1
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DeOliveira CC, Crane BR. A structural decryption of cryptochromes. Front Chem 2024; 12:1436322. [PMID: 39220829 PMCID: PMC11362059 DOI: 10.3389/fchem.2024.1436322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 08/01/2024] [Indexed: 09/04/2024] Open
Abstract
Cryptochromes (CRYs), which are signaling proteins related to DNA photolyases, play pivotal roles in sensory responses throughout biology, including growth and development, metabolic regulation, circadian rhythm entrainment and geomagnetic field sensing. This review explores the evolutionary relationships and functional diversity of cryptochromes from the perspective of their molecular structures. In general, CRY biological activities derive from their core structural architecture, which is based on a Photolyase Homology Region (PHR) and a more variable and functionally specific Cryptochrome C-terminal Extension (CCE). The α/β and α-helical domains within the PHR bind FAD, modulate redox reactive residues, accommodate antenna cofactors, recognize small molecules and provide conformationally responsive interaction surfaces for a range of partners. CCEs add structural complexity and divergence, and in doing so, influence photoreceptor reactivity and tailor function. Primary and secondary pockets within the PHR bind myriad moieties and collaborate with the CCEs to tune recognition properties and propagate chemical changes to downstream partners. For some CRYs, changes in homo and hetero-oligomerization couple to light-induced conformational changes, for others, changes in posttranslational modifications couple to cascades of protein interactions with partners and effectors. The structural exploration of cryptochromes underscores how a broad family of signaling proteins with close relationship to light-dependent enzymes achieves a wide range of activities through conservation of key structural and chemical properties upon which function-specific features are elaborated.
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Affiliation(s)
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States
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2
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Tariq D, Maurici N, Bartholomai BM, Chandrasekaran S, Dunlap JC, Bah A, Crane BR. Phosphorylation, disorder, and phase separation govern the behavior of Frequency in the fungal circadian clock. eLife 2024; 12:RP90259. [PMID: 38526948 PMCID: PMC10963029 DOI: 10.7554/elife.90259] [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] [Indexed: 03/27/2024] Open
Abstract
Circadian clocks are composed of transcription-translation negative feedback loops that pace rhythms of gene expression to the diurnal cycle. In the filamentous fungus Neurospora crassa, the proteins Frequency (FRQ), the FRQ-interacting RNA helicase (FRH), and Casein-Kinase I (CK1) form the FFC complex that represses expression of genes activated by the white-collar complex (WCC). FRQ orchestrates key molecular interactions of the clock despite containing little predicted tertiary structure. Spin labeling and pulse-dipolar electron spin resonance spectroscopy provide domain-specific structural insights into the 989-residue intrinsically disordered FRQ and the FFC. FRQ contains a compact core that associates and organizes FRH and CK1 to coordinate their roles in WCC repression. FRQ phosphorylation increases conformational flexibility and alters oligomeric state, but the changes in structure and dynamics are non-uniform. Full-length FRQ undergoes liquid-liquid phase separation (LLPS) to sequester FRH and CK1 and influence CK1 enzymatic activity. Although FRQ phosphorylation favors LLPS, LLPS feeds back to reduce FRQ phosphorylation by CK1 at higher temperatures. Live imaging of Neurospora hyphae reveals FRQ foci characteristic of condensates near the nuclear periphery. Analogous clock repressor proteins in higher organisms share little position-specific sequence identity with FRQ; yet, they contain amino acid compositions that promote LLPS. Hence, condensate formation may be a conserved feature of eukaryotic clocks.
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Affiliation(s)
- Daniyal Tariq
- Department of Chemistry & Chemical Biology, Cornell UniversityIthacaUnited States
| | - Nicole Maurici
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical UniversitySyracuseUnited States
| | - Bradley M Bartholomai
- Department of Molecular and Systems Biology, Geisel School of Medicine at DartmouthHanoverUnited States
| | | | - Jay C Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine at DartmouthHanoverUnited States
| | - Alaji Bah
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical UniversitySyracuseUnited States
| | - Brian R Crane
- Department of Chemistry & Chemical Biology, Cornell UniversityIthacaUnited States
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3
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Saft M, Schneider L, Ho CC, Maiterth E, Menke J, Sendker F, Steinchen W, Essen LO. One More for Light-triggered Conformational Changes in Cryptochromes: CryP from Phaeodactylum tricornutum. J Mol Biol 2024; 436:168408. [PMID: 38123123 DOI: 10.1016/j.jmb.2023.168408] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 12/01/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
Cryptochromes are a ubiquitously occurring class of photoreceptors. Together with photolyases, they form the Photolyase Cryptochrome Superfamily (PCSf) by sharing a common protein architecture and binding mode of the FAD chromophore. Despite these similarities, PCSf members exert different functions. Photolyases repair UV-induced DNA damage by photocatalytically driven electron transfer between FADH¯ and the DNA lesion, whereas cryptochromes are light-dependent signaling molecules and trigger various biological processes by photoconversion of their FAD redox and charge states. Given that most cryptochromes possess a C-terminal extension (CTE) of varying length, the functions of their CTE have not yet been fully elucidated and are hence highly debated. In this study, the role of the CTE was investigated for a novel subclass of the PCSf, the CryP-like cryptochromes, by hydrogen/deuterium exchange and mass-spectrometric analysis. Striking differences in the relative deuterium uptake were observed in different redox states of CryP from the diatom Phaeodactylum tricornutum. Based on these measurements we propose a model for light-triggered conformational changes in CryP-like cryptochromes that differs from other known cryptochrome families like the insect or plant cryptochromes.
