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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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Schroeder L, Diepold N, Gäfe S, Niemann HH, Kottke T. Coupling and regulation mechanisms of the flavin-dependent halogenase PyrH observed by infrared difference spectroscopy. J Biol Chem 2024; 300:107210. [PMID: 38519030 PMCID: PMC11021962 DOI: 10.1016/j.jbc.2024.107210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/29/2024] [Accepted: 03/15/2024] [Indexed: 03/24/2024] Open
Abstract
Flavin-dependent halogenases are central enzymes in the production of halogenated secondary metabolites in various organisms and they constitute highly promising biocatalysts for regioselective halogenation. The mechanism of these monooxygenases includes formation of hypohalous acid from a reaction of fully reduced flavin with oxygen and halide. The hypohalous acid then diffuses via a tunnel to the substrate-binding site for halogenation of tryptophan and other substrates. Oxidized flavin needs to be reduced for regeneration of the enzyme, which can be performed in vitro by a photoreduction with blue light. Here, we employed this photoreduction to study characteristic structural changes associated with the transition from oxidized to fully reduced flavin in PyrH from Streptomyces rugosporus as a model for tryptophan-5-halogenases. The effect of the presence of bromide and chloride or the absence of any halides on the UV-vis spectrum of the enzyme demonstrated a halide-dependent structure of the flavin-binding pocket. Light-induced FTIR difference spectroscopy was applied and the signals assigned by selective isotope labeling of the protein moiety. The identified structural changes in α-helix and β-sheet elements were strongly dependent on the presence of bromide, chloride, the substrate tryptophan, and the product 5-chloro-tryptophan, respectively. We identified a clear allosteric coupling in solution at ambient conditions between cofactor-binding site and substrate-binding site that is active in both directions, despite their separation by a tunnel. We suggest that this coupling constitutes a fine-tuned mechanism for the promotion of the enzymatic reaction of flavin-dependent halogenases in dependence of halide and substrate availability.
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Affiliation(s)
- Lea Schroeder
- Biophysical Chemistry and Diagnostics, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Niklas Diepold
- Biophysical Chemistry and Diagnostics, Department of Chemistry, Bielefeld University, Bielefeld, Germany; Biophysical Chemistry and Diagnostics, Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Simon Gäfe
- Biophysical Chemistry and Diagnostics, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Hartmut H Niemann
- Structural Biochemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Tilman Kottke
- Biophysical Chemistry and Diagnostics, Department of Chemistry, Bielefeld University, Bielefeld, Germany; Biophysical Chemistry and Diagnostics, Medical School OWL, Bielefeld University, Bielefeld, Germany.
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3
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Arinkin V, Granzin J, Jaeger KE, Willbold D, Krauss U, Batra-Safferling R. Conserved Signal Transduction Mechanisms and Dark Recovery Kinetic Tuning in the Pseudomonadaceae Short Light, Oxygen, Voltage (LOV) Protein Family. J Mol Biol 2024; 436:168458. [PMID: 38280482 DOI: 10.1016/j.jmb.2024.168458] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 01/21/2024] [Accepted: 01/23/2024] [Indexed: 01/29/2024]
Abstract
Light-Oxygen-Voltage (LOV) flavoproteins transduce a light signal into variable signaling outputs via a structural rearrangement in the sensory core domain, which is then relayed to fused effector domains via α-helical linker elements. Short LOV proteins from Pseudomonadaceae consist of a LOV sensory core and N- and C-terminal α-helices of variable length, providing a simple model system to study the molecular mechanism of allosteric activation. Here we report the crystal structures of two LOV proteins from Pseudomonas fluorescens - SBW25-LOV in the fully light-adapted state and Pf5-LOV in the dark-state. In a comparative analysis of the Pseudomonadaceae short LOVs, the structures demonstrate light-induced rotation of the core domains and splaying of the proximal A'α and Jα helices in the N and C-termini, highlighting evidence for a conserved signal transduction mechanism. Another distinguishing feature of the Pseudomonadaceae short LOV protein family is their highly variable dark recovery, ranging from seconds to days. Understanding this variability is crucial for tuning the signaling behavior of LOV-based optogenetic tools. At 37 °C, SBW25-LOV and Pf5-LOV exhibit adduct state lifetimes of 1470 min and 3.6 min, respectively. To investigate this remarkable difference in dark recovery rates, we targeted three residues lining the solvent channel entrance to the chromophore pocket where we introduced mutations by exchanging the non-conserved amino acids from SBW25-LOV into Pf5-LOV and vice versa. Dark recovery kinetics of the resulting mutants, as well as MD simulations and solvent cavity calculations on the crystal structures suggest a correlation between solvent accessibility and adduct lifetime.
