1
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Plaper T, Rihtar E, Železnik Ramuta T, Forstnerič V, Jazbec V, Ivanovski F, Benčina M, Jerala R. The art of designed coiled-coils for the regulation of mammalian cells. Cell Chem Biol 2024; 31:1460-1472. [PMID: 38971158 DOI: 10.1016/j.chembiol.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/04/2024] [Accepted: 06/11/2024] [Indexed: 07/08/2024]
Abstract
Synthetic biology aims to engineer complex biological systems using modular elements, with coiled-coil (CC) dimer-forming modules are emerging as highly useful building blocks in the regulation of protein assemblies and biological processes. Those small modules facilitate highly specific and orthogonal protein-protein interactions, offering versatility for the regulation of diverse biological functions. Additionally, their design rules enable precise control and tunability over these interactions, which are crucial for specific applications. Recent advancements showcase their potential for use in innovative therapeutic interventions and biomedical applications. In this review, we discuss the potential of CCs, exploring their diverse applications in mammalian cells, such as synthetic biological circuit design, transcriptional and allosteric regulation, cellular assemblies, chimeric antigen receptor (CAR) T cell regulation, and genome editing and their role in advancing the understanding and regulation of cellular processes.
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Affiliation(s)
- Tjaša Plaper
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Erik Rihtar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Taja Železnik Ramuta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Vida Forstnerič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Vid Jazbec
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Filip Ivanovski
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; Centre for Technologies of Gene and Cell Therapy, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; Centre for Technologies of Gene and Cell Therapy, Hajdrihova 19, 1000 Ljubljana, Slovenia.
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2
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Ramos Ferrer P, Sakiyama-Elbert S. Affinity-based drug delivery systems for the central nervous system: exploiting molecular interactions for local, precise targeting. J Neural Eng 2024; 21:041004. [PMID: 39059438 DOI: 10.1088/1741-2552/ad680a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 07/26/2024] [Indexed: 07/28/2024]
Abstract
Objective: The effective treatment of central nervous system (CNS) disorders remains a significant challenge, primarily due to its molecular and structural complexity. Clinical translation of promising therapeutic agents is limited by the lack of optimal drug delivery systems capable of targeted, localized release of drugs to the brain and spinal cord.Approach: This review provides an overview of the potential of affinity-based drug delivery systems, which leverage molecular interactions to enhance the delivery and efficacy of therapeutic agents within the CNS.Main results: Various approaches, including hydrogels, micro- and nanoparticles, and functionalized biomaterials, are examined for their ability to provide local, sustained release of proteins, growth factors and other drugs.Significance: Furthermore, we present a detailed analysis of design considerations for developing effective affinity-based systems, incorporating insights from both existing literature and our group's research. These considerations include the biochemical modification of delivery vehicles and the optimization of physical and chemical properties to improve therapeutic outcomes.
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Affiliation(s)
- Pablo Ramos Ferrer
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States of America
| | - Shelly Sakiyama-Elbert
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States of America
- Department of Bioengineering, University of Washington, Seattle, WA, United States of America
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3
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Zhou S, Nishimura F, Wada K, Fujii K, Kondo T, Watanabe K, Imai Y, Ohtsuki T, Kitamatsu M. Configuration of two cysteine residues in a ring within a stapled Bim peptide affects the secondary structure and apoptotic activity. Bioorg Med Chem Lett 2024; 112:129915. [PMID: 39127242 DOI: 10.1016/j.bmcl.2024.129915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/29/2024] [Accepted: 08/04/2024] [Indexed: 08/12/2024]
Abstract
Many reports have shown that stabilization of secondary structure by stapling functional peptides enhances the intracellular bioactivity. However, no report has discussed the correlation between stabilization and biological activity based on the configuration of amino acid residues used as anchors for stapling. To clarify this, we investigated the helix content and apoptotic efficiency of an apoptosis-inducing peptide, Bim, and four stapled Bim peptides containing stapling-related Cys residues introduced with different configurations within the sequence. The results demonstrated that the configuration of Cys residues in stapled Bim peptides affected the secondary structure and intracellular activity of the peptides, and furthermore, there was a correlation between these latter two variables.
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Affiliation(s)
- Shengli Zhou
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan
| | - Fuka Nishimura
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Kazuhaya Wada
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Kaho Fujii
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Takeshi Kondo
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Kazunori Watanabe
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan
| | - Yoshitane Imai
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Takashi Ohtsuki
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan.
| | - Mizuki Kitamatsu
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan.
