Rational Construction of Compact de Novo- Designed Biliverdin-Binding Proteins
Abstract
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.
- Publication Date:
- Research Org.:
- Energy Frontier Research Centers (EFRC) (United States). Photosynthetic Antenna Research Center (PARC); Univ. of Pennsylvania, Philadelphia, PA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES); National Inst. of Health (NIH) (United States); National Science Foundation (NSF)
- OSTI Identifier:
- 1485333
- Alternate Identifier(s):
- OSTI ID: 1508787
- Grant/Contract Number:
- SC0001035; 1R21DA040434; 1R21EY027562; 1R01NS101106; CBET 126497; MCB 1652003
- Resource Type:
- Published Article
- Journal Name:
- Biochemistry
- Additional Journal Information:
- Journal Name: Biochemistry Journal Volume: 57 Journal Issue: 49; Journal ID: ISSN 0006-2960
- Publisher:
- American Chemical Society (ACS)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Sheehan, Molly M., Magaraci, Michael S., Kuznetsov, Ivan A., Mancini, Joshua A., Kodali, Goutham, Moser, Christopher C., Dutton, P. Leslie, and Chow, Brian Y. Rational Construction of Compact de Novo- Designed Biliverdin-Binding Proteins. United States: N. p., 2018.
Web. doi:10.1021/acs.biochem.8b01076.
Sheehan, Molly M., Magaraci, Michael S., Kuznetsov, Ivan A., Mancini, Joshua A., Kodali, Goutham, Moser, Christopher C., Dutton, P. Leslie, & Chow, Brian Y. Rational Construction of Compact de Novo- Designed Biliverdin-Binding Proteins. United States. https://doi.org/10.1021/acs.biochem.8b01076
Sheehan, Molly M., Magaraci, Michael S., Kuznetsov, Ivan A., Mancini, Joshua A., Kodali, Goutham, Moser, Christopher C., Dutton, P. Leslie, and Chow, Brian Y. Fri .
"Rational Construction of Compact de Novo- Designed Biliverdin-Binding Proteins". United States. https://doi.org/10.1021/acs.biochem.8b01076.
@article{osti_1485333,
title = {Rational Construction of Compact de Novo- Designed Biliverdin-Binding Proteins},
author = {Sheehan, Molly M. and Magaraci, Michael S. and Kuznetsov, Ivan A. and Mancini, Joshua A. and Kodali, Goutham and Moser, Christopher C. and Dutton, P. Leslie and Chow, Brian Y.},
abstractNote = {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.},
doi = {10.1021/acs.biochem.8b01076},
journal = {Biochemistry},
number = 49,
volume = 57,
place = {United States},
year = {Fri Nov 23 00:00:00 EST 2018},
month = {Fri Nov 23 00:00:00 EST 2018}
}
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https://doi.org/10.1021/acs.biochem.8b01076
https://doi.org/10.1021/acs.biochem.8b01076
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Cited by: 9 works
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Figures / Tables:
Figure 1: Engineering de novo-designed proteins to stabilize biliverdin. (a) Self-assembling single-chain tetrahelical bundles created by binary patterning of hydrophobic and hydrophobic residues with a high α-helix formation propensity, described by the helical wheel. (b) Strategy for stabilizing biliverdin within the core. (c) Holoprotein stepwise construction.
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Figures / Tables found in this record:
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