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Affiliation(s)
- Vladimir Arinkin
- Institut für Biologische Informationsprozesse (IBI): Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Joachim Granzin
- Institut für Biologische Informationsprozesse (IBI): Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; Institut für Bio- und Geowissenschaften (IBG): Biotechnologie (IBG-1), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Dieter Willbold
- Institut für Biologische Informationsprozesse (IBI): Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; Institut für Bio- und Geowissenschaften (IBG): Biotechnologie (IBG-1), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Renu Batra-Safferling
- Institut für Biologische Informationsprozesse (IBI): Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany.
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4
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Ubeysinghe S, Kankanamge D, Thotamune W, Wijayaratna D, Mohan TM, Karunarathne A. Spatiotemporal Optical Control of Gαq-PLCβ Interactions. ACS Synth Biol 2024; 13:242-258. [PMID: 38092428 DOI: 10.1021/acssynbio.3c00490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2023]
Abstract
Cells experience time-varying and spatially heterogeneous chemokine signals in vivo, activating cell surface proteins including G protein-coupled receptors (GPCRs). The Gαq pathway activation by GPCRs is a major signaling axis with broad physiological and pathological significance. Compared with other Gα members, GαqGTP activates many crucial effectors, including PLCβ (Phospholipase Cβ) and Rho GEFs (Rho guanine nucleotide exchange factors). PLCβ regulates many key processes, such as hematopoiesis, synaptogenesis, and cell cycle, and is therefore implicated in terminal-debilitating diseases, including cancer, epilepsy, Huntington's Disease, and Alzheimer's Disease. However, due to a lack of genetic and pharmacological tools, examining how the dynamic regulation of PLCβ signaling controls cellular physiology has been difficult. Since activated PLCβ induces several abrupt cellular changes, including cell morphology, examining how the other pathways downstream of Gq-GPCRs contribute to the overall signaling has also been difficult. Here we show the engineering, validation, and application of a highly selective and efficient optogenetic inhibitor (Opto-dHTH) to completely disrupt GαqGTP-PLCβ interactions reversibly in user-defined cellular-subcellular regions on optical command. Using this newly gained PLCβ signaling control, our data indicate that the molecular competition between RhoGEFs and PLCβ for GαqGTP determines the potency of Gq-GPCR-governed directional cell migration.
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Affiliation(s)
- Sithurandi Ubeysinghe
- Department of Chemistry, Saint Louis University, St. Louis, Missouri 63103, United States
| | - Dinesh Kankanamge
- Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Waruna Thotamune
- Department of Chemistry, Saint Louis University, St. Louis, Missouri 63103, United States
| | - Dhanushan Wijayaratna
- Department of Chemistry, Saint Louis University, St. Louis, Missouri 63103, United States
| | - Thomas M Mohan
- Department of Chemistry, Saint Louis University, St. Louis, Missouri 63103, United States
| | - Ajith Karunarathne
- Department of Chemistry, Saint Louis University, St. Louis, Missouri 63103, United States
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5
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Ubeysinghe S, Kankanamge D, Thotamune W, Wijayaratna D, Mohan TM, Karunarathne A. Spatiotemporal optical control of Gαq-PLCβ interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552801. [PMID: 37609229 PMCID: PMC10441412 DOI: 10.1101/2023.08.10.552801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Cells experience time-varying and spatially heterogeneous chemokine signals in vivo, activating cell surface proteins, including G protein-coupled receptors (GPCRs). The Gαq pathway activation by GPCRs is a major signaling axis with a broad physiological and pathological significance. Compared to other Gα members, GαqGTP activates many crucial effectors, including PLCβ (Phospholipase Cβ) and Rho GEFs (Rho guanine nucleotide exchange factors). PLCβ regulates many key processes, such as hematopoiesis, synaptogenesis, and cell cycle, and is therefore implicated in terminal - debilitating diseases, including cancer, epilepsy, Huntington's Disease, and Alzheimer's Disease. However, due to a lack of genetic and pharmacological tools, examining how the dynamic regulation of PLCβ signaling controls cellular physiology has been difficult. Since activated PLCβ induces several abrupt cellular changes, including cell morphology, examining how the other pathways downstream of Gq-GPCRs contribute to the overall signaling has also been difficult. Here we show the engineering, validation, and application of a highly selective and efficient optogenetic inhibitor (Opto-dHTH) to completely disrupt GαqGTP-PLCβ interactions reversibly in user-defined cellular-subcellular regions on optical command. Using this newly gained PLCβ signaling control, our data indicate that the molecular competition between RhoGEFs and PLCβ for GαqGTP determines the potency of Gq-GPCR-governed directional cell migration.
