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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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Kim C, Yun SR, Lee SJ, Kim SO, Lee H, Choi J, Kim JG, Kim TW, You S, Kosheleva I, Noh T, Baek J, Ihee H. Structural dynamics of protein-protein association involved in the light-induced transition of Avena sativa LOV2 protein. Nat Commun 2024; 15:6991. [PMID: 39143073 PMCID: PMC11324726 DOI: 10.1038/s41467-024-51461-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 08/07/2024] [Indexed: 08/16/2024] Open
Abstract
The Light-oxygen-voltage-sensing domain (LOV) superfamily, found in enzymes and signal transduction proteins, plays a crucial role in converting light signals into structural signals, mediating various biological mechanisms. While time-resolved spectroscopic studies have revealed the dynamics of the LOV-domain chromophore's electronic structures, understanding the structural changes in the protein moiety, particularly regarding light-induced dimerization, remains challenging. Here, we utilize time-resolved X-ray liquidography to capture the light-induced dimerization of Avena sativa LOV2. Our analysis unveils that dimerization occurs within milliseconds after the unfolding of the A'α and Jα helices in the microsecond time range. Notably, our findings suggest that protein-protein interactions (PPIs) among the β-scaffolds, mediated by helix unfolding, play a key role in dimerization. In this work, we offer structural insights into the dimerization of LOV2 proteins following structural changes in the A'α and Jα helices, as well as mechanistic insights into the protein-protein association process driven by PPIs.
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Affiliation(s)
- Changin Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - So Ri Yun
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Sang Jin Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Seong Ok Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Hyosub Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Jungkweon Choi
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Tae Wu Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Seyoung You
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL, 60637, USA
| | - Taeyoon Noh
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Jonghoon Baek
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea.
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3
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Shim JG, Chuon K, Kim JH, Lee SJ, Song MC, Cho SG, Hour C, Jung KH. Proton-pumping photoreceptor controls expression of ABC transporter by regulating transcription factor through light. Commun Biol 2024; 7:789. [PMID: 38951607 PMCID: PMC11217422 DOI: 10.1038/s42003-024-06471-4] [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: 12/11/2023] [Accepted: 06/19/2024] [Indexed: 07/03/2024] Open
Abstract
Light is a significant factor for living organisms with photosystems, like microbial rhodopsin-a retinal protein that functions as an ion pump, channel, and sensory transduction. Gloeobacter violaceus PCC7421, has a proton-pumping rhodopsin gene, the Gloeobacter rhodopsin (GR). The helix-turn-helix family of transcriptional regulators has various motifs, and they regulate gene expression in the presence of various metal ions. Here, we report that active proton outward pumping rhodopsin interacted with the helix-turn-helix transcription regulator and regulated gene expression. This interaction is confirmed using ITC analysis (KD of 8 μM) and determined the charged residues required. During in vitro experiments using fluorescent and luciferase reporter systems, ATP-binding cassette (ABC) transporters and the self-regulation of G. violaceus transcriptional regulator (GvTcR) are regulated by light, and gene regulation is observed in G. violaceus using the real-time polymerase chain reaction. These results expand our understanding of the natural potential and limitations of microbial rhodopsin function.
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Affiliation(s)
- Jin-Gon Shim
- Department of Life Science, Sogang University, Seoul, South Korea
- Pharmacology Department, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Kimleng Chuon
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Ji-Hyun Kim
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Sang-Ji Lee
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Myung-Chul Song
- Department of Life Science, Sogang University, Seoul, South Korea
- Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - Shin-Gyu Cho
- Department of Life Science, Sogang University, Seoul, South Korea
- Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - Chenda Hour
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Kwang-Hwan Jung
- Department of Life Science, Sogang University, Seoul, South Korea.
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4
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Zhang L, Malkemper EP. Cryptochromes in mammals: a magnetoreception misconception? Front Physiol 2023; 14:1250798. [PMID: 37670767 PMCID: PMC10475740 DOI: 10.3389/fphys.2023.1250798] [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: 06/30/2023] [Accepted: 08/01/2023] [Indexed: 09/07/2023] Open
Abstract
Cryptochromes are flavoproteins related to photolyases that are widespread throughout the plant and animal kingdom. They govern blue light-dependent growth in plants, control circadian rhythms in a light-dependent manner in invertebrates, and play a central part in the circadian clock in vertebrates. In addition, cryptochromes might function as receptors that allow animals to sense the Earth's magnetic field. As cryptochromes are also present in mammals including humans, the possibility of a magnetosensitive protein is exciting. Here we attempt to provide a concise overview of cryptochromes in mammals. We briefly review their canonical role in the circadian rhythm from the molecular level to physiology, behaviour and diseases. We then discuss their disputed light sensitivity and proposed role in the magnetic sense in mammals, providing three mechanistic hypotheses. Specifically, mammalian cryptochromes could form light-induced radical pairs in particular cellular milieus, act as magnetoreceptors in darkness, or as secondary players in a magnetoreception signalling cascade. Future research can test these hypotheses to investigate if the role of mammalian cryptochromes extends beyond the circadian clock.
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Affiliation(s)
| | - E. Pascal Malkemper
- Max Planck Research Group Neurobiology of Magnetoreception, Max Planck Institute for Neurobiology of Behavior—caesar, Bonn, Germany
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Dikiy I, Swingle D, Toy K, Edupuganti UR, Rivera-Cancel G, Gardner KH. Diversity of function and higher-order structure within HWE sensor histidine kinases. J Biol Chem 2023; 299:104934. [PMID: 37331599 PMCID: PMC10359499 DOI: 10.1016/j.jbc.2023.104934] [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: 02/18/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/20/2023] Open
Abstract
Integral to the protein structure/function paradigm, oligomeric state is typically conserved along with function across evolution. However, notable exceptions such as the hemoglobins show how evolution can alter oligomerization to enable new regulatory mechanisms. Here, we examine this linkage in histidine kinases (HKs), a large class of widely distributed prokaryotic environmental sensors. While the majority of HKs are transmembrane homodimers, members of the HWE/HisKA2 family can deviate from this architecture as exemplified by our finding of a monomeric soluble HWE/HisKA2 HK (EL346, a photosensing light-oxygen-voltage [LOV]-HK). To further explore the diversity of oligomerization states and regulation within this family, we biophysically and biochemically characterized multiple EL346 homologs and found a range of HK oligomeric states and functions. Three LOV-HK homologs are primarily dimeric with differing structural and functional responses to light, while two Per-ARNT-Sim-HKs interconvert between differentially active monomers and dimers, suggesting dimerization might control enzymatic activity for these proteins. Finally, we examined putative interfaces in a dimeric LOV-HK, finding that multiple regions contribute to dimerization. Our findings suggest the potential for novel regulatory modes and oligomeric states beyond those traditionally defined for this important family of environmental sensors.
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Affiliation(s)
- Igor Dikiy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA
| | - Danielle Swingle
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA; PhD. Program in Biochemistry, The Graduate Center - City University of New York, New York, New York, USA
| | - Kaitlyn Toy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA; Department of Chemistry and Biochemistry, City College of New York, New York, New York, USA
| | - Uthama R Edupuganti
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA; PhD. Program in Biochemistry, The Graduate Center - City University of New York, New York, New York, USA
| | - Giomar Rivera-Cancel
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA; Department of Chemistry and Biochemistry, City College of New York, New York, New York, USA; PhD. Programs in Biochemistry, Biology, and Chemistry, The Graduate Center - City University of New York, New York, New York, USA.
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6
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Gao TT, Oh T, Mehta K, Huang YA, Camp T, Fan H, Han JW, Barnes CM, Zhang K. The clinical potential of optogenetic interrogation of pathogenesis. Clin Transl Med 2023; 13:e1243. [PMID: 37132114 PMCID: PMC10154842 DOI: 10.1002/ctm2.1243] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/05/2023] [Accepted: 04/13/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND Opsin-based optogenetics has emerged as a powerful biomedical tool using light to control protein conformation. Such capacity has been initially demonstrated to control ion flow across the cell membrane, enabling precise control of action potential in excitable cells such as neurons or muscle cells. Further advancement in optogenetics incorporates a greater variety of photoactivatable proteins and results in flexible control of biological processes, such as gene expression and signal transduction, with commonly employed light sources such as LEDs or lasers in optical microscopy. Blessed by the precise genetic targeting specificity and superior spatiotemporal resolution, optogenetics offers new biological insights into physiological and pathological mechanisms underlying health and diseases. Recently, its clinical potential has started to be capitalized, particularly for blindness treatment, due to the convenient light delivery into the eye. AIMS AND METHODS This work summarizes the progress of current clinical trials and provides a brief overview of basic structures and photophysics of commonly used photoactivable proteins. We highlight recent achievements such as optogenetic control of the chimeric antigen receptor, CRISPR-Cas system, gene expression, and organelle dynamics. We discuss conceptual innovation and technical challenges faced by current optogenetic research. CONCLUSION In doing so, we provide a framework that showcases ever-growing applications of optogenetics in biomedical research and may inform novel precise medicine strategies based on this enabling technology.
