1
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Zhou Y, Tang S, Chen Z, Zhou Z, Huang J, Kang XW, Zou S, Wang B, Zhang T, Ding B, Zhong D. Origin of the multi-phasic quenching dynamics in the BLUF domains across the species. Nat Commun 2024; 15:623. [PMID: 38245518 PMCID: PMC10799861 DOI: 10.1038/s41467-023-44565-5] [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: 07/27/2023] [Accepted: 12/19/2023] [Indexed: 01/22/2024] Open
Abstract
Blue light using flavin (BLUF) photoreceptors respond to light via one of nature's smallest photo-switching domains. Upon photo-activation, the flavin cofactor in the BLUF domain exhibits multi-phasic dynamics, quenched by a proton-coupled electron transfer reaction involving the conserved Tyr and Gln. The dynamic behavior varies drastically across different species, the origin of which remains controversial. Here, we incorporate site-specific fluorinated Trp into three BLUF proteins, i.e., AppA, OaPAC and SyPixD, and characterize the percentages for the Wout, WinNHin and WinNHout conformations using 19F nuclear magnetic resonance spectroscopy. Using femtosecond spectroscopy, we identify that one key WinNHin conformation can introduce a branching one-step proton transfer in AppA and a two-step proton transfer in OaPAC and SyPixD. Correlating the flavin quenching dynamics with the active-site structural heterogeneity, we conclude that the quenching rate is determined by the percentage of WinNHin, which encodes a Tyr-Gln configuration that is not conducive to proton transfer.
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Affiliation(s)
- 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
| | - 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
| | - Jiulong Huang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiu-Wen Kang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shuhua Zou
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bingyao Wang
- 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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2
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Woloschuk RM, Reed PMM, Jaikaran ASI, Demmans KZ, Youn J, Kanelis V, Uppalapati M, Woolley GA. Structure-based design of a photoswitchable affibody scaffold. Protein Sci 2021; 30:2359-2372. [PMID: 34590762 DOI: 10.1002/pro.4196] [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: 08/17/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 12/15/2022]
Abstract
Photo-control of affinity reagents offers a general approach for high-resolution spatiotemporal control of diverse molecular processes. In an effort to develop general design principles for a photo-controlled affinity reagent, we took a structure-based approach to the design of a photoswitchable Z-domain, among the simplest of affinity reagent scaffolds. A chimera, designated Z-PYP, of photoactive yellow protein (PYP) and the Z-domain, was designed based on the concept of mutually exclusive folding. NMR analysis indicated that, in the dark, the PYP domain of the chimera was folded, and the Z-domain was unfolded. Blue light caused loss of structure in PYP and a two- to sixfold change in the apparent affinity of Z-PYP for its target as determined using size exclusion chromatography, UV-Vis based assays, and enyzme-linked immunosorbent assay (ELISA). A thermodynamic model indicated that mutations to decrease Z-domain folding energy would alter target affinity without loss of switching. This prediction was confirmed experimentally with a double alanine mutant in helix 3 of the Z-domain of the chimera (Z-PYP-AA) showing >30-fold lower dark-state binding and no loss in switching. The effect of decreased dark-state binding affinity was tested in a two-hybrid transcriptional control format and enabled pronounced light/dark differences in yeast growth in vivo. Finally, the design was transferable to the αZ-Taq affibody enabling tunable light-dependent binding both in vitro and in vivo to the Z-Taq target. This system thus provides a framework for the focused development of light switchable affibodies for a range of targets.