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Affiliation(s)
- Martin Saft
- Department of Chemistry, Philipps University Marburg, 35032 Marburg, Germany
| | - Leonie Schneider
- Department of Chemistry, Philipps University Marburg, 35032 Marburg, Germany
| | - Chun-Chih Ho
- Department of Chemistry, Philipps University Marburg, 35032 Marburg, Germany
| | - Elias Maiterth
- Department of Chemistry, Philipps University Marburg, 35032 Marburg, Germany
| | - Josephine Menke
- Department of Chemistry, Philipps University Marburg, 35032 Marburg, Germany
| | - Franziska Sendker
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Wieland Steinchen
- Center of Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, 35032 Marburg, Germany
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps University Marburg, 35032 Marburg, Germany.
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4
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Schneps CM, Dunleavy R, Crane BR. Dissecting the Interaction between Cryptochrome and Timeless Reveals Underpinnings of Light-Dependent Recognition. Biochemistry 2024:10.1021/acs.biochem.3c00630. [PMID: 38294880 PMCID: PMC11289166 DOI: 10.1021/acs.biochem.3c00630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Circadian rhythms are determined by cell-autonomous transcription-translation feedback loops that entrain to environmental stimuli. In the model circadian clock of Drosophila melanogaster, the clock is set by the light-induced degradation of the core oscillator protein timeless (TIM) by the principal light-sensor cryptochrome (CRY). The cryo-EM structure of CRY bound to TIM revealed that within the extensive CRY:TIM interface, the TIM N-terminus binds into the CRY FAD pocket, in which FAD and the associated phosphate-binding loop (PBL) undergo substantial rearrangement. The TIM N-terminus involved in CRY binding varies in isoforms that facilitate the adaptation of flies to different light environments. Herein, we demonstrate, through peptide binding assays and pulsed-dipolar electron spin resonance (ESR) spectroscopy, that the TIM N-terminal peptide alone exhibits light-dependent binding to CRY and that the affinity of the interaction depends on the initiating methionine residue. Extensions to the TIM N-terminus that mimic less light-sensitive variants have substantially reduced interactions with CRY. Substitutions of CRY residues that couple to the flavin rearrangement in the CRY:TIM complex have dramatic effects on CRY light activation. CRY residues Arg237 on α8, Asn253, and Gln254 on the PBL are critical for the release of the CRY autoinhibitory C-terminal tail (CTT) and subsequent TIM binding. These key light-responsive elements of CRY are well conserved throughout Type I cryptochromes of invertebrates but not by cryptochromes of chordates and plants, which likely utilize a distinct light-activation mechanism.
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Affiliation(s)
| | - Robert Dunleavy
- Cornell University, Department of Chemistry & Chemical Biology, Ithaca, NY 14853
| | - Brian R. Crane
- Cornell University, Department of Chemistry & Chemical Biology, Ithaca, NY 14853
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5
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Yuan XN, Luo C, Zhao QF, Zhong SY, Hang Q, Dai TM, Pan ZH, Sima YH, Qiu JF, Xu SQ. The clock gene Cryptochrome 1 is involved in the photoresponse of embryonic hatching behavior in Bombyx mori. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 114:e22046. [PMID: 37583246 DOI: 10.1002/arch.22046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/17/2023]
Abstract
The hatching of insect eggs is a classic circadian behavior rhythm controlled by the biological clock. Its function is considered to impose a daily rhythm on the embryo, allowing it to hatch within a permissible time window. However, the molecular pathways through which the clock affects embryonic hatching behavior remain unclear. Here, we utilized a clock gene Cryptochrome1 (Cry1) knockout mutant to dissect the pathways by which the circadian clock affects embryonic hatching rhythm in the silkworm. In the Cry1 mutant, the embryo hatching rhythm was disrupted. Under the constant light or constant dark incubation conditions, mutant embryos lost their hatching rhythm, while wild-type embryos hatch exhibiting free-running rhythm. In the light-dark cycle (LD), the hatching rhythm of CRY1-deficient silkworms could not be entrained by the LD photoperiod during the incubation period. The messenger RNA levels and enzymatic activities of Cht and Hel in the mutant embryos were significantly reduced at circadian time 24 (CT24). Transcriptome analysis revealed significant differences in gene expression at CT24 between the Cry1 knockout mutant and the wild-type, with 2616 differentially expressed genes identified. The enriched Gene Ontology pathway includes enzyme activity, energy availability, and protein translation. Short neuropeptide F signaling was reduced in the CT24 embryonic brain of the mutant, the expression of the neuropeptide PTTH was also reduced and the rhythm was lost, which further affects ecdysteroid signaling. Our results suggested that the silkworm circadian clock affects neuropeptide-hormone signaling as well as physiological functions related to hatching, which may regulate the hatching rhythm.