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Affiliation(s)
- Tianyu Terry Gao
- University of Illinois at Urbana‐ChampaignDepartment of BiochemistryUrbanaIllinoisUSA
| | - Teak‐Jung Oh
- University of Illinois at Urbana‐ChampaignDepartment of BiochemistryUrbanaIllinoisUSA
| | - Kritika Mehta
- University of Illinois at Urbana‐ChampaignDepartment of BiochemistryUrbanaIllinoisUSA
| | - Yu‐En Andrew Huang
- University of Illinois at Urbana‐ChampaignCenter for Biophysics and Quantitative BiologyUrbanaIllinoisUSA
| | - Tyler Camp
- University of Illinois at Urbana‐ChampaignDepartment of BiochemistryUrbanaIllinoisUSA
| | - Huaxun Fan
- University of Illinois at Urbana‐ChampaignDepartment of BiochemistryUrbanaIllinoisUSA
| | - Jeong Won Han
- University of Illinois at Urbana‐ChampaignDepartment of BiochemistryUrbanaIllinoisUSA
| | - Collin Michael Barnes
- University of Illinois at Urbana‐ChampaignDepartment of BiochemistryUrbanaIllinoisUSA
| | - Kai Zhang
- University of Illinois at Urbana‐ChampaignDepartment of BiochemistryUrbanaIllinoisUSA
- University of Illinois at Urbana‐ChampaignCenter for Biophysics and Quantitative BiologyUrbanaIllinoisUSA
- Cancer Center at IllinoisUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
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7
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Demchenko AP. Proton transfer reactions: from photochemistry to biochemistry and bioenergetics. BBA ADVANCES 2023. [DOI: 10.1016/j.bbadva.2023.100085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
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Fan H, Barnes C, Hwang H, Zhang K, Yang J. Precise modulation of embryonic development through optogenetics. Genesis 2022; 60:e23505. [PMID: 36478118 PMCID: PMC9847014 DOI: 10.1002/dvg.23505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022]
Abstract
The past decade has witnessed enormous progress in optogenetics, which uses photo-sensitive proteins to control signal transduction in live cells and animals. The ever-increasing amount of optogenetic tools, however, could overwhelm the selection of appropriate optogenetic strategies. In this work, we summarize recent progress in this emerging field and highlight the application of opsin-free optogenetics in studying embryonic development, focusing on new insights gained into optical induction of morphogenesis, cell polarity, cell fate determination, tissue differentiation, neuronal regeneration, synaptic plasticity, and removal of cells during development.
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Affiliation(s)
- Huaxun Fan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Collin Barnes
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Hyojeong Hwang
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA
| | - Kai Zhang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA,Authors for correspondence: Kai Zhang, Ph.D., , 600 South Mathews Avenue, 314 B Roger Adams Laboratory,Urbana, Illinois 61801, USA, Phone: 1-217-300-0582; Jing Yang, Ph.D., , 2001 S Lincoln Ave, VMBSB3411, Urbana, Illinois 61802, USA, Phone: 1-217-333-6825
| | - Jing Yang
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA,Authors for correspondence: Kai Zhang, Ph.D., , 600 South Mathews Avenue, 314 B Roger Adams Laboratory,Urbana, Illinois 61801, USA, Phone: 1-217-300-0582; Jing Yang, Ph.D., , 2001 S Lincoln Ave, VMBSB3411, Urbana, Illinois 61802, USA, Phone: 1-217-333-6825
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Abstract
Sunlight drives phototrophic metabolism, which affects redox conditions and produces substrates for nonphototrophs. These environmental parameters fluctuate daily due to Earth’s rotation, and nonphototrophic organisms can therefore benefit from the ability to respond to, or even anticipate, such changes. Circadian rhythms, such as daily changes in body temperature, in host organisms can also affect local conditions for colonizing bacteria. Here, we investigated the effects of light/dark and temperature cycling on biofilms of the opportunistic pathogen Pseudomonas aeruginosa PA14. We grew biofilms in the presence of a respiratory indicator dye and found that enhanced dye reduction occurred in biofilm zones that formed during dark intervals and at lower temperatures. This pattern formation occurred with cycling of blue, red, or far-red light, and a screen of mutants representing potential sensory proteins identified two with defects in pattern formation, specifically under red light cycling. We also found that the physiological states of biofilm subzones formed under specific light and temperature conditions were retained during subsequent condition cycling. Light/dark and temperature cycling affected expression of genes involved in primary metabolic pathways and redox homeostasis, including those encoding electron transport chain components. Consistent with this, we found that cbb3-type oxidases contribute to dye reduction under light/dark cycling conditions. Together, our results indicate that cyclic changes in light exposure and temperature have lasting effects on redox metabolism in biofilms formed by a nonphototrophic, pathogenic bacterium.
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Li H, Liu T, Yang H. Amplifying Intermolecular Events by Streptavidin-Induced Proximity. J Am Chem Soc 2022; 144:11377-11385. [PMID: 35715211 DOI: 10.1021/jacs.2c03666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Weak interactions between biomolecules play important roles in many cellular functions. Structural and kinetic analyses of these interactions, however, have been hindered by the transient nature of such events. Here, we pointed out a general approach to overcome this obstacle─anchoring the molecular partners to streptavidin hosts─and achieved constrained proximity and stoichiometry for the sought-after molecular coupling. We elaborated this idea through a series of DNA hybridization reactions and quantitatively characterized them using single-molecule experiments. Compared to a nominally 1 μM solution, for example, the streptavidin-induced proximity (SIP) amounted to an effective molarity of ∼10-30 μM for the binding partners. There was also a significantly increased proportion of molecular association, manifested in both ensemble population and single-molecule residence time. As an application example, we showed how SIP enabled the observation and quantitative characterization of an unstable complex between Cas9-RNA and noncognate DNA substrates, interactions that had been challenging to characterize previously. Conceptually simple and implementationally robust, SIP was shown to considerably enhance the efficacy in capturing weak interactions and, as demonstrated here, could empower scientists to see the otherwise unseeable.
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Affiliation(s)
- Hao Li
- Department of Chemistry, Princeton University,, Princeton, New Jersey 08544, United States
| | - Tao Liu
- Department of Chemistry, Princeton University,, Princeton, New Jersey 08544, United States
| | - Haw Yang
- Department of Chemistry, Princeton University,, Princeton, New Jersey 08544, United States
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The nature of proton-coupled electron transfer in a blue light using flavin domain. Proc Natl Acad Sci U S A 2022; 119:e2203996119. [PMID: 35737837 PMCID: PMC9245699 DOI: 10.1073/pnas.2203996119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Proton-coupled electron transfer (PCET) is key to the activation of the blue light using flavin (BLUF) domain photoreceptors. Here, to elucidate the photocycle of the central FMN-Gln-Tyr motif in the BLUF domain of OaPAC, we eliminated the intrinsic interfering W90 in the mutant design. We integrated the stretched exponential function into the target analysis to account for the dynamic heterogeneity arising from the active-site solvation relaxation and the flexible H-bonding network as shown in the molecular dynamics simulation results, facilitating a simplified expression of the kinetics model. We find that, in both the functional wild-type (WT) and the nonfunctional Q48E and Q48A, forward PCET happens in the range of 105 ps to 344 ps, with a kinetic isotope effect (KIE) measured to be ∼1.8 to 2.4, suggesting that the nature of the forward PCET is concerted. Remarkably, only WT proceeds with an ultrafast reverse PCET process (31 ps, KIE = 4.0), characterized by an inverted kinetics of the intermediate FMNH˙. Our results reveal that the reverse PCET is driven by proton transfer via an intervening imidic Gln.
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12
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Crossman SH, Janovjak H. Light-activated receptor tyrosine kinases: Designs and applications. Curr Opin Pharmacol 2022; 63:102197. [PMID: 35245796 DOI: 10.1016/j.coph.2022.102197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 11/03/2022]
Abstract
Receptor tyrosine kinases (RTKs) are a large and essential membrane receptor family. The molecular mechanisms and physiological consequences of RTK activation depend on, for example, ligand identity, subcellular localization, and developmental or disease stage. In the past few years, genetically-encoded light-activated RTKs (Opto-RTKs) have been developed to dissect these complexities by providing reversible and spatio-temporal control over cell signaling. These methods have very recently matured to include highly-sensitive multi-color actuators. The new ability to regulate RTK activity with high precision has been recently harnessed to gain mechanistic insights in subcellular, tissue, and animal models. Because of their sophisticated engineering, Opto-RTKs may only mirror some aspects of natural activation mechanisms but nevertheless offer unique opportunities to study RTK signaling and physiology.
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Affiliation(s)
- Samuel H Crossman
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, 15 Innovation Walk, Clayton, Victoria 3800, Australia; European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, 15 Innovation Walk, Clayton, Victoria 3800, Australia
| | - Harald Janovjak
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, 15 Innovation Walk, Clayton, Victoria 3800, Australia; European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, 15 Innovation Walk, Clayton, Victoria 3800, Australia; Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Sturt Road, Bedford Park, South Australia 5042, Australia.
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Advances in Ophthalmic Optogenetics: Approaches and Applications. Biomolecules 2022; 12:biom12020269. [PMID: 35204770 PMCID: PMC8961521 DOI: 10.3390/biom12020269] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 02/04/2023] Open
Abstract
Recent advances in optogenetics hold promise for vision restoration in degenerative eye diseases. Optogenetics refers to techniques that use light to control the cellular activity of targeted cells. Although optogenetics is a relatively new technology, multiple therapeutic options are already being explored in pre-clinical and phase I/II clinical trials with the aim of developing novel, safe, and effective treatments for major blinding eye diseases, such as glaucoma and retinitis pigmentosa. Optogenetic approaches to visual restoration are primarily aimed at replacing lost or dysfunctional photoreceptors by inserting light-sensitive proteins into downstream retinal neurons that have no intrinsic light sensitivity. Such approaches are attractive because they are agnostic to the genetic causes of retinal degeneration, which raises hopes that all forms of retinal dystrophic and degenerative diseases could become treatable. Optogenetic strategies can also have a far-reaching impact on translational research by serving as important tools to study the pathogenesis of retinal degeneration and to identify clinically relevant therapeutic targets. For example, the CRY-CIBN optogenetic system has been recently applied to animal models of glaucoma, suggesting a potential role of OCRL in the regulation of intraocular pressure in trabecular meshwork. As optogenetic strategies are being intensely investigated, it appears crucial to consider the opportunities and challenges such therapies may offer. Here, we review the more recent promising optogenetic molecules, vectors, and applications of optogenetics for the treatment of retinal degeneration and glaucoma. We also summarize the preliminary results of ongoing clinical trials for visual restoration.
