1
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Zhang N, Sood D, Guo SC, Chen N, Antoszewski A, Marianchuk T, Chavan A, Dey S, Xiao Y, Hong L, Peng X, Baxa M, Partch C, Wang LP, Sosnick TR, Dinner AR, LiWang A. Temperature-Dependent Fold-Switching Mechanism of the Circadian Clock Protein KaiB. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.594594. [PMID: 38826295 PMCID: PMC11142059 DOI: 10.1101/2024.05.21.594594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The oscillator of the cyanobacterial circadian clock relies on the ability of the KaiB protein to switch reversibly between a stable ground-state fold (gsKaiB) and an unstable fold-switched fold (fsKaiB). Rare fold-switching events by KaiB provide a critical delay in the negative feedback loop of this post-translational oscillator. In this study, we experimentally and computationally investigate the temperature dependence of fold switching and its mechanism. We demonstrate that the stability of gsKaiB increases with temperature compared to fsKaiB and that the Q10 value for the gsKaiB → fsKaiB transition is nearly three times smaller than that for the reverse transition. Simulations and native-state hydrogen-deuterium exchange NMR experiments suggest that fold switching can involve both subglobally and near-globally unfolded intermediates. The simulations predict that the transition state for fold switching coincides with isomerization of conserved prolines in the most rapidly exchanging region, and we confirm experimentally that proline isomerization is a rate-limiting step for fold switching. We explore the implications of our results for temperature compensation, a hallmark of circadian clocks, through a kinetic model.
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2
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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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3
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Retamal-Farfán I, González-Higueras J, Galaz-Davison P, Rivera M, Ramírez-Sarmiento CA. Exploring the structural acrobatics of fold-switching proteins using simplified structure-based models. Biophys Rev 2023; 15:787-799. [PMID: 37681096 PMCID: PMC10480104 DOI: 10.1007/s12551-023-01087-0] [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: 03/27/2023] [Accepted: 06/22/2023] [Indexed: 09/09/2023] Open
Abstract
Metamorphic proteins are a paradigm of the protein folding process, by encoding two or more native states, highly dissimilar in terms of their secondary, tertiary, and even quaternary structure, on a single amino acid sequence. Moreover, these proteins structurally interconvert between these native states in a reversible manner at biologically relevant timescales as a result of different environmental cues. The large-scale rearrangements experienced by these proteins, and their sometimes high mass interacting partners that trigger their metamorphosis, makes the computational and experimental study of their structural interconversion challenging. Here, we present our efforts in studying the refolding landscapes of two quintessential metamorphic proteins, RfaH and KaiB, using simplified dual-basin structure-based models (SBMs), rigorously footed on the energy landscape theory of protein folding and the principle of minimal frustration. By using coarse-grained models in which the native contacts and bonded interactions extracted from the available experimental structures of the two native states of RfaH and KaiB are merged into a single Hamiltonian, dual-basin SBM models can be generated and savvily calibrated to explore their fold-switch in a reversible manner in molecular dynamics simulations. We also describe how some of the insights offered by these simulations have driven the design of experiments and the validation of the conformational ensembles and refolding routes observed using this simple and computationally efficient models.
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Affiliation(s)
- Ignacio Retamal-Farfán
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
- ANID — Millennium Science Initiative Program — Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Jorge González-Higueras
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
- ANID — Millennium Science Initiative Program — Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Pablo Galaz-Davison
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
- ANID — Millennium Science Initiative Program — Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Maira Rivera
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
- Department of Chemistry, Faculty of Science, McGill University, Montreal, Quebec H3A 0B8 Canada
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
- ANID — Millennium Science Initiative Program — Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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4
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Dimer dissociation is a key energetic event in the fold-switch pathway of KaiB. Biophys J 2022; 121:943-955. [PMID: 35151633 PMCID: PMC8943816 DOI: 10.1016/j.bpj.2022.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 12/14/2021] [Accepted: 02/09/2022] [Indexed: 11/21/2022] Open
Abstract
Cyanobacteria possesses the simplest circadian clock, composed of three proteins that act as a phosphorylation oscillator: KaiA, KaiB, and KaiC. The timing of this oscillator is determined by the fold-switch of KaiB, a structural rearrangement of its C-terminal half that is accompanied by a change in the oligomerization state. During the day, KaiB forms a stable tetramer (gsKaiB), whereas it adopts a monomeric thioredoxin-like fold during the night (fsKaiB). Although the structures and functions of both native states are well studied, little is known about the sequence and structure determinants that control their structural interconversion. Here, we used confinement molecular dynamics (CCR-MD) and folding simulations using structure-based models to show that the dissociation of the gsKaiB dimer is a key energetic event for the fold-switch. Hydrogen-deuterium exchange mass spectrometry (HDXMS) recapitulates the local stability of protein regions reported by CCR-MD, with both approaches consistently indicating that the energy and backbone flexibility changes are solely associated with the region that fold-switches between gsKaiB and fsKaiB and that the localized regions that differentially stabilize gsKaiB also involve regions outside the dimer interface. Moreover, two mutants (R23C and R75C) previously reported to be relevant for altering the rhythmicity of the Kai clock were also studied by HDXMS. Particularly, R75C populates dimeric and monomeric states with a deuterium incorporation profile comparable to the one observed for fsKaiB, emphasizing the importance of the oligomerization state of KaiB for the fold-switch. These findings suggest that the information necessary to control the rhythmicity of the cyanobacterial biological clock is, to a great extent, encoded within the KaiB sequence.