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Affiliation(s)
- Xiao-Nan Yuan
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, China
- Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou, China
| | - Cheng Luo
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, China
- Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou, China
| | - Qi-Fan Zhao
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, China
- Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou, China
| | - Si-Yin Zhong
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, China
- Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou, China
| | - Qi Hang
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, China
- Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou, China
| | - Tai-Ming Dai
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, China
- Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou, China
| | - Zhong-Hua Pan
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, China
- Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou, China
| | - Yang-Hu Sima
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, China
- Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou, China
| | - Jian-Feng Qiu
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, China
- Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou, China
| | - Shi-Qing Xu
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, China
- Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou, China
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6
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Vu HH, Behrmann H, Hanić M, Jeyasankar G, Krishnan S, Dannecker D, Hammer C, Gunkel M, Solov'yov IA, Wolf E, Behrmann E. A marine cryptochrome with an inverse photo-oligomerization mechanism. Nat Commun 2023; 14:6918. [PMID: 37903809 PMCID: PMC10616196 DOI: 10.1038/s41467-023-42708-2] [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: 06/01/2023] [Accepted: 10/19/2023] [Indexed: 11/01/2023] Open
Abstract
Cryptochromes (CRYs) are a structurally conserved but functionally diverse family of proteins that can confer unique sensory properties to organisms. In the marine bristle worm Platynereis dumerilii, its light receptive cryptochrome L-CRY (PdLCry) allows the animal to discriminate between sunlight and moonlight, an important requirement for synchronizing its lunar cycle-dependent mass spawning. Using cryo-electron microscopy, we show that in the dark, PdLCry adopts a dimer arrangement observed neither in plant nor insect CRYs. Intense illumination disassembles the dimer into monomers. Structural and functional data suggest a mechanistic coupling between the light-sensing flavin adenine dinucleotide chromophore, the dimer interface, and the C-terminal tail helix, with a likely involvement of the phosphate binding loop. Taken together, our work establishes PdLCry as a CRY protein with inverse photo-oligomerization with respect to plant CRYs, and provides molecular insights into how this protein might help discriminating the different light intensities associated with sunlight and moonlight.
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Affiliation(s)
- Hong Ha Vu
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Heide Behrmann
- University of Cologne, Faculty of Mathematics and Natural Sciences, Institute of Biochemistry, Zülpicher Straße 47, 50674, Cologne, Germany
| | - Maja Hanić
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129, Oldenburg, Germany
| | - Gayathri Jeyasankar
- University of Cologne, Faculty of Mathematics and Natural Sciences, Institute of Biochemistry, Zülpicher Straße 47, 50674, Cologne, Germany
| | - Shruthi Krishnan
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Dennis Dannecker
- University of Cologne, Faculty of Mathematics and Natural Sciences, Institute of Biochemistry, Zülpicher Straße 47, 50674, Cologne, Germany
| | - Constantin Hammer
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Monika Gunkel
- University of Cologne, Faculty of Mathematics and Natural Sciences, Institute of Biochemistry, Zülpicher Straße 47, 50674, Cologne, Germany
| | - Ilia A Solov'yov
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129, Oldenburg, Germany
- Research Center for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26111, Oldenburg, Germany
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, Ammerländer Heerstr. 114-118, 26129, Oldenburg, Germany
| | - Eva Wolf
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany.
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany.
| | - Elmar Behrmann
- University of Cologne, Faculty of Mathematics and Natural Sciences, Institute of Biochemistry, Zülpicher Straße 47, 50674, Cologne, Germany.
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7
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Hanić M, Antill LM, Gehrckens AS, Schmidt J, Görtemaker K, Bartölke R, El-Baba TJ, Xu J, Koch KW, Mouritsen H, Benesch JLP, Hore PJ, Solov'yov IA. Dimerization of European Robin Cryptochrome 4a. J Phys Chem B 2023. [PMID: 37428840 PMCID: PMC10364083 DOI: 10.1021/acs.jpcb.3c01305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Homo-dimer formation is important for the function of many proteins. Although dimeric forms of cryptochromes (Cry) have been found by crystallography and were recently observed in vitro for European robin Cry4a, little is known about the dimerization of avian Crys and the role it could play in the mechanism of magnetic sensing in migratory birds. Here, we present a combined experimental and computational investigation of the dimerization of robin Cry4a resulting from covalent and non-covalent interactions. Experimental studies using native mass spectrometry, mass spectrometric analysis of disulfide bonds, chemical cross-linking, and photometric measurements show that disulfide-linked dimers are routinely formed, that their formation is promoted by exposure to blue light, and that the most likely cysteines are C317 and C412. Computational modeling and molecular dynamics simulations were used to generate and assess a number of possible dimer structures. The relevance of these findings to the proposed role of Cry4a in avian magnetoreception is discussed.