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Abstract
Light activated proteins are at the heart of photobiology and optogenetics, so there is wide interest in understanding the mechanisms coupling optical excitation to protein function. In addition, such light activated proteins provide unique insights into the real-time dynamics of protein function. Using pump-probe spectroscopy, the function of a photoactive protein can be initiated by a sub-100 fs pulse of light, allowing subsequent protein dynamics to be probed from femtoseconds to milliseconds and beyond. Among the most interesting photoactive proteins are the blue light using flavin (BLUF) domain proteins, which regulate the response to light of a wide range of bacterial and some euglenoid processes. The photosensing mechanism of BLUF domains has long been a subject of debate. In contrast to other photoactive proteins, the electronic and nuclear structure of the chromophore (flavin) is the same in dark- and light-adapted states. Thus, the driving force for photoactivity is unclear.To address this question requires real-time observation of both chromophore excited state processes and their effect on the structure and dynamics of the surrounding protein matrix. In this Account we describe how time-resolved infrared (IR) experiments, coupled with chemical biology, provide important new insights into the signaling mechanism of BLUF domains. IR measurements are sensitive to changes in both chromophore electronic structure and protein hydrogen bonding interactions. These contributions are resolved by isotope labeling of the chromophore and protein separately. Further, a degree of control over BLUF photochemistry is achieved through mutagenesis, while unnatural amino acid substitution allows us to both fine-tune the photochemistry and time resolve protein dynamics with spatial resolution.Ultrafast studies of BLUF domains reveal non-single-exponential relaxation of the flavin excited state. That relaxation leads within one nanosecond to the original flavin ground state bound in a modified hydrogen-bonding network, as seen in transient and steady-state IR spectroscopy. The change in H-bond configuration arises from formation of an unusual enol (imine) form of a critical glutamine residue. The dynamics observed, complemented by quantum mechanical calculations, suggest a unique sequential electron then double proton transfer reaction as the driving force, followed by rapid reorganization in the binding site and charge recombination. Importantly, studies of several BLUF domains reveal an unexpected diversity in their dynamics, although the underlying structure appears highly conserved. It is suggested that this diversity reflects structural dynamics in the ground state at standard temperature, leading to a distribution of structures and photochemical outcomes. Time resolved IR measurements were extended to the millisecond regime for one BLUF domain, revealing signaling state formation on the microsecond time scale. The mechanism involves reorganization of a β-sheet connected to the chromophore binding pocket via a tryptophan residue. The potential of site-specific labeling amino acids with IR labels as a tool for probing protein structural dynamics was demonstrated.In summary, time-resolved IR studies of BLUF domains (along with related studies at visible wavelengths and quantum and molecular dynamics calculations) have resolved the photoactivation mechanism and real-time dynamics of signaling state formation. These measurements provide new insights into protein structural dynamics and will be important in optimizing the potential of BLUF domains in optobiology.
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Affiliation(s)
- Andras Lukacs
- Department of Biophysics, Medical School, University of Pécs, Szigeti str 12, 7624 Pécs, Hungary
| | - Peter J. Tonge
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, New York 11794-3400, United States
| | - Stephen R. Meech
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
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15
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Abstract
Light is a ubiquitous energy source and environmental signal that broadly impacts the lifestyle of a large number of photosynthetic/nonphotosynthetic microorganisms living in the euphotic layer. However, the responses of deep-sea microbes to light are largely unknown, even though blue light is proposed to be distributed in the deep ocean. Here, we successfully cultured a novel bacterial species, named Spongiibacter nanhainus CSC3.9, from deep-sea cold seep samples by a blue light induction approach. The growth of strain CSC3.9 was obviously promoted by the illumination of blue light. We next determined BLUF (a typical blue light photoreceptor) was the most essential factor directing light sensing of strain CSC3.9 through a combined proteomic and genetic method. The function of light sensing mediated by BLUF was further confirmed by the in vitro-synthesized protein. Notably, homologs of BLUF widely existed across the marine microorganisms (containing Spongiibacter species) derived from different environments, including cold seeps. This strongly indicates that the distribution of light utilization by the nonphototrophic bacteria living in the ocean is broad and has been substantially underestimated. IMPORTANCE Extensive studies have been conducted to explore the mechanisms of light sensing and utilization by microorganisms that live in the photic zone. Strikingly, accumulated evidence shows that light is distributed in the deep biosphere. However, the existence and process of light sensing and utilization by microbes inhabiting the deep ocean have been seldom reported. In the present study, a novel bacterial strain, Spongiibacter nanhainus CSC3.9, was enriched and purified from a deep-sea cold seep sample through a blue light induction method. Combined with genomic, proteomic, genetic, and biochemical approaches, the mechanism of this novel strain sensing blue light through a BLUF-dependent pathway was detailed. Our study provides a good model to study the mechanisms of light sensing mediated by deep-sea nonphototrophic bacteria.
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16
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Kang X, Chen Z, Zhou Z, Zhou Y, Tang S, Zhang Y, Zhang T, Ding B, Zhong D. Direct Observation of Ultrafast Proton Rocking in the BLUF Domain. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Xiu‐Wen Kang
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Zijing Chen
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Zhongneng Zhou
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Yalin Zhou
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Siwei Tang
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Yifei Zhang
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Tianyi Zhang
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Bei Ding
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Dongping Zhong
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
- Department of Physics Department of Chemistry and Biochemistry and Programs of Biophysics Chemical Physics, and Biochemistry The Ohio State University Columbus OH 43210 USA
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17
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Ding B, Kang XW, Chen Z, Zhou Z, Zhou Y, Tang S, Zhang Y, Zhang T, Zhong D. Direct Observation of Ultrafast Proton Rocking in the BLUF Domain. Angew Chem Int Ed Engl 2021; 61:e202114423. [PMID: 34927328 DOI: 10.1002/anie.202114423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Indexed: 11/10/2022]
Abstract
We present direct observation of ultrafast proton rocking in the central motif of a BLUF domain protein scaffold. The mutant design has taken considerations of modulating the proton-coupled electron transfer (PCET) driving forces by replacing Tyr in the original motif with Trp, as well as of removing the interference of a competing electron transfer pathway. Using femtosecond pump-probe spectroscopy and detailed kinetics analysis, we resolved an electron-transfer-coupled Grotthuss-type forward and reversed proton rocking along the FMN-Gln-Trp proton relay chain. The rates of forward and reversed proton transfer are determined to be very close, namely 51 ps vs 52 ps. The kinetic isotope effect (KIE) constants associated with the forward and reversed proton transfer are 3.9 and 5.3, respectively. The observation of ultrafast proton rocking is not only a crucial step towards revealing the nature of proton relay in BLUF domain, but also provides a new paradigm of proton transfer in proteins for theoretical investigations.
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Affiliation(s)
- Bei Ding
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, 800 Dongchuan Road, 200240, Shanghai, CHINA
| | - Xiu-Wen Kang
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Zijing Chen
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Zhongneng Zhou
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Yalin Zhou
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Siwei Tang
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Yifei Zhang
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Tianyi Zhang
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Dongping Zhong
- The Ohio State University, Department of Chemical and Biomolecular Engineering, CHINA
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18
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Directed evolution approaches for optogenetic tool development. Biochem Soc Trans 2021; 49:2737-2748. [PMID: 34783342 DOI: 10.1042/bst20210700] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/16/2021] [Accepted: 10/21/2021] [Indexed: 12/30/2022]
Abstract
Photoswitchable proteins enable specific molecular events occurring in complex biological settings to be probed in a rapid and reversible fashion. Recent progress in the development of photoswitchable proteins as components of optogenetic tools has been greatly facilitated by directed evolution approaches in vitro, in bacteria, or in yeast. We review these developments and suggest future directions for this rapidly advancing field.
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19
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Fujisawa T, Masuda S, Takeuchi S, Tahara T. Femtosecond Time-Resolved Absorption Study of Signaling State of a BLUF Protein PixD from the Cyanobacterium Synechocystis: Hydrogen-Bond Rearrangement Completes during Forward Proton-Coupled Electron Transfer. J Phys Chem B 2021; 125:12154-12165. [PMID: 34726926 DOI: 10.1021/acs.jpcb.1c05957] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Femtosecond time-resolved absorption measurements were carried out for the dark and signaling states of a BLUF (Blue Light Using FAD) protein, PixD, from the cyanobacterium Synechocystis. When the dark state was excited, FAD semiquinone radical (FADH•) was produced from the S1 state, and FADH• led to the signaling state. On the other hand, photoexcitation of the signaling state generated FADH• and FAD anion radical (FAD•-), and they decayed back to the original signaling state. In both cases, FADH• was formed and decayed with a proton-coupled electron transfer (PCET) via the hydrogen-bond network that involves FAD, Gln50, and Tyr8, and hence the kinetics of FADH• directly reflects the hydrogen-bond structure in the FAD-binding sites. It was found that the formation rate of FADH• was significantly different between the dark and signaling states, whereas the decay rate was the same. This indicates that the hydrogen-bond network of FAD-Gln50-Tyr8 in the dark and signaling states is initially different but it becomes indistinguishable after FADH• is formed, implying that the FAD-Gln50-Tyr8 hydrogen-bond network is rearranged during the PCET to generate FADH•. The present results best agree with the model in which the Gln tautomerizes without rotation in the signaling-state formation.