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Affiliation(s)
- Ryan M Woloschuk
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | | | - Anna S I Jaikaran
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Karl Z Demmans
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jeffrey Youn
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Voula Kanelis
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Maruti Uppalapati
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - G Andrew Woolley
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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3
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Lee SJ, Kim Y, Kim TW, Yang C, Thamilselvan K, Jeong H, Hyun J, Ihee H. Reversible molecular motional switch based on circular photoactive protein oligomers exhibits unexpected photo-induced contraction. CELL REPORTS. PHYSICAL SCIENCE 2021; 2:100512. [PMID: 35509376 PMCID: PMC9062587 DOI: 10.1016/j.xcrp.2021.100512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Molecular switches alterable between two stable states by environmental stimuli, such as light and temperature, offer the potential for controlling biological functions. Here, we report a circular photoswitchable protein complex made of multiple protein molecules that can rapidly and reversibly switch with significant conformational changes. The structural and photochromic properties of photoactive yellow protein (PYP) are harnessed to construct circular oligomer PYPs (coPYPs) of desired sizes. Considering the light-induced N-terminal protrusion of monomer PYP, we expected coPYPs would expand upon irradiation, but time-resolved X-ray scattering data reveal that the late intermediate has a pronounced light-induced contraction motion. This work not only provides an approach to engineering a novel protein-based molecular switch based on circular oligomers of well-known protein units but also demonstrates the importance of characterizing the structural dynamics of designed molecular switches.
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Affiliation(s)
- Sang Jin Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- These authors contributed equally
| | - Youngmin Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- These authors contributed equally
| | - Tae Wu Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Cheolhee Yang
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Kamatchi Thamilselvan
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Hyeongseop Jeong
- Center for Research Equipment, Korea Basic Science Institute (KBSI), Cheongju-si, Chungcheongbuk-do 28119, Republic of Korea
| | - Jaekyung Hyun
- Center for Research Equipment, Korea Basic Science Institute (KBSI), Cheongju-si, Chungcheongbuk-do 28119, Republic of Korea
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology (OIST), Okinawa 904-0495, Japan
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Lead contact
- Correspondence:
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4
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Woloschuk RM, Reed PMM, McDonald S, Uppalapati M, Woolley GA. Yeast Two-Hybrid Screening of Photoswitchable Protein-Protein Interaction Libraries. J Mol Biol 2020; 432:3113-3126. [PMID: 32198111 DOI: 10.1016/j.jmb.2020.03.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/04/2020] [Accepted: 03/09/2020] [Indexed: 02/08/2023]
Abstract
Although widely used in the detection and characterization of protein-protein interactions, Y2H screening has been under-used for the engineering of new optogenetic tools or the improvement of existing tools. Here we explore the feasibility of using Y2H selection and screening to evaluate libraries of photoswitchable protein-protein interactions. We targeted the interaction between circularly permuted photoactive yellow protein (cPYP) and its binding partner binder of PYP dark-state (BoPD) by mutating a set of four surface residues of cPYP that contribute to the binding interface. A library of ~10,000 variants was expressed in yeast together with BoPD in a Y2H format. An initial selection for the cPYP/BoPD interaction was performed using a range of concentrations of the cPYP chromophore. As expected, the majority (>90% of cPYP variants) no longer bound to BoPD. Replica plating was then used to evaluate the photoswitchability of the surviving clones. Photoswitchable cPYP variants with BoPD affinities equal to, or higher than, native cPYP were recovered in addition to variants with altered photocycles and binders that interacted with BoPD as apo-proteins. Y2H results reflected protein-protein interaction affinity, expression, photoswitchability, and chromophore uptake, and correlated well with results obtained both in vitro and in mammalian cells. Thus, by systematic variation of selection parameters, Y2H screens can be effectively used to generate new optogenetic tools for controlling protein-protein interactions for use in diverse settings.
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Affiliation(s)
- Ryan M Woloschuk
- Department of Chemistry, University of Toronto, 80 St. George St, Toronto, Canada, M5S 3H6
| | - P Maximilian M Reed
- Department of Chemistry, University of Toronto, 80 St. George St, Toronto, Canada, M5S 3H6
| | - Sherin McDonald
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, SK, Canada, S7N 5E5
| | - Maruti Uppalapati
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, SK, Canada, S7N 5E5
| | - G Andrew Woolley
- Department of Chemistry, University of Toronto, 80 St. George St, Toronto, Canada, M5S 3H6.