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Affiliation(s)
- Maja Hanić
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Lewis M Antill
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura Ward, Saitama 338-8570, Japan
- Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Angela S Gehrckens
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Jessica Schmidt
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Katharina Görtemaker
- Department of Neuroscience, Division of Biochemistry, Carl von Ossietzky University of Oldenburg, Oldenburg D-26111, Germany
| | - Rabea Bartölke
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Tarick J El-Baba
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
- Kavli Institute for NanoScience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, U.K
| | - Jingjing Xu
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Karl-Wilhelm Koch
- Department of Neuroscience, Division of Biochemistry, Carl von Ossietzky University of Oldenburg, Oldenburg D-26111, Germany
- Research Center for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26111, Germany
| | - Henrik Mouritsen
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
- Research Center for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26111, Germany
| | - Justin L P Benesch
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
- Kavli Institute for NanoScience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, U.K
| | - P J Hore
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Ilia A Solov'yov
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
- Research Center for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26111, Germany
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, Ammerländer Heerstr. 114-118, Oldenburg 26129, Germany
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8
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Lin C, Feng S, DeOliveira CC, Crane BR. Cryptochrome-Timeless structure reveals circadian clock timing mechanisms. Nature 2023; 617:194-199. [PMID: 37100907 PMCID: PMC11034853 DOI: 10.1038/s41586-023-06009-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/23/2023] [Indexed: 04/28/2023]
Abstract
Circadian rhythms influence many behaviours and diseases1,2. They arise from oscillations in gene expression caused by repressor proteins that directly inhibit transcription of their own genes. The fly circadian clock offers a valuable model for studying these processes, wherein Timeless (Tim) plays a critical role in mediating nuclear entry of the transcriptional repressor Period (Per) and the photoreceptor Cryptochrome (Cry) entrains the clock by triggering Tim degradation in light2,3. Here, through cryogenic electron microscopy of the Cry-Tim complex, we show how a light-sensing cryptochrome recognizes its target. Cry engages a continuous core of amino-terminal Tim armadillo repeats, resembling how photolyases recognize damaged DNA, and binds a C-terminal Tim helix, reminiscent of the interactions between light-insensitive cryptochromes and their partners in mammals. The structure highlights how the Cry flavin cofactor undergoes conformational changes that couple to large-scale rearrangements at the molecular interface, and how a phosphorylated segment in Tim may impact clock period by regulating the binding of Importin-α and the nuclear import of Tim-Per4,5. Moreover, the structure reveals that the N terminus of Tim inserts into the restructured Cry pocket to replace the autoinhibitory C-terminal tail released by light, thereby providing a possible explanation for how the long-short Tim polymorphism adapts flies to different climates6,7.
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Affiliation(s)
- Changfan Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Shi Feng
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | | | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
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9
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Dunleavy R, Chandrasekaran S, Crane BR. Enzymatic Spin-Labeling of Protein N- and C-Termini for Electron Paramagnetic Resonance Spectroscopy. Bioconjug Chem 2023:10.1021/acs.bioconjchem.3c00029. [PMID: 36921260 PMCID: PMC10502183 DOI: 10.1021/acs.bioconjchem.3c00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for investigating the structure and dynamics of proteins. The introduction of paramagnetic moieties at specific positions in a protein enables precise measurement of local structure and dynamics. This technique, termed site-directed spin-labeling, has traditionally been performed using cysteine-reactive radical-containing probes. However, large proteins are more likely to contain multiple cysteine residues and cysteine labeling at specific sites may be infeasible or impede function. To address this concern, we applied three peptide-ligating enzymes (sortase, asparaginyl endopeptidase, and inteins) for nitroxide labeling of N- and C-termini of select monomeric and dimeric proteins. Continuous wave and pulsed EPR (double electron electron resonance) experiments reveal specific attachment of nitroxide probes to ether N-termini (OaAEP1) or C-termini (sortase and intein) across three test proteins (CheY, CheA, and iLOV), thereby enabling a straightforward, highly specific, and general method for protein labeling. Importantly, the linker length (3, 5, and 9 residues for OaAEP1, intein, and sortase reactions, respectively) between the probe and the target protein has a large impact on the utility of distance measurements by pulsed EPR, with longer linkers leading to broader distributions. As these methods are only dependent on accessible N- and C-termini, we anticipate application to a wide range of protein targets for biomolecular EPR spectroscopy.
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Affiliation(s)
- Robert Dunleavy
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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10
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Foroutannejad S, Good LL, Lin C, Carter ZI, Tadesse MG, Lucius AL, Crane BR, Maillard RA. The cofactor-dependent folding mechanism of Drosophila cryptochrome revealed by single-molecule pulling experiments. Nat Commun 2023; 14:1057. [PMID: 36828841 PMCID: PMC9958137 DOI: 10.1038/s41467-023-36701-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 02/10/2023] [Indexed: 02/26/2023] Open
Abstract
The link between cofactor binding and protein activity is well-established. However, how cofactor interactions modulate folding of large proteins remains unknown. We use optical tweezers, clustering and global fitting to dissect the folding mechanism of Drosophila cryptochrome (dCRY), a 542-residue protein that binds FAD, one of the most chemically and structurally complex cofactors in nature. We show that the first dCRY parts to fold are independent of FAD, but later steps are FAD-driven as the remaining polypeptide folds around the cofactor. FAD binds to largely unfolded intermediates, yet with association kinetics above the diffusion-limit. Interestingly, not all FAD moieties are required for folding: whereas the isoalloxazine ring linked to ribitol and one phosphate is sufficient to drive complete folding, the adenosine ring with phosphates only leads to partial folding. Lastly, we propose a dCRY folding model where regions that undergo conformational transitions during signal transduction are the last to fold.
