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Nam KH, Xu Y. Structural Analysis of the Large Stokes Shift Red Fluorescent Protein tKeima. Molecules 2024; 29:2579. [PMID: 38893454 PMCID: PMC11173989 DOI: 10.3390/molecules29112579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
The Keima family comprises large Stokes shift fluorescent proteins that are useful for dual-color fluorescence cross-correlation spectroscopy and multicolor imaging. The tKeima is a tetrameric large Stokes shift fluorescent protein and serves as the ancestor fluorescent protein for both dKeima and mKeima. The spectroscopic properties of tKeima have been previously reported; however, its structural basis and molecular properties have not yet been elucidated. In this study, we present the crystallographic results of the large Stokes shift fluorescent protein tKeima. The purified tKeima protein spontaneously crystallized after purification without further crystallization. The crystal structure of tKeima was determined at 3.0 Å resolution, revealing a β-barrel fold containing the Gln-Tyr-Gly chromophores mainly with cis-conformation. The tetrameric interfaces of tKeima were stabilized by numerous hydrogen bonds and salt-bridge interactions. These key residues distinguish the substituted residues in dKeima and mKeima. The key structure-based residues involved in the tetramer formation of tKeima provide insights into the generation of a new type of monomeric mKeima. This structural analysis expands our knowledge of the Keima family and provides insights into its protein engineering.
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Affiliation(s)
- Ki Hyun Nam
- College of General Education, Kookmin University, Seoul 02707, Republic of Korea
| | - Yongbin Xu
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
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2
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Wang W. Protein-Based Tools for Studying Neuromodulation. ACS Chem Biol 2024; 19:788-797. [PMID: 38581649 PMCID: PMC11129172 DOI: 10.1021/acschembio.4c00037] [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] [Indexed: 04/08/2024]
Abstract
Neuromodulators play crucial roles in regulating neuronal activity and affecting various aspects of brain functions, including learning, memory, cognitive functions, emotional states, and pain modulation. In this Account, we describe our group's efforts in designing sensors and tools for studying neuromodulation. Our lab focuses on developing new classes of integrators that can detect neuromodulators across the whole brain while leaving a mark for further imaging analysis at high spatial resolution. Our lab also designed chemical- and light-dependent protein switches for controlling peptide activity to potentially modulate the endogenous receptors of the neuromodulatory system in order to study the causal effects of selective neuronal pathways.
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Affiliation(s)
- Wenjing Wang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
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Gao Y, Ma M, Li W, Lei X. Chemoproteomics, A Broad Avenue to Target Deconvolution. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305608. [PMID: 38095542 PMCID: PMC10885659 DOI: 10.1002/advs.202305608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/29/2023] [Indexed: 12/22/2023]
Abstract
As a vital project of forward chemical genetic research, target deconvolution aims to identify the molecular targets of an active hit compound. Chemoproteomics, either with chemical probe-facilitated target enrichment or probe-free, provides a straightforward and effective approach to profile the target landscape and unravel the mechanisms of action. Canonical methods rely on chemical probes to enable target engagement, enrichment, and identification, whereas click chemistry and photoaffinity labeling techniques improve the efficiency, sensitivity, and spatial accuracy of target recognition. In comparison, recently developed probe-free methods detect protein-ligand interactions without the need to modify the ligand molecule. This review provides a comprehensive overview of different approaches and recent advancements for target identification and highlights the significance of chemoproteomics in investigating biological processes and advancing drug discovery processes.
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Affiliation(s)
- Yihui Gao
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Mingzhe Ma
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijing100871China
| | - Wenyang Li
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijing100871China
- Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijing100871China
- Institute for Cancer ResearchShenzhen Bay LaboratoryShenzhenChina
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4
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Nerella SG, Telu S, Liow JS, Jenkins MD, Zoghbi SS, Gomez JL, Michaelides M, Eldridge MAG, Richmond BJ, Innis RB, Pike VW. Synthesis and preclinical evaluation of [ 11C]uPSEM792 for PSAM 4-GlyR based chemogenetics. Sci Rep 2024; 14:1886. [PMID: 38253691 PMCID: PMC10803328 DOI: 10.1038/s41598-024-51307-0] [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: 07/03/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024] Open
Abstract
Chemogenetic tools are designed to control neuronal signaling. These tools have the potential to contribute to the understanding of neuropsychiatric disorders and to the development of new treatments. One such chemogenetic technology comprises modified Pharmacologically Selective Actuator Modules (PSAMs) paired with Pharmacologically Selective Effector Molecules (PSEMs). PSAMs are receptors with ligand-binding domains that have been modified to interact only with a specific small-molecule agonist, designated a PSEM. PSAM4 is a triple mutant PSAM derived from the α7 nicotinic receptor (α7L131G,Q139L,Y217F). Although having no constitutive activity as a ligand-gated ion channel, PSAM4 has been coupled to the serotonin 5-HT3 receptor (5-HT3R) and to the glycine receptor (GlyR). Treatment with the partner PSEM to activate PSAM4-5-HT3 or PSAM4-GlyR, causes neuronal activation or silencing, respectively. A suitably designed radioligand may enable selective visualization of the expression and location of PSAMs with positron emission tomography (PET). Here, we evaluated uPSEM792, an ultrapotent PSEM for PSAM4-GlyR, as a possible lead for PET radioligand development. We labeled uPSEM792 with the positron-emitter, carbon-11 (t1/2 = 20.4 min), in high radiochemical yield by treating a protected precursor with [11C]iodomethane followed by base deprotection. PET experiments with [11C]uPSEM792 in rodents and in a monkey transduced with PSAM4-GlyR showed low peak radioactivity uptake in brain. This low uptake was probably due to high polarity of the radioligand, as evidenced by physicochemical measurements, and to the vulnerability of the radioligand to efflux transport at the blood-brain barrier. These findings can inform the design of a more effective PSAM4 based PET radioligand, based on the uPSEM792 chemotype.