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4
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Albanese KI, Petrenas R, Pirro F, Naudin EA, Borucu U, Dawson WM, Scott DA, Leggett GJ, Weiner OD, Oliver TAA, Woolfson DN. Rationally seeded computational protein design of ɑ-helical barrels. Nat Chem Biol 2024; 20:991-999. [PMID: 38902458 PMCID: PMC11288890 DOI: 10.1038/s41589-024-01642-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 05/09/2024] [Indexed: 06/22/2024]
Abstract
Computational protein design is advancing rapidly. Here we describe efficient routes starting from validated parallel and antiparallel peptide assemblies to design two families of α-helical barrel proteins with central channels that bind small molecules. Computational designs are seeded by the sequences and structures of defined de novo oligomeric barrel-forming peptides, and adjacent helices are connected by loop building. For targets with antiparallel helices, short loops are sufficient. However, targets with parallel helices require longer connectors; namely, an outer layer of helix-turn-helix-turn-helix motifs that are packed onto the barrels. Throughout these computational pipelines, residues that define open states of the barrels are maintained. This minimizes sequence sampling, accelerating the design process. For each of six targets, just two to six synthetic genes are made for expression in Escherichia coli. On average, 70% of these genes express to give soluble monomeric proteins that are fully characterized, including high-resolution structures for most targets that match the design models with high accuracy.
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Affiliation(s)
- Katherine I Albanese
- School of Chemistry, University of Bristol, Bristol, UK
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK
| | | | - Fabio Pirro
- School of Chemistry, University of Bristol, Bristol, UK
| | | | - Ufuk Borucu
- School of Biochemistry, University of Bristol, Medical Sciences Building, Bristol, UK
| | | | - D Arne Scott
- Rosa Biotech, Science Creates St Philips, Bristol, UK
| | | | - Orion D Weiner
- Cardiovascular Research Institute, Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | | | - Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, UK.
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK.
- School of Biochemistry, University of Bristol, Medical Sciences Building, Bristol, UK.
- Bristol BioDesign Institute, University of Bristol, Bristol, UK.
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5
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Cross JA, Dawson WM, Shukla SR, Weijman JF, Mantell J, Dodding MP, Woolfson DN. A de novo designed coiled coil-based switch regulates the microtubule motor kinesin-1. Nat Chem Biol 2024; 20:916-923. [PMID: 38849529 PMCID: PMC11213707 DOI: 10.1038/s41589-024-01640-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 05/09/2024] [Indexed: 06/09/2024]
Abstract
Many enzymes are allosterically regulated via conformational change; however, our ability to manipulate these structural changes and control function is limited. Here we install a conformational switch for allosteric activation into the kinesin-1 microtubule motor in vitro and in cells. Kinesin-1 is a heterotetramer that accesses open active and closed autoinhibited states. The equilibrium between these states centers on a flexible elbow within a complex coiled-coil architecture. We target the elbow to engineer a closed state that can be opened with a de novo designed peptide. The alternative states are modeled computationally and confirmed by biophysical measurements and electron microscopy. In cells, peptide-driven activation increases kinesin transport, demonstrating a primary role for conformational switching in regulating motor activity. The designs are enabled by our understanding of ubiquitous coiled-coil structures, opening possibilities for controlling other protein activities.
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Affiliation(s)
- Jessica A Cross
- School of Biochemistry, University of Bristol, Bristol, UK.
- School of Chemistry, University of Bristol, Bristol, UK.
| | | | - Shivam R Shukla
- School of Biochemistry, University of Bristol, Bristol, UK
- School of Chemistry, University of Bristol, Bristol, UK
| | | | - Judith Mantell
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Mark P Dodding
- School of Biochemistry, University of Bristol, Bristol, UK.
- Bristol BioDesign Institute, University of Bristol, Bristol, UK.
| | - Derek N Woolfson
- School of Biochemistry, University of Bristol, Bristol, UK.
- School of Chemistry, University of Bristol, Bristol, UK.
- Bristol BioDesign Institute, University of Bristol, Bristol, UK.
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6
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Kortemme T. De novo protein design-From new structures to programmable functions. Cell 2024; 187:526-544. [PMID: 38306980 PMCID: PMC10990048 DOI: 10.1016/j.cell.2023.12.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/03/2023] [Accepted: 12/19/2023] [Indexed: 02/04/2024]
Abstract
Methods from artificial intelligence (AI) trained on large datasets of sequences and structures can now "write" proteins with new shapes and molecular functions de novo, without starting from proteins found in nature. In this Perspective, I will discuss the state of the field of de novo protein design at the juncture of physics-based modeling approaches and AI. New protein folds and higher-order assemblies can be designed with considerable experimental success rates, and difficult problems requiring tunable control over protein conformations and precise shape complementarity for molecular recognition are coming into reach. Emerging approaches incorporate engineering principles-tunability, controllability, and modularity-into the design process from the beginning. Exciting frontiers lie in deconstructing cellular functions with de novo proteins and, conversely, constructing synthetic cellular signaling from the ground up. As methods improve, many more challenges are unsolved.
