1
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Vázquez Torres S, Leung PJY, Venkatesh P, Lutz ID, Hink F, Huynh HH, Becker J, Yeh AHW, Juergens D, Bennett NR, Hoofnagle AN, Huang E, MacCoss MJ, Expòsit M, Lee GR, Bera AK, Kang A, De La Cruz J, Levine PM, Li X, Lamb M, Gerben SR, Murray A, Heine P, Korkmaz EN, Nivala J, Stewart L, Watson JL, Rogers JM, Baker D. De novo design of high-affinity binders of bioactive helical peptides. Nature 2024; 626:435-442. [PMID: 38109936 PMCID: PMC10849960 DOI: 10.1038/s41586-023-06953-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 12/07/2023] [Indexed: 12/20/2023]
Abstract
Many peptide hormones form an α-helix on binding their receptors1-4, and sensitive methods for their detection could contribute to better clinical management of disease5. De novo protein design can now generate binders with high affinity and specificity to structured proteins6,7. However, the design of interactions between proteins and short peptides with helical propensity is an unmet challenge. Here we describe parametric generation and deep learning-based methods for designing proteins to address this challenge. We show that by extending RFdiffusion8 to enable binder design to flexible targets, and to refining input structure models by successive noising and denoising (partial diffusion), picomolar-affinity binders can be generated to helical peptide targets by either refining designs generated with other methods, or completely de novo starting from random noise distributions without any subsequent experimental optimization. The RFdiffusion designs enable the enrichment and subsequent detection of parathyroid hormone and glucagon by mass spectrometry, and the construction of bioluminescence-based protein biosensors. The ability to design binders to conformationally variable targets, and to optimize by partial diffusion both natural and designed proteins, should be broadly useful.
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Affiliation(s)
- Susana Vázquez Torres
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA
| | - Philip J Y Leung
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA
| | - Preetham Venkatesh
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA
| | - Isaac D Lutz
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Fabian Hink
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Huu-Hien Huynh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Jessica Becker
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Andy Hsien-Wei Yeh
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - David Juergens
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA
| | - Nathaniel R Bennett
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Eric Huang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Marc Expòsit
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA
| | - Gyu Rie Lee
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Joshmyn De La Cruz
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Paul M Levine
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Xinting Li
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Mila Lamb
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Stacey R Gerben
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Analisa Murray
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Piper Heine
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Elif Nihal Korkmaz
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jeff Nivala
- School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Joseph L Watson
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
| | - Joseph M Rogers
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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2
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Lutz ID, Wang S, Norn C, Courbet A, Borst AJ, Zhao YT, Dosey A, Cao L, Xu J, Leaf EM, Treichel C, Litvicov P, Li Z, Goodson AD, Rivera-Sánchez P, Bratovianu AM, Baek M, King NP, Ruohola-Baker H, Baker D. Top-down design of protein architectures with reinforcement learning. Science 2023; 380:266-273. [PMID: 37079676 DOI: 10.1126/science.adf6591] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 03/21/2023] [Indexed: 04/22/2023]
Abstract
As a result of evolutionary selection, the subunits of naturally occurring protein assemblies often fit together with substantial shape complementarity to generate architectures optimal for function in a manner not achievable by current design approaches. We describe a "top-down" reinforcement learning-based design approach that solves this problem using Monte Carlo tree search to sample protein conformers in the context of an overall architecture and specified functional constraints. Cryo-electron microscopy structures of the designed disk-shaped nanopores and ultracompact icosahedra are very close to the computational models. The icosohedra enable very-high-density display of immunogens and signaling molecules, which potentiates vaccine response and angiogenesis induction. Our approach enables the top-down design of complex protein nanomaterials with desired system properties and demonstrates the power of reinforcement learning in protein design.
