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Wayment-Steele HK, Otten R, Pitsawong W, Ojoawo AM, Glaser A, Calderone LA, Kern D. The conformational landscape of fold-switcher KaiB is tuned to the circadian rhythm timescale. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597139. [PMID: 38895306 PMCID: PMC11185700 DOI: 10.1101/2024.06.03.597139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
How can a single protein domain encode a conformational landscape with multiple stably-folded states, and how do those states interconvert? Here, we use real-time and relaxation-dispersion NMR to characterize the conformational landscape of the circadian rhythm protein KaiB from Rhodobacter sphaeroides. Unique among known natural metamorphic proteins, this KaiB variant spontaneously interconverts between two monomeric states: the "Ground" and "Fold-switched" (FS) state. KaiB in its FS state interacts with multiple binding partners, including the central KaiC protein, to regulate circadian rhythms. We find that KaiB itself takes hours to interconvert between the Ground and FS state, underscoring the ability of a single sequence to encode the slow process needed for function. We reveal the rate-limiting step between the Ground and FS state is the cis-trans isomerization of three prolines in the fold-switching region by demonstrating interconversion acceleration by the prolyl isomerase CypA. The interconversion proceeds through a "partially disordered" (PD) state, where the C-terminal half becomes disordered while the N-terminal half remains stably folded. We discovered two additional properties of KaiB's landscape. Firstly, the Ground state experiences cold denaturation: at 4°C, the PD state becomes the majorly populated state. Secondly, the Ground state exchanges with a fourth state, the "Enigma" state, on the millisecond timescale. We combine AlphaFold2-based predictions and NMR chemical shift predictions to predict this "Enigma" state is a beta-strand register shift that eases buried charged residues, and support this structure experimentally. These results provide mechanistic insight in how evolution can design a single sequence that achieves specific timing needed for its function.
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Affiliation(s)
- Hannah K Wayment-Steele
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
| | - Renee Otten
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
- Present address: Treeline Biosciences, Watertown, MA, USA
| | - Warintra Pitsawong
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
- Present address: Biomolecular Discovery, Relay Therapeutics, Cambridge, MA, USA
| | - Adedolapo M Ojoawo
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
| | - Andrew Glaser
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
| | - Logan A Calderone
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
| | - Dorothee Kern
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
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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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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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Wayment-Steele HK, Ojoawo A, Otten R, Apitz JM, Pitsawong W, Hömberger M, Ovchinnikov S, Colwell L, Kern D. Predicting multiple conformations via sequence clustering and AlphaFold2. Nature 2024; 625:832-839. [PMID: 37956700 PMCID: PMC10808063 DOI: 10.1038/s41586-023-06832-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/03/2023] [Indexed: 11/15/2023]
Abstract
AlphaFold2 (ref. 1) has revolutionized structural biology by accurately predicting single structures of proteins. However, a protein's biological function often depends on multiple conformational substates2, and disease-causing point mutations often cause population changes within these substates3,4. We demonstrate that clustering a multiple-sequence alignment by sequence similarity enables AlphaFold2 to sample alternative states of known metamorphic proteins with high confidence. Using this method, named AF-Cluster, we investigated the evolutionary distribution of predicted structures for the metamorphic protein KaiB5 and found that predictions of both conformations were distributed in clusters across the KaiB family. We used nuclear magnetic resonance spectroscopy to confirm an AF-Cluster prediction: a cyanobacteria KaiB variant is stabilized in the opposite state compared with the more widely studied variant. To test AF-Cluster's sensitivity to point mutations, we designed and experimentally verified a set of three mutations predicted to flip KaiB from Rhodobacter sphaeroides from the ground to the fold-switched state. Finally, screening for alternative states in protein families without known fold switching identified a putative alternative state for the oxidoreductase Mpt53 in Mycobacterium tuberculosis. Further development of such bioinformatic methods in tandem with experiments will probably have a considerable impact on predicting protein energy landscapes, essential for illuminating biological function.
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Affiliation(s)
- Hannah K Wayment-Steele
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
| | - Adedolapo Ojoawo
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
| | - Renee Otten
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
- Treeline Biosciences, Watertown, MA, USA
| | - Julia M Apitz
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
| | - Warintra Pitsawong
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
- Biomolecular Discovery, Relay Therapeutics, Cambridge, MA, USA
| | - Marc Hömberger
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
- Treeline Biosciences, Watertown, MA, USA
| | | | - Lucy Colwell
- Google Research, Cambridge, MA, USA
- Cambridge University, Cambridge, UK
| | - Dorothee Kern
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA.