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Affiliation(s)
| | - Lydia L Good
- Department of Chemistry, Georgetown University, Washington, DC, USA
| | - Changfan Lin
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Zachariah I Carter
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mahlet G Tadesse
- Department of Mathematics and Statistics, Georgetown University, Washington, DC, USA
| | - Aaron L Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Brian R Crane
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY, USA
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11
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Au DD, Liu JC, Nguyen TH, Foden AJ, Park SJ, Dimalanta M, Yu Z, Holmes TC. Nocturnal mosquito Cryptochrome 1 mediates greater electrophysiological and behavioral responses to blue light relative to diurnal mosquito Cryptochrome 1. Front Neurosci 2022; 16:1042508. [PMID: 36532283 PMCID: PMC9749892 DOI: 10.3389/fnins.2022.1042508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/04/2022] [Indexed: 12/05/2022] Open
Abstract
Nocturnal Anopheles mosquitoes exhibit strong behavioral avoidance to blue-light while diurnal Aedes mosquitoes are behaviorally attracted to blue-light and a wide range of other wavelengths of light. To determine the molecular mechanism of these effects, we expressed light-sensing Anopheles gambiae (AgCRY1) and Aedes aegypti (AeCRY1) Cryptochrome 1 (CRY) genes under a crypGAL4-24 driver line in a mutant Drosophila genetic background lacking native functional CRY, then tested behavioral and electrophysiological effects of mosquito CRY expression relative to positive and negative CRY control conditions. Neither mosquito CRY stops the circadian clock as shown by robust circadian behavioral rhythmicity in constant darkness in flies expressing either AgCRY1 or AeCRY1. AgCRY1 and AeCRY1 both mediate acute increases in large ventral lateral neuronal firing rate evoked by 450 nm blue-light, corresponding to CRY's peak absorbance in its base state, indicating that both mosquito CRYs are functional, however, AgCRY1 mediates significantly stronger sustained electrophysiological light-evoked depolarization in response to blue-light relative to AeCRY1. In contrast, neither AgCRY1 nor AeCRY1 expression mediates measurable increases in large ventral lateral neuronal firing rates in response to 405 nm violet-light, the peak of the Rhodopsin-7 photoreceptor that is co-expressed in the large lateral ventral neurons. These results are consistent with the known action spectra of type 1 CRYs and lack of response in cry-null controls. AgCRY1 and AeCRY1 expressing flies show behavioral attraction to low intensity blue-light, but AgCRY1 expressing flies show behavioral avoidance to higher intensity blue-light. These results show that nocturnal and diurnal mosquito Cryptochrome 1 proteins mediate differential physiological and behavioral responses to blue-light that are consistent with species-specific mosquito behavior.
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Affiliation(s)
- David D. Au
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Jenny C. Liu
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Thanh H. Nguyen
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Alexander J. Foden
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Soo Jee Park
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Mia Dimalanta
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Zhaoxia Yu
- Department of Statistics, Donald Bren School of Information and Computer Sciences, University of California, Irvine, Irvine, CA, United States,Center for Neural Circuit Mapping, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Todd C. Holmes
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, Irvine, CA, United States,Center for Neural Circuit Mapping, School of Medicine, University of California, Irvine, Irvine, CA, United States,*Correspondence: Todd C. Holmes,
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12
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Yagi M, Miller S, Nagai Y, Inuki S, Sato A, Hirota T. A methylbenzimidazole derivative regulates mammalian circadian rhythms by targeting Cryptochrome proteins. F1000Res 2022; 11:1016. [PMID: 36226040 PMCID: PMC9523283 DOI: 10.12688/f1000research.124658.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/26/2022] [Indexed: 01/13/2023] Open
Abstract
Background: Impairment of the circadian clock has been associated with numerous diseases, including sleep disorders and metabolic disease. Although small molecules that modulate clock function may form the basis of drug discovery of clock-related diseases, only a few compounds that selectively target core clock proteins have been identified. Three scaffolds were previously discovered as small-molecule activators of the clock protein Cryptochrome (CRY), and they have been providing powerful tools to understand and control the circadian clock system. Identifying new scaffolds will expand the possibilities of drug discovery. Methods: A methylbenzimidazole derivative TH401 identified from cell-based circadian screens was characterized. Effects of TH401 on circadian rhythms were evaluated in cellular assays. Functional assays and X-ray crystallography were used to elucidate the effects of the compound on CRY1 and CRY2 isoforms. Results: TH401 lengthened the period of circadian rhythms and stabilized both CRY1 and CRY2. The compound repressed Per2 reporter activity, which was reduced by Cry1 or Cry2 knockout and abolished by Cry1/Cry2 double knockout, indicating the dependence on CRY isoforms. Thermal shift assays showed slightly higher interaction of TH401 with CRY2 over CRY1. The crystal structure of CRY1 in complex with TH401 revealed a conformational change of the gatekeeper W399, which is involved in isoform-selectivity determination. Conclusions: The present study identified a new small molecule TH401 that targets both CRY isoforms. This compound has expanded the chemical diversity of CRY activators, and will ultimately aid in the development of therapeutics against circadian clock-related disorders.