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Affiliation(s)
- Tomotsumi Fujisawa
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Shinji Masuda
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Satoshi Takeuchi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
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20
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Genetic Factors Affect the Survival and Behaviors of Selected Bacteria during Antimicrobial Blue Light Treatment. Int J Mol Sci 2021; 22:ijms221910452. [PMID: 34638788 PMCID: PMC8508746 DOI: 10.3390/ijms221910452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/26/2022] Open
Abstract
Antimicrobial resistance is a global, mounting and dynamic issue that poses an immediate threat to human, animal, and environmental health. Among the alternative antimicrobial treatments proposed to reduce the external use of antibiotics is electromagnetic radiation, such as blue light. The prevailing mechanistic model is that blue light can be absorbed by endogenous porphyrins within the bacterial cell, inducing the production of reactive oxygen species, which subsequently inflict oxidative damages upon different cellular components. Nevertheless, it is unclear whether other mechanisms are involved, particularly those that can affect the efficacy of antimicrobial blue light treatments. In this review, we summarize evidence of inherent factors that may confer protection to a selected group of bacteria against blue light-induced oxidative damages or modulate the physiological characteristics of the treated bacteria, such as virulence and motility. These include descriptions of three major photoreceptors in bacteria, chemoreceptors, SOS-dependent DNA repair and non-SOS protective mechanisms. Future directions are also provided to assist with research efforts to increase the efficacy of antimicrobial blue light and to minimize the development of blue light-tolerant phenotypes.
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21
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Stierschneider A, Grünstäudl P, Colleselli K, Atzler J, Klein CT, Hundsberger H, Wiesner C. Light-Inducible Spatio-Temporal Control of TLR4 and NF-κB-Gluc Reporter in Human Pancreatic Cell Line. Int J Mol Sci 2021; 22:ijms22179232. [PMID: 34502140 PMCID: PMC8431472 DOI: 10.3390/ijms22179232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 11/18/2022] Open
Abstract
Augmented Toll-like receptor 4 (TLR4) expression was found in nearly 70% of patients with pancreatic adenocarcinoma, which is correlated with increased tumorigenesis and progression. In this study, we engineered a new light-oxygen-voltage-sensing (LOV) domain-based optogenetic cell line (opto-TLR4 PANC-1) that enables time-resolved activation of the NF-κB and extracellular-signal regulated kinases (ERK)1/2 signalling pathway upon blue light-sensitive homodimerisation of the TLR4-LOV fusion protein. Continuous stimulation with light indicated strong p65 and ERK1/2 phosphorylation even after 24 h, whereas brief light exposure peaked at 8 h and reached the ground level 24 h post-illumination. The cell line further allows a voltage-dependent TLR4 activation, which can be continuously monitored, turned on by light or off in the dark. Using this cell line, we performed different phenotypic cell-based assays with 2D and 3D cultures, with the aim of controlling cellular activity with spatial and temporal precision. Light exposure enhanced cell attachment, the formation and extension of invadopodia, and cell migration in 3D spheroid cultures, but no significant changes in proliferation or viability could be detected. We conclude that the opto-TLR4 PANC-1 cell line is an ideal tool for investigating the underlying molecular mechanisms of TLR4, thereby providing strategies for new therapeutic options.
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Affiliation(s)
- Anna Stierschneider
- Department of Medical and Pharmaceutical Biotechnology, IMC University of Applied Sciences, 3500 Krems, Austria; (A.S.); (P.G.); (K.C.); (C.T.K.); (H.H.)
| | - Petra Grünstäudl
- Department of Medical and Pharmaceutical Biotechnology, IMC University of Applied Sciences, 3500 Krems, Austria; (A.S.); (P.G.); (K.C.); (C.T.K.); (H.H.)
| | - Katrin Colleselli
- Department of Medical and Pharmaceutical Biotechnology, IMC University of Applied Sciences, 3500 Krems, Austria; (A.S.); (P.G.); (K.C.); (C.T.K.); (H.H.)
| | - Josef Atzler
- Molecular Devices, LLC, 5071 Wals-Siezenheim, Austria;
| | - Christian T. Klein
- Department of Medical and Pharmaceutical Biotechnology, IMC University of Applied Sciences, 3500 Krems, Austria; (A.S.); (P.G.); (K.C.); (C.T.K.); (H.H.)
| | - Harald Hundsberger
- Department of Medical and Pharmaceutical Biotechnology, IMC University of Applied Sciences, 3500 Krems, Austria; (A.S.); (P.G.); (K.C.); (C.T.K.); (H.H.)
| | - Christoph Wiesner
- Department of Medical and Pharmaceutical Biotechnology, IMC University of Applied Sciences, 3500 Krems, Austria; (A.S.); (P.G.); (K.C.); (C.T.K.); (H.H.)
- Correspondence:
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22
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Song Y, Wang X, Wang L, Dong Z, Fan S, Huang P, Zeng J, Cheng P. Visible-light promoted allylation of N-substituted tetrahydroisoquinoline using riboflavin tetra-acetate as photocatalyst. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.153286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Trozzi F, Wang F, Verkhivker G, Zoltowski BD, Tao P. Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE. PLoS Comput Biol 2021; 17:e1009168. [PMID: 34310591 PMCID: PMC8341706 DOI: 10.1371/journal.pcbi.1009168] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 08/05/2021] [Accepted: 06/10/2021] [Indexed: 11/19/2022] Open
Abstract
In Arabidopsis thaliana, the Light-Oxygen-Voltage (LOV) domain containing protein ZEITLUPE (ZTL) integrates light quality, intensity, and duration into regulation of the circadian clock. Recent structural and biochemical studies of ZTL indicate that the protein diverges from other members of the LOV superfamily in its allosteric mechanism, and that the divergent allosteric mechanism hinges upon conservation of two signaling residues G46 and V48 that alter dynamic motions of a Gln residue implicated in signal transduction in all LOV proteins. Here, we delineate the allosteric mechanism of ZTL via an integrated computational approach that employs atomistic simulations of wild type and allosteric variants of ZTL in the functional dark and light states, together with Markov state and supervised machine learning classification models. This approach has unveiled key factors of the ZTL allosteric mechanisms, and identified specific interactions and residues implicated in functional allosteric changes. The final results reveal atomic level insights into allosteric mechanisms of ZTL function that operate via a non-trivial combination of population-shift and dynamics-driven allosteric pathways.
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Affiliation(s)
- Francesco Trozzi
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, United States of America
| | - Feng Wang
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, United States of America
| | - Gennady Verkhivker
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Chapman University School of Pharmacy, Irvine, California, United States of America
| | - Brian D. Zoltowski
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, United States of America
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, United States of America
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24
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Chen Z, Huang S, Liu M. The review of the light parameters and mechanisms of Photobiomodulation on melanoma cells. PHOTODERMATOLOGY PHOTOIMMUNOLOGY & PHOTOMEDICINE 2021; 38:3-11. [PMID: 34181781 DOI: 10.1111/phpp.12715] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 05/27/2021] [Accepted: 06/25/2021] [Indexed: 11/30/2022]
Abstract
Photobiomodulation (PBM) uses low-intensity visible or near-infrared light to produce beneficial effects on cells or tissues, such as brain therapy, wound healing. Still there is no consistent recommendation on the parameters (dose, light mode, wavelength, irradiance) and protocols (repetition, treatment duration) for its clinical application. Herein, we summarize the current PBM parameters for the treatment of melanoma, and we also discuss the potential photoreceptors and downstream signaling mechanisms in the PBM treatment of melanoma cells. It is hypothesized that PBM may inhibit the melanoma cells by activating mitochondria, OPNs, and other receptors. Regardless of the underlying mechanisms, PBM has been shown to be beneficial in treating melanoma. Through further in-depth studies of the underlying potential mechanisms, it can strengthen the applications of PBM for the therapy of melanoma.
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Affiliation(s)
- Zeqing Chen
- Institute of Future Lighting, Academy for Engineering and Technology, Fudan University, Shanghai, China
| | - Shijie Huang
- Zhongshan Fudan Joint Innovation Center, Zhongshan City, China.,Institute for Electric Light Sources, Fudan University, Shanghai, China
| | - Muqing Liu
- Institute of Future Lighting, Academy for Engineering and Technology, Fudan University, Shanghai, China.,Zhongshan Fudan Joint Innovation Center, Zhongshan City, China.,Institute for Electric Light Sources, Fudan University, Shanghai, China
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25
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Reprogramming signal transduction through a designer receptor tyrosine kinase. Commun Biol 2021; 4:752. [PMID: 34140621 PMCID: PMC8211861 DOI: 10.1038/s42003-021-02287-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 06/01/2021] [Indexed: 11/30/2022] Open
Abstract
Controlling signal transduction with artificial designer receptors is a promising approach to realize future medicine for intractable diseases. Although several functional artificial receptors have been reported by domain engineering, more sophisticated engineering within domains has yet to be thoroughly investigated. Here we demonstrate motif-based engineering of a receptor tyrosine kinase for reprogramming signal transduction. We design a scaffold-less tyrosine kinase domain that does not recruit any signal transducers but retains its kinase function. The resultant scaffold-less tyrosine kinase domain is linked to a tyrosine motif that recruits a target signaling molecule upon its phosphorylation. The engineered tyrosine motif–kinase fusion protein is further connected to a small molecule- or light-dependent dimerizing domain that can switch on the kinase activity in response to an external stimulus. The resultant designer receptors attain specific chemical- or photo-activation of signaling molecules of interest in mammalian cells. Thus, our designer receptor tyrosine kinase proves the possibility of rationally reprogramming intracellular signal transduction on a motif basis. The motif-based receptor engineering may realize tailor-made functional receptors useful in the fields of biology and medicine. Kongkrongtong et al. present motif-based engineering of tyrosine kinase receptor for reprogramming signal transduction. Here, by swapping internal tyrosine of receptor with those that bind intracellular STAT signaling proteins, they demonstrate that specificity of this receptor can be reprogrammed with this approach.
