1
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Zheng C, Tang E. A topological mechanism for robust and efficient global oscillations in biological networks. Nat Commun 2024; 15:6453. [PMID: 39085205 PMCID: PMC11291491 DOI: 10.1038/s41467-024-50510-x] [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: 03/22/2023] [Accepted: 07/11/2024] [Indexed: 08/02/2024] Open
Abstract
Long and stable timescales are often observed in complex biochemical networks, such as in emergent oscillations. How these robust dynamics persist remains unclear, given the many stochastic reactions and shorter time scales demonstrated by underlying components. We propose a topological model that produces long oscillations around the network boundary, reducing the system dynamics to a lower-dimensional current in a robust manner. Using this to model KaiC, which regulates the circadian rhythm in cyanobacteria, we compare the coherence of oscillations to that in other KaiC models. Our topological model localizes currents on the system edge, with an efficient regime of simultaneously increased precision and decreased cost. Further, we introduce a new predictor of coherence from the analysis of spectral gaps, and show that our model saturates a global thermodynamic bound. Our work presents a new mechanism and parsimonious description for robust emergent oscillations in complex biological networks.
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Affiliation(s)
- Chongbin Zheng
- Center for Theoretical Biological Physics, Rice University, Houston, TX, 77005, USA
- Department of Physics and Astronomy, Rice University, Houston, TX, 77005, USA
| | - Evelyn Tang
- Center for Theoretical Biological Physics, Rice University, Houston, TX, 77005, USA.
- Department of Physics and Astronomy, Rice University, Houston, TX, 77005, USA.
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2
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Ando T, Fukuda S, Ngo KX, Flechsig H. High-Speed Atomic Force Microscopy for Filming Protein Molecules in Dynamic Action. Annu Rev Biophys 2024; 53:19-39. [PMID: 38060998 DOI: 10.1146/annurev-biophys-030722-113353] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Structural biology is currently undergoing a transformation into dynamic structural biology, which reveals the dynamic structure of proteins during their functional activity to better elucidate how they function. Among the various approaches in dynamic structural biology, high-speed atomic force microscopy (HS-AFM) is unique in the ability to film individual molecules in dynamic action, although only topographical information is acquirable. This review provides a guide to the use of HS-AFM for biomolecular imaging and showcases several examples, as well as providing information on up-to-date progress in HS-AFM technology. Finally, we discuss the future prospects of HS-AFM in the context of dynamic structural biology in the upcoming era.
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Affiliation(s)
- Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan;
| | - Shingo Fukuda
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan;
| | - Kien X Ngo
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan;
| | - Holger Flechsig
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan;
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3
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van Ewijk C, Xu F, Maity S, Sheng J, Stuart MCA, Feringa BL, Roos WH. Light-Triggered Disassembly of Molecular Motor-based Supramolecular Polymers Revealed by High-Speed AFM. Angew Chem Int Ed Engl 2024; 63:e202319387. [PMID: 38372499 DOI: 10.1002/anie.202319387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/02/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
Photoresponsive supramolecular polymers have a major potential for applications in responsive materials that are externally triggered by light with spatio-temporal control of their polymerisation state. While changes in macroscopic properties revealed the adaptive nature of these materials, it remains challenging to capture the dynamic depolymerisation process at the molecular level, which requires fast observation techniques combined with in situ irradiation. By implementing in situ UV illumination into a High-Speed Atomic Force Microscope (HS-AFM) setup, we have been able to capture the disassembly of a light-driven molecular motor-based supramolecular polymer. The real-time visualisation of the light-triggered disassembly process not only reveals cooperative depolymerisation, it also shows that this process continues after illumination is halted. Combining the data with cryo-electron microscopy and spectroscopy approaches, we obtain a molecular-level description of the motor-based polymer dynamics reminiscent of actin chain-end depolymerisation. Our detailed understanding of supramolecular depolymerisation will drive the development of future responsive polymer systems.
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Affiliation(s)
- Chris van Ewijk
- Molecular Biophysics, Zernike Institute for Advanced Materials Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The, Netherlands
| | - Fan Xu
- Synthetic Organic Chemistry, Stratingh Institute for Chemistry Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The, Netherlands
| | - Sourav Maity
- Molecular Biophysics, Zernike Institute for Advanced Materials Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The, Netherlands
| | - Jinyu Sheng
- Synthetic Organic Chemistry, Stratingh Institute for Chemistry Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The, Netherlands
| | - Marc C A Stuart
- Synthetic Organic Chemistry, Stratingh Institute for Chemistry Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The, Netherlands
| | - Ben L Feringa
- Synthetic Organic Chemistry, Stratingh Institute for Chemistry Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The, Netherlands
| | - Wouter H Roos
- Molecular Biophysics, Zernike Institute for Advanced Materials Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The, Netherlands
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4
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Leech G, Melcher L, Chiu M, Nugent M, Burton L, Kang J, Kim SJ, Roy S, Farhadi L, Ross JL, Das M, Rust MJ, Robertson-Anderson RM. Timed material self-assembly controlled by circadian clock proteins. ARXIV 2024:arXiv:2303.00779v2. [PMID: 36911279 PMCID: PMC10002811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Active biological molecules present a powerful, yet largely untapped, opportunity to impart autonomous regulation to materials. Because these systems can function robustly to regulate when and where chemical reactions occur, they have the ability to bring complex, life-like behavior to synthetic materials. Here, we achieve this design feat by using functionalized circadian clock proteins, KaiB and KaiC, to engineer time-dependent crosslinking of colloids. The resulting material self-assembles with programmable kinetics, producing macroscopic changes in material properties, via molecular assembly of KaiB-KaiC complexes. We show that colloid crosslinking depends strictly on the phosphorylation state of KaiC, with kinetics that are synced with KaiB-KaiC complexing. Our microscopic image analyses and computational models indicate that the stability of colloidal super-structures depends sensitively on the number of Kai complexes per colloid connection. Consistent with our model predictions, a high concentration stabilizes the material against dissolution after a robust self-assembly phase, while a low concentration allows circadian oscillation of material structure. This work introduces the concept of harnessing biological timers to control synthetic materials; and, more generally, opens the door to using protein-based reaction networks to endow synthetic systems with life-like functional properties.