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Affiliation(s)
- Moeri Yagi
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan,Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, 464-8601, Japan
| | - Simon Miller
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan
| | - Yoshiko Nagai
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan
| | - Shinsuke Inuki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Ayato Sato
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan,Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, 464-8601, Japan,
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13
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Direct experimental observation of blue-light-induced conformational change and intermolecular interactions of cryptochrome. Commun Biol 2022; 5:1103. [PMID: 36257983 PMCID: PMC9579160 DOI: 10.1038/s42003-022-04054-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 09/30/2022] [Indexed: 11/30/2022] Open
Abstract
Cryptochromes are blue light receptors that mediate circadian rhythm and magnetic sensing in various organisms. A typical cryptochrome consists of a conserved photolyase homology region domain and a varying carboxyl-terminal extension across species. The structure of the flexible carboxyl-terminal extension and how carboxyl-terminal extension participates in cryptochrome’s signaling function remain mostly unknown. In this study, we uncover the potential missing link between carboxyl-terminal extension conformational changes and downstream signaling functions. Specifically, we discover that the blue-light induced opening of carboxyl-terminal extension in C. reinhardtii animal-like cryptochrome can structurally facilitate its interaction with Rhythm Of Chloroplast 15, a circadian-clock-related protein. Our finding is made possible by two technical advances. Using single-molecule Förster resonance energy transfer technique, we directly observe the displacement of carboxyl-terminal extension by about 15 Å upon blue light excitation. Combining structure prediction and solution X-ray scattering methods, we propose plausible structures of full-length cryptochrome under dark and lit conditions. The structures provide molecular basis for light active conformational changes of cryptochrome and downstream regulatory functions. Refined structures, protein-docking analysis and single molecule assays provides insights into light-induced conformational changes in the cryptochrome CraCRY.
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14
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Maschmann ZA, Chua TK, Chandrasekaran S, Ibáñez H, Crane BR. Redox properties and PAS domain structure of the Escherichia coli energy sensor Aer indicate a multistate sensing mechanism. J Biol Chem 2022; 298:102598. [PMID: 36252616 PMCID: PMC9668731 DOI: 10.1016/j.jbc.2022.102598] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022] Open
Abstract
The Per-Arnt-Sim (PAS; named for the representative proteins: Period, Aryl hydrocarbon receptor nuclear translocator protein and Single-minded) domain of the dimeric Escherichia coli aerotaxis receptor Aer monitors cellular respiration through a redox-sensitive flavin adenine dinucleotide (FAD) cofactor. Conformational shifts in the PAS domain instigated by the oxidized FAD (FADOX)/FAD anionic semiquinone (FADASQ) redox couple traverse the HAMP (histidine kinases, adenylate cyclases, methyl-accepting chemotaxis proteins, and phosphatases) and kinase control domains of the Aer dimer to regulate CheA kinase activity. The PAS domain of Aer is unstable and has not been previously purified. Here, residue substitutions that rescue FAD binding in an FAD binding-deficient full-length Aer variant were used in combination to stabilize the Aer PAS domain. We solved the 2.4 Å resolution crystal structure of this variant, Aer-PAS-GVV, and revealed a PAS fold that contains distinct features associated with FAD-based redox sensing, such as a close contact between the Arg115 side chain and N5 of the isoalloxazine ring and interactions of the flavin with the side chains of His53 and Asn85 that are poised to convey conformational signals from the cofactor to the protein surface. In addition, we determined the FADox/FADASQ formal potentials of Aer-PAS-GVV and full-length Aer reconstituted into nanodiscs. The Aer redox couple is remarkably low at -289.6 ± 0.4 mV. In conclusion, we propose a model for Aer energy sensing based on the low potential of Aer-PAS-FADox/FADASQ couple and the inability of Aer-PAS to bind to the fully reduced FAD hydroquinone.
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Affiliation(s)
- Zachary A Maschmann
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Teck Khiang Chua
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | | | - Héctor Ibáñez
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA.
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15
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Schneps CM, Ganguly A, Crane BR. Room-temperature serial synchrotron crystallography of Drosophila cryptochrome. Acta Crystallogr D Struct Biol 2022; 78:975-985. [PMID: 35916222 PMCID: PMC9344480 DOI: 10.1107/s2059798322007008] [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: 04/06/2022] [Accepted: 07/08/2022] [Indexed: 11/10/2022] Open
Abstract
Fixed-target serial crystallography allows the high-throughput collection of diffraction data from small crystals at room temperature. This methodology is particularly useful for difficult samples that have sensitivity to radiation damage or intolerance to cryoprotection measures; fixed-target methods also have the added benefit of low sample consumption. Here, this method is applied to the structure determination of the circadian photoreceptor cryptochrome (CRY), previous structures of which have been determined at cryogenic temperature. In determining the structure, several data-filtering strategies were tested for combining observations from the hundreds of crystals that contributed to the final data set. Removing data sets based on the average correlation coefficient among equivalent reflection intensities between a given data set and all others was most effective at improving the data quality and maintaining overall completeness. CRYs are light sensors that undergo conformational photoactivation. Comparisons between the cryogenic and room-temperature CRY structures reveal regions of enhanced mobility at room temperature in loops that have functional importance within the CRY family of proteins. The B factors of the room-temperature structure correlate well with those predicted from molecular-dynamics simulations.