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6
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Nagasawa Y, Ueda HH, Kawabata H, Murakoshi H. LOV2-based photoactivatable CaMKII and its application to single synapses: Local Optogenetics. Biophys Physicobiol 2023; 20:e200027. [PMID: 38496236 PMCID: PMC10941968 DOI: 10.2142/biophysico.bppb-v20.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/02/2023] [Indexed: 03/19/2024] Open
Abstract
Optogenetic techniques offer a high spatiotemporal resolution to manipulate cellular activity. For instance, Channelrhodopsin-2 with global light illumination is the most widely used to control neuronal activity at the cellular level. However, the cellular scale is much larger than the diffraction limit of light (<1 μm) and does not fully exploit the features of the "high spatial resolution" of optogenetics. For instance, until recently, there were no optogenetic methods to induce synaptic plasticity at the level of single synapses. To address this, we developed an optogenetic tool named photoactivatable CaMKII (paCaMKII) by fusing a light-sensitive domain (LOV2) to CaMKIIα, which is a protein abundantly expressed in neurons of the cerebrum and hippocampus and essential for synaptic plasticity. Combining photoactivatable CaMKII with two-photon excitation, we successfully activated it in single spines, inducing synaptic plasticity (long-term potentiation) in hippocampal neurons. We refer to this method as "Local Optogenetics", which involves the local activation of molecules and measurement of cellular responses. In this review, we will discuss the characteristics of LOV2, the recent development of its derivatives, and the development and application of paCaMKII.
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Affiliation(s)
- Yutaro Nagasawa
- Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
- Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Hiromi H Ueda
- Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
- Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Haruka Kawabata
- Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
- Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Hideji Murakoshi
- Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
- Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
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7
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Reynolds JA, Vishweshwaraiah YL, Chirasani VR, Pritchard JR, Dokholyan NV. An engineered N-acyltransferase-LOV2 domain fusion protein enables light-inducible allosteric control of enzymatic activity. J Biol Chem 2023; 299:103069. [PMID: 36841477 PMCID: PMC10060751 DOI: 10.1016/j.jbc.2023.103069] [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: 12/16/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023] Open
Abstract
Transferases are ubiquitous across all known life. While much work has been done to understand and describe these essential enzymes, there have been minimal efforts to exert tight and reversible control over their activity for various biotechnological applications. Here, we apply a rational, computation-guided methodology to design and test a transferase-class enzyme allosterically regulated by light-oxygen-voltage 2 sensing domain. We utilize computational techniques to determine the intrinsic allosteric networks within N-acyltransferase (Orf11/∗Dbv8) and identify potential allosteric sites on the protein's surface. We insert light-oxygen-voltage 2 sensing domain at the predicted allosteric site, exerting reversible control over enzymatic activity. We demonstrate blue-light regulation of N-acyltransferase (Orf11/∗Dbv8) function. Our study for the first time demonstrates optogenetic regulation of a transferase-class enzyme as a proof-of-concept for controllable transferase design. This successful design opens the door for many future applications in metabolic engineering and cellular programming.