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Affiliation(s)
- Gregor Leech
- Department of Physics and Biophysics, University of San Diego, San Diego, California 92110, United States
| | - Lauren Melcher
- School of Mathematical Sciences, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Michelle Chiu
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, Illinois 60637, United States
| | - Maya Nugent
- Department of Physics and Biophysics, University of San Diego, San Diego, California 92110, United States
| | - Lily Burton
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, Illinois 60637, United States
| | - Janet Kang
- Department of Molecular Genetics and Cell Biology and Department of Physics, University of Chicago, Chicago, Illinois 60637, United States
| | - Soo Ji Kim
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, Illinois 60637, United States
| | - Sourav Roy
- Department of Physics, Syracuse University, Syracuse, New York 13244, United States
| | - Leila Farhadi
- Department of Physics, Syracuse University, Syracuse, New York 13244, United States
| | - Jennifer L Ross
- Department of Physics, Syracuse University, Syracuse, New York 13244, United States
| | - Moumita Das
- School of Mathematical Sciences, Rochester Institute of Technology, Rochester, New York 14623, United States
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Michael J Rust
- Department of Molecular Genetics and Cell Biology and Department of Physics, University of Chicago, Chicago, Illinois 60637, United States
| | - Rae M Robertson-Anderson
- Department of Physics and Biophysics, University of San Diego, San Diego, California 92110, United States
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5
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Chavan A, Heisler J, Chang YG, Golden SS, Partch CL, LiWang A. Protocols for in vitro reconstitution of the cyanobacterial circadian clock. Biopolymers 2024; 115:e23559. [PMID: 37421636 PMCID: PMC10772220 DOI: 10.1002/bip.23559] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/26/2023] [Accepted: 06/16/2023] [Indexed: 07/10/2023]
Abstract
Circadian clocks are intracellular systems that orchestrate metabolic processes in anticipation of sunrise and sunset by providing an internal representation of local time. Because the ~24-h metabolic rhythms they produce are important to health across diverse life forms there is growing interest in their mechanisms. However, mechanistic studies are challenging in vivo due to the complex, that is, poorly defined, milieu of live cells. Recently, we reconstituted the intact circadian clock of cyanobacteria in vitro. It oscillates autonomously and remains phase coherent for many days with a fluorescence-based readout that enables real-time observation of individual clock proteins and promoter DNA simultaneously under defined conditions without user intervention. We found that reproducibility of the reactions required strict adherence to the quality of each recombinant clock protein purified from Escherichia coli. Here, we provide protocols for preparing in vitro clock samples so that other labs can ask questions about how changing environments, like temperature, metabolites, and protein levels are reflected in the core oscillator and propagated to regulation of transcription, providing deeper mechanistic insights into clock biology.
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Affiliation(s)
- Archana Chavan
- Center for Circadian Biology, University of California – San Diego, La Jolla, CA 92093
- School of Natural Sciences, University of California – Merced, Merced, CA 95343
| | - Joel Heisler
- Center for Circadian Biology, University of California – San Diego, La Jolla, CA 92093
- School of Natural Sciences, University of California – Merced, Merced, CA 95343
| | - Yong-Gang Chang
- Center for Circadian Biology, University of California – San Diego, La Jolla, CA 92093
- School of Natural Sciences, University of California – Merced, Merced, CA 95343
| | - Susan S. Golden
- Center for Circadian Biology, University of California – San Diego, La Jolla, CA 92093
- Department of Molecular Biology, University of California – San Diego, La Jolla, CA 92093
| | - Carrie L. Partch
- Center for Circadian Biology, University of California – San Diego, La Jolla, CA 92093
- Department of Chemistry & Biochemistry, University of California – Santa Cruz, Santa Cruz, CA 95064
| | - Andy LiWang
- Center for Circadian Biology, University of California – San Diego, La Jolla, CA 92093
- School of Natural Sciences, University of California – Merced, Merced, CA 95343
- Department of Chemistry & Biochemistry, University of California – Merced, Merced, CA 95343
- Center for Cellular and Biomolecular Machines, University of California – Merced, Merced, CA 95343
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6
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Fang M, LiWang A, Golden SS, Partch CL. The inner workings of an ancient biological clock. Trends Biochem Sci 2024; 49:236-246. [PMID: 38185606 PMCID: PMC10939747 DOI: 10.1016/j.tibs.2023.12.007] [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: 09/09/2023] [Revised: 11/30/2023] [Accepted: 12/15/2023] [Indexed: 01/09/2024]
Abstract
Circadian clocks evolved in diverse organisms as an adaptation to the daily swings in ambient light and temperature that derive from Earth's rotation. These timing systems, based on intracellular molecular oscillations, synchronize organisms' behavior and physiology with the 24-h environmental rhythm. The cyanobacterial clock serves as a special model for understanding circadian rhythms because it can be fully reconstituted in vitro. This review summarizes recent advances that leverage new biochemical, biophysical, and mathematical approaches to shed light on the molecular mechanisms of cyanobacterial Kai proteins that support the clock, and their homologues in other bacteria. Many questions remain in circadian biology, and the tools developed for the Kai system will bring us closer to the answers.
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Affiliation(s)
- Mingxu Fang
- Department of Molecular Biology, University of California - San Diego, La Jolla, CA 92093, USA; Center for Circadian Biology, University of California - San Diego, La Jolla, CA 92093, USA
| | - Andy LiWang
- Center for Circadian Biology, University of California - San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California - Merced, Merced, CA 95343, USA; Center for Cellular and Biomolecular Machines, University of California - Merced, Merced, CA 95343, USA
| | - Susan S Golden
- Department of Molecular Biology, University of California - San Diego, La Jolla, CA 92093, USA; Center for Circadian Biology, University of California - San Diego, La Jolla, CA 92093, USA
| | - Carrie L Partch
- Center for Circadian Biology, University of California - San Diego, La Jolla, CA 92093, USA; Department of Chemistry & Biochemistry, University of California - Santa Cruz, Santa Cruz, CA 95064, USA.
