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Title: Receptor subtype discrimination using extensive shape complementary designed interfaces

Abstract

To discriminate between closely related members of a protein family that differ at a limited number of spatially distant positions is a challenge for drug discovery. Here, we describe a combined computational design and experimental selection approach for generating binders targeting functional sites with large, shape complementary interfaces to read out subtle sequence differences for subtype-specific antagonism. Repeat proteins are computationally docked against a functionally relevant region of the target protein surface that varies in the different subtypes, and the interface sequences are optimized for affinity and specificity first computationally and then experimentally. We used this approach to generate a series of human Frizzled (Fz) subtype-selective antagonists with extensive shape complementary interaction surfaces considerably larger than those of repeat proteins selected from random libraries. In vivo administration revealed that Wnt-dependent pericentral liver gene expression involves multiple Fz subtypes, while maintenance of the intestinal crypt stem cell compartment involves only a limited subset.

Authors:
 [1]; ORCiD logo [2];  [3];  [3];  [4];  [5]; ORCiD logo [6];  [6];  [3];  [3];  [3];  [7];  [3];  [6]; ORCiD logo [1]
  1. Univ. of Washington, Seattle, WA (United States). Dept. of Biochemistry; Univ. of Washington, Seattle, WA (United States). Inst. for Protein Design; Univ. of Washington, Seattle, WA (United States). Howard Hughes Medical Inst.
  2. Stanford Univ., CA (United States). Dept. of Molecular and Cellular Physiology; Stanford Univ., CA (United States). School of Medicine, Dept. of Structural Biology; Stanford Univ., CA (United States). Howard Hughes Medical Inst.
  3. Stanford Univ., CA (United States). Dept. of Medicine, Division of Hematology
  4. Korea Inst. of Science and Technology, Gangneung (China). Systems Biotechnology Research Center
  5. Stanford Univ., CA (United States). Dept. of Molecular and Cellular Physiology; Stanford Univ., CA (United States). School of Medicine, Dept. of Structural Biology; Stanford Univ., CA (United States). Howard Hughes Medical Inst.; Princess Máxima Center for Pediatric Oncology, Utrecht (The Netherlands)
  6. Stanford Univ., CA (United States). Dept. of Molecular and Cellular Physiology; Stanford Univ., CA (United States). School of Medicine, Dept. of Structural Biology; Stanford Univ., CA (United States). Howard Hughes Medical Inst.
  7. Stanford Univ., CA (United States). School of Medicine, Dept. of Comparative Medicine
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); National Institutes of Health (NIH)
OSTI Identifier:
1532481
Grant/Contract Number:  
AC02-76SF00515; AC02-06CH11357; AC02-05CH11231; 1S10OD012289-01A1; U01DK085527; U19AI116484; R01NS100904; U01CA217851
Resource Type:
Accepted Manuscript
Journal Name:
Nature Structural & Molecular Biology
Additional Journal Information:
Journal Volume: 26; Journal Issue: 6; Journal ID: ISSN 1545-9993
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING

Citation Formats

Dang, Luke T., Miao, Yi, Ha, Andrew, Yuki, Kanako, Park, Keunwan, Janda, Claudia Y., Jude, Kevin M., Mohan, Kritika, Ha, Nhi, Vallon, Mario, Yuan, Jenny, Vilches-Moure, José G., Kuo, Calvin J., Garcia, K. Christopher, and Baker, David. Receptor subtype discrimination using extensive shape complementary designed interfaces. United States: N. p., 2019. Web. doi:10.1038/s41594-019-0224-z.
Dang, Luke T., Miao, Yi, Ha, Andrew, Yuki, Kanako, Park, Keunwan, Janda, Claudia Y., Jude, Kevin M., Mohan, Kritika, Ha, Nhi, Vallon, Mario, Yuan, Jenny, Vilches-Moure, José G., Kuo, Calvin J., Garcia, K. Christopher, & Baker, David. Receptor subtype discrimination using extensive shape complementary designed interfaces. United States. doi:10.1038/s41594-019-0224-z.
Dang, Luke T., Miao, Yi, Ha, Andrew, Yuki, Kanako, Park, Keunwan, Janda, Claudia Y., Jude, Kevin M., Mohan, Kritika, Ha, Nhi, Vallon, Mario, Yuan, Jenny, Vilches-Moure, José G., Kuo, Calvin J., Garcia, K. Christopher, and Baker, David. Mon . "Receptor subtype discrimination using extensive shape complementary designed interfaces". United States. doi:10.1038/s41594-019-0224-z.
@article{osti_1532481,
title = {Receptor subtype discrimination using extensive shape complementary designed interfaces},
author = {Dang, Luke T. and Miao, Yi and Ha, Andrew and Yuki, Kanako and Park, Keunwan and Janda, Claudia Y. and Jude, Kevin M. and Mohan, Kritika and Ha, Nhi and Vallon, Mario and Yuan, Jenny and Vilches-Moure, José G. and Kuo, Calvin J. and Garcia, K. Christopher and Baker, David},
abstractNote = {To discriminate between closely related members of a protein family that differ at a limited number of spatially distant positions is a challenge for drug discovery. Here, we describe a combined computational design and experimental selection approach for generating binders targeting functional sites with large, shape complementary interfaces to read out subtle sequence differences for subtype-specific antagonism. Repeat proteins are computationally docked against a functionally relevant region of the target protein surface that varies in the different subtypes, and the interface sequences are optimized for affinity and specificity first computationally and then experimentally. We used this approach to generate a series of human Frizzled (Fz) subtype-selective antagonists with extensive shape complementary interaction surfaces considerably larger than those of repeat proteins selected from random libraries. In vivo administration revealed that Wnt-dependent pericentral liver gene expression involves multiple Fz subtypes, while maintenance of the intestinal crypt stem cell compartment involves only a limited subset.},
doi = {10.1038/s41594-019-0224-z},
journal = {Nature Structural & Molecular Biology},
number = 6,
volume = 26,
place = {United States},
year = {2019},
month = {5}
}

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Works referenced in this record:

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