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Buhrke D, Tavraz NN, Shcherbakova DM, Sauthof L, Moldenhauer M, Vélazquez Escobar F, Verkhusha VV, Hildebrandt P, Friedrich T. Chromophore binding to two cysteines increases quantum yield of near-infrared fluorescent proteins. Sci Rep 2019; 9:1866. [PMID: 30755663 PMCID: PMC6372600 DOI: 10.1038/s41598-018-38433-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 12/27/2018] [Indexed: 12/16/2022] Open
Abstract
Phytochromes are red/far-red light sensing photoreceptors employing linear tetrapyrroles as chromophores, which are covalently bound to a cysteine (Cys) residue in the chromophore-binding domain (CBD, composed of a PAS and a GAF domain). Recently, near-infrared (NIR) fluorescent proteins (FPs) engineered from bacterial phytochromes binding biliverdin IXα (BV), such as the iRFP series, have become invaluable probes for multicolor fluorescence microscopy and in vivo imaging. However, all current NIR FPs suffer from relatively low brightness. Here, by combining biochemical, spectroscopic and resonance Raman (RR) assays, we purified and characterized an iRFP variant that contains a BV chromophore simultaneously bound to two cysteines. This protein with the unusual double-Cys attached BV showed the highest fluorescence quantum yield (FQY) of 16.6% reported for NIR FPs, whereas the initial iRFP appeared to be a mixture of species with a mean FQY of 11.1%. The purified protein was also characterized with 1.3-fold higher extinction coefficient that together with FQY resulted in almost two-fold brighter fluorescence than the original iRFP as isolated. This work shows that the high FQY of iRFPs with two cysteines is a direct consequence of the double attachment. The PAS-Cys, GAF-Cys and double-Cys attachment each entails distinct configurational constraints of the BV adduct, which can be identified by distinct RR spectroscopic features, i.e. the marker band including the C=C stretching coordinate of the ring A-B methine bridge, which was previously identified as being characteristic for rigid chromophore embedment and high FQY. Our findings can be used to rationally engineer iRFP variants with enhanced FQYs.
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Affiliation(s)
- David Buhrke
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Neslihan N Tavraz
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Daria M Shcherbakova
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Luisa Sauthof
- Charité - Universitätsmedizin Berlin, Institute of Medical Physics and Biophysics (CC2), Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, 10117, Berlin, Germany
| | - Marcus Moldenhauer
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Francisco Vélazquez Escobar
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Vladislav V Verkhusha
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Peter Hildebrandt
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Thomas Friedrich
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.
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