecular manipulation method in the self-spreading lipid bilayer membrane by combining Brownian ratchet and molecular filtering effects is reported. The newly designed ratchet obstacle was developed to effectively separate dye-lipid molecules. The self-spreading lipid bilayer acted as both a molecular transport system and a manipulation medium. By controlling the size and shape of ratchet obstacles, we achieved a significant increase in the separation angle for dye-lipid molecules compared to that with the previous ratchet obstacle. A clear difference was observed between the experimental results and the simple random walk simulation that takes into consideration only the geometrical effect of the ratchet obstacles. This difference was explained by considering an obstacle-dependent local decrease in molecular diffusivity near the obstacles, known as the molecular filtering effect at nanospace. Our experimental findings open up a novel controlling factor in the Brownian ratchet manipulation that allow the efficient separation of molecules in the lipid bilayer based on the combination of Brownian ratchet and molecular filtering effects.
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Affiliation(s)
- Toshinori Motegi
- Department of Chemistry, Faculty of Science, Hokkaido University , Sapporo 060-0810, Japan
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Abstract
Neurotrophins are a family of target-derived growth factors that support survival, development, and maintenance of innervating neurons. Owing to the unique architecture of neurons, neurotrophins that act locally on the axonal terminals must convey their signals across the entire axon for subsequent regulation of gene transcription in the cell nucleus. This long-distance retrograde signaling, a motor-driven process that can take hours or days, has been a subject of intense interest. In the last decade, live-cell imaging with high sensitivity has significantly increased our capability to track the transport of neurotrophins, their receptors, and subsequent signals in real time. This review summarizes recent research progress in understanding neurotrophin-receptor interactions at the axonal terminal and their transport dynamics along the axon. We emphasize high-resolution studies at the single-molecule level and also discuss recent technical advances in the field.
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Hall D, Hoshino M. Effects of macromolecular crowding on intracellular diffusion from a single particle perspective. Biophys Rev 2010; 2:39-53. [PMID: 21088688 PMCID: PMC2957576 DOI: 10.1007/s12551-010-0029-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Accepted: 01/08/2010] [Indexed: 01/07/2023] Open
Abstract
Compared to biochemical reactions taking place in relatively well-defined aqueous solutions in vitro, the corresponding reactions happening in vivo occur in extremely complex environments containing only 60-70% water by volume, with the remainder consisting of an undefined array of bio-molecules. In a biological setting, such extremely complex and volume-occupied solution environments are termed 'crowded'. Through a range of intermolecular forces and pseudo-forces, this complex background environment may cause biochemical reactions to behave differently to their in vitro counterparts. In this review, we seek to highlight how the complex background environment of the cell can affect the diffusion of substances within it. Engaging the subject from the perspective of a single particle's motion, we place the focus of our review on two areas: (1) experimental procedures for conducting single particle tracking experiments within cells along with methods for extracting information from these experiments; (2) theoretical factors affecting the translational diffusion of single molecules within crowded two-dimensional membrane and three-dimensional solution environments. We conclude by discussing a number of recent publications relating to intracellular diffusion in light of the reviewed material.
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Affiliation(s)
- Damien Hall
- Institute of Basic Medical Science, University of Tsukuba, Lab 225-B, Building D, 1-1-1 Tennodai, Tsukuba-shi, Ibaraki-ken 305-8577 Japan
| | - Masaru Hoshino
- Department of Pharmaceutical Science, Kyoto University, 46-29 Yoshida-Shimo-Adachi-cho, Sakyo-ku Kyoto, 606-8501 Japan
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Tracking single proteins in live cells using single-chain antibody fragment-fluorescent quantum dot affinity pair. Methods Enzymol 2010; 475:61-79. [PMID: 20627153 DOI: 10.1016/s0076-6879(10)75003-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Quantum dots (QDs) are extremely bright fluorescent imaging probes that are particularly useful for tracking individual molecules in living cells. Here, we show how a two-component system composed of a high-affinity single-chain fragment antibody and its cognate hapten (fluorescein) can be utilized for tracking individual proteins in various cell types. The single-chain fragment antibody against fluorescein is genetically appended to the protein of interest, while the hapten fluorescein is attached to the end of the peptide that is used to coat the QDs. We describe (i) the method used to functionalize QDs with fluorescein peptides; (ii) the method used to control the stoichiometry of the hapten on the surface of the QD; and (iii) the technical details necessary to observe single molecules in living cells.
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Hibino K, Shibata T, Yanagida T, Sako Y. A RasGTP-induced conformational change in C-RAF is essential for accurate molecular recognition. Biophys J 2009; 97:1277-87. [PMID: 19720015 DOI: 10.1016/j.bpj.2009.05.048] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Revised: 05/22/2009] [Accepted: 05/28/2009] [Indexed: 10/20/2022] Open
Abstract
The dysregulation of Ras-RAF signaling is associated with many types of human cancer. However, the kinetic and dynamic features of the mutual molecular recognition of Ras and RAF remain unknown. Here, we developed a technique for imaging single-pair fluorescence resonance energy transfer in living cells, and coupled this technique to single-molecule kinetic analysis to investigate how C-RAF (a subtype of RAF) molecules distinguish the active form of Ras (RasGTP) from the inactive form (RasGDP). Functional fragments of C-RAF containing the Ras-binding domains did not detect the switch in Ras activity in living cells as efficiently as did C-RAF. Single-molecule analysis showed that RasGDP associates with closed-conformation C-RAF, whereas the association of C-RAF with RasGTP immediately triggers the open RAF conformation, which induces an effective interaction between C-RAF and RasGTP. Spontaneous conformational changes from closed C-RAF to the open form rarely occur in quiescent cells. The conformational change in C-RAF is so important to Ras-RAF molecular recognition that C-RAF mutants lacking the conformational change cannot distinguish between RasGDP and RasGTP. The manipulation of the conformation of an effector molecule is a newly identified function of RasGTP.
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Affiliation(s)
- Kayo Hibino
- Cellular Informatics Laboratory, RIKEN, Wako, Japan
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