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Affiliation(s)
- J A Reynolds
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania, USA
| | - Y L Vishweshwaraiah
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - V R Chirasani
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - J R Pritchard
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania, USA
| | - N V Dokholyan
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania, USA; Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania, USA; Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania, USA; Department of Chemistry, Penn State University, University Park, Pennsylvania, USA.
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8
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Kroll KL, French AR, Sosnick TR, Rock RS. LILAC: enhanced actin imaging with an optogenetic Lifeact. Nat Methods 2023; 20:214-217. [PMID: 36717692 PMCID: PMC10986358 DOI: 10.1038/s41592-022-01761-3] [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: 09/10/2021] [Accepted: 12/20/2022] [Indexed: 01/31/2023]
Abstract
Lifeact is a popular peptide-based label of actin filaments in live cells. We have designed an improved Lifeact variant, LILAC, that binds to actin in light using the LOV2 protein. Light control allows the user to modulate actin labeling, enabling image analysis that leverages modulation for an enhanced view of F-actin dynamics in cells. Furthermore, the tool reduces actin perturbations and cell sickness caused by Lifeact overexpression.
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Affiliation(s)
- Kourtney L Kroll
- Biophysical Sciences Graduate Program, The University of Chicago, Chicago, IL, USA
| | - Alexander R French
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Tobin R Sosnick
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA.
| | - Ronald S Rock
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
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9
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Ibrahim MT, Trozzi F, Tao P. Dynamics of hydrogen bonds in the secondary structures of allosteric protein Avena Sativa phototropin 1. Comput Struct Biotechnol J 2022; 20:50-64. [PMID: 34976311 PMCID: PMC8671528 DOI: 10.1016/j.csbj.2021.11.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/28/2021] [Accepted: 11/28/2021] [Indexed: 11/06/2022] Open
Abstract
The Light-Oxygen-Voltage 2 (LOV2) domain of Avena Sativa phototropin 1 (AsLOV2) protein is one of the most studied domains in the field of designing photoswitches. This is due to the several unique features in the AsLOV2, such as the monomeric structure of the protein in both light and dark states and the relatively short transition time between the two states. Despite that, not many studies focus on the effect of the secondary structures on the drastic conformational change between the light and dark states. In this study, we focus on the role of A’α helix as a key player in the transition between both states using various computational tools as: 1.5 μs molecular dynamics simulations for each configuration, Markov state model, different machine learning techniques, and community analysis. The impact of the A’α helix was studied on the atomistic level by introducing two groups of mutations, helicity enhancing mutations (T406A and T407A) and helicity disrupting mutations (L408D and R410P), as well as on the overall secondary structure by using the community analysis. Maintaining the N-terminal hydrogen bond network was found to be essential for the transition between the two states. Via in-depth hydrogen bonding and contact analysis we were able to identify key residues (Thr407 and Arg410) involved in the functional conformational switch and their impact on the overall protein dynamics. Moreover, the community analysis highlighted the significant role of the β sheets in the overall protein allosteric process.
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Affiliation(s)
- Mayar Tarek Ibrahim
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, United States
| | - Francesco Trozzi
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, United States
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, United States
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10
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Sharma S, Sanyal SK, Sushmita K, Chauhan M, Sharma A, Anirudhan G, Veetil SK, Kateriya S. Modulation of Phototropin Signalosome with Artificial Illumination Holds Great Potential in the Development of Climate-Smart Crops. Curr Genomics 2021; 22:181-213. [PMID: 34975290 PMCID: PMC8640849 DOI: 10.2174/1389202922666210412104817] [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: 09/17/2020] [Revised: 01/21/2021] [Accepted: 03/01/2021] [Indexed: 11/22/2022] Open
Abstract
Changes in environmental conditions like temperature and light critically influence crop production. To deal with these changes, plants possess various photoreceptors such as Phototropin (PHOT), Phytochrome (PHY), Cryptochrome (CRY), and UVR8 that work synergistically as sensor and stress sensing receptors to different external cues. PHOTs are capable of regulating several functions like growth and development, chloroplast relocation, thermomorphogenesis, metabolite accumulation, stomatal opening, and phototropism in plants. PHOT plays a pivotal role in overcoming the damage caused by excess light and other environmental stresses (heat, cold, and salinity) and biotic stress. The crosstalk between photoreceptors and phytohormones contributes to plant growth, seed germination, photo-protection, flowering, phototropism, and stomatal opening. Molecular genetic studies using gene targeting and synthetic biology approaches have revealed the potential role of different photoreceptor genes in the manipulation of various beneficial agronomic traits. Overexpression of PHOT2 in Fragaria ananassa leads to the increase in anthocyanin content in its leaves and fruits. Artificial illumination with blue light alone and in combination with red light influence the growth, yield, and secondary metabolite production in many plants, while in algal species, it affects growth, chlorophyll content, lipid production and also increases its bioremediation efficiency. Artificial illumination alters the morphological, developmental, and physiological characteristics of agronomic crops and algal species. This review focuses on PHOT modulated signalosome and artificial illumination-based photo-biotechnological approaches for the development of climate-smart crops.
