Exploring the repeat protein universe through computational protein design

Brunette, TJ; Parmeggiani, Fabio; Huang, Po-Ssu; Bhabha, Gira; Ekiert, Damian C.; Tsutakawa, Susan E.; Hura, Greg L.; Tainer, John A.; Baker, David

doi:10.1038/nature16162

Title: Exploring the repeat protein universe through computational protein design

Journal Article · Wed Dec 16 00:00:00 EST 2015 · Nature (London)

DOI:https://doi.org/10.1038/nature16162· OSTI ID:1378707

Brunette, TJ ^[1]; Parmeggiani, Fabio ^[1]; Huang, Po-Ssu ^[1]; Bhabha, Gira ^[2]; Ekiert, Damian C. ^[3]; Tsutakawa, Susan E. ^[4]; Hura, Greg L. ^[5]; Tainer, John A. ^[6]; Baker, David ^[7]

Univ. of Washington, Seattle, WA (United States). Dept. of Biochemistry. Inst. for Protein Design
Univ. of California, San Francisco, CA (United States). Dept. of Cellular and Molecular Pharmacology
Univ. of California, San Francisco, CA (United States). Dept. of Microbiology and Immunology
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging; Univ. of California, Santa Cruz, CA (United States). Dept. of Chemistry and Biochemistry
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging; Univ. of Texas M. D. Anderson Cancer Center, Houston, TX (United States). Dept. of Molecular and Cellular Oncology
Univ. of Washington, Seattle, WA (United States). Dept. of Biochemistry. Inst. for Protein Design. Howard Hughes Medical Inst.

A central question in protein evolution is the extent to which naturally occurring proteins sample the space of folded structures accessible to the polypeptide chain. Repeat proteins composed of multiple tandem copies of a modular structure unit are widespread in nature and have critical roles in molecular recognition, signalling, and other essential biological processes. Naturally occurring repeat proteins have been re-engineered for molecular recognition and modular scaffolding applications. In this paper, we use computational protein design to investigate the space of folded structures that can be generated by tandem repeating a simple helix–loop–helix–loop structural motif. Eighty-three designs with sequences unrelated to known repeat proteins were experimentally characterized. Of these, 53 are monomeric and stable at 95 °C, and 43 have solution X-ray scattering spectra consistent with the design models. Crystal structures of 15 designs spanning a broad range of curvatures are in close agreement with the design models with root mean square deviations ranging from 0.7 to 2.5 Å. Finally, our results show that existing repeat proteins occupy only a small fraction of the possible repeat protein sequence and structure space and that it is possible to design novel repeat proteins with precisely specified geometries, opening up a wide array of new possibilities for biomolecular engineering.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); National Science Foundation (NSF); Defense Threat Reduction Agency (DTRA) (United States); US Air Force Office of Scientific Research (AFOSR); Howard Hughes Medical Inst. (HHMI) (United States); National Inst. of Health (NIH) (United States); Damon Runyon Cancer Research Foundation (United States); Swiss National Science Foundation (SNSF); Human Frontier Science Program (HFSP) (France)

Contributing Organization:: Univ. of California, Santa Cruz, CA (United States); Univ. of Texas M. D. Anderson Cancer Center, Houston, TX (United States)

Grant/Contract Number:: AC02-05CH11231; MCB-1445201; CHE-1332907; FA950-12-10112; HHMI-027779; GM105404; K99GM112982; DRG-2140-12; DRG-2136-12; PBZHP3-125470; LT000070/2009-L

OSTI ID:: 1378707

Journal Information:: Nature (London), Vol. 528, Issue 7583; ISSN 0028-0836

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 161 works

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59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
protein design
protein structure predictions

Title: Exploring the repeat protein universe through computational protein design

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