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5
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Banerjee S, Mitra D. Structural Basis of Design and Engineering for Advanced Plant Optogenetics. TRENDS IN PLANT SCIENCE 2020; 25:35-65. [PMID: 31699521 DOI: 10.1016/j.tplants.2019.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 09/12/2019] [Accepted: 10/03/2019] [Indexed: 06/10/2023]
Abstract
In optogenetics, light-sensitive proteins are specifically expressed in target cells and light is used to precisely control the activity of these proteins at high spatiotemporal resolution. Optogenetics initially used naturally occurring photoreceptors to control neural circuits, but has expanded to include carefully designed and engineered photoreceptors. Several optogenetic constructs are based on plant photoreceptors, but their application to plant systems has been limited. Here, we present perspectives on the development of plant optogenetics, considering different levels of design complexity. We discuss how general principles of light-driven signal transduction can be coupled with approaches for engineering protein folding to develop novel optogenetic tools. Finally, we explore how the use of computation, networks, circular permutation, and directed evolution could enrich optogenetics.
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Affiliation(s)
- Sudakshina Banerjee
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, India
| | - Devrani Mitra
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, India.
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6
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Ui M, Miyauchi Y, Inoue M, Murakami M, Araki Y, Wada T, Kinbara K. Development of an Engineered Photoactive Yellow Protein as a Cross‐Linking Junction for Construction of Photoresponsive Protein‐Polymer Conjugates. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mihoko Ui
- Institute of Multidisciplinary Research for Advanced MaterialsTohoku University 2-1-1, Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Yusuke Miyauchi
- Institute of Multidisciplinary Research for Advanced MaterialsTohoku University 2-1-1, Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Masataka Inoue
- School of Life Science and TechnologyTokyo Institute of Technology 4259 B58, Nagatsuta-cho, Midori-ku Yokohama 226-8501 Japan
| | - Makoto Murakami
- Institute of Multidisciplinary Research for Advanced MaterialsTohoku University 2-1-1, Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Yasuyuki Araki
- Institute of Multidisciplinary Research for Advanced MaterialsTohoku University 2-1-1, Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Takehiko Wada
- Institute of Multidisciplinary Research for Advanced MaterialsTohoku University 2-1-1, Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Kazushi Kinbara
- School of Life Science and TechnologyTokyo Institute of Technology 4259 B58, Nagatsuta-cho, Midori-ku Yokohama 226-8501 Japan
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7
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Brechun KE, Zhen D, Jaikaran A, Borisenko V, Kumauchi M, Hoff WD, Arndt KM, Woolley GA. Detection of Incorporation of p-Coumaric Acid into Photoactive Yellow Protein Variants in Vivo. Biochemistry 2019; 58:2682-2694. [DOI: 10.1021/acs.biochem.9b00279] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Katherine E. Brechun
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Potsdam, Brandenburg 14476, Germany
| | - Danlin Zhen
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Anna Jaikaran
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Vitali Borisenko
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Masato Kumauchi
- Department of Microbiology and Molecular Genetics, Oklahoma State University, 307 Life Sciences East, Stillwater, Oklahoma 74078, United States
| | - Wouter D. Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, 307 Life Sciences East, Stillwater, Oklahoma 74078, United States
| | - Katja M. Arndt
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Potsdam, Brandenburg 14476, Germany
| | - G. Andrew Woolley
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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8
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Lu H, Mazumder M, Jaikaran ASI, Kumar A, Leis EK, Xu X, Altmann M, Cochrane A, Woolley GA. A Yeast System for Discovering Optogenetic Inhibitors of Eukaryotic Translation Initiation. ACS Synth Biol 2019; 8:744-757. [PMID: 30901519 DOI: 10.1021/acssynbio.8b00386] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The precise spatiotemporal regulation of protein synthesis is essential for many complex biological processes such as memory formation, embryonic development, and tumor formation. Current methods used to study protein synthesis offer only a limited degree of spatiotemporal control. Optogenetic methods, in contrast, offer the prospect of controlling protein synthesis noninvasively within minutes and with a spatial scale as small as a single synapse. Here, we present a hybrid yeast system where growth depends on the activity of human eukaryotic initiation factor 4E (eIF4E) that is suitable for screening optogenetic designs for the down-regulation of protein synthesis. We used this system to screen a diverse initial panel of 15 constructs designed to couple a light switchable domain (PYP, RsLOV, AsLOV, Dronpa) to 4EBP2 (eukaryotic initiation factor 4E binding protein 2), a native inhibitor of translation initiation. We identified cLIPS1 (circularly permuted LOV inhibitor of protein synthesis 1), a fusion of a segment of 4EBP2 and a circularly permuted version of the LOV2 domain from Avena sativa, as a photoactivated inhibitor of translation. Adapting the screen for higher throughput, we tested small libraries of cLIPS1 variants and found cLIPS2, a construct with an improved degree of optical control. We show that these constructs can both inhibit translation in yeast harboring a human eIF4E in vivo, and bind human eIF4E in vitro in a light-dependent manner. This hybrid yeast system thus provides a convenient way for discovering optogenetic constructs that can regulate human eIF4E-dependent translation initiation in a mechanistically defined manner.