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Affiliation(s)
- Sunita Sharma
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sibaji K. Sanyal
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Kumari Sushmita
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manisha Chauhan
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi-110025, India
| | - Amit Sharma
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi-110025, India
| | - Gireesh Anirudhan
- Integrated Science Education and Research Centre (ISERC), Institute of Science (Siksha Bhavana), Visva Bharati (A Central University), Santiniketan (PO), West Bengal, 731235, India
| | - Sindhu K. Veetil
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Suneel Kateriya
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
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11
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Ding Y, Zhao Z, Matysik J, Gärtner W, Losi A. Mapping the role of aromatic amino acids within a blue-light sensing LOV domain. Phys Chem Chem Phys 2021; 23:16767-16775. [PMID: 34319324 DOI: 10.1039/d1cp02217b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Photosensing LOV (Light, Oxygen, Voltage) domains detect and respond to UVA/Blue (BL) light by forming a covalent adduct between the flavin chromophore and a nearby cysteine, via the decay of the flavin triplet excited state. LOV domains where the reactive cysteine has been mutated are valuable fluorescent tools for microscopy and as genetically encoded photosensitisers for reactive oxygen species. Besides being convenient tools for applications, LOV domains without the reactive cysteine (naturally occurring or engineered) can still be functionally photoactivated via formation of a neutral flavin radical. Tryptophans and tyrosines are held as the main partners as potential electron donors to the flavin excited states. In this work, we explore the relevance of aromatic amino acids in determining the photophysical features of the LOV protein Mr4511 from Methylobacterium radiotolerans by introducing point mutations into the C71S variant that does not form the covalent adduct. By using an array of spectroscopic techniques we measured the fluorescence quantum yields and lifetimes, the triplet yields and lifetimes, and the efficiency of singlet oxygen (SO) formation for eleven Mr4511 variants. Insertion of Trp residues at distances between 0.6 and 1.5 nm from the flavin chromophore results in strong quenching of the flavin excited triplet state and, at the shorter distances even of the singlet excited state. The mutation F130W (ca. 0.6 nm) completely quenches the singlet excited state, preventing triplet formation: in this case, even if the cysteine is present, the photo-adduct is not formed. Tyrosines are also quenchers for the flavin excited states, although not as efficient as Trp residues, as demonstrated with their substitution with the inert phenylalanine. For one of these variants, C71S/Y116F, we found that the quantum yield of formation for singlet oxygen is 0.44 in aqueous aerobic solution, vs 0.17 for C71S. Based on our study with Mr4511 and on literature data for other LOV domains we suggest that Trp and Tyr residues too close to the flavin chromophore (at distances less than 0.9 nm) reduce the yield of photoproduct formation and that introduction of inert Phe residues in key positions can help in developing efficient, LOV-based photosensitisers.