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26
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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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27
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Duan HD, Khan SA, Miller AF. Photogeneration and reactivity of flavin anionic semiquinone in a bifurcating electron transfer flavoprotein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148415. [PMID: 33727071 DOI: 10.1016/j.bbabio.2021.148415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 02/15/2021] [Accepted: 03/10/2021] [Indexed: 02/04/2023]
Abstract
Electron transfer bifurcation allows production of a strongly reducing carrier at the expense of a weaker one, by redistributing energy among a pair of electrons. Thus, two weakly-reducing electrons from NADH are consumed to produce a strongly reducing ferredoxin or flavodoxin, paid for by reduction of an oxidizing acceptor. The prevailing mechanism calls for participation of a strongly reducing flavin semiquinone which has been difficult to observe with site-certainly in multi-flavin systems. Using blue light (450 nm) to photoexcite the flavins of bifurcating electron transfer flavoprotein (ETF), we demonstrate accumulation of anionic flavin semiquinone in excess of what is observed in equilibrium titrations, and establish its ability to reduce the low-potential electron acceptor benzyl viologen. This must occur at the bifurcating flavin because the midpoint potentials of the electron transfer (ET) flavin are not sufficiently negative. We show that bis-tris propane buffer is an effective electron donor to the flavin photoreduction, but that if the system is prepared with the ET flavin chemically reduced, so that only the bifurcating flavin is oxidized and photochemically active, flavin anionic semiquinone is formed more rapidly. Thus, excited bifurcating flavin is able to draw on an electron stored at the ET flavin. Flavin semiquinone photogenerated at the bifurcation site must therefore be accompanied by additional semiquinone formation by oxidation of the ET flavin. Consistent with the expected instability of bifurcating flavin semiquinone, it subsides immediately upon cessation of illumination. However comparison with yields of semiquinone in equilibrium titrations suggest that during continuous illumination at pH 9 a steady state population of 0.3 equivalents of bifurcating flavin semiquinone accumulates, and then undergoes further photoreduction to the hydroquinone. Although transient, the population of bifurcating flavin semiquinone explains the system's ability to conduct light-driven electron transfer from bis-tris propane to benzyl viologen, in effect trapping energy from light.
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Affiliation(s)
- H Diessel Duan
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
| | - Sharique A Khan
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
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28
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Chandrasekaran S, Schneps CM, Dunleavy R, Lin C, DeOliveira CC, Ganguly A, Crane BR. Tuning flavin environment to detect and control light-induced conformational switching in Drosophila cryptochrome. Commun Biol 2021; 4:249. [PMID: 33637846 PMCID: PMC7910608 DOI: 10.1038/s42003-021-01766-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
Light-induction of an anionic semiquinone (SQ) flavin radical in Drosophila cryptochrome (dCRY) alters the dCRY conformation to promote binding and degradation of the circadian clock protein Timeless (TIM). Specific peptide ligation with sortase A attaches a nitroxide spin-probe to the dCRY C-terminal tail (CTT) while avoiding deleterious side reactions. Pulse dipolar electron-spin resonance spectroscopy from the CTT nitroxide to the SQ shows that flavin photoreduction shifts the CTT ~1 nm and increases its motion, without causing full displacement from the protein. dCRY engineered to form the neutral SQ serves as a dark-state proxy to reveal that the CTT remains docked when the flavin ring is reduced but uncharged. Substitutions of flavin-proximal His378 promote CTT undocking in the dark or diminish undocking in the light, consistent with molecular dynamics simulations and TIM degradation activity. The His378 variants inform on recognition motifs for dCRY cellular turnover and strategies for developing optogenetic tools. Chandrasekaran et al. engineered the Drosophila circadian clock protein Cryptochrome (dCRY) to form the neutral semiquinone, which serves as a dark-state proxy. They find that the C-terminal tail of dCRY remains docked when the flavin ring is reduced but uncharged. dCRY His378 variants provide insights into the recognition motifs for dCRY turnover and strategies for optogenetic tools.
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Affiliation(s)
| | - Connor M Schneps
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Robert Dunleavy
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Changfan Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | | | - Abir Ganguly
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
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29
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Einholz C, Nohr D, Rodriguez R, Topitsch A, Kern M, Goldmann J, Chileshe E, Okasha M, Weber S, Schleicher E. pH-dependence of signaling-state formation in Drosophila cryptochrome. Arch Biochem Biophys 2021; 700:108787. [PMID: 33545100 DOI: 10.1016/j.abb.2021.108787] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 11/30/2022]
Abstract
Cryptochromes, FAD-dependent blue light photoreceptors, undergo a series of electron transfer reactions after light excitation. Time-resolved optical spectroscopy was employed to investigate the pH dependence of all light-dependent reactions in the cryptochrome from fruit flies. Signal state formation experiments on a time scale of seconds were found to be strongly pH dependent, and formation of both anionic and neutral FAD radicals could be detected, with reaction rates increasing by a factor of ~2.5 from basic to neutral pH values. Additionally, the influence of the amino acid His378 was investigated in further detail: Two protein variants, DmCry H378A and H378Q, showed significantly reduced rate constants for signal state formation, which again differed at neutral and alkaline pH values. Hence, His378 was identified as an amino acid responsible for the pronounced pH dependence; however, this amino acid can be excluded as a proton donor for the protonation of the anionic FAD radical. Other conserved amino acids appear to alter the overall polarity of the binding pocket and thus to be responsible for the pronounced pH dependence. Furthermore, the influence of pH and other experimental parameters, such as temperature, glycerol or ferricyanide concentrations, on the intermediately formed FAD-tryptophan radical pair was explored, which deprotonates on a microsecond time scale with a clear pH dependence, and subsequently recombines within milliseconds. Surprisingly, the latter reaction showed no pH dependence; potential reasons are discussed. All results are reviewed in terms of the photoreceptor and potential magnetoreceptor functions of Drosophila cryptochrome.
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Affiliation(s)
- Christopher Einholz
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Daniel Nohr
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Ryan Rodriguez
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Annika Topitsch
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Maria Kern
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Jacqueline Goldmann
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Emma Chileshe
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Moustafa Okasha
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany.
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30
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Pudasaini A, Green R, Song YH, Blumenfeld A, Karki N, Imaizumi T, Zoltowski BD. Steric and Electronic Interactions at Gln154 in ZEITLUPE Induce Reorganization of the LOV Domain Dimer Interface. Biochemistry 2021; 60:95-103. [PMID: 33337855 PMCID: PMC8211391 DOI: 10.1021/acs.biochem.0c00819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Plants measure light quality, intensity, and duration to coordinate growth and development with daily and seasonal changes in environmental conditions; however, the molecular details linking photochemistry to signal transduction remain incomplete. Two closely related light, oxygen, or voltage (LOV) domain-containing photoreceptor proteins, ZEITLUPE (ZTL) and FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1), divergently regulate the protein stability of circadian clock and photoperiodic flowering components to mediate daily and seasonal development. Using structural approaches, we identified that mutations at the Gly46 position led to global rearrangements of the ZTL dimer interface in the isolated ZTL-LOV domain. Specifically, G46S and G46A variants induce a 180° rotation about the ZTL-LOV dimer interface that is coupled to ordering of N- and C-terminal signaling elements. These conformational changes hinge upon rotation of a C-terminal Gln residue (Gln154) analogous to that present in light-state structures of ZTL. In contrast to other LOV proteins, a Q154L variant retains light-state interactions with GIGANTEA (GI), thereby indicating N5 protonation is not required for ZTL signaling. The results presented herein confirm a divergent signaling mechanism within ZTL, whereby steric and electronic effects following adduct formation can be sufficient for signal propagation in LOV proteins containing a Gly residue at position 46. Examination of bacterial LOV structures with Gly residues at the equivalent position suggests that mechanisms of signal transduction in LOV proteins may be fluid across the LOV protein family.