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7
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Yanaka S, Watanabe H, Yogo R, Kongsema M, Kondo S, Yagi H, Uchihashi T, Kato K. Quantitative Analysis of Therapeutic Antibody Interactions with Fcγ Receptors Using High-Speed Atomic Force Microscopy. Biol Pharm Bull 2024; 47:334-338. [PMID: 38143078 DOI: 10.1248/bpb.b23-00751] [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] [Indexed: 12/26/2023]
Abstract
This study employed high-speed atomic force microscopy to quantitatively analyze the interactions between therapeutic antibodies and Fcγ receptors (FcγRs). Antibodies are essential components of the immune system and are integral to biopharmaceuticals. The focus of this study was on immunoglobulin G molecules, which are crucial for antigen binding via the Fab segments and cytotoxic functions through their Fc portions. We conducted real-time, label-free observations of the interactions of rituximab and mogamulizumab with the recombinant FcγRIIIa and FcγRIIa. The dwell times of FcγR binding were measured at the single-molecule level, which revealed an extended interaction duration of mogamulizumab with FcγRIIIa compared with that of rituximab. This is linked to enhanced antibody-dependent cellular cytotoxicity that is attributed to the absence of the core fucosylation of Fc-linked N-glycan. This study also emphasizes the crucial role of the Fab segments in the interaction with FcγRIIa as well as that with FcγRIIIa. This approach provided quantitative insight into therapeutic antibody interactions and exemplified kinetic proofreading, where cellular discrimination relies on ligand residence times. Observing the dwell times of antibodies on the effector molecules has emerged as a robust indicator of therapeutic antibody efficacy. Ultimately, these findings pave the way for the development of refined therapeutic antibodies with tailored interactions with specific FcγRs. This research contributes to the advancement of biopharmaceutical antibody design and optimizing antibody-based treatments for enhanced efficacy and precision.
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Affiliation(s)
- Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
- Graduate School of Pharmaceutical Sciences, Kyushu University
| | - Hiroki Watanabe
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences
| | - Rina Yogo
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
| | | | - Sachiko Kondo
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Hirokazu Yagi
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Takayuki Uchihashi
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences
- Department of Physics and Institute for Glyco-core Research (iGCORE), Nagoya University
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
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8
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van Ewijk C, Maity S, Roos WH. Visualizing Molecular Dynamics by High-Speed Atomic Force Microscopy. Methods Mol Biol 2024; 2694:355-372. [PMID: 37824013 DOI: 10.1007/978-1-0716-3377-9_17] [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] [Indexed: 10/13/2023]
Abstract
Dynamic processes and structural changes of biological molecules are essential to life. While conventional atomic force microscopy (AFM) is able to visualize molecules and supramolecular assemblies at sub-nanometer resolution, it cannot capture dynamics because of its low imaging rate. The introduction of high-speed atomic force microscopy (HS-AFM) solved this problem by providing a large increase in imaging velocity. Using HS-AFM, one is able to visualize dynamic molecular events with high spatiotemporal resolution under near-to physiological conditions. This approach opened new windows as finally dynamics of biomolecules at sub-nanometer resolution could be studied. Here we describe the working principles and an operation protocol for HS-AFM imaging and characterization of biological samples in liquid.
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Affiliation(s)
- Chris van Ewijk
- Molecular Biophysics, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Sourav Maity
- Molecular Biophysics, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Wouter H Roos
- Molecular Biophysics, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands.
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9
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Lakin-Thomas P. The Case for the Target of Rapamycin Pathway as a Candidate Circadian Oscillator. Int J Mol Sci 2023; 24:13307. [PMID: 37686112 PMCID: PMC10488232 DOI: 10.3390/ijms241713307] [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: 08/09/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
The molecular mechanisms that drive circadian (24 h) rhythmicity have been investigated for many decades, but we still do not have a complete picture of eukaryotic circadian systems. Although the transcription/translation feedback loop (TTFL) model has been the primary focus of research, there are many examples of circadian rhythms that persist when TTFLs are not functioning, and we lack any good candidates for the non-TTFL oscillators driving these rhythms. In this hypothesis-driven review, the author brings together several lines of evidence pointing towards the Target of Rapamycin (TOR) signalling pathway as a good candidate for a non-TTFL oscillator. TOR is a ubiquitous regulator of metabolism in eukaryotes and recent focus in circadian research on connections between metabolism and rhythms makes TOR an attractive candidate oscillator. In this paper, the evidence for a role for TOR in regulating rhythmicity is reviewed, and the advantages of TOR as a potential oscillator are discussed. Evidence for extensive feedback regulation of TOR provides potential mechanisms for a TOR-driven oscillator. Comparison with ultradian yeast metabolic cycles provides an example of a potential TOR-driven self-sustained oscillation. Unanswered questions and problems to be addressed by future research are discussed.
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10
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Sasai M. Role of the reaction-structure coupling in temperature compensation of the KaiABC circadian rhythm. PLoS Comput Biol 2022; 18:e1010494. [PMID: 36067222 PMCID: PMC9481178 DOI: 10.1371/journal.pcbi.1010494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 09/16/2022] [Accepted: 08/17/2022] [Indexed: 11/19/2022] Open
Abstract
When the mixture solution of cyanobacterial proteins, KaiA, KaiB, and KaiC, is incubated with ATP in vitro, the phosphorylation level of KaiC shows stable oscillations with the temperature-compensated circadian period. Elucidating this temperature compensation is essential for understanding the KaiABC circadian clock, but its mechanism has remained a mystery. We analyzed the KaiABC temperature compensation by developing a theoretical model describing the feedback relations among reactions and structural transitions in the KaiC molecule. The model showed that the reduced structural cooperativity should weaken the negative feedback coupling among reactions and structural transitions, which enlarges the oscillation amplitude and period, explaining the observed significant period extension upon single amino-acid residue substitution. We propose that an increase in thermal fluctuations similarly attenuates the reaction-structure feedback, explaining the temperature compensation in the KaiABC clock. The model explained the experimentally observed responses of the oscillation phase to the temperature shift or the ADP-concentration change and suggested that the ATPase reactions in the CI domain of KaiC affect the period depending on how the reaction rates are modulated. The KaiABC clock provides a unique opportunity to analyze how the reaction-structure coupling regulates the system-level synchronized oscillations of molecules.