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Affiliation(s)
- Huixin Lu
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Mostafizur Mazumder
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Anna S. I. Jaikaran
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Anil Kumar
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Eric K. Leis
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Xiuling Xu
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Michael Altmann
- Institut für Biochemie und Molekulare Medizin, Universität Bern, Bühlstr. 28, CH-3012 Bern, Switzerland
| | - Alan Cochrane
- Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - G. Andrew Woolley
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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9
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Regulation of Protein Structural Changes by Incorporation of a Small-Molecule Linker. Int J Mol Sci 2018; 19:ijms19123714. [PMID: 30469528 PMCID: PMC6321067 DOI: 10.3390/ijms19123714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 11/16/2018] [Accepted: 11/19/2018] [Indexed: 12/12/2022] Open
Abstract
Proteins have the potential to serve as nanomachines with well-controlled structural movements, and artificial control of their conformational changes is highly desirable for successful applications exploiting their dynamic structural characteristics. Here, we demonstrate an experimental approach for regulating the degree of conformational change in proteins by incorporating a small-molecule linker into a well-known photosensitive protein, photoactive yellow protein (PYP), which is sensitized by blue light and undergoes a photo-induced N-terminal protrusion coupled with chromophore-isomerization-triggered conformational changes. Specifically, we introduced thiol groups into specific sites of PYP through site-directed mutagenesis and then covalently conjugated a small-molecule linker into these sites, with the expectation that the linker is likely to constrain the structural changes associated with the attached positions. To investigate the structural dynamics of PYP incorporated with the small-molecule linker (SML-PYP), we employed the combination of small-angle X-ray scattering (SAXS), transient absorption (TA) spectroscopy and experiment-restrained rigid-body molecular dynamics (MD) simulation. Our results show that SML-PYP exhibits much reduced structural changes during photo-induced signaling as compared to wild-type PYP. This demonstrates that incorporating an external molecular linker can limit photo-induced structural dynamics of the protein and may be used as a strategy for fine control of protein structural dynamics in nanomachines.
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10
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Reis JM, Xu X, McDonald S, Woloschuk RM, Jaikaran ASI, Vizeacoumar FS, Woolley GA, Uppalapati M. Discovering Selective Binders for Photoswitchable Proteins Using Phage Display. ACS Synth Biol 2018; 7:2355-2364. [PMID: 30203962 DOI: 10.1021/acssynbio.8b00123] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nature provides an array of proteins that change conformation in response to light. The discovery of a complementary array of proteins that bind only the light-state or dark-state conformation of their photoactive partner proteins would allow each light-switchable protein to be used as an optogenetic tool to control protein-protein interactions. However, as many photoactive proteins have no known binding partner, the advantages of optogenetic control-precise spatial and temporal resolution-are currently restricted to a few well-defined natural systems. In addition, the affinities and kinetics of native interactions are often suboptimal and are difficult to engineer in the absence of any structural information. We report a phage display strategy using a small scaffold protein that can be used to discover new binding partners for both light and dark states of a given light-switchable protein. We used our approach to generate binding partners that interact specifically with the light state or the dark state conformation of two light-switchable proteins: PYP, a test case for a protein with no known partners, and AsLOV2, a well-characterized protein. We show that these novel light-switchable protein-protein interactions can function in living cells to control subcellular localization processes.