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5
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Mutoh R, Iwata K, Iida T, Ishiura M, Onai K. Rhythmic adenosine triphosphate release from the cyanobacterial circadian clock protein KaiC revealed by real-time monitoring of bioluminescence using firefly luciferase. Genes Cells 2021; 26:83-93. [PMID: 33341998 DOI: 10.1111/gtc.12825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/16/2020] [Accepted: 12/16/2020] [Indexed: 11/27/2022]
Abstract
The cyanobacterial circadian clock is composed of three clock proteins, KaiA, KaiB and KaiC. This KaiABC clock system can be reconstituted in vitro in the presence of adenosine triphosphate (ATP) and Mg2+ , and shows circadian rhythms in the phosphorylation level and ATPase activity of KaiC. Previously, we found that ATP regulates a complex formation between KaiB and KaiC, and KaiC releases ATP from KaiC itself (PLoS One, 8, 2013, e80200). In this study, we examined whether the ATP release from KaiC shows any rhythms in vitro. We monitored the release of ATP from wild-type and ATPase motif mutants of KaiC as a bioluminescence in real time using a firefly luciferase assay in vitro and obtained the following results: (a) ATP release from KaiC oscillated even without KaiA and KaiB although period of the oscillation was not 24 hr; (b) ATP was mainly released from the N-terminal domain of KaiC; and (c) the ATP release was enhanced and suppressed by KaiB and KaiA, respectively. These results suggest that KaiC can generate basal oscillation as a core clock without KaiA and KaiB, whereas these two proteins contribute to adjusting and stabilizing the oscillation.
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Affiliation(s)
- Risa Mutoh
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Keita Iwata
- Center for Gene Research, Nagoya University, Nagoya, Japan.,Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Takahiro Iida
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Masahiro Ishiura
- Center for Gene Research, Nagoya University, Nagoya, Japan.,Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Kiyoshi Onai
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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6
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Li J, Zhang L, Xiong J, Cheng X, Huang Y, Su Z, Yi M, Liu S. Polyamines Disrupt the KaiABC Oscillator by Inducing Protein Denaturation. Molecules 2019; 24:E3351. [PMID: 31540079 PMCID: PMC6767301 DOI: 10.3390/molecules24183351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/06/2019] [Accepted: 09/13/2019] [Indexed: 11/16/2022] Open
Abstract
Polyamines are positively charged small molecules ubiquitously existing in all living organisms, and they are considered as one kind of the most ancient cellular components. The most common polyamines are spermidine, spermine, and their precursor putrescine generated from ornithine. Polyamines play critical roles in cells by stabilizing chromatin structure, regulating DNA replication, modulating gene expression, etc., and they also affect the structure and function of proteins. A few studies have investigated the impact of polyamines on protein structure and function previously, but no reports have focused on a protein-based biological module with a dedicated function. In this report, we investigated the impact of polyamines (putrescine, spermidine, and spermine) on the cyanobacterial KaiABC circadian oscillator. Using an established in vitro reconstitution system, we noticed that polyamines could disrupt the robustness of the KaiABC oscillator by inducing the denaturation of the Kai proteins (KaiA, KaiB, and KaiC). Further experiments showed that the denaturation was likely due to the induced change of the thermal stability of the clock proteins. Our study revealed an intriguing role of polyamines as a component in complex cellular environments and would be of great importance for elucidating the biological function of polyamines in future.
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Affiliation(s)
- Jinkui Li
- Key Laboratory of Fermentation Engineering (HBUT, Ministry of Education) and National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China.
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, Medical College of China Three Gorges University, Yichang 443002, China.
| | - Lingya Zhang
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, Medical College of China Three Gorges University, Yichang 443002, China.
| | - Junwen Xiong
- Key Laboratory of Fermentation Engineering (HBUT, Ministry of Education) and National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China.