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Affiliation(s)
- Masaki Sasai
- Department of Applied Physics, Nagoya University, Nagoya, Japan
- Department of Complex Systems Science, Nagoya University, Nagoya, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto, Japan
- * E-mail:
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11
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Lee D, Woo Y, Lim JS, Park I, Park SK, Park JW. Quantification of a Neurological Protein in a Single Cell Without Amplification. ACS OMEGA 2022; 7:20165-20171. [PMID: 35722002 PMCID: PMC9201896 DOI: 10.1021/acsomega.2c02009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Proteins are key biomolecules that not only play various roles in the living body but also are used as biomarkers. If these proteins can be quantified at the level of a single cell, understanding the role of proteins will be deepened and diagnosing diseases and abnormality will be further upgraded. In this study, we quantified a neurological protein in a single cell using atomic force microscopy (AFM). After capturing specifically disrupted-in-schizophrenia 1 (DISC1) in a single cell onto a microspot immobilizing the corresponding antibody on the surface, force mapping with AFM was followed to visualize individual DISC1. Although a large variation of the number of DISC1 in a cell was observed, the average number is 4.38 × 103, and the number agrees with the ensemble-averaged value. The current AFM approach for the quantitative analysis of proteins in a single cell should be useful to study molecular behavior of proteins in depth and to follow physiological change of individual cells in response to external stimuli.
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Affiliation(s)
- Donggyu Lee
- Department
of Life Sciences, Pohang University of Science
and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Youngsik Woo
- Department
of Life Sciences, Pohang University of Science
and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Ji-seon Lim
- Department
of Chemistry, Pohang University of Science
and Technology, 77 Cheongam-Ro,
Nam-Gu, Pohang 37673, Republic of Korea
| | - Ikbum Park
- Analysis
and Assessment Research Center, Research
Institute of Industrial Science and Technology, 67 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic
of Korea
| | - Sang Ki Park
- Department
of Life Sciences, Pohang University of Science
and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Joon Won Park
- Department
of Chemistry, Pohang University of Science
and Technology, 77 Cheongam-Ro,
Nam-Gu, Pohang 37673, Republic of Korea
- Institute
of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic
of Korea
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12
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Lim JS, Kim HJ, Park I, Woo S, Kim JH, Park JW. Force Mapping Reveals the Spatial Distribution of Individual Proteins in a Neuron. NANO LETTERS 2022; 22:3865-3871. [PMID: 35549313 DOI: 10.1021/acs.nanolett.1c04395] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Conventional methods for studying the spatial distribution and expression level of proteins within neurons have primarily relied on immunolabeling and/or signal amplification. Here, we present an atomic force microscopy (AFM)-based nanoscale force mapping method, where Anti-LIMK1-tethered AFM probes were used to visualize individual LIMK1 proteins in cultured neurons directly through force measurements. We observed that the number density of LIMK1 decreased in neuronal somas after the cells were depolarized. We also elucidated the spatial distribution of LIMK1 in single spine areas and found that the protein predominantly locates at heads of spines rather than dendritic shafts. The study demonstrates that our method enables unveiling of the abundance and spatial distribution of a protein of interest in neurons without signal amplification or labeling. We expected that this approach should facilitate the studies of protein expression phenomena in depth in a wide range of biological systems.
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Affiliation(s)
- Ji-Seon Lim
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Hyun Jin Kim
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Ikbum Park
- Analysis and Assessment Research Center, Research Institute of Industrial Science and Technology, 67 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Sungwook Woo
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Joung-Hun Kim
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Joon Won Park
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
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13
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Abstract
KaiC, a core clock protein in the cyanobacterial circadian clock system, hydrolyzes adenosine triphosphate (ATP) at two distinct sites in a slow but ordered manner to measure the circadian timescale. We used biochemical and structural biology techniques to characterize the properties and interplay of dual-adenosine triphosphatase (ATPase) active sites. Our results show that the N-terminal and C-terminal ATPases communicate with each other through an interface between the N-terminal and C-terminal domains in KaiC. The dual-ATPase sites are regulated rhythmically in a concerted or opposing manner dependent on the phase of the circadian clock system, controlling the affinities of KaiC for other clock proteins, KaiA and KaiB. KaiC is a dual adenosine triphosphatase (ATPase), with one active site in its N-terminal domain and another in its C-terminal domain, that drives the circadian clock system of cyanobacteria through sophisticated coordination of the two sites. To elucidate the coordination mechanism, we studied the contribution of the dual-ATPase activities in the ring-shaped KaiC hexamer and these structural bases for activation and inactivation. At the N-terminal active site, a lytic water molecule is sequestered between the N-terminal domains, and its reactivity to adenosine triphosphate (ATP) is controlled by the quaternary structure of the N-terminal ring. The C-terminal ATPase activity is regulated mostly by water-incorporating voids between the C-terminal domains, and the size of these voids is sensitive to phosphoryl modification of S431. The up-regulatory effect on the N-terminal ATPase activity inversely correlates with the affinity of KaiC for KaiB, a clock protein constitutes the circadian oscillator together with KaiC and KaiA, and the complete dissociation of KaiB from KaiC requires KaiA-assisted activation of the dual ATPase. Delicate interactions between the N-terminal and C-terminal rings make it possible for the components of the dual ATPase to work together, thereby driving the assembly and disassembly cycle of KaiA and KaiB.
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14
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Yunoki Y, Matsumoto A, Morishima K, Martel A, Porcar L, Sato N, Yogo R, Tominaga T, Inoue R, Yagi-Utsumi M, Okuda A, Shimizu M, Urade R, Terauchi K, Kono H, Yagi H, Kato K, Sugiyama M. Overall structure of fully assembled cyanobacterial KaiABC circadian clock complex by an integrated experimental-computational approach. Commun Biol 2022; 5:184. [PMID: 35273347 PMCID: PMC8913699 DOI: 10.1038/s42003-022-03143-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/08/2022] [Indexed: 12/24/2022] Open
Abstract
In the cyanobacterial circadian clock system, KaiA, KaiB and KaiC periodically assemble into a large complex. Here we determined the overall structure of their fully assembled complex by integrating experimental and computational approaches. Small-angle X-ray and inverse contrast matching small-angle neutron scatterings coupled with size-exclusion chromatography provided constraints to highlight the spatial arrangements of the N-terminal domains of KaiA, which were not resolved in the previous structural analyses. Computationally built 20 million structural models of the complex were screened out utilizing the constrains and then subjected to molecular dynamics simulations to examine their stabilities. The final model suggests that, despite large fluctuation of the KaiA N-terminal domains, their preferential positionings mask the hydrophobic surface of the KaiA C-terminal domains, hindering additional KaiA-KaiC interactions. Thus, our integrative approach provides a useful tool to resolve large complex structures harboring dynamically fluctuating domains. The revealed full KaiA12B6C6 complex is assembled including the dynamic and asynchronous KaiA N-terminal domains that have been missing in cryo-EM structures.