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Affiliation(s)
- Isaac D Lutz
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Shunzhi Wang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Christoffer Norn
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- BioInnovation Institute, DK2200 Copenhagen N, Denmark
| | - Alexis Courbet
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Andrew J Borst
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Yan Ting Zhao
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Oral Health Sciences, University of Washington, Seattle, WA, USA
| | - Annie Dosey
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Longxing Cao
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Jinwei Xu
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Elizabeth M Leaf
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Catherine Treichel
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Patrisia Litvicov
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Zhe Li
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alexander D Goodson
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | | | - Minkyung Baek
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Oral Health Sciences, University of Washington, Seattle, WA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
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3
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Filsinger GT, Wannier TM, Pedersen FB, Lutz ID, Zhang J, Stork DA, Debnath A, Gozzi K, Kuchwara H, Volf V, Wang S, Rios X, Gregg CJ, Lajoie MJ, Shipman SL, Aach J, Laub MT, Church GM. Characterizing the portability of phage-encoded homologous recombination proteins. Nat Chem Biol 2021; 17:394-402. [PMID: 33462496 PMCID: PMC7990699 DOI: 10.1038/s41589-020-00710-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 11/02/2020] [Accepted: 11/13/2020] [Indexed: 01/29/2023]
Abstract
Efficient genome editing methods are essential for biotechnology and fundamental research. Homologous recombination (HR) is the most versatile method of genome editing, but techniques that rely on host RecA-mediated pathways are inefficient and laborious. Phage-encoded single-stranded DNA annealing proteins (SSAPs) improve HR 1,000-fold above endogenous levels. However, they are not broadly functional. Using Escherichia coli, Lactococcus lactis, Mycobacterium smegmatis, Lactobacillus rhamnosus and Caulobacter crescentus, we investigated the limited portability of SSAPs. We find that these proteins specifically recognize the C-terminal tail of the host's single-stranded DNA-binding protein (SSB) and are portable between species only if compatibility with this host domain is maintained. Furthermore, we find that co-expressing SSAPs with SSBs can significantly improve genome editing efficiency, in some species enabling SSAP functionality even without host compatibility. Finally, we find that high-efficiency HR far surpasses the mutational capacity of commonly used random mutagenesis methods, generating exceptional phenotypes that are inaccessible through sequential nucleotide conversions.
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Affiliation(s)
- Gabriel T. Filsinger
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA.,Correspondence to: ,
| | - Timothy M. Wannier
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Felix B. Pedersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Isaac D. Lutz
- Institute for Protein Design, University of Washington, Seattle, Washington, USA.,Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Julie Zhang
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Devon A. Stork
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Anik Debnath
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Tenza Inc., Cambridge, MA
| | - Kevin Gozzi
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Helene Kuchwara
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Verena Volf
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA.,Harvard University John A. Paulson School of Engineering and Applied Sciences, Cambridge, Massachusetts, USA
| | - Stan Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Xavier Rios
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Marc J. Lajoie
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Seth L. Shipman
- Gladstone Institutes, San Francisco, CA,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA
| | - John Aach
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael T. Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - George M. Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Correspondence to: ,
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4
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Crowe LB, Hughes PF, Alcorta DA, Osada T, Smith AP, Totzke J, Loiselle DR, Lutz ID, Gargesha M, Roy D, Roques J, Darr D, Lyerly HK, Spector NL, Haystead TA. A Fluorescent Hsp90 Probe Demonstrates the Unique Association between Extracellular Hsp90 and Malignancy in Vivo. ACS Chem Biol 2017; 12:1047-1055. [PMID: 28103010 DOI: 10.1021/acschembio.7b00006] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Extracellular expression of heat shock protein 90 (eHsp90) by tumor cells is correlated with malignancy. Development of small molecule probes that can detect eHsp90 in vivo may therefore have utility in the early detection of malignancy. We synthesized a cell impermeable far-red fluorophore-tagged Hsp90 inhibitor to target eHsp90 in vivo. High resolution confocal and lattice light sheet microscopy show that probe-bound eHsp90 accumulates in punctate structures on the plasma membrane of breast tumor cells and is actively internalized. The extent of internalization correlates with tumor cell aggressiveness, and this process can be induced in benign cells by overexpressing p110HER2. Whole body cryoslicing, imaging, and histology of flank and spontaneous tumor-bearing mice strongly suggests that eHsp90 expression and internalization is a phenomenon unique to tumor cells in vivo and may provide an "Achilles heel" for the early diagnosis of metastatic disease and targeted drug delivery.
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Affiliation(s)
- Lauren B. Crowe
- Department of Cell
Biology, Duke University, Durham, North Carolina 27710, United States
| | - Philip F. Hughes
- Department
of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710, United States
| | - David A. Alcorta
- Department of Medicine, Duke University, Durham, North Carolina 27710, United States
| | - Takuya Osada
- Department of Surgery, Duke University, Durham, North Carolina 27710, United States
| | - Aaron P. Smith
- Department
of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710, United States
| | - Juliane Totzke
- Department
of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710, United States
| | - David R. Loiselle
- Department
of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710, United States
| | - Isaac D. Lutz
- Department
of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710, United States
| | | | - Debasish Roy
- BioInVision, Inc., Mayfield Village, Ohio 44143, United States
| | - Jose Roques
- Lineberger Comprehensive
Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - David Darr
- Lineberger Comprehensive
Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - H. Kim Lyerly
- Department of Surgery, Duke University, Durham, North Carolina 27710, United States
| | - Neil L. Spector
- Department
of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710, United States
| | - Timothy A.J. Haystead
- Department
of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710, United States
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