Journal Article

De novo design of protein structure and function with RFdiffusion

Courbet, Alexis, Ragotte, Robert J., Ovchinnikov, Sergey, Venkatesh, Preetham, Trippe, Brian L., Watson, Joseph L., Torres, Susana Vázquez, Sheffler, William, Sappington, Isaac, De Bortoli, Valentin, Baker, David, Wang, Jue, Borst, Andrew J., DiMaio, Frank, Pellock, Samuel J., Jaakkola, Tommi S., Yim, Jason, Mathieu, Emile, Baek, Minkyung, Lauko, Anna, Eisenach, Helen E., Bennett, Nathaniel R., Milles, Lukas F., Juergens, David, Wicky, Basile I. M., Ahern, Woody, Barzilay, Regina, Hanikel, Nikita

2023

Overview

There has been considerable recent progress in designing new proteins using deep-learning methods 1 – 9 . Despite this progress, a general deep-learning framework for protein design that enables solution of a wide range of design challenges, including de novo binder design and design of higher-order symmetric architectures, has yet to be described. Diffusion models 10 , 11 have had considerable success in image and language generative modelling but limited success when applied to protein modelling, probably due to the complexity of protein backbone geometry and sequence–structure relationships. Here we show that by fine-tuning the RoseTTAFold structure prediction network on protein structure denoising tasks, we obtain a generative model of protein backbones that achieves outstanding performance on unconditional and topology-constrained protein monomer design, protein binder design, symmetric oligomer design, enzyme active site scaffolding and symmetric motif scaffolding for therapeutic and metal-binding protein design. We demonstrate the power and generality of the method, called RoseTTAFold diffusion (RFdiffusion), by experimentally characterizing the structures and functions of hundreds of designed symmetric assemblies, metal-binding proteins and protein binders. The accuracy of RFdiffusion is confirmed by the cryogenic electron microscopy structure of a designed binder in complex with influenza haemagglutinin that is nearly identical to the design model. In a manner analogous to networks that produce images from user-specified inputs, RFdiffusion enables the design of diverse functional proteins from simple molecular specifications. Fine-tuning the RoseTTAFold structure prediction network on protein structure denoising tasks yields a generative model for protein design that achieves outstanding performance on a wide range of protein structure and function design challenges.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 101/28 / 631/114/1305 / 631/114/469 / 631/45/612 / 82 / 82/83 / Amino acid sequence / Binders / Catalytic Domain / Complexity / Cryoelectron Microscopy / Deep Learning / Design / Design specifications / Diffusion models / Electron microscopy / Hemagglutinin Glycoproteins, Influenza Virus - chemistry / Hemagglutinin Glycoproteins, Influenza Virus - metabolism / Hemagglutinin Glycoproteins, Influenza Virus - ultrastructure / Hemagglutinins / Humanities and Social Sciences / Modelling / multidisciplinary / Protein Binding / Protein structure / Proteins / Proteins - chemistry / Proteins - metabolism / Proteins - ultrastructure / Scaffolding / Science / Science & Technology - Other Topics / Science (multidisciplinary) / Structure-function relationships / Success / Topology