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Affiliation(s)
- Yasuhiro Yunoki
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya, 467-8603, Japan.,Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Atsushi Matsumoto
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology (QST), Umemidai, Kizu, Kyoto, 619-0215, Japan
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Anne Martel
- Institut Laue-Langevin, 71, avenue des martyrs, 38042, Grenoble, France
| | - Lionel Porcar
- Institut Laue-Langevin, 71, avenue des martyrs, 38042, Grenoble, France
| | - Nobuhiro Sato
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Rina Yogo
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya, 467-8603, Japan.,Biomedical Research Centre, School of Biomedical Engineering, The University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Taiki Tominaga
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), Tokai, Ibaraki, 319-1106, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya, 467-8603, Japan
| | - Aya Okuda
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Masahiro Shimizu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Reiko Urade
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Kazuki Terauchi
- Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Hidetoshi Kono
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology (QST), Umemidai, Kizu, Kyoto, 619-0215, Japan.
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya, 467-8603, Japan.
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, 444-8787, Japan. .,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya, 467-8603, Japan.
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan.
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15
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Jabbur ML, Johnson CH. Spectres of Clock Evolution: Past, Present, and Yet to Come. Front Physiol 2022; 12:815847. [PMID: 35222066 PMCID: PMC8874327 DOI: 10.3389/fphys.2021.815847] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/22/2021] [Indexed: 01/20/2023] Open
Abstract
Circadian clocks are phylogenetically widespread biological oscillators that allow organisms to entrain to environmental cycles and use their steady-state phase relationship to anticipate predictable daily phenomena – such as the light-dark transitions of a day – and prepare accordingly. Present from cyanobacteria to mammals, circadian clocks are evolutionarily ancient and are thought to increase the fitness of the organisms that possess them by allowing for better resource usage and/or proper internal temporal order. Here, we review literature with respect to the ecology and evolution of circadian clocks, with a special focus on cyanobacteria as model organisms. We first discuss what can be inferred about future clock evolution in response to climate change, based on data from latitudinal clines and domestication. We then address our current understanding of the role that circadian clocks might be contributing to the adaptive fitness of cyanobacteria at the present time. Lastly, we discuss what is currently known about the oldest known circadian clock, and the early Earth conditions that could have led to its evolution.
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16
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Tyler J, Lu Y, Dunlap J, Forger DB. Evolution of the repression mechanisms in circadian clocks. Genome Biol 2022; 23:17. [PMID: 35012616 PMCID: PMC8751359 DOI: 10.1186/s13059-021-02571-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/07/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Circadian (daily) timekeeping is essential to the survival of many organisms. An integral part of all circadian timekeeping systems is negative feedback between an activator and repressor. However, the role of this feedback varies widely between lower and higher organisms. RESULTS Here, we study repression mechanisms in the cyanobacterial and eukaryotic clocks through mathematical modeling and systems analysis. We find a common mathematical model that describes the mechanism by which organisms generate rhythms; however, transcription's role in this has diverged. In cyanobacteria, protein sequestration and phosphorylation generate and regulate rhythms while transcription regulation keeps proteins in proper stoichiometric balance. Based on recent experimental work, we propose a repressor phospholock mechanism that models the negative feedback through transcription in clocks of higher organisms. Interestingly, this model, when coupled with activator phosphorylation, allows for oscillations over a wide range of protein stoichiometries, thereby reconciling the negative feedback mechanism in Neurospora with that in mammals and cyanobacteria. CONCLUSIONS Taken together, these results paint a picture of how circadian timekeeping may have evolved.
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Affiliation(s)
- Jonathan Tyler
- Department of Mathematics, University of Michigan, Ann Arbor, 48109 MI USA
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Michigan, Ann Arbor, 48109 MI USA
| | - Yining Lu
- Department of Mathematics, University of Michigan, Ann Arbor, 48109 MI USA
| | - Jay Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, 03755 NH USA
| | - Daniel B. Forger
- Department of Mathematics, University of Michigan, Ann Arbor, 48109 MI USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, 48109 MI USA
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17
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Kim P, Thati N, Peshori S, Jang HI, Kim YI. Shift in Conformational Equilibrium Underlies the Oscillatory Phosphoryl Transfer Reaction in the Circadian Clock. Life (Basel) 2021; 11:life11101058. [PMID: 34685430 PMCID: PMC8538168 DOI: 10.3390/life11101058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 11/26/2022] Open
Abstract
Oscillatory phosphorylation/dephosphorylation can be commonly found in a biological system as a means of signal transduction though its pivotal presence in the workings of circadian clocks has drawn significant interest: for example in a significant portion of the physiology of Synechococcus elongatus PCC 7942. The biological oscillatory reaction in the cyanobacterial circadian clock can be visualized through its reconstitution in a test tube by mixing three proteins—KaiA, KaiB and KaiC—with adenosine triphosphate and magnesium ions. Surprisingly, the oscillatory phosphorylation/dephosphorylation of the hexameric KaiC takes place spontaneously and almost indefinitely in a test tube as long as ATP is present. This autonomous post-translational modification is tightly regulated by the conformational change of the C-terminal peptide of KaiC called the “A-loop” between the exposed and the buried states, a process induced by the time-course binding events of KaiA and KaiB to KaiC. There are three putative hydrogen-bond forming residues of the A-loop that are important for stabilizing its buried conformation. Substituting the residues with alanine enabled us to observe KaiB’s role in dephosphorylating hyperphosphorylated KaiC, independent of KaiA’s effect. We found a novel role of KaiB that its binding to KaiC induces the A-loop toward its buried conformation, which in turn activates the autodephosphorylation of KaiC. In addition to its traditional role of sequestering KaiA, KaiB’s binding contributes to the robustness of cyclic KaiC phosphorylation by inhibiting it during the dephosphorylation phase, effectively shifting the equilibrium toward the correct phase of the clock.