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Affiliation(s)
- Yonghong Ding
- Institute for Analytical Chemistry, University of Leipzig, Linnéstrasse 3, 04103 Leipzig, Germany
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Photoreaction of photoactivated adenylate cyclase from cyanobacterium Microcoleus chthonoplastes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2021; 221:112252. [PMID: 34265548 DOI: 10.1016/j.jphotobiol.2021.112252] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 05/19/2021] [Accepted: 06/28/2021] [Indexed: 11/21/2022]
Abstract
The photochemical reaction of photoactivated adenylate cyclase from cyanobacterium Microcoleus chthonoplastes PCC 7420 (mPAC), which consists of a Per-Arnt-Sim (PAS), a light‑oxygene-voltage (LOV), and an adenylate cyclase (AC) domain, was investigated mainly using the time-resolved transient grating method. An absorption spectral change associated with an adduct formation between its chromophore (flavin mononucleotide) and a cysteine residue was observed with a time constant of 0.66 μs. After this reaction, a significant diffusion coefficient (D)-change was observed with a time constant of 38 ms. The determined D-value was concentration-dependent indicating a rapid equilibrium between the dimer and tetramer. Combining the results of size exclusion chromatography and CD spectroscopy, we concluded that the photoinduced D-change was mainly attributed to the equilibrium shift from the dimer rich to the tetramer rich states upon light exposure. Since the reaction rate does not depend on concentration, the rate determining step of the tetramer formation is not the collision of proteins by diffusion, but a conformation change. The roles of the PAS and AC domains as well as the N- and C-terminal flanking helices of the LOV domain (A'α- and Jα-helices) were investigated using various truncated mutants. The PAS domain was found to be a strong dimerization site and is related to efficient signal transduction. It was found that simultaneous existence of the A'α- and Jα-helices in mPAC is important for the light-induced conformation change to lead the conformation change which induces the tetramer formation. The results suggest that the angle changes of the coiled-coil structures in the A'α and Jα-helices are essential for this conformation change. The reaction scheme of mPAC is proposed.
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Andrikopoulos PC, Chaudhari AS, Liu Y, Konold PE, Kennis JTM, Schneider B, Fuertes G. QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors. Phys Chem Chem Phys 2021; 23:13934-13950. [PMID: 34142688 PMCID: PMC8246142 DOI: 10.1039/d1cp00447f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 06/04/2021] [Indexed: 11/21/2022]
Abstract
Photosensory receptors containing the flavin-binding light-oxygen-voltage (LOV) domain are modular proteins that fulfil a variety of biological functions ranging from gene expression to phototropism. The LOV photocycle is initiated by blue-light and involves a cascade of intermediate species, including an electronically excited triplet state, that leads to covalent bond formation between the flavin mononucleotide (FMN) chromophore and a nearby cysteine residue. Subsequent conformational changes in the polypeptide chain arise due to the remodelling of the hydrogen bond network in the cofactor binding pocket, whereby a conserved glutamine residue plays a key role in coupling FMN photochemistry with LOV photobiology. Although the dark-to-light transition of LOV photosensors has been previously addressed by spectroscopy and computational approaches, the mechanistic basis of the underlying reactions is still not well understood. Here we present a detailed computational study of three distinct LOV domains: EL222 from Erythrobacter litoralis, AsLOV2 from the second LOV domain of Avena sativa phototropin 1, and RsLOV from Rhodobacter sphaeroides LOV protein. Extended protein-chromophore models containing all known crucial residues involved in the initial steps (femtosecond-to-microsecond) of the photocycle were employed. Energies and rotational barriers were calculated for possible rotamers and tautomers of the critical glutamine side chain, which allowed us to postulate the most energetically favoured glutamine orientation for each LOV domain along the assumed reaction path. In turn, for each evolving species, infrared difference spectra were constructed and compared to experimental EL222 and AsLOV2 transient infrared spectra, the former from original work presented here and the latter from the literature. The good agreement between theory and experiment permitted the assignment of the majority of observed bands, notably the ∼1635 cm-1 transient of the adduct state to the carbonyl of the glutamine side chain after rotation. Moreover, both the energetic and spectroscopic approaches converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and more so for AsLOV2, while for RsLOV the glutamine keeps its initial configuration. Additionally, the computed infrared shifts of the glutamine and interacting residues could guide experimental research addressing early events of signal transduction in LOV proteins.