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Affiliation(s)
- Sridhar Goud Nerella
- Molecular Imaging Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Sanjay Telu
- Molecular Imaging Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA.
| | - Jeih-San Liow
- Molecular Imaging Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Madeline D Jenkins
- Molecular Imaging Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Sami S Zoghbi
- Molecular Imaging Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Juan L Gomez
- Biobehavioral Imaging and Molecular Neuropsychopharmacology Unit, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, USA
| | - Michael Michaelides
- Biobehavioral Imaging and Molecular Neuropsychopharmacology Unit, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, USA
| | - Mark A G Eldridge
- Laboratory of Neuropsychology, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Barry J Richmond
- Laboratory of Neuropsychology, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Robert B Innis
- Molecular Imaging Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Victor W Pike
- Molecular Imaging Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA.
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Finkelstein DS, Du Bois J. Trifunctional Saxitoxin Conjugates for Covalent Labeling of Voltage-Gated Sodium Channels. Chembiochem 2023; 24:e202300493. [PMID: 37746898 PMCID: PMC10863845 DOI: 10.1002/cbic.202300493] [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: 07/04/2023] [Revised: 08/24/2023] [Indexed: 09/26/2023]
Abstract
Voltage-gated sodium ion channels (NaV s) are integral membrane protein complexes responsible for electrical signal conduction in excitable cells. Methods that enable selective labeling of NaV s hold potential value for understanding how channel regulation and post-translational modification are influenced during development and in response to diseases and disorders of the nervous system. We have developed chemical reagents patterned after (+)-saxitoxin (STX) - a potent and reversible inhibitor of multiple NaV isoforms - and affixed with a reactive electrophile and either a biotin cofactor, fluorophore, or 'click' functional group for labeling wild-type channels. Our studies reveal enigmatic structural effects of the probes on the potency and efficiency of covalent protein modification. Among the compounds analyzed, a STX-maleimide-coumarin derivative is most effective at irreversibly blocking Na+ conductance when applied to recombinant NaV s and endogenous channels expressed in hippocampal neurons. Mechanistic analysis supports the conclusion that high-affinity toxin binding is a prerequisite for covalent protein modification. Results from these studies are guiding the development of next-generation tool compounds for selective modification of NaV s expressed in the plasma membranes of cells.
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Affiliation(s)
- Darren S Finkelstein
- Department of Chemistry, Stanford University, 337 Campus Dr., Stanford, CA 94305, USA
- Present address: Pliant Therapeutics, 260 Littlefield Avenue, South San Francisco, CA 94080, USA
| | - J Du Bois
- Department of Chemistry, Stanford University, 337 Campus Dr., Stanford, CA 94305, USA
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Nerella SG, Michaelides M, Minamimoto T, Innis RB, Pike VW, Eldridge MAG. PET reporter systems for the brain. Trends Neurosci 2023; 46:941-952. [PMID: 37734962 PMCID: PMC10592100 DOI: 10.1016/j.tins.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/18/2023] [Accepted: 08/23/2023] [Indexed: 09/23/2023]
Abstract
Positron emission tomography (PET) can be used as a noninvasive method to longitudinally monitor and quantify the expression of proteins in the brain in vivo. It can be used to monitor changes in biomarkers of mental health disorders, and to assess therapeutic interventions such as stem cell and molecular genetic therapies. The utility of PET monitoring depends on the availability of a radiotracer with good central nervous system (CNS) penetration and high selectivity for the target protein. This review evaluates existing methods for the visualization of reporter proteins and/or protein function using PET imaging, focusing on engineered systems, and discusses possible approaches for future success in the development of high-sensitivity and high-specificity PET reporter systems for the brain.