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Affiliation(s)
- Pyonghwa Kim
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA;
| | - Neha Thati
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ 07102, USA; (N.T.); (S.P.)
| | - Shreya Peshori
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ 07102, USA; (N.T.); (S.P.)
| | - Hye-In Jang
- School of Cosmetic Science and Beauty Biotechnology, Semyung University, Jecheon 27136, Korea
- Correspondence: (H.-I.J.); (Y.-I.K.)
| | - Yong-Ick Kim
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA;
- Institute for Brain and Neuroscience Research, New Jersey Institute of Technology, Newark, NJ 07102, USA
- Correspondence: (H.-I.J.); (Y.-I.K.)
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18
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Alqabandi M, de Franceschi N, Maity S, Miguet N, Bally M, Roos WH, Weissenhorn W, Bassereau P, Mangenot S. The ESCRT-III isoforms CHMP2A and CHMP2B display different effects on membranes upon polymerization. BMC Biol 2021; 19:66. [PMID: 33832485 PMCID: PMC8033747 DOI: 10.1186/s12915-021-00983-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 02/16/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND ESCRT-III proteins are involved in many membrane remodeling processes including multivesicular body biogenesis as first discovered in yeast. In humans, ESCRT-III CHMP2 exists as two isoforms, CHMP2A and CHMP2B, but their physical characteristics have not been compared yet. RESULTS Here, we use a combination of techniques on biomimetic systems and purified proteins to study their affinity and effects on membranes. We establish that CHMP2B binding is enhanced in the presence of PI(4,5)P2 lipids. In contrast, CHMP2A does not display lipid specificity and requires CHMP3 for binding significantly to membranes. On the micrometer scale and at moderate bulk concentrations, CHMP2B forms a reticular structure on membranes whereas CHMP2A (+CHMP3) binds homogeneously. Thus, CHMP2A and CHMP2B unexpectedly induce different mechanical effects to membranes: CHMP2B strongly rigidifies them while CHMP2A (+CHMP3) has no significant effect. CONCLUSIONS We therefore conclude that CHMP2B and CHMP2A exhibit different mechanical properties and might thus contribute differently to the diverse ESCRT-III-catalyzed membrane remodeling processes.
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Affiliation(s)
- Maryam Alqabandi
- Laboratoire Physico Chimie Curie, Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, 75005, Paris, France
| | - Nicola de Franceschi
- Laboratoire Physico Chimie Curie, Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, 75005, Paris, France
| | - Sourav Maity
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Nolwenn Miguet
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000, Grenoble, France
| | - Marta Bally
- Umeå University, Department of Clinical Microbiology & Wallenberg Centre for Molecular Medicine, 90185, Umeå, Sweden
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Winfried Weissenhorn
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000, Grenoble, France
| | - Patricia Bassereau
- Laboratoire Physico Chimie Curie, Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, 75005, Paris, France
| | - Stéphanie Mangenot
- Laboratoire Physico Chimie Curie, Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, 75005, Paris, France.
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19
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Mechanism of autonomous synchronization of the circadian KaiABC rhythm. Sci Rep 2021; 11:4713. [PMID: 33633230 PMCID: PMC7907350 DOI: 10.1038/s41598-021-84008-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/11/2021] [Indexed: 11/28/2022] Open
Abstract
The cyanobacterial circadian clock can be reconstituted by mixing three proteins, KaiA, KaiB, and KaiC, in vitro. In this protein mixture, oscillations of the phosphorylation level of KaiC molecules are synchronized to show the coherent oscillations of the ensemble of many molecules. However, the molecular mechanism of this synchronization has not yet been fully elucidated. In this paper, we explain a theoretical model that considers the multifold feedback relations among the structure and reactions of KaiC. The simulated KaiC hexamers show stochastic switch-like transitions at the level of single molecules, which are synchronized in the ensemble through the sequestration of KaiA into the KaiC–KaiB–KaiA complexes. The proposed mechanism quantitatively reproduces the synchronization that was observed by mixing two solutions oscillating in different phases. The model results suggest that biochemical assays with varying concentrations of KaiA or KaiB can be used to test this hypothesis.
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20
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Okumura M, Noi K, Inaba K. Visualization of structural dynamics of protein disulfide isomerase enzymes in catalysis of oxidative folding and reductive unfolding. Curr Opin Struct Biol 2020; 66:49-57. [PMID: 33176263 DOI: 10.1016/j.sbi.2020.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/18/2020] [Accepted: 10/08/2020] [Indexed: 02/06/2023]
Abstract
Time-resolved single-molecule observations by high-speed atomic force microscopy (HS-AFM), have greatly advanced our understanding of how proteins operate to fulfill their unique functions. Using this device, we succeeded in visualizing two members of the protein disulfide isomerase family (PDIs) that act to catalyze oxidative folding and reductive unfolding in the endoplasmic reticulum (ER). ERdj5, an ER-resident disulfide reductase that promotes ER-associated degradation, reduces nonnative disulfide bonds of misfolded proteins utilizing the dynamics of its N-terminal and C-terminal clusters. With unfolded substrates, canonical PDI assembles to form a face-to-face dimer with a central hydrophobic cavity and multiple redox-active sites to accelerate oxidative folding inside the cavity. Altogether, PDIs exert highly dynamic mechanisms to ensure the protein quality control in the ER.
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Affiliation(s)
- Masaki Okumura
- Frontier Research Institute for Interdisciplinary Sciences, Aramaki aza Aoba 6-3, Aoba-ku, Sendai 980-8578, Japan
| | - Kentaro Noi
- Institute of Nanoscience Design, Osaka University, Machikaneyamatyou 1-3, Toyonaka 560-8531, Japan
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.