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Affiliation(s)
- Connor M. Schneps
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850, USA
| | - Abir Ganguly
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850, USA
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16
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Lin C, Schneps CM, Chandrasekaran S, Ganguly A, Crane BR. Mechanistic insight into light-dependent recognition of Timeless by Drosophila Cryptochrome. Structure 2022; 30:851-861.e5. [PMID: 35397203 DOI: 10.1016/j.str.2022.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/24/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022]
Abstract
Cryptochrome (CRY) entrains the fly circadian clock by binding to Timeless (TIM) in light. Undocking of a helical C-terminal tail (CTT) in response to photoreduction of the CRY flavin cofactor gates TIM recognition. We present a generally applicable select western-blot-free tagged-protein interaction (SWFTI) assay that allowed the quantification of CRY binding to TIM in dark and light. The assay was used to study CRY variants with residue substitutions in the flavin pocket and correlate their TIM affinities with CTT undocking, as measured by pulse-dipolar ESR spectroscopy and evaluated by molecular dynamics simulations. CRY variants with the CTT removed or undocked bound TIM constitutively, whereas those incapable of photoreduction bound TIM weakly. In response to the flavin redox state, two conserved histidine residues contributed to a robust on/off switch by mediating CTT interactions with the flavin pocket and TIM. Our approach provides an expeditious means to quantify the interactions of difficult-to-produce proteins.
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Affiliation(s)
- Changfan Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Connor M Schneps
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | - Abir Ganguly
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
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17
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Miller S, Hirota T. Structural and Chemical Biology Approaches Reveal Isoform-Selective Mechanisms of Ligand Interactions in Mammalian Cryptochromes. Front Physiol 2022; 13:837280. [PMID: 35153842 PMCID: PMC8831909 DOI: 10.3389/fphys.2022.837280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/05/2022] [Indexed: 01/27/2023] Open
Abstract
Cryptochromes (CRYs) are core components of the circadian feedback loop in mammals, which regulates circadian rhythmicity in a variety of physiological processes including sleep–wake cycles and metabolism. Dysfunction of CRY1 and CRY2 isoforms has been associated with a host of diseases, such as sleep phase disorder and metabolic diseases. Accumulating evidence for distinct roles of CRY1 and CRY2 has highlighted the need for CRY isoform-selective regulation; however, highly conserved sequences in CRY ligand-binding sites have hindered the design of isoform-selective compounds. Chemical biology approaches have been identifying small-molecule modulators of CRY proteins, which act in isoform-non-selective and also isoform-selective manners. In this review, we describe advances in our understanding of CRY isoform selectivity by comparing X-ray crystal structures of mammalian CRY isoforms in apo form and in complexes with compounds. We discuss how intrinsic conformational differences in identical residues of CRY1 and CRY2 contribute to unique interactions with different compound moieties for isoform selectivity.
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18
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Zadeh-Haghighi H, Simon C. Radical pairs can explain magnetic field and lithium effects on the circadian clock. Sci Rep 2022; 12:269. [PMID: 34997158 PMCID: PMC8742017 DOI: 10.1038/s41598-021-04334-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/14/2021] [Indexed: 12/21/2022] Open
Abstract
Drosophila's circadian clock can be perturbed by magnetic fields, as well as by lithium administration. Cryptochromes are critical for the circadian clock. Further, the radical pairs in cryptochrome also can explain magnetoreception in animals. Based on a simple radical pair mechanism model of the animal magnetic compass, we show that both magnetic fields and lithium can influence the spin dynamics of the naturally occurring radical pairs and hence modulate the circadian clock's rhythms. Using a simple chemical oscillator model for the circadian clock, we show that the spin dynamics influence a rate in the chemical oscillator model, which translates into a change in the circadian period. Our model can reproduce the results of two independent experiments, magnetic field and lithium effects on the circadian clock. Our model predicts that stronger magnetic fields would shorten the clock's period. We also predict that lithium influences the clock in an isotope-dependent manner. Furthermore, our model also predicts that magnetic fields and hyperfine interactions modulate oxidative stress. The findings of this work suggest that the quantum nature of radical pairs might play roles in the brain, as another piece of evidence in addition to recent results on xenon anesthesia and lithium effects on hyperactivity.
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Affiliation(s)
- Hadi Zadeh-Haghighi
- Department of Physics and Astronomy, University of Calgary, Calgary, AB, T2N 1N4, Canada.
- Institute for Quantum Science and Technology, University of Calgary, Calgary, AB, T2N 1N4, Canada.