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Affiliation(s)
- Ashutosh Pudasaini
- Department of Chemistry, Southern Methodist University, Dallas, TX 75275, USA Center for Drug Discovery, Design and Delivery, Southern Methodist University
| | - Robert Green
- Department of Chemistry, Southern Methodist University, Dallas, TX 75275, USA Center for Drug Discovery, Design and Delivery, Southern Methodist University
| | - Young Hun Song
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
| | - Abby Blumenfeld
- Department of Chemistry, Southern Methodist University, Dallas, TX 75275, USA Center for Drug Discovery, Design and Delivery, Southern Methodist University
| | - Nischal Karki
- Department of Chemistry, Southern Methodist University, Dallas, TX 75275, USA Center for Drug Discovery, Design and Delivery, Southern Methodist University
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, WA, 98195-1800, USA
| | - Brian D. Zoltowski
- Department of Chemistry, Southern Methodist University, Dallas, TX 75275, USA Center for Drug Discovery, Design and Delivery, Southern Methodist University,corresponding author: Brian D. Zoltowski, Associate Professor, Department of Chemistry, Southern Methodist University, Dallas, TX 75275-0314, t. 214-768-2640, f. 214-768-4089,
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31
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Deb A, Grewal RK, Roy S, Mitra D. Residue interaction dynamics in
Vaucheria
aureochrome1 light‐oxygen‐voltage: Bridging theory and experiments. Proteins 2020; 88:1660-1674. [DOI: 10.1002/prot.25984] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/04/2020] [Accepted: 07/12/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Anwesha Deb
- Department of Life Sciences Presidency University Kolkata India
| | | | - Soumen Roy
- Department of Physics Bose Institute Kolkata India
| | - Devrani Mitra
- Department of Life Sciences Presidency University Kolkata India
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32
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Chen H, Li K, Cai Y, Wang P, Gong W, Wu LF, Song T. Light regulation of resistance to oxidative damage and magnetic crystal biogenesis in Magnetospirillum magneticum mediated by a Cys-less LOV-like protein. Appl Microbiol Biotechnol 2020; 104:7927-7941. [PMID: 32780289 DOI: 10.1007/s00253-020-10807-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/01/2020] [Accepted: 08/02/2020] [Indexed: 12/20/2022]
Abstract
Light-oxygen-voltage (LOV) proteins are ubiquitous photoreceptors that can interact with other regulatory proteins and then mediate their activities, which results in cellular adaptation and subsequent physiological changes. Upon blue-light irradiation, a conserved cysteine (Cys) residue in LOV covalently binds to flavin to form a flavin-Cys adduct, which triggers a subsequent cascade of signal transduction and reactions. We found a group of natural Cys-less LOV-like proteins in magnetotactic bacteria (MTB) and investigated its physiological functions by conducting research on one of these unusual LOV-like proteins, Amb2291, in Magnetospirillum magneticum. In-frame deletion of amb2291 or site-directive substitution of alanine-399 for Cys mutants impaired the protective responses against hydrogen peroxide, thereby causing stress and growth impairment. Consequently, gene expression and magnetosome formation were affected, which led to high sensitivity to oxidative damage and defective phototactic behaviour. The purified wild-type and A399C-mutated LOV-like proteins had similar LOV blue-light response spectra, but Amb2291A399C exhibited a faster reaction to blue light. We especially showed that LOV-like protein Amb2291 plays a role in magnetosome synthesis and resistance to oxidative stress of AMB-1 when this bacterium was exposed to red light and hydrogen peroxide. This finding expands our knowledge of the physiological function of this widely distributed group of photoreceptors and deepens our understanding of the photoresponse of MTB. KEY POINTS: • We found a group of Cys-less light-oxygen-voltage (LOV) photoreceptors in magnetotactic bacteria, which prompted us to study the light-response and biological roles of these proteins in these non-photosynthetic bacteria. • The Cys-less LOV-like protein participates in the light-regulated signalling pathway and improves resistance to oxidative damage and magnetic crystal biogenesis in Magnetospirillum magneticum. • This result will contribute to our understanding of the structural and functional diversity of the LOV-like photoreceptor and help us understand the complexity of light-regulated model organisms.
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Affiliation(s)
- Haitao Chen
- Beijing Key Laboratory of Biological Electromagnetism, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-CAS, Beijing, 100190, China
| | - Kefeng Li
- Beijing Key Laboratory of Biological Electromagnetism, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing, 100190, China.,Shandong Sport University, Jinan, 250102, China
| | - Yao Cai
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Pingping Wang
- Beijing Key Laboratory of Biological Electromagnetism, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing, 100190, China.,France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-CAS, Beijing, 100190, China
| | - Weimin Gong
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Long-Fei Wu
- France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-CAS, Beijing, 100190, China. .,Aix Marseille University, CNRS, LCB, 13402, Marseille, France.
| | - Tao Song
- Beijing Key Laboratory of Biological Electromagnetism, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing, 100190, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-CAS, Beijing, 100190, China.
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33
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Light-Mediated Decreases in Cyclic di-GMP Levels Inhibit Structure Formation in Pseudomonas aeruginosa Biofilms. J Bacteriol 2020; 202:JB.00117-20. [PMID: 32366589 DOI: 10.1128/jb.00117-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/28/2020] [Indexed: 12/22/2022] Open
Abstract
Light is known to trigger regulatory responses in diverse organisms, including slime molds, animals, plants, and phototrophic bacteria. However, light-dependent processes in nonphototrophic bacteria, and those of pathogens in particular, have received comparatively little research attention. In this study, we examined the impact of light on multicellular development in Pseudomonas aeruginosa, a leading cause of biofilm-based bacterial infections. We grew P. aeruginosa strain PA14 in a colony morphology assay and found that growth under prolonged exposure to low-intensity blue light inhibited biofilm matrix production and thereby the formation of vertical biofilm structures (i.e., "wrinkles"). Light-dependent inhibition of biofilm wrinkling was correlated with low levels of cyclic di-GMP (c-di-GMP), consistent with the role of this signal in stimulating matrix production. A screen of enzymes with the potential to catalyze c-di-GMP synthesis or degradation identified c-di-GMP phosphodiesterases that contribute to light-dependent inhibition of biofilm wrinkling. One of these, RmcA, was previously characterized by our group for its role in mediating the effect of redox-active P. aeruginosa metabolites called phenazines on biofilm wrinkle formation. Our results suggest that an RmcA sensory domain that is predicted to bind a flavin cofactor is involved in light-dependent inhibition of wrinkling. Together, these findings indicate that P. aeruginosa integrates information about light exposure and redox state in its regulation of biofilm development.IMPORTANCE Light exposure tunes circadian rhythms, which modulate the immune response and affect susceptibility to infection in plants and animals. Though molecular responses to light are defined for model plant and animal hosts, analogous pathways that function in bacterial pathogens are understudied. We examined the response to light exposure in biofilms (matrix-encased multicellular assemblages) of the nonphotosynthetic bacterium Pseudomonas aeruginosa We found that light at intensities that are not harmful to human cells inhibited biofilm maturation via effects on cellular signals. Because biofilm formation is a critical factor in many types of P. aeruginosa infections, including burn wound infections that may be exposed to light, these effects could be relevant for pathogenicity.
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34
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Brosi R, Illarionov B, Heidinger L, Kim RR, Fischer M, Weber S, Bacher A, Bittl R, Schleicher E. Coupled Methyl Group Rotation in FMN Radicals Revealed by Selective Deuterium Labeling. J Phys Chem B 2020; 124:1678-1690. [PMID: 32011886 DOI: 10.1021/acs.jpcb.9b11331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Flavin semiquinones are common intermediate redox states in flavoproteins, and thus, knowledge of their electronic structure is essential for fully understanding their chemistry and chemical versatility. In this contribution, we use a combination of high-field electron nuclear double resonance spectroscopy and selective deuterium labeling of flavin mononucleotide (FMN) with subsequent incorporation as cofactor into a variant Avena sativa LOV domain to extract missing traits of the electronic structure of a protein-bound FMN radical. From these experiments, precise values of small proton hyperfine and deuterium nuclear quadrupole couplings could be extracted. Specifically, isotropic hyperfine couplings of -3.34, -0.11, and +0.91 MHz were obtained for the protons H(6), H(9), and H(7α), respectively. These values are discussed in the light of specific protein-cofactor interactions. Furthermore, the temperature behavior of the H(7α) methyl-group rotation elicited by its energy landscape was analyzed in greater detail. Pronounced interplay between the two methyl groups at C(7) and C(8) of FMN could be revealed. Most strikingly, this rotational behavior could be modulated by selective deuterium editing.
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Affiliation(s)
- Richard Brosi
- Fachbereich Physik, Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Boris Illarionov
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Lorenz Heidinger
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Ryu-Ryun Kim
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Adelbert Bacher
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany.,Fakultät für Chemie, Technische Universität München, Lichtenbergstr. 4, 80247 Garching, Germany
| | - Robert Bittl
- Fachbereich Physik, Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
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35
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Magerl K, Dick B. Dimerization of LOV domains of Rhodobacter sphaeroides (RsLOV) studied with FRET and stopped-flow experiments. Photochem Photobiol Sci 2020; 19:159-170. [DOI: 10.1039/c9pp00424f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
LOV (light-oxygen-voltage) proteins function as light sensors in plants, fungi, and bacteria. RsLOV is unique as the light state is a monomer but the dark state is a dimer. These dimers exchange their monomer units on a time-scale of seconds.
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Affiliation(s)
- Kathrin Magerl
- Institut für Physikalische und Theoretische Chemie
- Universität Regensburg
- 93053 Regensburg
- Germany
| | - Bernhard Dick
- Institut für Physikalische und Theoretische Chemie
- Universität Regensburg
- 93053 Regensburg
- Germany
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36
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Seifert S, Ehrt C, Lückfeldt L, Lubeck M, Schramm F, Brakmann S. Optical Control of Transcription: Genetically Encoded Photoswitchable Variants of T7 RNA Polymerase. Chembiochem 2019; 20:2813-2817. [PMID: 31192518 DOI: 10.1002/cbic.201900298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Indexed: 01/07/2023]
Abstract
Light-sensing protein domains that link an exogenous light signal to the activity of an enzyme have attracted much attention for the engineering of new regulatory mechanisms into proteins and for studying the dynamic behavior of intracellular reactions and reaction cascades. Light-oxygen-voltage (LOV) photoreceptors are blue-light-sensing modules that have been intensely characterized for this purpose and linked to several proteins of interest. For the successful application of these tools, it is crucial to identify appropriate fusion strategies for combining sensor and enzyme domains that sustain activity and light-induced responsivity. Terminal fusion of LOV domains is the natural strategy; however, this is not transferrable to T7 RNA polymerase because both of its termini are involved in catalysis. It is shown herein that it is possible to covalently insert LOV domains into the polymerase protein, while preserving its activity and generating new light-responsive allosteric coupling.