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21
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Hong L, Lavrentovich DO, Chavan A, Leypunskiy E, Li E, Matthews C, LiWang A, Rust MJ, Dinner AR. Bayesian modeling reveals metabolite-dependent ultrasensitivity in the cyanobacterial circadian clock. Mol Syst Biol 2020; 16:e9355. [PMID: 32496641 PMCID: PMC7271899 DOI: 10.15252/msb.20199355] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 12/22/2022] Open
Abstract
Mathematical models can enable a predictive understanding of mechanism in cell biology by quantitatively describing complex networks of interactions, but such models are often poorly constrained by available data. Owing to its relative biochemical simplicity, the core circadian oscillator in Synechococcus elongatus has become a prototypical system for studying how collective dynamics emerge from molecular interactions. The oscillator consists of only three proteins, KaiA, KaiB, and KaiC, and near-24-h cycles of KaiC phosphorylation can be reconstituted in vitro. Here, we formulate a molecularly detailed but mechanistically naive model of the KaiA-KaiC subsystem and fit it directly to experimental data within a Bayesian parameter estimation framework. Analysis of the fits consistently reveals an ultrasensitive response for KaiC phosphorylation as a function of KaiA concentration, which we confirm experimentally. This ultrasensitivity primarily results from the differential affinity of KaiA for competing nucleotide-bound states of KaiC. We argue that the ultrasensitive stimulus-response relation likely plays an important role in metabolic compensation by suppressing premature phosphorylation at nighttime.
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Affiliation(s)
- Lu Hong
- Graduate Program in Biophysical SciencesUniversity of ChicagoChicagoILUSA
| | - Danylo O Lavrentovich
- Department of ChemistryUniversity of ChicagoChicagoILUSA
- Present address:
Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMAUSA
| | - Archana Chavan
- School of Natural SciencesUniversity of CaliforniaMercedCAUSA
| | - Eugene Leypunskiy
- Graduate Program in Biophysical SciencesUniversity of ChicagoChicagoILUSA
| | - Eileen Li
- Department of StatisticsUniversity of ChicagoChicagoILUSA
| | - Charles Matthews
- Department of StatisticsUniversity of ChicagoChicagoILUSA
- Present address:
School of MathematicsUniversity of EdinburghEdinburghUK
| | - Andy LiWang
- School of Natural SciencesUniversity of CaliforniaMercedCAUSA
- Quantitative and Systems BiologyUniversity of CaliforniaMercedCAUSA
- Center for Circadian BiologyUniversity of CaliforniaSan Diego, La JollaCAUSA
- Chemistry and Chemical BiologyUniversity of CaliforniaMercedCAUSA
- Health Sciences Research InstituteUniversity of CaliforniaMercedCAUSA
- Center for Cellular and Biomolecular MachinesUniversity of CaliforniaMercedCAUSA
| | - Michael J Rust
- Department of Molecular Genetics and Cell BiologyUniversity of ChicagoChicagoILUSA
- Institute for Biophysical DynamicsUniversity of ChicagoChicagoILUSA
- Institute for Genomics and Systems BiologyUniversity of ChicagoChicagoILUSA
| | - Aaron R Dinner
- Department of ChemistryUniversity of ChicagoChicagoILUSA
- Institute for Biophysical DynamicsUniversity of ChicagoChicagoILUSA
- James Franck InstituteUniversity of ChicagoChicagoILUSA
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22
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Recent advances in bioimaging with high-speed atomic force microscopy. Biophys Rev 2020; 12:363-369. [PMID: 32172451 DOI: 10.1007/s12551-020-00670-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/26/2020] [Indexed: 01/13/2023] Open
Abstract
Among various microscopic techniques for characterizing protein structures and functions, high-speed atomic force microscopy (HS-AFM) is a unique technique in that it allows direct visualization of structural changes and molecular interactions of proteins without any labeling in a liquid environment. Since the development of the HS-AFM was first reported in 2001, it has been applied to analyze the dynamics of various types of proteins, including motor proteins, membrane proteins, DNA-binding proteins, amyloid proteins, and artificial proteins. This method has now become a versatile tool indispensable for biophysical research. This short review summarizes some bioimaging applications of HS-AFM reported in the last few years and novel applications of HS-AFM utilizing the unique ability of AFM to gain mechanical properties of samples in addition to structural information.
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23
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Direct visualization of avian influenza H5N1 hemagglutinin precursor and its conformational change by high-speed atomic force microscopy. Biochim Biophys Acta Gen Subj 2020; 1864:129313. [DOI: 10.1016/j.bbagen.2019.02.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/19/2019] [Accepted: 02/26/2019] [Indexed: 01/06/2023]
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24
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Li M, Xi N, Wang Y, Liu L. Atomic Force Microscopy as a Powerful Multifunctional Tool for Probing the Behaviors of Single Proteins. IEEE Trans Nanobioscience 2020; 19:78-99. [DOI: 10.1109/tnb.2019.2954099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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25
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Dibner C. The importance of being rhythmic: Living in harmony with your body clocks. Acta Physiol (Oxf) 2020; 228:e13281. [PMID: 30980501 DOI: 10.1111/apha.13281] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/05/2019] [Accepted: 04/08/2019] [Indexed: 02/06/2023]
Abstract
Circadian rhythms have developed in all light-sensitive organisms, including humans, as a fundamental anticipatory mechanism that enables proactive adaptation to environmental changes. The circadian system is organized in a highly hierarchical manner, with clocks operative in most cells of the body ensuring the temporal coordination of physiological processes. Circadian misalignment, stemming from modern life style, draws increasing attention due to its tight association with the development of metabolic, cardiovascular, inflammatory and mental diseases as well as cancer. This review highlights recent findings emphasizing the role of the circadian system in the temporal orchestration of physiology, with a particular focus on implications of circadian misalignment in human pathologies.
