Rational Construction of Compact de Novo- Designed Biliverdin-Binding Proteins

Sheehan, Molly M.; Magaraci, Michael S.; Kuznetsov, Ivan A.; Mancini, Joshua A.; Kodali, Goutham; Moser, Christopher C.; Dutton, P. Leslie; Chow, Brian Y.

doi:10.1021/acs.biochem.8b01076

Title: Rational Construction of Compact de Novo- Designed Biliverdin-Binding Proteins

Journal Article · Fri Nov 23 00:00:00 EST 2018 · Biochemistry

DOI:https://doi.org/10.1021/acs.biochem.8b01076· OSTI ID:1485333

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; Mancini, Joshua A.;

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We report the rational construction of de novo-designed biliverdin-binding proteins by first principles of protein design, informed by energy minimization modeling in Rosetta. The self-assembling tetrahelical bundles bind biliverdin IXa (BV) cofactor autocatalytically in vitro, like photosensory proteins that bind BV (and related bilins or linear tetrapyrroles) despite lacking sequence and structural homology to the natural counterparts. Upon identification of a suitable site for ligation of the cofactor to the protein scaffold, stepwise placement of residues stabilized BV within the hydrophobic core. Rosetta modeling was used in the absence of a high-resolution structure to inform the structure-function relationships of the cofactor binding pocket. Holoprotein formation stabilized BV, resulting in increased far-red BV fluorescence. Via removal of segments extraneous to cofactor stabilization or bundle stability, the initial 15 kDa de novo-designed fluorescence-activating protein was truncated without any change to its optical properties, down to a miniature 10 kDa “mini”, in which the protein scaffold extends only a half-heptad repeat beyond the hypothetical position of the bilin D-ring. This work demonstrates how highly compact holoprotein fluorochromes can be rationally constructed using de novo protein design technology and natural cofactors.

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Research Organization:: Energy Frontier Research Centers (EFRC) (United States). Photosynthetic Antenna Research Center (PARC); Univ. of Pennsylvania, Philadelphia, PA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); National Inst. of Health (NIH) (United States); National Science Foundation (NSF)

Grant/Contract Number:: SC0001035; 1R21DA040434; 1R21EY027562; 1R01NS101106; CBET 126497; MCB 1652003

OSTI ID:: 1485333

Alternate ID(s):: OSTI ID: 1508787

Journal Information:: Biochemistry, Journal Name: Biochemistry Vol. 57 Journal Issue: 49; ISSN 0006-2960

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 9 works

Citation information provided by
Web of Science

References (29)