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Affiliation(s)
- Swantje Seifert
- Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Christiane Ehrt
- Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Lena Lückfeldt
- Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Melissa Lubeck
- Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Frederik Schramm
- Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Susanne Brakmann
- Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
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37
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Hu W, Li Q, Li B, Ma K, Zhang C, Fu X. Optogenetics sheds new light on tissue engineering and regenerative medicine. Biomaterials 2019; 227:119546. [PMID: 31655444 DOI: 10.1016/j.biomaterials.2019.119546] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 10/09/2019] [Accepted: 10/14/2019] [Indexed: 01/23/2023]
Abstract
Optogenetics has demonstrated great potential in the fields of tissue engineering and regenerative medicine, from basic research to clinical applications. Spatiotemporal encoding during individual development has been widely identified and is considered a novel strategy for regeneration. A as a noninvasive method with high spatiotemporal resolution, optogenetics are suitable for this strategy. In this review, we discuss roles of dynamic signal coding in cell physiology and embryonic development. Several optogenetic systems are introduced as ideal optogenetic tools, and their features are compared. In addition, potential applications of optogenetics for tissue engineering are discussed, including light-controlled genetic engineering and regulation of signaling pathways. Furthermore, we present how emerging biomaterials and photoelectric technologies have greatly promoted the clinical application of optogenetics and inspired new concepts for optically controlled therapies. Our summation of currently available data conclusively demonstrates that optogenetic tools are a promising method for elucidating and simulating developmental processes, thus providing vast prospects for tissue engineering and regenerative medicine applications.
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Affiliation(s)
- Wenzhi Hu
- Wound Healing and Cell Biology Laboratory, Institute of Basic Medicine Science, College of Life Science, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, PR China; Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China
| | - Qiankun Li
- Wound Healing and Cell Biology Laboratory, Institute of Basic Medicine Science, College of Life Science, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, PR China; Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China
| | - Bingmin Li
- Wound Healing and Cell Biology Laboratory, Institute of Basic Medicine Science, College of Life Science, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, PR China; Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China
| | - Kui Ma
- Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China
| | - Cuiping Zhang
- Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China.
| | - Xiaobing Fu
- Wound Healing and Cell Biology Laboratory, Institute of Basic Medicine Science, College of Life Science, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, PR China; Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China.
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38
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Hall CR, Tolentino Collado J, Iuliano JN, Gil AA, Adamczyk K, Lukacs A, Greetham GM, Sazanovich I, Tonge PJ, Meech SR. Site-Specific Protein Dynamics Probed by Ultrafast Infrared Spectroscopy of a Noncanonical Amino Acid. J Phys Chem B 2019; 123:9592-9597. [DOI: 10.1021/acs.jpcb.9b09425] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - James N. Iuliano
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Agnieszka A. Gil
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Katrin Adamczyk
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Andras Lukacs
- Department of Biophysics, Medical School, University of Pecs, Szigeti ut 12, 7624 Pecs, Hungary
| | - Gregory M. Greetham
- Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Igor Sazanovich
- Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Peter J. Tonge
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Stephen R. Meech
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
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39
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Zoltowski BD, Chelliah Y, Wickramaratne A, Jarocha L, Karki N, Xu W, Mouritsen H, Hore PJ, Hibbs RE, Green CB, Takahashi JS. Chemical and structural analysis of a photoactive vertebrate cryptochrome from pigeon. Proc Natl Acad Sci U S A 2019; 116:19449-19457. [PMID: 31484780 PMCID: PMC6765304 DOI: 10.1073/pnas.1907875116] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Computational and biochemical studies implicate the blue-light sensor cryptochrome (CRY) as an endogenous light-dependent magnetosensor enabling migratory birds to navigate using the Earth's magnetic field. Validation of such a mechanism has been hampered by the absence of structures of vertebrate CRYs that have functional photochemistry. Here we present crystal structures of Columba livia (pigeon) CRY4 that reveal evolutionarily conserved modifications to a sequence of Trp residues (Trp-triad) required for CRY photoreduction. In ClCRY4, the Trp-triad chain is extended to include a fourth Trp (W369) and a Tyr (Y319) residue at the protein surface that imparts an unusually high quantum yield of photoreduction. These results are consistent with observations of night migratory behavior in animals at low light levels and could have implications for photochemical pathways allowing magnetosensing.
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Affiliation(s)
- Brian D Zoltowski
- Department of Chemistry, Southern Methodist University, Dallas, TX 75275
- Center for Drug Discovery, Design, and Delivery, Southern Methodist University, Dallas, TX 75275
| | - Yogarany Chelliah
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Anushka Wickramaratne
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Lauren Jarocha
- Department of Chemistry, University of Oxford, OX1 3QZ Oxford, United Kingdom
| | - Nischal Karki
- Department of Chemistry, Southern Methodist University, Dallas, TX 75275
- Center for Drug Discovery, Design, and Delivery, Southern Methodist University, Dallas, TX 75275
| | - Wei Xu
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Henrik Mouritsen
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, DE-26111 Oldenburg, Germany
- Research Center for Neurosensory Sciences, University of Oldenburg, DE-26111 Oldenburg, Germany
| | - Peter J Hore
- Department of Chemistry, University of Oxford, OX1 3QZ Oxford, United Kingdom
| | - Ryan E Hibbs
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Carla B Green
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390;
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
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40
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Nohr D, Weber S, Schleicher E. EPR spectroscopy on flavin radicals in flavoproteins. Methods Enzymol 2019; 620:251-275. [PMID: 31072489 DOI: 10.1016/bs.mie.2019.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Flavin semiquinone redox states are important intermediates in a broad variety of reactions catalyzed by flavoproteins. As paramagnetic states they can be favorably probed by EPR spectroscopy in all its flavors. This review summarizes recent results in the characterization of flavin radicals. On the one hand, flavin radical states, e.g., trapped as reaction intermediates, can be characterized using modern pulsed EPR methods to unravel their electronic structure and to gain information about the surrounding environment and its changes on protein action. On the other hand, short-lived intermediate flavin radical states generated, e.g., photochemically, can be followed by time-resolved EPR, which allows a direct tracking of flavin-dependent reactions with a temporal resolution reaching nanoseconds.
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Affiliation(s)
- Daniel Nohr
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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41
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Abstract
Molecular mechanisms of dark-to-light state transitions in flavoprotein photoreceptors have been the subject of intense investigation. Blue-light sensing flavoproteins fall into three general classes that share aspects of their activation processes: LOV domains, BLUF proteins, and cryptochromes. In all cases, light-induced changes in flavin redox, protonation, and bonding states result in hydrogen-bond and conformational rearrangements important for regulation of downstream targets. Physical characterization of these flavoprotein states can provide valuable insights into biological function, but clear conclusions are often challenging to draw owing to complexities of data collection and interpretation. In this chapter, we briefly review the three classes of flavoprotein photoreceptors and provide methods for their recombinant production, reconstitution with flavin cofactor, and characterization. We then relate best practices and special considerations for the application of several types of spectroscopies, redox potential measurements, and X-ray scattering experiments to photosensitive flavoproteins. The methods presented are generally accessible to most laboratories.
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Affiliation(s)
- Estella F Yee
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States
| | | | - Changfan Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States.
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42
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Garza ZCF, Born M, Hilbers PAJ, van Riel NAW, Liebmann J. Visible Blue Light Therapy: Molecular Mechanisms and Therapeutic Opportunities. Curr Med Chem 2019; 25:5564-5577. [PMID: 28748760 DOI: 10.2174/0929867324666170727112206] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/28/2017] [Accepted: 06/28/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND Visible light is absorbed by photoacceptors in pigmented and non-pigmented mammalian cells, activating signaling cascades and downstream mechanisms that lead to the modulation of cellular processes. Most studies have investigated the molecular mechanisms and therapeutic applications of UV and the red to near infrared regions of the visible spectrum. Considerably less effort has been dedicated to the blue, UV-free part of the spectrum. OBJECTIVE In this review, we discuss the current advances in the understanding of the molecular photoacceptors, signaling mechanisms, and corresponding therapeutic opportunities of blue light photoreception in non-visual mammalian cells in the context of inflammatory skin conditions. METHODS The literature was scanned for peer-reviewed articles focusing on the molecular mechanisms, cellular effects, and therapeutic applications of blue light. RESULTS At a molecular level, blue light is absorbed by flavins, porphyrins, nitrosated proteins, and opsins; inducing the generation of ROS, nitric oxide release, and the activation of G protein coupled signaling. Limited and contrasting results have been reported on the cellular effects of blue light induced signaling. Some investigations describe a regulation of proliferation and differentiation or a modulation of inflammatory parameters; others show growth inhibition and apoptosis. Regardless of the elusive underlying mechanism, clinical studies show that blue light is beneficial in the treatment of inflammatory skin conditions. CONCLUSION To strengthen the use of blue light for therapeutic purposes, further in depth studies are clearly needed with regard to its underlying molecular and cellular mechanisms, and their translation into clinical applications.