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Affiliation(s)
- Jakeb M. Reis
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
| | - Xiuling Xu
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
| | - Sherin McDonald
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A2, Canada
| | - Ryan M. Woloschuk
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
| | - Anna S. I. Jaikaran
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
| | - Frederick S. Vizeacoumar
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A2, Canada
| | - G. Andrew Woolley
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
| | - Maruti Uppalapati
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A2, Canada
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11
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Tebo AG, Pimenta FM, Zoumpoulaki M, Kikuti C, Sirkia H, Plamont MA, Houdusse A, Gautier A. Circularly Permuted Fluorogenic Proteins for the Design of Modular Biosensors. ACS Chem Biol 2018; 13:2392-2397. [PMID: 30088915 DOI: 10.1021/acschembio.8b00417] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescent reporters are essential components for the design of optical biosensors that are able to image intracellular analytes in living cells. Herein, we describe the development of circularly permuted variants of Fluorescence-Activating and absorption-Shifting Tag (FAST) and demonstrate their potential as reporting module in biosensors. Circularly permutated FAST (cpFAST) variants allow one to condition the binding and activation of a fluorogenic ligand (and thus fluorescence) to analyte recognition by coupling them with analyte-binding domains. We demonstrated their use for biosensor design by generating multicolor plug-and-play fluorogenic biosensors for imaging the intracellular levels of Ca2+ in living mammalian cells in real time.
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Affiliation(s)
- Alison G. Tebo
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Frederico M. Pimenta
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Martha Zoumpoulaki
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Carlos Kikuti
- Structural Motility, Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France
| | - Helena Sirkia
- Structural Motility, Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France
| | - Marie-Aude Plamont
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Anne Houdusse
- Structural Motility, Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France
| | - Arnaud Gautier
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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12
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Kumar A, Nokhrin S, Woloschuk RM, Woolley GA. Duplication of a Single Strand in a β-Sheet Can Produce a New Switching Function in a Photosensory Protein. Biochemistry 2018; 57:4093-4104. [PMID: 29897240 DOI: 10.1021/acs.biochem.8b00445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Duplication of a single β-strand that forms part of a β-sheet in photoactive yellow protein (PYP) was found to produce two approximately isoenergetic protein conformations, in which either the first or the second copy of the duplicated β-strand participates in the β-sheet. Whereas one conformation (big-loop) is more stable at equilibrium in the dark, the other conformation (long-tail) is populated after recovery from blue light irradiation. By appending a recognition motif (E-helix) to the C-terminus of the protein, we show that β-strand duplication, and the resulting possibility of β-strand slippage, can lead to a new switchable protein-protein interaction. We suggest that β-strand duplication may be a general means of introducing two-state switching activity into protein structures.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , ON M5S 3H6 , Canada
| | - Sergiy Nokhrin
- Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , ON M5S 3H6 , Canada
| | - Ryan M Woloschuk
- Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , ON M5S 3H6 , Canada
| | - G Andrew Woolley
- Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , ON M5S 3H6 , Canada
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13
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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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14
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Strategies for the photo-control of endogenous protein activity. Curr Opin Struct Biol 2017; 45:53-58. [DOI: 10.1016/j.sbi.2016.11.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/13/2016] [Indexed: 11/21/2022]
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15
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Optogenetic Inhibitor of the Transcription Factor CREB. ACTA ACUST UNITED AC 2016; 22:1531-1539. [PMID: 26590638 DOI: 10.1016/j.chembiol.2015.09.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 09/11/2015] [Accepted: 09/24/2015] [Indexed: 01/28/2023]
Abstract
Current approaches for optogenetic control of transcription do not mimic the activity of endogenous transcription factors, which act at numerous sites in the genome in a complex interplay with other factors. Optogenetic control of dominant negative versions of endogenous transcription factors provides a mechanism for mimicking the natural regulation of gene expression. Here we describe opto-DN-CREB, a blue-light-controlled inhibitor of the transcription factor CREB created by fusing the dominant negative inhibitor A-CREB to photoactive yellow protein (PYP). A light-driven conformational change in PYP prevents coiled-coil formation between A-CREB and CREB, thereby activating CREB. Optogenetic control of CREB function was characterized in vitro, in HEK293T cells, and in neurons where blue light enabled control of expression of the CREB targets NR4A2 and c-Fos. Dominant negative inhibitors exist for numerous transcription factors; linking these to optogenetic domains offers a general approach for spatiotemporal control of native transcriptional events.