- Institute of Biomedical and Pharmaceutical Sciences, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China.
| | - Xiyao Cheng
- Key Laboratory of Fermentation Engineering (HBUT, Ministry of Education) and National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China.
- Institute of Biomedical and Pharmaceutical Sciences, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China.
| | - Yongqi Huang
- Key Laboratory of Fermentation Engineering (HBUT, Ministry of Education) and National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China.
- Institute of Biomedical and Pharmaceutical Sciences, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China.
| | - Zhengding Su
- Key Laboratory of Fermentation Engineering (HBUT, Ministry of Education) and National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China.
- Institute of Biomedical and Pharmaceutical Sciences, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China.
| | - Ming Yi
- School of Mathematics and Physics, China University of Geosciences, Wuhan 430074, China.
| | - Sen Liu
- Key Laboratory of Fermentation Engineering (HBUT, Ministry of Education) and National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China.
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, Medical College of China Three Gorges University, Yichang 443002, China.
- Institute of Biomedical and Pharmaceutical Sciences, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China.
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7
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Cooperative Binding of KaiB to the KaiC Hexamer Ensures Accurate Circadian Clock Oscillation in Cyanobacteria. Int J Mol Sci 2019; 20:ijms20184550. [PMID: 31540310 PMCID: PMC6769508 DOI: 10.3390/ijms20184550] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/08/2019] [Accepted: 09/11/2019] [Indexed: 12/01/2022] Open
Abstract
The central oscillator generating cyanobacterial circadian rhythms comprises KaiA, KaiB, and KaiC proteins. Their interactions cause KaiC phosphorylation and dephosphorylation cycles over approximately 24 h. KaiB interacts with phosphorylated KaiC in competition with SasA, an output protein harboring a KaiB-homologous domain. Structural data have identified KaiB–KaiC interaction sites; however, KaiB mutations distal from the binding surfaces can impair KaiB–KaiC interaction and the circadian rhythm. Reportedly, KaiB and KaiC exclusively form a complex in a 6:6 stoichiometry, indicating that KaiB–KaiC hexamer binding shows strong positive cooperativity. Here, mutational analysis was used to investigate the functional significance of this cooperative interaction. Results demonstrate that electrostatic complementarity between KaiB protomers promotes their cooperative assembly, which is indispensable for accurate rhythm generation. SasA does not exhibit such electrostatic complementarity and noncooperatively binds to KaiC. Thus, the findings explain KaiB distal mutation effects, providing mechanistic insights into clock protein interplay.
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8
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Abstract
Life has adapted to Earth's day-night cycle with the evolution of endogenous biological clocks. Whereas these circadian rhythms typically involve extensive transcription-translation feedback in higher organisms, cyanobacteria have a circadian clock, which functions primarily as a protein-based post-translational oscillator. Known as the Kai system, it consists of three proteins KaiA, KaiB, and KaiC. In this chapter, we provide a detailed structural overview of the Kai components and how they interact to produce circadian rhythms of global gene expression in cyanobacterial cells. We discuss how the circadian oscillation is coupled to gene expression, intertwined with transcription-translation feedback mechanisms, and entrained by input from the environment. We discuss the use of mathematical models and summarize insights into the cyanobacterial circadian clock from theoretical studies. The molecular details of the Kai system are well documented for the model cyanobacterium Synechococcus elongatus, but many less understood varieties of the Kai system exist across the highly diverse phylum of Cyanobacteria. Several species contain multiple kai-gene copies, while others like marine Prochlorococcus strains have a reduced kaiBC-only system, lacking kaiA. We highlight recent findings on the genomic distribution of kai genes in Bacteria and Archaea and finally discuss hypotheses on the evolution of the Kai system.
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Affiliation(s)
- Joost Snijder
- Snijder Bioscience, Zevenwouden 143, 3524CN, Utrecht, The Netherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Ilka Maria Axmann
- Synthetic Microbiology, Biology Department, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
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9
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Brown J, Horrocks MH. A sticky situation: Aberrant protein-protein interactions in Parkinson's disease. Semin Cell Dev Biol 2018; 99:65-77. [PMID: 29738882 DOI: 10.1016/j.semcdb.2018.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 02/21/2018] [Accepted: 05/04/2018] [Indexed: 12/13/2022]
Abstract
The aberrant aggregation of normally soluble proteins into amyloid fibrils is the pathological hallmark of several neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. Understanding this process will be key to developing both diagnostic and therapeutic approaches for neurodegenerative diseases. Recent advances in biophysical techniques, coupled with kinetic analyses have enabled a thorough description of the key molecular steps involved in protein aggregation. In this review, we discuss these advances and how they have been applied to study the ability of one such protein, α-Synuclein, to form neurotoxic oligomers.
