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Charette M, Rosenblum C, Shade O, Deiters A. Optogenetics with Atomic Precision─A Comprehensive Review of Optical Control of Protein Function through Genetic Code Expansion. Chem Rev 2025; 125:1663-1717. [PMID: 39928721 PMCID: PMC11869211 DOI: 10.1021/acs.chemrev.4c00224] [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: 03/22/2024] [Revised: 10/03/2024] [Accepted: 10/08/2024] [Indexed: 02/12/2025]
Abstract
Conditional control of protein activity is important in order to elucidate the particular functions and interactions of proteins, their regulators, and their substrates, as well as their impact on the behavior of a cell or organism. Optical control provides a perhaps optimal means of introducing spatiotemporal control over protein function as it allows for tunable, rapid, and noninvasive activation of protein activity in its native environment. One method of introducing optical control over protein activity is through the introduction of photocaged and photoswitchable noncanonical amino acids (ncAAs) through genetic code expansion in cells and animals. Genetic incorporation of photoactive ncAAs at key residues in a protein provides a tool for optical activation, or sometimes deactivation, of protein activity. Importantly, the incorporation site can typically be rationally selected based on structural, mechanistic, or computational information. In this review, we comprehensively summarize the applications of photocaged lysine, tyrosine, cysteine, serine, histidine, glutamate, and aspartate derivatives, as well as photoswitchable phenylalanine analogues. The extensive and diverse list of proteins that have been placed under optical control demonstrates the broad applicability of this methodology.
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Affiliation(s)
- Maura Charette
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Carolyn Rosenblum
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Olivia Shade
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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Yang X, Su XC, Xuan W. Genetically Encoded Photocaged Proteinogenic and Non-Proteinogenic Amino Acids. Chembiochem 2024; 25:e202400393. [PMID: 38831474 DOI: 10.1002/cbic.202400393] [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: 04/30/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/05/2024]
Abstract
Photocaged amino acids could be genetically encoded into proteins via genetic code expansion (GCE) and constitute unique tools for innovative protein engineering. There are a number of photocaged proteinogenic amino acids that allow strategic conversion of proteins into their photocaged variants, thus enabling spatiotemporal and non-invasive regulation of protein functions using light. Meanwhile, there are a hand of photocaged non-proteinogenic amino acids that address the challenges in directly encoding certain non-canonical amino acids (ncAAs) that structurally resemble proteinogenic ones or possess highly reactive functional groups. Herein, we would like to summarize the efforts in encoding photocaged proteinogenic and non-proteinogenic amino acids, hoping to draw more attention to this fruitful and exciting scientific campaign.
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Affiliation(s)
- Xiaochen Yang
- Frontier Science Center for Synthetic Biology (Ministry of Education), School of Life Sciences, Faculty of Medicine, Tianjin University, Tianjin, 300072, China
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xun-Cheng Su
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Weimin Xuan
- Frontier Science Center for Synthetic Biology (Ministry of Education), School of Life Sciences, Faculty of Medicine, Tianjin University, Tianjin, 300072, China
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Pham PN, Zahradník J, Kolářová L, Schneider B, Fuertes G. Regulation of IL-24/IL-20R2 complex formation using photocaged tyrosines and UV light. Front Mol Biosci 2023; 10:1214235. [PMID: 37484532 PMCID: PMC10361524 DOI: 10.3389/fmolb.2023.1214235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023] Open
Abstract
Human interleukin 24 (IL-24) is a multifunctional cytokine that represents an important target for autoimmune diseases and cancer. Since the biological functions of IL-24 depend on interactions with membrane receptors, on-demand regulation of the affinity between IL-24 and its cognate partners offers exciting possibilities in basic research and may have applications in therapy. As a proof-of-concept, we developed a strategy based on recombinant soluble protein variants and genetic code expansion technology to photocontrol the binding between IL-24 and one of its receptors, IL-20R2. Screening of non-canonical ortho-nitrobenzyl-tyrosine (NBY) residues introduced at several positions in both partners was done by a combination of biophysical and cell signaling assays. We identified one position for installing NBY, tyrosine70 of IL-20R2, which results in clear impairment of heterocomplex assembly in the dark. Irradiation with 365-nm light leads to decaging and reconstitutes the native tyrosine of the receptor that can then associate with IL-24. Photocaged IL-20R2 may be useful for the spatiotemporal control of the JAK/STAT phosphorylation cascade.