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16
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Abstract
Photoswitchable proteins are becoming increasingly common tools for manipulating cellular processes with high spatial and temporal precision. Photoactive yellow protein (PYP) is a small, water-soluble protein that undergoes a blue light induced change in conformation. It can serve as a scaffold for designing new tools to manipulate biological processes, but with respect to other protein scaffolds it presents some technical challenges. Here, we present practical information on how to overcome these, including how to synthesize the PYP chromophore, how to express and purify PYP, and how to screen for desired activity.
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Affiliation(s)
- Jakeb M Reis
- Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, Canada, M5S 3H6
| | - G Andrew Woolley
- Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, Canada, M5S 3H6.
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17
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Kumar A, Ali AM, Woolley GA. Photo-control of DNA binding by an engrailed homeodomain-photoactive yellow protein hybrid. Photochem Photobiol Sci 2015. [PMID: 26204102 DOI: 10.1039/c5pp00160a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A photo-controlled version of the engrailed homeodomain (zENG) was created by inserting the homeodomain into a surface loop of a circularly permuted version of the photoactive yellow protein (cPYP). The two proteins fold independently as judged by NMR and fluorescence denaturation measurements. In the dark, the affinity of the zENG domain for its cognate DNA is inhibited >100-fold compared to wild-type zENG. Blue-light irradiation of the hybrid protein leads to enhanced conformational dynamics of the cPYP portion and a two-fold enhancement of the DNA binding affinity of the zENG domain. These results suggest that insertion into a surface loop of cPYP can be a general approach for conferring an initial level of photo-control on a given target protein. Focussed mutation/selection strategies may then be used to enhance the degree of photo-control.
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Affiliation(s)
- A Kumar
- Dept. of Chemistry, University of Toronto, 80 St. George St., Toronto, CanadaM5S 3H6.
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18
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O'Neill PR, Gautam N. Optimizing optogenetic constructs for control over signaling and cell behaviours. Photochem Photobiol Sci 2015; 14:1578-85. [PMID: 26135203 DOI: 10.1039/c5pp00171d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Optogenetic tools have recently been developed that enable dynamic control over the activities of select signaling proteins. They provide the unique ability to rapidly turn signaling events on or off with subcellular control in living cells and organisms. This capability is leading to new insights into how the spatial and temporal coordination of signaling events governs dynamic cell behaviours such as migration and neurite outgrowth. These tools can also be used to dissect a protein's signaling functions at different organelles. Here we review the properties of photoreceptors from diverse organisms that have been leveraged to control signaling in mammalian cells. We emphasize recent engineering approaches that have been used to create optogenetic constructs with optimized spectral, kinetic, and signaling properties for controlling cell behaviours.
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Affiliation(s)
- P R O'Neill
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
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19
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Kumar A, Woolley GA. Origins of the Intermediate Spectral Form in M100 Mutants of Photoactive Yellow Protein. Photochem Photobiol 2015; 91:985-91. [PMID: 25946641 DOI: 10.1111/php.12464] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 04/26/2015] [Indexed: 12/11/2022]
Abstract
Numerous single-site mutants of photoactive yellow protein (PYP) from Halorhodospira halophila and as well as PYP homologs from other species exhibit a shoulder on the short wavelength side of the absorbance maximum in their dark-adapted states. The structural basis for the occurrence of this shoulder, called the "intermediate spectral form," has only been investigated in detail for the Y42F mutation. Here we explore the structural basis for occurrence of the intermediate spectral form in a M121E derivative of a circularly permuted H. halophila PYP (M121E-cPYP). The M121 site in M121E-cPYP corresponds to the M100 site in wild-type H. halophila PYP. High-resolution NMR measurements with a salt-tolerant cryoprobe enabled identification of those residues directly affected by increasing concentrations of ammonium chloride, a salt that greatly enhances the fraction of the intermediate spectra form. Residues in the surface loop containing the M121E (M100E) mutation were found to be affected by ammonium chloride as well as a discrete set of residues that link this surface loop to the buried hydroxyl group of the chromophore via a hydrogen bond network. Localized changes in the conformational dynamics of a surface loop can thereby produce structural rearrangements near the buried hydroxyl group chromophore while leaving the large majority of residues in the protein unaffected.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