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Affiliation(s)
- James Brown
- EMBL Australia Node in Single Molecule Science, The University of New South Wales, Sydney, NSW, 2032, Australia.
| | - Mathew H Horrocks
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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10
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Chen Q, Liu S, Yang L, Zhang L, Li J. The reversible function switching of the circadian clock protein KaiA is encoded in its structure. Biochim Biophys Acta Gen Subj 2017; 1861:2535-2542. [DOI: 10.1016/j.bbagen.2017.08.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 08/20/2017] [Accepted: 08/23/2017] [Indexed: 10/19/2022]
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11
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Abstract
Chronobiological studies of prokaryotic organisms have generally lagged far behind the study of endogenous circadian clocks in eukaryotes, in which such systems are essentially ubiquitous. However, despite only being studied during the past 25 years, cyanobacteria have become important model organisms for the study of circadian rhythms and, presently, their timekeeping mechanism is the best understood of any system in terms of biochemistry, structural biology, biophysics and adaptive importance. Nevertheless, intrinsic daily rhythmicity among bacteria other than cyanobacteria is essentially unknown; some tantalizing information suggests widespread daily timekeeping among Eubacteria and Archaea through mechanisms that share common elements with the cyanobacterial clock but are distinct. Moreover, the recent surge of information about microbiome-host interactions has largely neglected the temporal dimension and yet daily cycles control important aspects of their relationship.
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12
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Murakami R, Mutoh R, Ishii K, Ishiura M. Circadian oscillations of KaiA-KaiC and KaiB-KaiC complex formations in an in vitro
reconstituted KaiABC clock oscillator. Genes Cells 2016; 21:890-900. [DOI: 10.1111/gtc.12392] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 05/31/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Reiko Murakami
- Center for Gene Research; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8602 Japan
| | - Risa Mutoh
- Center for Gene Research; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8602 Japan
| | - Ketaro Ishii
- Center for Gene Research; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8602 Japan
| | - Masahiro Ishiura
- Center for Gene Research; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8602 Japan
- Division of Biological Sciences; Nagoya University; Furo-cho Chikusa Nagoya 464-8602 Japan
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13
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Stadler AM, Ramírez J, Lehn JM, Vincent B. Supramolecular reactions of metallo-architectures: Ag 2-double-helicate/Zn 4-grid, Pb 4-grid/Zn 4-grid interconversions, and Ag 2-double-helicate fusion. Chem Sci 2016; 7:3689-3693. [PMID: 30008998 PMCID: PMC6008726 DOI: 10.1039/c5sc04403k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 02/03/2016] [Indexed: 01/29/2023] Open
Abstract
Supramolecular reactions are of importance in many fields. We report herein three examples where complexes of hydrazone-based ligands are involved. A Ag2-double-helicate was converted, by treatment with Zn(OTf)2, into a Zn4-grid (exchange of metal ions and change of the nature of the initial complex). A Pb4-grid was converted, upon reaction with ZnCl2 or ZnBr2, into a Zn4-grid (exchange of metal ions, but conservation of the nature of the initial complex). The reverse conversions were also achieved. The fusion of a Ag2-double-helicate with another Ag2-double-helicate was performed (exchange of ligands, but conservation of the nature of the complexes) and resulted in a mixture of three helicates (two homostranded ones and one heterostranded one).
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Affiliation(s)
- Adrian-Mihail Stadler
- Université de Strasbourg , CNRS , UMR 7006 , ISIS , 8 Allée G. Monge , Strasbourg , France .
- Institute of Nanotechnology (INT) , Karlsruhe Institute of Technolgoy (KIT) , 76344 , Eggenstein-Leopoldshafen , Germany
| | - Juan Ramírez
- Institut Pasteur Paris , 28 Rue du Docteur Roux , 75015 Paris , France
| | - Jean-Marie Lehn
- Université de Strasbourg , CNRS , UMR 7006 , ISIS , 8 Allée G. Monge , Strasbourg , France .