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, T2N 1N4, Canada.
| | - Christoph Simon
- Department of Physics and Astronomy, University of Calgary, Calgary, AB, T2N 1N4, Canada.
- Institute for Quantum Science and Technology, University of Calgary, Calgary, AB, T2N 1N4, Canada.
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, T2N 1N4, Canada.
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19
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Goett-Zink L, Kottke T. Plant Cryptochromes Illuminated: A Spectroscopic Perspective on the Mechanism. Front Chem 2021; 9:780199. [PMID: 34900940 PMCID: PMC8653763 DOI: 10.3389/fchem.2021.780199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Abstract
Plant cryptochromes are central blue light receptors for the control of land plant and algal development including the circadian clock and the cell cycle. Cryptochromes share a photolyase homology region with about 500 amino acids and bind the chromophore flavin adenine dinucleotide. Characteristic for plant cryptochromes is a conserved aspartic acid close to flavin and an exceptionally long C-terminal extension. The mechanism of activation by excitation and reduction of the chromophore flavin adenine dinucleotide has been controversially discussed for many years. Various spectroscopic techniques have contributed to our understanding of plant cryptochromes by providing high time resolution, ambient conditions and even in-cell approaches. As a result, unifying and differing aspects of photoreaction and signal propagation have been revealed in comparison to members from other cryptochrome subfamilies. Here, we review the insight from spectroscopy on the flavin photoreaction in plant cryptochromes and present the current models on the signal propagation from flavin reduction to dissociation of the C-terminal extension.
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Affiliation(s)
- Lukas Goett-Zink
- Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Tilman Kottke
- Department of Chemistry, Bielefeld University, Bielefeld, Germany.,Biophysical Chemistry and Diagnostics, Medical School OWL, Bielefeld University, Bielefeld, Germany
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20
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Karki N, Vergish S, Zoltowski BD. Cryptochromes: Photochemical and structural insight into magnetoreception. Protein Sci 2021; 30:1521-1534. [PMID: 33993574 DOI: 10.1002/pro.4124] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 12/21/2022]
Abstract
Cryptochromes (CRYs) function as blue light photoreceptors in diverse physiological processes in nearly all kingdoms of life. Over the past several decades, they have emerged as the most likely candidates for light-dependent magnetoreception in animals, however, a long history of conflicts between in vitro photochemistry and in vivo behavioral data complicate validation of CRYs as a magnetosensor. In this review, we highlight the origins of conflicts regarding CRY photochemistry and signal transduction, and identify recent data that provides clarity on potential mechanisms of signal transduction in magnetoreception. The review primarily focuses on examining differences in photochemistry and signal transduction in plant and animal CRYs, and identifies potential modes of convergent evolution within these independent lineages that may identify conserved signaling pathways.
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Affiliation(s)
- Nischal Karki
- Department of Chemistry, Southern Methodist University, Dallas, Texas, USA
| | - Satyam Vergish
- Department of Chemistry, Southern Methodist University, Dallas, Texas, USA
| | - Brian D Zoltowski
- Department of Chemistry, Southern Methodist University, Dallas, Texas, USA
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21
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Yee EF, Oldemeyer S, Böhm E, Ganguly A, York DM, Kottke T, Crane BR. Peripheral Methionine Residues Impact Flavin Photoreduction and Protonation in an Engineered LOV Domain Light Sensor. Biochemistry 2021; 60:1148-1164. [PMID: 33787242 PMCID: PMC8107827 DOI: 10.1021/acs.biochem.1c00064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Proton-coupled electron transfer reactions play critical roles in many aspects of sensory phototransduction. In the case of flavoprotein light sensors, reductive quenching of flavin excited states initiates chemical and conformational changes that ultimately transmit light signals to downstream targets. These reactions generally require neighboring aromatic residues and proton-donating side chains for rapid and coordinated electron and proton transfer to flavin. Although photoreduction of flavoproteins can produce either the anionic (ASQ) or neutral semiquinone (NSQ), the factors that favor one over the other are not well understood. Here we employ a biologically active variant of the light-oxygen-voltage (LOV) domain protein VVD devoid of the adduct-forming Cys residue (VVD-III) to probe the mechanism of flavin photoreduction and protonation. A series of isosteric and conservative residue replacements studied by rate measurements, fluorescence quantum yields, FTIR difference spectroscopy, and molecular dynamics simulations indicate that tyrosine residues facilitate charge recombination reactions that limit sustained flavin reduction, whereas methionine residues facilitate radical propagation and quenching and also gate solvent access for flavin protonation. Replacement of a single surface Met residue with Leu favors formation of the ASQ over the NSQ and desensitizes photoreduction to oxidants. In contrast, increasing site hydrophilicity by Gln substitution promotes rapid NSQ formation and weakens the influence of the redox environment. Overall, the photoreactivity of VVD-III can be understood in terms of redundant electron donors, internal hole quenching, and coupled proton transfer reactions that all depend upon protein conformation, dynamics, and solvent penetration.
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Affiliation(s)
- Estella F. Yee
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Sabine Oldemeyer
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Elena Böhm
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Abir Ganguly
- Laboratory for Biomolecular Simulation Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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