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Affiliation(s)
- Sridhar Goud Nerella
- Molecular Imaging Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Michael Michaelides
- Biobehavioral Imaging and Molecular Neuropsychopharmacology Unit, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD 21224, USA
| | - Takafumi Minamimoto
- Department of Functional Brain Imaging, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Robert B Innis
- Molecular Imaging Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Victor W Pike
- Molecular Imaging Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark A G Eldridge
- Laboratory of Neuropsychology, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA.
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Ojima K, Kakegawa W, Yamasaki T, Miura Y, Itoh M, Michibata Y, Kubota R, Doura T, Miura E, Nonaka H, Mizuno S, Takahashi S, Yuzaki M, Hamachi I, Kiyonaka S. Coordination chemogenetics for activation of GPCR-type glutamate receptors in brain tissue. Nat Commun 2022; 13:3167. [PMID: 35710788 PMCID: PMC9203742 DOI: 10.1038/s41467-022-30828-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/19/2022] [Indexed: 11/20/2022] Open
Abstract
Direct activation of cell-surface receptors is highly desirable for elucidating their physiological roles. A potential approach for cell-type-specific activation of a receptor subtype is chemogenetics, in which both point mutagenesis of the receptors and designed ligands are used. However, ligand-binding properties are affected in most cases. Here, we developed a chemogenetic method for direct activation of metabotropic glutamate receptor 1 (mGlu1), which plays essential roles in cerebellar functions in the brain. Our screening identified a mGlu1 mutant, mGlu1(N264H), that was activated directly by palladium complexes. A palladium complex showing low cytotoxicity successfully activated mGlu1 in mGlu1(N264H) knock-in mice, revealing that activation of endogenous mGlu1 is sufficient to evoke the critical cellular mechanism of synaptic plasticity, a basis of motor learning in the cerebellum. Moreover, cell-type-specific activation of mGlu1 was demonstrated successfully using adeno-associated viruses in mice, which shows the potential utility of this chemogenetics for clarifying the physiological roles of mGlu1 in a cell-type-specific manner. Cell-type-specific activation of receptors is desirable for elucidating their roles in tissues or animals. Here, the authors developed a chemogenetic method for direct activation of mGlu1, a GPCR-type glutamate receptor subtype, and demonstrate its use in mouse brain tissue.
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Affiliation(s)
- Kento Ojima
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan.,Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Wataru Kakegawa
- Department of Neurophysiology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Tokiwa Yamasaki
- Department of Neurophysiology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Yuta Miura
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Masayuki Itoh
- Department of Neurophysiology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Yukiko Michibata
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Tomohiro Doura
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Eriko Miura
- Department of Neurophysiology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Hiroshi Nonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center in Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, 305-8575, Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center in Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, 305-8575, Japan
| | - Michisuke Yuzaki
- Department of Neurophysiology, Keio University School of Medicine, Tokyo, 160-8582, Japan.
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan.
| | - Shigeki Kiyonaka
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan. .,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, 464-8603, Japan.
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Miura Y, Ojima K, Kiyonaka S. [Coordination chemogenetics for regulation of glutamate receptors in neuron]. Nihon Yakurigaku Zasshi 2022; 157:366-370. [PMID: 36047155 DOI: 10.1254/fpj.22047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Transmembrane receptors transmit extracellular information into cells. In many cases, protein families are composed of highly homologous subtypes, each of which has unique cellular functions. Therefore, it is highly desired for understanding the physiological roles of the receptor in tissues or animals. However, it is difficult to control the activity of receptors in a cell-type- and subtype-specific manner with high temporal resolution using traditional pharmacological or genetic engineering methods. Recently, chemogenetics has been focused on controlling the cellular signaling in a cell-type-specific manner, which allows for elucidating the function of specific cell types with high temporal resolution. However, conventional chemogenetics are not suitable for understanding the roles of each receptor. Therefore, we have developed a chemogenetic method, termed coordination chemogenetics, in which coordination chemistry and genetic engineering are combined. The coordination chemogenetics enabled artificial activation of ionotropic glutamate receptor (GluA2) and metabotropic glutamate receptor (mGlu1). A palladium (Pd) complex successfully activated mGlu1 in mGlu1(N264H) knock-in mice, demonstrating that endogenous mGlu1 activation is sufficient to evoke a key cellular mechanism of synaptic plasticity that underlies motor learning in the cerebellum. We also expanded the coordination chemogenetics for orthogonal activation of mGlu1 activity using Cu2+, Zn2+, and Pd complexes for analyzing the individual roles of mGlu1 simultaneously. Notably, coordination chemogenetics can be expanded to apply selective inhibition of transmembrane receptors, and the dissociation is much slower than that of conventional inhibitors. Thus, coordination chemogenetics would be a unique method for controlling mGlu1 in a cell-type-specific manner.
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Affiliation(s)
- Yuta Miura
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University
| | - Kento Ojima
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University
| | - Shigeki Kiyonaka
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University
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