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Affiliation(s)
- Phuong Ngoc Pham
- Laboratory of Biomolecular Recognition, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
- Faculty of Science, Charles University, Prague, Czechia
| | - Jiří Zahradník
- First Faculty of Medicine, BIOCEV Center, Charles University, Prague, Czechia
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Lucie Kolářová
- Laboratory of Biomolecular Recognition, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
| | - Bohdan Schneider
- Laboratory of Biomolecular Recognition, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
| | - Gustavo Fuertes
- Laboratory of Biomolecular Recognition, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
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Schulz EC, Yorke BA, Pearson AR, Mehrabi P. Best practices for time-resolved serial synchrotron crystallography. Acta Crystallogr D Struct Biol 2022; 78:14-29. [PMID: 34981758 PMCID: PMC8725164 DOI: 10.1107/s2059798321011621] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/03/2021] [Indexed: 11/10/2022] Open
Abstract
With recent developments in X-ray sources, instrumentation and data-analysis tools, time-resolved crystallographic experiments, which were originally the preserve of a few expert groups, are becoming simpler and can be carried out at more radiation sources, and are thus increasingly accessible to a growing user base. However, these experiments are just that: discrete experiments, not just `data collections'. As such, careful planning and consideration of potential pitfalls is required to enable a successful experiment. Here, some of the key factors that should be considered during the planning and execution of a time-resolved structural study are outlined, with a particular focus on synchrotron-based experiments.
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Affiliation(s)
- Eike C. Schulz
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Briony A. Yorke
- School of Chemistry and Bioscience, University of Bradford, Bradford BD7 1DP, United Kingdom
| | - Arwen R. Pearson
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Pedram Mehrabi
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
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Nwafor J, Salguero C, Welcome F, Durmus S, Glasser RN, Zimmer M, Schneider TL. Why Are Gly31, Gly33, and Gly35 Highly Conserved in All Fluorescent Proteins? Biochemistry 2021; 60:3762-3770. [PMID: 34806355 DOI: 10.1021/acs.biochem.1c00587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Green fluorescent protein (GFP)-like fluorescent proteins have been found in more than 120 species. Although the proteins have little sequence identity, Gly31, 33, and 35 are 87, 100, and 95% conserved across all species, respectively. All GFP-like proteins have a β-barrel structure composed of 11 β-sheets, and the 3 conserved glycines are located in the second β-sheet. Molecular dynamics (MD) simulations have shown that mutating one or more of the glycines to alanines most likely does not reduce chromophore formation in correctly folded immature fluorescent proteins. MD and protein characterization of alanine mutants indicate that mutation of the conserved glycines leads to misfolding. Gly31, 33, and 35 are essential to maintain the integrity of the β1-3 triad that is the last structural element to slot in place in the formation of the canonical fluorescent protein β-barrel. Glycines located in β-sheets may have a similar role in the formation of other non-GFP β-barrels.
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Affiliation(s)
- Justin Nwafor
- Chemistry Department, Connecticut College, New London, Connecticut 06320, United States
| | - Christian Salguero
- Chemistry Department, Connecticut College, New London, Connecticut 06320, United States
| | - Franceine Welcome
- Chemistry Department, Connecticut College, New London, Connecticut 06320, United States
| | - Sercan Durmus
- Chemistry Department, Connecticut College, New London, Connecticut 06320, United States
| | - Rachel N Glasser
- Chemistry Department, Connecticut College, New London, Connecticut 06320, United States
| | - Marc Zimmer
- Chemistry Department, Connecticut College, New London, Connecticut 06320, United States
| | - Tanya L Schneider
- Chemistry Department, Connecticut College, New London, Connecticut 06320, United States
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Protein Secondary Structure Affects Glycan Clustering in Native Mass Spectrometry. Life (Basel) 2021; 11:life11060554. [PMID: 34208397 PMCID: PMC8231113 DOI: 10.3390/life11060554] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 01/01/2023] Open
Abstract
Infection by the humannoroviruses (hNoV), for the vast majority of strains, requires attachment of the viral capsid to histo blood group antigens (HBGAs). The HBGA-binding pocket is formed by dimers of the protruding domain (P dimers) of the capsid protein VP1. Several studies have focused on HBGA binding to P dimers, reporting binding affinities and stoichiometries. However, nuclear magnetic resonance spectroscopy (NMR) and native mass spectrometry (MS) analyses yielded incongruent dissociation constants (KD) for the binding of HBGAs to P dimers and, in some cases, disagreed on whether glycans bind at all. We hypothesized that glycan clustering during electrospray ionization in native MS critically depends on the physicochemical properties of the protein studied. It follows that the choice of a reference protein is crucial. We analysed carbohydrate clustering using various P dimers and eight non-glycan binding proteins serving as possible references. Data from native and ion mobility MS indicate that the mass fraction of β-sheets has a strong influence on the degree of glycan clustering. Therefore, the determination of specific glycan binding affinities from native MS must be interpreted cautiously.
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