De novo design of protein homodimers containing tunable symmetric protein pockets

Hicks, Derrick R.; Kennedy, Madison A.; Thompson, Kirsten A.; DeWitt, Michelle; Coventry, Brian; Kang, Alex; Bera, Asim K.; Brunette, T. J.; Sankaran, Banumathi; Stoddard, Barry; Baker, David

doi:10.1073/pnas.2113400119

De novo design of protein homodimers containing tunable symmetric protein pockets

Journal Article · Thu Jul 21 04:00:00 EDT 2022 · Proceedings of the National Academy of Sciences of the United States of America

DOI:https://doi.org/10.1073/pnas.2113400119· OSTI ID:1904172

^[1]; ^[2]; ^[1]; DeWitt, Michelle ^[1]; Coventry, Brian ^[1]; Kang, Alex ^[1]; ^[1]; ^[1]; Sankaran, Banumathi ^[3]; Stoddard, Barry ^[4]; ^[1]

Univ. of Washington, Seattle, WA (United States)
Univ. of Washington, Seattle, WA (United States); Fred Hutchinson Cancer Center, Seattle, WA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Fred Hutchinson Cancer Center, Seattle, WA (United States)

Function follows form in biology, and the binding of small molecules requires proteins with pockets that match the shape of the ligand. For design of binding to symmetric ligands, protein homo-oligomers with matching symmetry are advantageous as each protein subunit can make identical interactions with the ligand. Here, we describe a general approach to designing hyperstable C2 symmetric proteins with pockets of diverse size and shape. We first designed repeat proteins that sample a continuum of curvatures but have low helical rise, then docked these into C2 symmetric homodimers to generate an extensive range of C2 symmetric cavities. We used this approach to design thousands of C2 symmetric homodimers, and characterized 101 of them experimentally. Of these, the geometry of 31 were confirmed by small angle X-ray scattering and 2 were shown by crystallographic analyses to be in close agreement with the computational design models. These scaffolds provide a rich set of starting points for binding a wide range of C2 symmetric compounds.

View Accepted Manuscript (DOE)

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

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Basic Energy Sciences (BES); National Science Foundation (NSF); National Institute of General Medical Sciences (NIGMS); National Institutes of Health (NIH); National Institute of Aging

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1904172

Journal Information:: Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Issue: 30 Vol. 119; ISSN 0027-8424

Publisher:: National Academy of SciencesCopyright Statement

Country of Publication:: United States

Language:: English

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
homodimer
protein design
repeat protein
scaffold
symmetry

De novo design of protein homodimers containing tunable symmetric protein pockets

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