Diffusing protein binders to intrinsically disordered proteins
Caixuan Liu, Kejia Wu, Hojun Choi, Hannah L. Han, Xueli Zhang, Joseph L. Watson, Green Ahn, Jason Z. Zhang, Sara Shijo, Lydia L. Good, Charlotte M. Fischer, Asim K. Bera, Alex Kang, Evans Brackenbrough, Brian Coventry, Derrick R. Hicks, Seema Qamar, Xinting Li, Justin Decarreau, Stacey Gerben, Wei Yang, Inna Goreshnik, Dionne Vafeados, Xinru Wang, Mila Lamb, Analisa Murray, Sebastian Kenny, Magnus S. Bauer, Andrew N. Hoofnagle, Ping Zhu, Tuomas P. J. Knowles, David Baker
Abstract
Proteins that bind to intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) with high affinity and specificity could be useful for therapeutic and diagnostic applications1–4. However, a general methodology for targeting IDPs or IDRs has yet to be developed. Here we show that starting only from the target sequence of the input, and freely sampling both target and binding protein conformations, RFdiffusion5 can generate binders to IDPs and IDRs in a wide range of conformations. We used this approach to generate binders to the IDPs amylin, C-peptide, VP48 and BRCA1_ARATH in diverse conformations with a dissociation constant (Kd) ranging from 3 to 100 nM. For the IDRs G3BP1, common cytokine receptor γ-chain (IL-2RG) and prion protein, we diffused binders to β-strand conformations of the targets, obtaining Kd between 10 and 100 nM. Fluorescence imaging experiments show that the binders bind to their respective targets in cells. The G3BP1 binder disrupts stress granule formation in cells, and the amylin binder inhibits amyloid fibril formation and dissociates existing fibres, enables targeting of both monomeric and fibrillar amylin to lysosomes, and increases the sensitivity of mass spectrometry-based amylin detection. Our approach should be useful for creating binders to flexible IDPs or IDRs spanning a wide range of intrinsic conformational preferences. Using RFdiffusion, a general method for targeting intrinsically disordered proteins and regions for protein design has been developed.