Improved protein binder design using beta-pairing targeted RFdiffusion Article Swipe
David Baker
,
Isaac Sappington
,
Martin Toul
,
David Lee
,
Stephanie A. Robinson
,
Inna Goreshnik
,
Clara McCurdy
,
Tung Ching Chan
,
Nic Buccholz
,
Buwei Huang
,
Dionne Vafeados
,
Mariana Garcia-Sanchez
,
Nicole Roullier
,
Matthias Glögl
,
Christopher J. Kim
,
Joseph L. Watson
,
Susana Vázquez Torres
,
Koen H. G. Verschueren
,
Kenneth Verstraete
,
Cynthia S. Hinck
,
Melisa Bénard-Valle
,
Brian Coventry
,
Jeremiah Nelson Sims
,
Green Ahn
,
Xinru Wang
,
Andrew P. Hinck
,
Timothy P. Jenkins
,
Hannele Ruohola‐Baker
,
Steven M. Banik
,
Savvas N. Savvides
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.rs-5473963/v1
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.rs-5473963/v1
Despite recent advances in the computational design of protein binders, designing proteins that bind with high affinity to polar protein targets remains an outstanding problem. Here we show that RFdiffusion can be conditioned to efficiently generate protein scaffolds that form geometrically matched extended beta-sheets with target protein edge beta-strands in which polar groups on the target are nearly perfectly complemented with hydrogen bonding groups on the design. We use this approach to design binders against a set of therapeutically relevant polar targets (KIT, PDGFRɑ, ALK-2, ALK-3, FCRL5, and NRP1) and find that beta-strand-targeted design yields higher affinities and success rates than unconditioned RFdiffusion. All by all binding experiments show that the designs have affinities ranging from 137 pM to mid nM for their targets and essentially no off target binding despite the sharing of beta-strand interactions, likely reflecting the precise customization of interacting beta-strand geometry and additional designed binder-target interactions. A co-crystal structure of one such design in complex with the KIT receptor is nearly identical to the computational design model confirming the accuracy of the design approach. The ability to robustly generate binders displaying high affinity and specificity to polar interaction surfaces with exposed beta-strands considerably increases the range and capabilities of computational binder design.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.21203/rs.3.rs-5473963/v1
- OA Status
- gold
- Cited By
- 2
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4406450580
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4406450580Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.21203/rs.3.rs-5473963/v1Digital Object Identifier
- Title
-
Improved protein binder design using beta-pairing targeted RFdiffusionWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2025Year of publication
- Publication date
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2025-01-17Full publication date if available
- Authors
-
David Baker, Isaac Sappington, Martin Toul, David Lee, Stephanie A. Robinson, Inna Goreshnik, Clara McCurdy, Tung Ching Chan, Nic Buccholz, Buwei Huang, Dionne Vafeados, Mariana Garcia-Sanchez, Nicole Roullier, Matthias Glögl, Christopher J. Kim, Joseph L. Watson, Susana Vázquez Torres, Koen H. G. Verschueren, Kenneth Verstraete, Cynthia S. Hinck, Melisa Bénard-Valle, Brian Coventry, Jeremiah Nelson Sims, Green Ahn, Xinru Wang, Andrew P. Hinck, Timothy P. Jenkins, Hannele Ruohola‐Baker, Steven M. Banik, Savvas N. SavvidesList of authors in order
- Landing page
-
https://doi.org/10.21203/rs.3.rs-5473963/v1Publisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://doi.org/10.21203/rs.3.rs-5473963/v1Direct OA link when available
- Concepts
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Pairing, BETA (programming language), Computer science, Physics, Programming language, Condensed matter physics, SuperconductivityTop concepts (fields/topics) attached by OpenAlex
- Cited by
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2Total citation count in OpenAlex
- Citations by year (recent)
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2025: 2Per-year citation counts (last 5 years)
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.targets | 21, 82, 124 |
| abstract_inverted_index.PDGFRɑ, | 84 |
| abstract_inverted_index.accuracy | 174 |
| abstract_inverted_index.advances | 3 |
| abstract_inverted_index.affinity | 17, 187 |
| abstract_inverted_index.approach | 71 |
| abstract_inverted_index.binders, | 10 |
| abstract_inverted_index.designed | 148 |
| abstract_inverted_index.extended | 43 |
| abstract_inverted_index.generate | 36, 183 |
| abstract_inverted_index.geometry | 145 |
| abstract_inverted_index.hydrogen | 62 |
| abstract_inverted_index.problem. | 25 |
| abstract_inverted_index.proteins | 12 |
| abstract_inverted_index.receptor | 163 |
| abstract_inverted_index.relevant | 80 |
| abstract_inverted_index.robustly | 182 |
| abstract_inverted_index.surfaces | 193 |
| abstract_inverted_index.approach. | 178 |
| abstract_inverted_index.designing | 11 |
| abstract_inverted_index.identical | 166 |
| abstract_inverted_index.increases | 198 |
| abstract_inverted_index.perfectly | 59 |
| abstract_inverted_index.scaffolds | 38 |
| abstract_inverted_index.structure | 153 |
| abstract_inverted_index.additional | 147 |
| abstract_inverted_index.affinities | 97, 114 |
| abstract_inverted_index.co-crystal | 152 |
| abstract_inverted_index.confirming | 172 |
| abstract_inverted_index.displaying | 185 |
| abstract_inverted_index.reflecting | 138 |
| abstract_inverted_index.RFdiffusion | 30 |
| abstract_inverted_index.beta-sheets | 44 |
| abstract_inverted_index.beta-strand | 135, 144 |
| abstract_inverted_index.conditioned | 33 |
| abstract_inverted_index.efficiently | 35 |
| abstract_inverted_index.essentially | 126 |
| abstract_inverted_index.experiments | 108 |
| abstract_inverted_index.interacting | 143 |
| abstract_inverted_index.interaction | 192 |
| abstract_inverted_index.outstanding | 24 |
| abstract_inverted_index.specificity | 189 |
| abstract_inverted_index.RFdiffusion. | 103 |
| abstract_inverted_index.beta-strands | 49, 196 |
| abstract_inverted_index.capabilities | 202 |
| abstract_inverted_index.complemented | 60 |
| abstract_inverted_index.considerably | 197 |
| abstract_inverted_index.binder-target | 149 |
| abstract_inverted_index.computational | 6, 169, 204 |
| abstract_inverted_index.customization | 141 |
| abstract_inverted_index.geometrically | 41 |
| abstract_inverted_index.interactions, | 136 |
| abstract_inverted_index.interactions. | 150 |
| abstract_inverted_index.unconditioned | 102 |
| abstract_inverted_index.therapeutically | 79 |
| abstract_inverted_index.beta-strand-targeted | 93 |
| abstract_inverted_index.<title>Abstract</title> | 0 |
| cited_by_percentile_year.max | 97 |
| cited_by_percentile_year.min | 95 |
| countries_distinct_count | 3 |
| institutions_distinct_count | 30 |
| citation_normalized_percentile.value | 0.866926 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | True |