| | - Bruno Vincent
- Service de RMN , Faculté de Chimie , 1 Rue B. Pascal , Strasbourg , France
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14
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Gambin Y, Polinkovsky M, Francois B, Giles N, Bhumkar A, Sierecki E. Confocal Spectroscopy to Study Dimerization, Oligomerization and Aggregation of Proteins: A Practical Guide. Int J Mol Sci 2016; 17:ijms17050655. [PMID: 27144560 PMCID: PMC4881481 DOI: 10.3390/ijms17050655] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/15/2016] [Accepted: 04/20/2016] [Indexed: 12/25/2022] Open
Abstract
Protein self-association is a key feature that can modulate the physiological role of proteins or lead to deleterious effects when uncontrolled. Protein oligomerization is a simple way to modify the activity of a protein, as the modulation of binding interfaces allows for self-activation or inhibition, or variation in the selectivity of binding partners. As such, dimerization and higher order oligomerization is a common feature in signaling proteins, for example, and more than 70% of enzymes have the potential to self-associate. On the other hand, protein aggregation can overcome the regulatory mechanisms of the cell and can have disastrous physiological effects. This is the case in a number of neurodegenerative diseases, where proteins, due to mutation or dysregulation later in life, start polymerizing and often fibrillate, leading to the creation of protein inclusion bodies in cells. Dimerization, well-defined oligomerization and random aggregation are often difficult to differentiate and characterize experimentally. Single molecule “counting” methods are particularly well suited to the study of self-oligomerization as they allow observation and quantification of behaviors in heterogeneous conditions. However, the extreme dilution of samples often causes weak complexes to dissociate, and rare events can be overlooked. Here, we discuss a straightforward alternative where the principles of single molecule detection are used at higher protein concentrations to quantify oligomers and aggregates in a background of monomers. We propose a practical guide for the use of confocal spectroscopy to quantify protein oligomerization status and also discuss about its use in monitoring changes in protein aggregation in drug screening assays.
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Affiliation(s)
- Yann Gambin
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
| | - Mark Polinkovsky
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
| | - Bill Francois
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
| | - Nichole Giles
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
| | - Akshay Bhumkar
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
| | - Emma Sierecki
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
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15
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Dong P, Fan Y, Sun J, Lv M, Yi M, Tan X, Liu S. A dynamic interaction process between KaiA and KaiC is critical to the cyanobacterial circadian oscillator. Sci Rep 2016; 6:25129. [PMID: 27113386 PMCID: PMC4844972 DOI: 10.1038/srep25129] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 04/12/2016] [Indexed: 11/09/2022] Open
Abstract
The core circadian oscillator of cyanobacteria consists of three proteins, KaiA, KaiB, and KaiC. This circadian oscillator could be functionally reconstituted in vitro with these three proteins, and therefore has been a very important model in circadian rhythm research. KaiA can bind to KaiC and then stimulate its phosphorylation, but their interaction mechanism remains elusive. In this study, we followed the "second-site suppressor" strategy to investigate the interaction mechanism of KaiA and KaiC. Using protein sequence analyses, we showed that there exist co-varying residues in the binding interface of KaiA and KaiC. The followed mutagenesis study verified that these residues are important to the functions of KaiA and KaiC, but their roles could not be fully explained by the reported complex structures of KaiA and KaiC derived peptides. Combining our data with previous reports, we suggested a dynamic interaction mechanism in KaiA-KaiC interaction, in which both KaiA and the intrinsically disordered tail of KaiC undergo significant structural changes through conformational selection and induced fit during the binding process. At last, we presented a mathematic model to support this hypothesis and explained the importance of this interaction mechanism for the KaiABC circadian oscillator.
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Affiliation(s)
- Pei Dong
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China.,College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Ying Fan
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Jianqiang Sun
- School of Statistics, Shandong Institute of Business and Technology, Yantai, 264005, China
| | - Mengting Lv
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Ming Yi
- Department of Physics, College of Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiao Tan
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China.,College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Sen Liu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China.,College of Medical Science, China Three Gorges University, Yichang 443002, China
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Abstract
Life on earth is subject to daily and predictable fluctuations in light intensity, temperature, and humidity created by rotation of the earth. Circadian rhythms, generated by a circadian clock, control temporal programs of cellular physiology to facilitate adaptation to daily environmental changes. Circadian rhythms are nearly ubiquitous and are found in both prokaryotic and eukaryotic organisms. Here we introduce the molecular mechanism of the circadian clock in the model cyanobacterium Synechococcus elongatus PCC 7942. We review the current understanding of the cyanobacterial clock, emphasizing recent work that has generated a more comprehensive understanding of how the circadian oscillator becomes synchronized with the external environment and how information from the oscillator is transmitted to generate rhythms of biological activity. These results have changed how we think about the clock, shifting away from a linear model to one in which the clock is viewed as an interactive network of multifunctional components that are integrated into the context of the cell in order to pace and reset the oscillator. We conclude with a discussion of how this basic timekeeping mechanism differs in other cyanobacterial species and how information gleaned from work in cyanobacteria can be translated to understanding rhythmic phenomena in other prokaryotic systems.
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