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Title: De novo design of tunable, pH-driven conformational changes

Abstract

The ability of naturally occurring proteins to change conformation in response to environmental changes is critical to biological function. Although there have been advances in the de novo design of stable proteins with a single, deep free-energy minimum, the design of conformational switches remains challenging. We present a general strategy to design pH-responsive protein conformational changes by precisely preorganizing histidine residues in buried hydrogen-bond networks. We design homotrimers and heterodimers that are stable above pH 6.5 but undergo cooperative, large-scale conformational changes when the pH is lowered and electrostatic and steric repulsion builds up as the network histidine residues become protonated. The transition pH and cooperativity can be controlled through the number of histidine-containing networks and the strength of the surrounding hydrophobic interactions. Upon disassembly, the designed proteins disrupt lipid membranes both in vitro and after being endocytosed in mammalian cells. Our results demonstrate that environmentally triggered conformational changes can now be programmed by de novo protein design.

Authors:
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Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1545927
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Science
Additional Journal Information:
Journal Name: Science Journal Volume: 364 Journal Issue: 6441; Journal ID: ISSN 0036-8075
Publisher:
American Association for the Advancement of Science (AAAS)
Country of Publication:
United States
Language:
English

Citation Formats

Boyken, Scott E., Benhaim, Mark A., Busch, Florian, Jia, Mengxuan, Bick, Matthew J., Choi, Heejun, Klima, Jason C., Chen, Zibo, Walkey, Carl, Mileant, Alexander, Sahasrabuddhe, Aniruddha, Wei, Kathy Y., Hodge, Edgar A., Byron, Sarah, Quijano-Rubio, Alfredo, Sankaran, Banumathi, King, Neil P., Lippincott-Schwartz, Jennifer, Wysocki, Vicki H., Lee, Kelly K., and Baker, David. De novo design of tunable, pH-driven conformational changes. United States: N. p., 2019. Web. doi:10.1126/science.aav7897.
Boyken, Scott E., Benhaim, Mark A., Busch, Florian, Jia, Mengxuan, Bick, Matthew J., Choi, Heejun, Klima, Jason C., Chen, Zibo, Walkey, Carl, Mileant, Alexander, Sahasrabuddhe, Aniruddha, Wei, Kathy Y., Hodge, Edgar A., Byron, Sarah, Quijano-Rubio, Alfredo, Sankaran, Banumathi, King, Neil P., Lippincott-Schwartz, Jennifer, Wysocki, Vicki H., Lee, Kelly K., & Baker, David. De novo design of tunable, pH-driven conformational changes. United States. doi:10.1126/science.aav7897.
Boyken, Scott E., Benhaim, Mark A., Busch, Florian, Jia, Mengxuan, Bick, Matthew J., Choi, Heejun, Klima, Jason C., Chen, Zibo, Walkey, Carl, Mileant, Alexander, Sahasrabuddhe, Aniruddha, Wei, Kathy Y., Hodge, Edgar A., Byron, Sarah, Quijano-Rubio, Alfredo, Sankaran, Banumathi, King, Neil P., Lippincott-Schwartz, Jennifer, Wysocki, Vicki H., Lee, Kelly K., and Baker, David. Thu . "De novo design of tunable, pH-driven conformational changes". United States. doi:10.1126/science.aav7897.
@article{osti_1545927,
title = {De novo design of tunable, pH-driven conformational changes},
author = {Boyken, Scott E. and Benhaim, Mark A. and Busch, Florian and Jia, Mengxuan and Bick, Matthew J. and Choi, Heejun and Klima, Jason C. and Chen, Zibo and Walkey, Carl and Mileant, Alexander and Sahasrabuddhe, Aniruddha and Wei, Kathy Y. and Hodge, Edgar A. and Byron, Sarah and Quijano-Rubio, Alfredo and Sankaran, Banumathi and King, Neil P. and Lippincott-Schwartz, Jennifer and Wysocki, Vicki H. and Lee, Kelly K. and Baker, David},
abstractNote = {The ability of naturally occurring proteins to change conformation in response to environmental changes is critical to biological function. Although there have been advances in the de novo design of stable proteins with a single, deep free-energy minimum, the design of conformational switches remains challenging. We present a general strategy to design pH-responsive protein conformational changes by precisely preorganizing histidine residues in buried hydrogen-bond networks. We design homotrimers and heterodimers that are stable above pH 6.5 but undergo cooperative, large-scale conformational changes when the pH is lowered and electrostatic and steric repulsion builds up as the network histidine residues become protonated. The transition pH and cooperativity can be controlled through the number of histidine-containing networks and the strength of the surrounding hydrophobic interactions. Upon disassembly, the designed proteins disrupt lipid membranes both in vitro and after being endocytosed in mammalian cells. Our results demonstrate that environmentally triggered conformational changes can now be programmed by de novo protein design.},
doi = {10.1126/science.aav7897},
journal = {Science},
number = 6441,
volume = 364,
place = {United States},
year = {2019},
month = {5}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1126/science.aav7897

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