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Affiliation(s)
- Charna Dibner
- Division of Endocrinology, Diabetes, Hypertension and Nutrition, Department of Medicine University Hospital of Geneva Geneva Switzerland
- Department of Cell Physiology and Metabolism, Faculty of Medicine University of Geneva Geneva Switzerland
- Diabetes Center, Faculty of Medicine University of Geneva Geneva Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3) Geneva Switzerland
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26
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Ando T. High-speed atomic force microscopy. Curr Opin Chem Biol 2019; 51:105-112. [DOI: 10.1016/j.cbpa.2019.05.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 04/23/2019] [Accepted: 05/13/2019] [Indexed: 11/28/2022]
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27
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Sumino A, Sumikama T, Uchihashi T, Oiki S. High-speed AFM reveals accelerated binding of agitoxin-2 to a K + channel by induced fit. SCIENCE ADVANCES 2019; 5:eaax0495. [PMID: 31281899 PMCID: PMC6609221 DOI: 10.1126/sciadv.aax0495] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 05/23/2019] [Indexed: 06/09/2023]
Abstract
Agitoxin-2 (AgTx2) from scorpion venom is a potent blocker of K+ channels. The docking model has been elucidated, but it remains unclear whether binding dynamics are described by a two-state model (AgTx2-bound and AgTx2-unbound) or a more complicated mechanism, such as induced fit or conformational selection. Here, we observed the binding dynamics of AgTx2 to the KcsA channel using high-speed atomic force microscopy. From images of repeated binding and dissociation of AgTx2 to the channel, single-molecule kinetic analyses revealed that the affinity of the channel for AgTx2 increased during persistent binding and decreased during persistent dissociation. We propose a four-state model, including high- and low-affinity states of the channel, with relevant rate constants. An induced-fit pathway was dominant and accelerated binding by 400 times. This is the first analytical imaging of scorpion toxin binding in real time, which is applicable to various biological dynamics including channel ligands, DNA-modifier proteins, and antigen-antibody complexes.
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Affiliation(s)
- A. Sumino
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
- Institute for Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan
- PRESTO, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
- Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - T. Sumikama
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
- Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - T. Uchihashi
- Department of Physics and Structural Biology Research Center, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
- Exploratory Research Center on Life and Living Systems, National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - S. Oiki
- Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
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28
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Yunoki Y, Ishii K, Yagi-Utsumi M, Murakami R, Uchiyama S, Yagi H, Kato K. ATP hydrolysis by KaiC promotes its KaiA binding in the cyanobacterial circadian clock system. Life Sci Alliance 2019; 2:2/3/e201900368. [PMID: 31160381 PMCID: PMC6549140 DOI: 10.26508/lsa.201900368] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 12/01/2022] Open
Abstract
ATP hydrolysis in the KaiC hexamer triggers the exposure of its C-terminal segments into the solvent so as to capture KaiA, providing mechanistic insights into the circadian periodicity regulation. The cyanobacterial clock is controlled via the interplay among KaiA, KaiB, and KaiC, which generate a periodic oscillation of KaiC phosphorylation in the presence of ATP. KaiC forms a homohexamer harboring 12 ATP-binding sites and exerts ATPase activities associated with its autophosphorylation and dephosphorylation. The KaiC nucleotide state is a determining factor of the KaiB–KaiC interaction; however, its relationship with the KaiA–KaiC interaction has not yet been elucidated. With the attempt to address this, our native mass spectrometric analyses indicated that ATP hydrolysis in the KaiC hexamer promotes its interaction with KaiA. Furthermore, our nuclear magnetic resonance spectral data revealed that ATP hydrolysis is coupled with conformational changes in the flexible C-terminal segments of KaiC, which carry KaiA-binding sites. From these data, we conclude that ATP hydrolysis in KaiC is coupled with the exposure of its C-terminal KaiA-binding sites, resulting in its high affinity for KaiA. These findings provide mechanistic insights into the ATP-mediated circadian periodicity.
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Affiliation(s)
- Yasuhiro Yunoki
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Japan
| | - Kentaro Ishii
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Japan
| | - Maho Yagi-Utsumi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Japan
| | - Reiko Murakami
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Susumu Uchiyama
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan .,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Japan
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29
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Ewald M, Henry S, Lambert E, Feuillie C, Bobo C, Cullin C, Lecomte S, Molinari M. High speed atomic force microscopy to investigate the interactions between toxic Aβ 1-42 peptides and model membranes in real time: impact of the membrane composition. NANOSCALE 2019; 11:7229-7238. [PMID: 30924478 DOI: 10.1039/c8nr08714h] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Due to an aging population, neurodegenerative diseases have become a major health issue, the most common being Alzheimer's disease. The mechanisms leading to neuronal loss still remain unclear but recent studies suggest that soluble Aβ oligomers have deleterious effects on neuronal membranes. Here, high-speed atomic force microscopy was used to assess the effect of oligomeric species of a variant of Aβ1-42 amyloid peptide on model membranes with various lipid compositions. Results showed that the peptide does not interact with membranes composed of phosphatidylcholine and sphingomyelin. Ganglioside GM1, but not cholesterol, is required for the peptide to interact with the membrane. Interestingly, when they are both present, a fast disruption of the membrane was observed. It suggests that the presence of ganglioside GM1 and cholesterol in membranes promotes the interaction of the oligomeric Aβ1-42 peptide with the membrane. This interaction leads to the membrane's destruction in a few seconds. This study highlights the power of high-speed atomic force microscopy to explore lipid-protein interactions with high spatio-temporal resolution.
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Affiliation(s)
- M Ewald
- LRN EA 4682, Université de Reims Champagne-Ardenne, F-51685 Reims, France.
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30
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Sasai M. Effects of Stochastic Single-Molecule Reactions on Coherent Ensemble Oscillations in the KaiABC Circadian Clock. J Phys Chem B 2019; 123:702-713. [PMID: 30629448 DOI: 10.1021/acs.jpcb.8b10584] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
How do many constituent molecules in a biochemical system synchronize, giving rise to coherent system-level oscillations? One system that is particularly suitable for use in studying this problem is a mixture solution of three cyanobacterial proteins, KaiA, KaiB, and KaiC: the phosphorylation level of KaiC shows stable oscillations with a period of approximately 24 h when these three Kai proteins are incubated with ATP in vitro. Here, we analyze the mechanism behind synchronization in the KaiABC system theoretically by enhancing a model previously developed by the present author. Our simulation results suggest that positive feedback between stochastic ATP hydrolysis and the allosteric structural transitions in KaiC molecules drives oscillations of individual molecules and promotes synchronization of oscillations of many KaiC molecules. Our simulations also show that the ATPase activity of KaiC is correlated with the oscillation frequency of an ensemble of KaiC molecules. These results suggest that stochastic ATP hydrolysis in each KaiC molecule plays an important role in regulating the coherent system-level oscillations. This property is robust against changes in the binding and unbinding rate constants for KaiA to/from KaiC or KaiB, but the oscillations are sensitive to the rate constants of the KaiC phosphorylation and dephosphorylation reactions.
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Affiliation(s)
- Masaki Sasai
- Department of Applied Physics , Nagoya University , Nagoya 464-8603 , Japan
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