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Affiliation(s)
- Prokopis C Andrikopoulos
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Czechia.
| | - Aditya S Chaudhari
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Czechia.
| | - Yingliang Liu
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Czechia.
| | - Patrick E Konold
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, 1081 De Boelelaan, 1081HV Amsterdam, The Netherlands
| | - John T M Kennis
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, 1081 De Boelelaan, 1081HV Amsterdam, The Netherlands
| | - Bohdan Schneider
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Czechia.
| | - Gustavo Fuertes
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Czechia.
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Iuliano JN, Collado JT, Gil AA, Ravindran PT, Lukacs A, Shin S, Woroniecka HA, Adamczyk K, Aramini JM, Edupuganti UR, Hall CR, Greetham GM, Sazanovich IV, Clark IP, Daryaee T, Toettcher JE, French JB, Gardner KH, Simmerling CL, Meech SR, Tonge PJ. Unraveling the Mechanism of a LOV Domain Optogenetic Sensor: A Glutamine Lever Induces Unfolding of the Jα Helix. ACS Chem Biol 2020; 15:2752-2765. [PMID: 32880430 DOI: 10.1021/acschembio.0c00543] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Light-activated protein domains provide a convenient, modular, and genetically encodable sensor for optogenetics and optobiology. Although these domains have now been deployed in numerous systems, the precise mechanism of photoactivation and the accompanying structural dynamics that modulate output domain activity remain to be fully elucidated. In the C-terminal light-oxygen-voltage (LOV) domain of plant phototropins (LOV2), blue light activation leads to formation of an adduct between a conserved Cys residue and the embedded FMN chromophore, rotation of a conserved Gln (Q513), and unfolding of a helix (Jα-helix) which is coupled to the output domain. In the present work, we focus on the allosteric pathways leading to Jα helix unfolding in Avena sativa LOV2 (AsLOV2) using an interdisciplinary approach involving molecular dynamics simulations extending to 7 μs, time-resolved infrared spectroscopy, solution NMR spectroscopy, and in-cell optogenetic experiments. In the dark state, the side chain of N414 is hydrogen bonded to the backbone N-H of Q513. The simulations predict a lever-like motion of Q513 after Cys adduct formation resulting in a loss of the interaction between the side chain of N414 and the backbone C═O of Q513, and formation of a transient hydrogen bond between the Q513 and N414 side chains. The central role of N414 in signal transduction was evaluated by site-directed mutagenesis supporting a direct link between Jα helix unfolding dynamics and the cellular function of the Zdk2-AsLOV2 optogenetic construct. Through this multifaceted approach, we show that Q513 and N414 are critical mediators of protein structural dynamics, linking the ultrafast (sub-ps) excitation of the FMN chromophore to the microsecond conformational changes that result in photoreceptor activation and biological function.
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Affiliation(s)
- James N. Iuliano
- Department of Chemistry, Stony Brook University, New York, 11794, United States
| | | | - Agnieszka A. Gil
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Pavithran T. Ravindran
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Andras Lukacs
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
- Department of Biophysics, Medical School, University of Pecs, Szigeti út 12, 7624 Pecs, Hungary
| | - SeungYoun Shin
- Department of Chemistry, Stony Brook University, New York, 11794, United States
| | | | - Katrin Adamczyk
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - James M. Aramini
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, New York 10031, United States
| | - Uthama R. Edupuganti
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, New York 10031, United States
- Ph.D. Program in Biochemistry, CUNY Graduate Center, New York, New York, United States
| | - Christopher R. Hall
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Gregory M. Greetham
- Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0QX, United Kingdom
| | - Igor V. Sazanovich
- Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0QX, United Kingdom
| | - Ian P. Clark
- Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0QX, United Kingdom
| | - Taraneh Daryaee
- Department of Chemistry, Stony Brook University, New York, 11794, United States
| | - Jared E. Toettcher
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Jarrod B. French
- Department of Chemistry, Stony Brook University, New York, 11794, United States
- Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Kevin H. Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, New York 10031, United States
- Ph.D. Programs in Biochemistry, Biology, and Chemistry, CUNY Graduate Center, New York, New York, United States
- Department of Chemistry and Biochemistry, City College of New York, New York, New York, United States
| | | | - Stephen R. Meech
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Peter J. Tonge
- Department of Chemistry, Stony Brook University, New York, 11794, United States
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