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20
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A. Rohrdanz M, Zheng W, Lambeth B, Vreede J, Clementi C. Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble. PLoS Comput Biol 2014; 10:e1003797. [PMID: 25356903 PMCID: PMC4214557 DOI: 10.1371/journal.pcbi.1003797] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 07/08/2014] [Indexed: 02/04/2023] Open
Abstract
The nature of the optical cycle of photoactive yellow protein (PYP) makes its elucidation challenging for both experiment and theory. The long transition times render conventional simulation methods ineffective, and yet the short signaling-state lifetime makes experimental data difficult to obtain and interpret. Here, through an innovative combination of computational methods, a prediction and analysis of the biological signaling state of PYP is presented. Coarse-grained modeling and locally scaled diffusion map are first used to obtain a rough bird's-eye view of the free energy landscape of photo-activated PYP. Then all-atom reconstruction, followed by an enhanced sampling scheme; diffusion map-directed-molecular dynamics are used to focus in on the signaling-state region of configuration space and obtain an ensemble of signaling state structures. To the best of our knowledge, this is the first time an all-atom reconstruction from a coarse grained model has been performed in a relatively unexplored region of molecular configuration space. We compare our signaling state prediction with previous computational and more recent experimental results, and the comparison is favorable, which validates the method presented. This approach provides additional insight to understand the PYP photo cycle, and can be applied to other systems for which more direct methods are impractical. Many protein systems of biological interest undergo dynamical changes on a time scale too long to be modeled using standard computational methods. One example is photoactive yellow protein (PYP), found in several bacterial species. Blue light, potentially harmful for DNA, triggers several structural changes in PYP, eventually resulting in a conformation that changes the swimming behavior of bacteria. This conformation is difficult to investigate, as it is too short lived. In addition, understanding this “signaling state” is computationally difficult because of the long timescale of the transition. We overcome this by constructing a coarse-grained model to rapidly induce transitions to the signaling state. We then reconstruct and further sample the all-atom configurations from these coarse-grained representations. Our results are consistent with all available experimental and computational evidence.
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Affiliation(s)
- Mary A. Rohrdanz
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
- Chemistry Department, Rice University, Houston, Texas, United States of America
| | - Wenwei Zheng
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
- Chemistry Department, Rice University, Houston, Texas, United States of America
| | - Bradley Lambeth
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
| | - Jocelyne Vreede
- van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Cecilia Clementi
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
- Chemistry Department, Rice University, Houston, Texas, United States of America
- * E-mail:
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21
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Reis JM, Burns DC, Woolley GA. Optical control of protein-protein interactions via blue light-induced domain swapping. Biochemistry 2014; 53:5008-16. [PMID: 25003701 PMCID: PMC4372075 DOI: 10.1021/bi500622x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The design of new optogenetic tools
for controlling protein function
would be facilitated by the development of protein scaffolds that
undergo large, well-defined structural changes upon exposure to light.
Domain swapping, a process in which a structural element of a monomeric
protein is replaced by the same element of another copy of the same
protein, leads to a well-defined change in protein structure. We observe
domain swapping in a variant of the blue light photoreceptor photoactive
yellow protein in which a surface loop is replaced by a well-characterized
protein–protein interaction motif, the E-helix. In the domain-swapped
dimer, the E-helix sequence specifically binds a partner K-helix sequence,
whereas in the monomeric form of the protein, the E-helix sequence
is unable to fold into a binding-competent conformation and no interaction
with the K-helix is seen. Blue light irradiation decreases the extent
of domain swapping (from Kd = 10 μM
to Kd = 300 μM) and dramatically
enhances the rate, from weeks to <1 min. Blue light-induced domain
swapping thus provides a novel mechanism for controlling of protein–protein
interactions in which light alters both the stability and the kinetic
accessibility of binding-competent states.
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Affiliation(s)
- Jakeb M Reis
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, ON M5S 3H6, Canada
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