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Wang J, Xia L. Investigation of effects of Circadian Rhythm in Sport: A bibliometric analysis. Medicine (Baltimore) 2023; 102:e34229. [PMID: 38134095 PMCID: PMC10735098 DOI: 10.1097/md.0000000000034229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/15/2023] [Indexed: 12/24/2023] Open
Abstract
PURPOSE This study conducted a bibliometric analysis of the literature on circadian rhythms and sports to identify research trends, knowledge gaps, and future directions. METHODS A total of 301 manuscripts, including 245 articles and 56 reviews, were extracted from the Web of Science Core Collection (WoSCC) database, and the bibliometric analysis was performed using VOSviewer 1.6.16. RESULTS The analysis revealed a continuous increase in the volume of literature on circadian rhythms and sports over the past 38 years, with a focus on the effects of circadian rhythms on physical performance, sleep quality, and jet lag. The study identified 1107 authors who have contributed to this field, with the highest number of publications from Reilly T, Chtourou H, and Atkinson G. The publications were from 512 institutions in 59 countries/regions, with Liverpool John Moores University, University of Sfax, and Manouba University being the leading institutions. The USA, UK, and Australia had the largest number of publications. The top 3 journals were Chronobiology International, Biological Rhythm Research, and Sports Medicine. CONCLUSION Despite the increase in research, there are still several underexplored areas, such as the effects of circadian rhythms on cognitive and emotional processes in sports, the role of individual differences in circadian rhythms on sports outcomes, and the potential applications of circadian interventions for sports performance optimization. Future research should address these gaps to advance our understanding of the complex relationship between circadian rhythms and sports.
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Affiliation(s)
- Jie Wang
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Lina Xia
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Hall JG. The importance of age-specific gene expression. Am J Med Genet A 2023; 191:2801-2805. [PMID: 37458230 DOI: 10.1002/ajmg.a.63354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 11/14/2023]
Affiliation(s)
- Judith G Hall
- Faculty of Medicine, University of British Columbia, Vancouver, Canada
- Medical Genetics, British Columbia Children's Hospital, Vancouver, Canada
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Clark AD, Cumpstey AF, Santolini J, Jackson AA, Feelisch M. Uncoupled redox stress: how a temporal misalignment of redox-regulated processes and circadian rhythmicity exacerbates the stressed state. Open Biol 2023; 13:230151. [PMID: 37669692 PMCID: PMC10480010 DOI: 10.1098/rsob.230151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023] Open
Abstract
Diurnal and seasonal rhythmicity, entrained by environmental and nutritional cues, is a vital part of all life on Earth operating at every level of organization; from individual cells, to multicellular organisms, whole ecosystems and societies. Redox processes are intrinsic to physiological function and circadian regulation, but how they are integrated with other regulatory processes at the whole-body level is poorly understood. Circadian misalignment triggered by a major stressor (e.g. viral infection with SARS-CoV-2) or recurring stressors of lesser magnitude such as shift work elicit a complex stress response that leads to desynchronization of metabolic processes. This in turn challenges the system's ability to achieve redox balance due to alterations in metabolic fluxes (redox rewiring). We infer that the emerging 'alternative redox states' do not always revert readily to their evolved natural states; 'Long COVID' and other complex disorders of unknown aetiology are the clinical manifestations of such rearrangements. To better support and successfully manage bodily resilience to major stress and other redox challenges needs a clear perspective on the pattern of the hysteretic response for the interaction between the redox system and the circadian clock. Characterization of this system requires repeated (ideally continuous) recording of relevant clinical measures of the stress responses and whole-body redox state (temporal redox phenotyping). The human/animal body is a complex 'system of systems' with multi-level buffering capabilities, and it requires consideration of the wider dynamic context to identify a limited number of stress-markers suitable for routine clinical decision making. Systematically mapping the patterns and dynamics of redox biomarkers along the stressor/disease trajectory will provide an operational model of whole-body redox regulation/balance that can serve as basis for the identification of effective interventions which promote health by enhancing resilience.
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Affiliation(s)
- Anna D. Clark
- Perioperative and Critical Care Research Group, Southampton NIHR Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Andrew F. Cumpstey
- Perioperative and Critical Care Research Group, Southampton NIHR Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Jérôme Santolini
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Universite Paris-Saclay, F-91198, Gif-sur-Yvette Cedex, France
| | - Alan A. Jackson
- Human Nutrition, University of Southampton and University Hospital Southampton, Tremona Road, Southampton, SO16 6YD, UK
| | - Martin Feelisch
- Perioperative and Critical Care Research Group, Southampton NIHR Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
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Larrondo LF. Circadian entrainment of in vitro reactions, in real time, and around the clock. Proc Natl Acad Sci U S A 2023; 120:e2303566120. [PMID: 37094142 PMCID: PMC10161006 DOI: 10.1073/pnas.2303566120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Affiliation(s)
- Luis F. Larrondo
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150Santiago, Chile
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology, 7500565Santiago, Chile
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