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Affiliation(s)
- Z C Félix Garza
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - M Born
- Philips GmbH, Innovative Technologies, Aachen, Germany
| | - P A J Hilbers
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - N A W van Riel
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - J Liebmann
- Philips GmbH, Innovative Technologies, Aachen, Germany
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43
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Lin L, Xie K, Beaucamp M, Job N, Penhoat M. Riboflavin as a Bioorganic Solar Fuel: Photoredox Chemistry Rationalized and Accelerated in a Miniaturized Flow Photoreactor. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201800236] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lyangya Lin
- USR 3290 MSAP, Miniaturisation pour la Synthèse l'Analyse et la Protéomique
- FR 2638, Institut Eugène-Michel ChevreulUniversité de Lille F-59000 Lille France
| | - Kaihui Xie
- USR 3290 MSAP, Miniaturisation pour la Synthèse l'Analyse et la Protéomique
- FR 2638, Institut Eugène-Michel ChevreulUniversité de Lille F-59000 Lille France
| | | | - Nathalie Job
- Department of Chemical Engineering – Nanomaterials, Catalysis, Electrochemistry (NCE) building B6a B-4000 Liège Belgium
| | - Maël Penhoat
- USR 3290 MSAP, Miniaturisation pour la Synthèse l'Analyse et la Protéomique
- FR 2638, Institut Eugène-Michel ChevreulUniversité de Lille F-59000 Lille France
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44
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Zhou H, Dong Z, Verkhivker G, Zoltowski BD, Tao P. Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis. PLoS Comput Biol 2019; 15:e1006801. [PMID: 30779735 PMCID: PMC6396943 DOI: 10.1371/journal.pcbi.1006801] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 03/01/2019] [Accepted: 01/17/2019] [Indexed: 01/16/2023] Open
Abstract
The fungal circadian clock photoreceptor Vivid (VVD) contains a photosensitive allosteric light, oxygen, voltage (LOV) domain that undergoes a large N-terminal conformational change. The mechanism by which a blue-light driven covalent bond formation leads to a global conformational change remains unclear, which hinders the further development of VVD as an optogenetic tool. We answered this question through a novel computational platform integrating Markov state models, machine learning methods, and newly developed community analysis algorithms. Applying this new integrative approach, we provided a quantitative evaluation of the contribution from the covalent bond to the protein global conformational change, and proposed an atomistic allosteric mechanism leading to the discovery of the unexpected importance of A'α/Aβ and previously overlooked Eα/Fα loops in the conformational change. This approach could be applicable to other allosteric proteins in general to provide interpretable atomistic representations of their otherwise elusive allosteric mechanisms.
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Affiliation(s)
- Hongyu Zhou
- Department of Chemistry, Center for Scientific Computation, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, United States of America
| | - Zheng Dong
- Department of Chemistry, Center for Scientific Computation, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, United States of America
| | - Gennady Verkhivker
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Chapman University School of Pharmacy, Irvine, California, United States of America
| | - Brian D. Zoltowski
- Department of Chemistry, Center for Scientific Computation, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, United States of America
| | - Peng Tao
- Department of Chemistry, Center for Scientific Computation, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, United States of America
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45
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Nazarenko VV, Remeeva A, Yudenko A, Kovalev K, Dubenko A, Goncharov IM, Kuzmichev P, Rogachev AV, Buslaev P, Borshchevskiy V, Mishin A, Dhoke GV, Schwaneberg U, Davari MD, Jaeger KE, Krauss U, Gordeliy V, Gushchin I. A thermostable flavin-based fluorescent protein from Chloroflexus aggregans: a framework for ultra-high resolution structural studies. Photochem Photobiol Sci 2019; 18:1793-1805. [DOI: 10.1039/c9pp00067d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A new thermostable fluorescent protein is shown to be a promising model for ultra-high resolution structural studies of LOV domains and for application as a fluorescent reporter.
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46
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Khamo JS, Krishnamurthy VV, Chen Q, Diao J, Zhang K. Optogenetic Delineation of Receptor Tyrosine Kinase Subcircuits in PC12 Cell Differentiation. Cell Chem Biol 2018; 26:400-410.e3. [PMID: 30595532 DOI: 10.1016/j.chembiol.2018.11.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 08/13/2018] [Accepted: 11/02/2018] [Indexed: 01/19/2023]
Abstract
Nerve growth factor elicits signaling outcomes by interacting with both its high-affinity receptor, TrkA, and its low-affinity receptor, p75NTR. Although these two receptors can regulate distinct cellular outcomes, they both activate the extracellular-signal-regulated kinase pathway upon nerve growth factor stimulation. To delineate TrkA subcircuits in PC12 cell differentiation, we developed an optogenetic system whereby light was used to specifically activate TrkA signaling in the absence of nerve growth factor. By using tyrosine mutants of the optogenetic TrkA in combination with pathway-specific pharmacological inhibition, we find that Y490 and Y785 each contributes to PC12 cell differentiation through the extracellular-signal-regulated kinase pathway in an additive manner. Optogenetic activation of TrkA eliminates the confounding effect of p75NTR and other potential off-target effects of the ligand. This approach can be generalized for the mechanistic study of other receptor-mediated signaling pathways.
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Affiliation(s)
- John S Khamo
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Vishnu V Krishnamurthy
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Qixin Chen
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
| | - Kai Zhang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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47
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Tsukuno H, Ozeki K, Kobayashi I, Hisatomi O, Mino H. Flavin-Radical Formation in the Light-Oxygen-Voltage-Sensing Domain of the Photozipper Blue-light Sensor Protein. J Phys Chem B 2018; 122:8819-8823. [PMID: 30157376 DOI: 10.1021/acs.jpcb.8b05808] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Formation of the neutral flavin radical in the light-oxygen-voltage-sensing (LOV-sensing) domain of photozipper, based on VfAUREO1, was investigated by electron paramagnetic resonance spectroscopy. The flavin radical was observed in the presence of dithiothreitol by illumination of a LOV-domain mutant (C254S), in which a photoactive cysteine residue in close proximity to flavin was replaced with a serine. The radical did not form under low initial protein-concentration conditions (less than 20 μM). The flavin radicals accumulated with logistic time-dependent kinetics when the protein concentrations were higher than 30 μM. These results indicate that the radical is produced by concerted reactions involving protein interactions and that the radical is formed from the LOV dimer but not the LOV monomer. In contrast, logistic time dependencies were not observed for the sample adapted to the dark following radical formation by illumination, indicating that initialization of the proton pathway is essential for this fast sensing reaction.
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Affiliation(s)
- Hiroyuki Tsukuno
- Division of Material Science, Graduate School of Science , Nagoya University , Chikusa-ku, Furo-cho, Nagoya 464-8602 , Japan
| | - Kohei Ozeki
- Division of Material Science, Graduate School of Science , Nagoya University , Chikusa-ku, Furo-cho, Nagoya 464-8602 , Japan
| | - Itsuki Kobayashi
- Department of Earth and Space Science, Graduate School of Science , Osaka University , Osaka 560-0043 , Japan
| | - Osamu Hisatomi
- Department of Earth and Space Science, Graduate School of Science , Osaka University , Osaka 560-0043 , Japan
| | - Hiroyuki Mino
- Division of Material Science, Graduate School of Science , Nagoya University , Chikusa-ku, Furo-cho, Nagoya 464-8602 , Japan
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48
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Abstract
In nature, a multitude of mechanisms have emerged for regulating biological processes and, specifically, protein activity. Light as a natural regulatory element is of outstanding interest for studying and modulating protein activity because it can be precisely applied with regard to a site of action, instant of time, or intensity. Naturally occurring photoresponsive proteins, predominantly those containing a light-oxygen-voltage (LOV) domain, have been characterized structurally and mechanistically and also conjugated to various proteins of interest. Immediate advantages of these new photoresponsive proteins such as genetic encoding, no requirement of chemical modification, and reversibility are paid for by difficulties in predicting the envisaged activity or type and site of domain fusion. In this article, we summarize recent advances and give a survey on currently available design concepts for engineering photoswitchable proteins.
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Affiliation(s)
- Swantje Seifert
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Susanne Brakmann
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
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49
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Krishnamurthy VV, Zhang K. Chemical physics in living cells — Using light to visualize and control intracellular signal transduction. CHINESE J CHEM PHYS 2018. [DOI: 10.1063/1674-0068/31/cjcp1806152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Vishnu V. Krishnamurthy
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Kai Zhang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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50
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Abstract
Sensory photoreceptors underpin light-dependent adaptations of organismal physiology, development, and behavior in nature. Adapted for optogenetics, sensory photoreceptors become genetically encoded actuators and reporters to enable the noninvasive, spatiotemporally accurate and reversible control by light of cellular processes. Rooted in a mechanistic understanding of natural photoreceptors, artificial photoreceptors with customized light-gated function have been engineered that greatly expand the scope of optogenetics beyond the original application of light-controlled ion flow. As we survey presently, UV/blue-light-sensitive photoreceptors have particularly allowed optogenetics to transcend its initial neuroscience applications by unlocking numerous additional cellular processes and parameters for optogenetic intervention, including gene expression, DNA recombination, subcellular localization, cytoskeleton dynamics, intracellular protein stability, signal transduction cascades, apoptosis, and enzyme activity. The engineering of novel photoreceptors benefits from powerful and reusable design strategies, most importantly light-dependent protein association and (un)folding reactions. Additionally, modified versions of these same sensory photoreceptors serve as fluorescent proteins and generators of singlet oxygen, thereby further enriching the optogenetic toolkit. The available and upcoming UV/blue-light-sensitive actuators and reporters enable the detailed and quantitative interrogation of cellular signal networks and processes in increasingly more precise and illuminating manners.
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Affiliation(s)
- Aba Losi
- Department of Mathematical, Physical and Computer Sciences , University of Parma , Parco Area delle Scienze 7/A-43124 Parma , Italy
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center , New York , New York 10031 , United States.,Department of Chemistry and Biochemistry, City College of New York , New York , New York 10031 , United States.,Ph.D. Programs in Biochemistry, Chemistry, and Biology , The Graduate Center of the City University of New York , New York , New York 10016 , United States
| | - Andreas Möglich
- Lehrstuhl für Biochemie , Universität Bayreuth , 95447 Bayreuth , Germany.,Research Center for Bio-Macromolecules , Universität Bayreuth , 95447 Bayreuth , Germany.,Bayreuth Center for Biochemistry & Molecular Biology , Universität Bayreuth , 95447 Bayreuth , Germany
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