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Li Z, Wang S, Nattermann U, Bera AK, Borst AJ, Yaman MY, Bick MJ, Yang EC, Sheffler W, Lee B, Seifert S, Hura GL, Nguyen H, Kang A, Dalal R, Lubner JM, Hsia Y, Haddox H, Courbet A, Dowling Q, Miranda M, Favor A, Etemadi A, Edman NI, Yang W, Weidle C, Sankaran B, Negahdari B, Ross MB, Ginger DS, Baker D. Accurate computational design of three-dimensional protein crystals. Nat Mater 2023; 22:1556-1563. [PMID: 37845322 DOI: 10.1038/s41563-023-01683-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 09/07/2023] [Indexed: 10/18/2023]
Abstract
Protein crystallization plays a central role in structural biology. Despite this, the process of crystallization remains poorly understood and highly empirical, with crystal contacts, lattice packing arrangements and space group preferences being largely unpredictable. Programming protein crystallization through precisely engineered side-chain-side-chain interactions across protein-protein interfaces is an outstanding challenge. Here we develop a general computational approach for designing three-dimensional protein crystals with prespecified lattice architectures at atomic accuracy that hierarchically constrains the overall number of degrees of freedom of the system. We design three pairs of oligomers that can be individually purified, and upon mixing, spontaneously self-assemble into >100 µm three-dimensional crystals. The structures of these crystals are nearly identical to the computational design models, closely corresponding in both overall architecture and the specific protein-protein interactions. The dimensions of the crystal unit cell can be systematically redesigned while retaining the space group symmetry and overall architecture, and the crystals are extremely porous and highly stable. Our approach enables the computational design of protein crystals with high accuracy, and the designed protein crystals, which have both structural and assembly information encoded in their primary sequences, provide a powerful platform for biological materials engineering.
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Affiliation(s)
- Zhe Li
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, 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
| | - Una Nattermann
- 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 & 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
| | - Andrew J Borst
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Muammer Y Yaman
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Matthew J Bick
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Erin C Yang
- 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 & Design, University of Washington, Seattle, WA, USA
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Byeongdu Lee
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL, USA
| | - Soenke Seifert
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL, USA
| | - Greg L Hura
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hannah Nguyen
- 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
| | - Radhika Dalal
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Joshua M Lubner
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Yang Hsia
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hugh Haddox
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alexis Courbet
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- HHMI, University of Washington, Seattle, WA, USA
| | - Quinton Dowling
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Marcos Miranda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Andrew Favor
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
| | - Ali Etemadi
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Natasha I Edman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Wei Yang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Connor Weidle
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Babak Negahdari
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Michael B Ross
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, USA
| | - David S Ginger
- Department of Chemistry, 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.
- HHMI, University of Washington, Seattle, WA, USA.
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Lubner JM, Dodge-Kafka KL, Carlson CR, Church GM, Chou MF, Schwartz D. Cushing's syndrome mutant PKA L205R exhibits altered substrate specificity. FEBS Lett 2017; 591:459-467. [PMID: 28100013 DOI: 10.1002/1873-3468.12562] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/10/2017] [Accepted: 01/12/2017] [Indexed: 12/22/2022]
Abstract
The PKAL205R hotspot mutation has been implicated in Cushing's syndrome through hyperactive gain-of-function PKA signaling; however, its influence on substrate specificity has not been investigated. Here, we employ the Proteomic Peptide Library (ProPeL) approach to create high-resolution models for PKAWT and PKAL205R substrate specificity. We reveal that the L205R mutation reduces canonical hydrophobic preference at the substrate P + 1 position, and increases acidic preference in downstream positions. Using these models, we designed peptide substrates that exhibit altered selectivity for specific PKA variants, and demonstrate the feasibility of selective PKAL205R loss-of-function signaling. Through these results, we suggest that substrate rewiring may contribute to Cushing's syndrome disease etiology, and introduce a powerful new paradigm for investigating mutation-induced kinase substrate rewiring in human disease.
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Affiliation(s)
- Joshua M Lubner
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, USA
| | - Kimberly L Dodge-Kafka
- Pat and Jim Calhoun Center for Cardiology, Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Cathrine R Carlson
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Norway
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Michael F Chou
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Daniel Schwartz
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, USA
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