Phycofluor probes Glazer, Alexander N.; Stryer, Lubert Trends in Biochemical Sciences, Vol. 9, Issue 10 https://doi.org/10.1016/0968-0004(84)90146-4	journal	October 1984
Origins of Fluorescence in Evolved Bacteriophytochromes Bhattacharya, Shyamosree; Auldridge, Michele E.; Lehtivuori, Heli Journal of Biological Chemistry, Vol. 289, Issue 46 https://doi.org/10.1074/jbc.M114.589739	journal	September 2014
Characterization of a helical protein designed from first principles Regan, L.; DeGrado, W. F. Science, Vol. 241, Issue 4868, p. 976-978 https://doi.org/10.1126/science.3043666	journal	August 1988
Minimal domain of bacterial phytochrome required for chromophore binding and fluorescence Rumyantsev, Konstantin A.; Shcherbakova, Daria M.; Zakharova, Natalia I. Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep18348	journal	December 2015
A Bilirubin-Inducible Fluorescent Protein from Eel Muscle Kumagai, Akiko; Ando, Ryoko; Miyatake, Hideyuki Cell, Vol. 153, Issue 7 https://doi.org/10.1016/j.cell.2013.05.038	journal	June 2013
Design and synthesis of multi-haem proteins Robertson, Dan E.; Farid, Ramy S.; Moser, Christopher C. Nature, Vol. 368, Issue 6470, p. 425-432 https://doi.org/10.1038/368425a0	journal	March 1994
The phytofluors: a new class of fluorescent protein probes Murphy, John T.; Lagarias, J.Clark Current Biology, Vol. 7, Issue 11, p. 870-876 https://doi.org/10.1016/S0960-9822(06)00375-7	journal	November 1997
The coming of age of de novo protein design Huang, Po-Ssu; Boyken, Scott E.; Baker, David Nature, Vol. 537, Issue 7620 https://doi.org/10.1038/nature19946	journal	September 2016
Near-infrared fluorescent proteins engineered from bacterial phytochromes Shcherbakova, Daria M.; Baloban, Mikhail; Verkhusha, Vladislav V. Current Opinion in Chemical Biology, Vol. 27 https://doi.org/10.1016/j.cbpa.2015.06.005	journal	August 2015
Protein Design: The Choice of de Novo Sequences Beasley, James R.; Hecht, Michael H. Journal of Biological Chemistry, Vol. 272, Issue 4 https://doi.org/10.1074/jbc.272.4.2031	journal	January 1997
Design, synthesis, and characterization of a photoactivatable flavocytochrome molecular maquette Sharp, R. E.; Moser, C. C.; Rabanal, F. Proceedings of the National Academy of Sciences, Vol. 95, Issue 18 https://doi.org/10.1073/pnas.95.18.10465	journal	September 1998
De Novo Protein Design: Fully Automated Sequence Selection Dahiyat, Bassil I.; Mayo, Stephen L. Science, Vol. 278, Issue 5335 https://doi.org/10.1126/science.278.5335.82	journal	October 1997
High thermodynamic stability of parametrically designed helical bundles Huang, Po-Ssu; Oberdorfer, Gustav; Xu, Chunfu Science, Vol. 346, Issue 6208 https://doi.org/10.1126/science.1257481	journal	October 2014
A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids O'Neil, K.; DeGrado, W. Science, Vol. 250, Issue 4981 https://doi.org/10.1126/science.2237415	journal	November 1990
De novo synthetic biliprotein design, assembly and excitation energy transfer Mancini, Joshua A.; Sheehan, Molly; Kodali, Goutham Journal of The Royal Society Interface, Vol. 15, Issue 141 https://doi.org/10.1098/rsif.2018.0021	journal	April 2018
Biliverdin Amides Reveal Roles for Propionate Side Chains in Bilin Reductase Recognition and in Holophytochrome Assembly and Photoconversion Shang, Lixia; Rockwell, Nathan C.; Martin, Shelley S. Biochemistry, Vol. 49, Issue 29 https://doi.org/10.1021/bi100756x	journal	July 2010
Continuous Fluorescence Assay of Phytochrome Assembly in Vitro Li, Liming; Murphy, John T.; Lagarias, J. Clark Biochemistry, Vol. 34, Issue 24 https://doi.org/10.1021/bi00024a017	journal	June 1995
De novo design of a hyperstable non-natural protein–ligand complex with sub-Å accuracy Polizzi, Nicholas F.; Wu, Yibing; Lemmin, Thomas Nature Chemistry, Vol. 9, Issue 12 https://doi.org/10.1038/nchem.2846	journal	August 2017
Removal of Chromophore-Proximal Polar Atoms Decreases Water Content and Increases Fluorescence in a Near Infrared Phytofluor Lehtivuori, Heli; Bhattacharya, Shyamosree; Angenent-Mari, Nicolaas M. Frontiers in Molecular Biosciences, Vol. 2 https://doi.org/10.3389/fmolb.2015.00065	journal	November 2015
The HP-1 maquette: From an apoprotein structure to a structured hemoprotein designed to promote redox-coupled proton exchange Huang, S. S.; Koder, R. L.; Lewis, M. Proceedings of the National Academy of Sciences, Vol. 101, Issue 15 https://doi.org/10.1073/pnas.0306676101	journal	March 2004
Structural and Biochemical Characterization of the Bilin Lyase CpcS from Thermosynechococcus elongatus Kronfel, Christina M.; Kuzin, Alexandre P.; Forouhar, Farhad Biochemistry, Vol. 52, Issue 48 https://doi.org/10.1021/bi401192z	journal	November 2013
ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility Meiler, Jens; Baker, David Proteins: Structure, Function, and Bioinformatics, Vol. 65, Issue 3 https://doi.org/10.1002/prot.21086	journal	November 2006
Defining the Bilin Lyase Domain: Lessons from the Extended Phytochrome Superfamily ^† Wu, Shu-Hsing; Lagarias, J. Clark Biochemistry, Vol. 39, Issue 44 https://doi.org/10.1021/bi001123z	journal	November 2000
Blue protein with red fluorescence Ghosh, Swagatha; Yu, Chi-Li; Ferraro, Daniel J. Proceedings of the National Academy of Sciences, Vol. 113, Issue 41 https://doi.org/10.1073/pnas.1525622113	journal	September 2016
Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome Shu, X.; Royant, A.; Lin, M. Z. Science, Vol. 324, Issue 5928 https://doi.org/10.1126/science.1168683	journal	May 2009
De novo design of a fluorescence-activating β-barrel Dou, Jiayi; Vorobieva, Anastassia A.; Sheffler, William Nature, Vol. 561, Issue 7724 https://doi.org/10.1038/s41586-018-0509-0	journal	September 2018
The Biliverdin Chromophore Binds Covalently to a Conserved Cysteine Residue in the N-Terminus of Agrobacterium Phytochrome Agp1 ^† Lamparter, Tilman; Carrascal, Montserrat; Michael, Norbert Biochemistry, Vol. 43, Issue 12 https://doi.org/10.1021/bi035693l	journal	March 2004
Computational de novo design of a four-helix bundle protein-DND_4HB: De Novo Design of a Helical Bundle Murphy, Grant S.; Sathyamoorthy, Bharatwaj; Der, Bryan S. Protein Science, Vol. 24, Issue 4 https://doi.org/10.1002/pro.2577	journal	November 2014
A far-red fluorescent protein evolved from a cyanobacterial phycobiliprotein Rodriguez, Erik A.; Tran, Geraldine N.; Gross, Larry A. Nature Methods, Vol. 13, Issue 9 https://doi.org/10.1038/nmeth.3935	journal	August 2016