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Affiliation(s)
- Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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7
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Goldbach N, Benna I, Wicky BIM, Croft JT, Carter L, Bera AK, Nguyen H, Kang A, Sankaran B, Yang EC, Lee KK, Baker D. De novo design of monomeric helical bundles for pH-controlled membrane lysis. Protein Sci 2023; 32:e4769. [PMID: 37632837 PMCID: PMC10578055 DOI: 10.1002/pro.4769] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/10/2023] [Accepted: 08/24/2023] [Indexed: 08/28/2023]
Abstract
Targeted intracellular delivery via receptor-mediated endocytosis requires the delivered cargo to escape the endosome to prevent lysosomal degradation. This can in principle be achieved by membrane lysis tightly restricted to endosomal membranes upon internalization to avoid general membrane insertion and lysis. Here, we describe the design of small monomeric proteins with buried histidine containing pH-responsive hydrogen bond networks and membrane permeating amphipathic helices. Of the 30 designs that were experimentally tested, all expressed in Escherichia coli, 13 were monomeric with the expected secondary structure, and 4 designs disrupted artificial liposomes in a pH-dependent manner. Mutational analysis showed that the buried histidine hydrogen bond networks mediate pH-responsiveness and control lysis of model membranes within a very narrow range of pH (6.0-5.5) with almost no lysis occurring at neutral pH. These tightly controlled lytic monomers could help mediate endosomal escape in designed targeted delivery platforms.
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Affiliation(s)
- Nicolas Goldbach
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Molecular Life SciencesTechnical University of MunichMunichGermany
| | - Issa Benna
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BioengineeringUniversity of WashingtonSeattleWashingtonUSA
| | - Basile I. M. Wicky
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Jacob T. Croft
- Department of Medicinal ChemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Lauren Carter
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Asim K. Bera
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Hannah Nguyen
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Alex Kang
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated BioimagingLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Erin C. Yang
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
- Biological Physics, Structure and Design Graduate ProgramUniversity of WashingtonSeattleWashingtonUSA
| | - Kelly K. Lee
- Department of Medicinal ChemistryUniversity of WashingtonSeattleWashingtonUSA
- Biological Physics, Structure and Design Graduate ProgramUniversity of WashingtonSeattleWashingtonUSA
- Department of MicrobiologyUniversity of WashingtonSeattleWashingtonUSA
| | - David Baker
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
- Howard Hughes Medical InstituteUniversity of WashingtonSeattleWashingtonUSA
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8
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Smith A, Naudin EA, Edgell CL, Baker EG, Mylemans B, FitzPatrick L, Herman A, Rice HM, Andrews DM, Tigue N, Woolfson DN, Savery NJ. Design and Selection of Heterodimerizing Helical Hairpins for Synthetic Biology. ACS Synth Biol 2023; 12:1845-1858. [PMID: 37224449 PMCID: PMC10278171 DOI: 10.1021/acssynbio.3c00231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Indexed: 05/26/2023]
Abstract
Synthetic biology applications would benefit from protein modules of reduced complexity that function orthogonally to cellular components. As many subcellular processes depend on peptide-protein or protein-protein interactions, de novo designed polypeptides that can bring together other proteins controllably are particularly useful. Thanks to established sequence-to-structure relationships, helical bundles provide good starting points for such designs. Typically, however, such designs are tested in vitro and function in cells is not guaranteed. Here, we describe the design, characterization, and application of de novo helical hairpins that heterodimerize to form 4-helix bundles in cells. Starting from a rationally designed homodimer, we construct a library of helical hairpins and identify complementary pairs using bimolecular fluorescence complementation in E. coli. We characterize some of the pairs using biophysics and X-ray crystallography to confirm heterodimeric 4-helix bundles. Finally, we demonstrate the function of an exemplar pair in regulating transcription in both E. coli and mammalian cells.
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Affiliation(s)
- Abigail
J. Smith
- School
of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K.
| | - Elise A. Naudin
- School
of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Caitlin L. Edgell
- School
of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K.
- School
of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Emily G. Baker
- School
of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K.
- School
of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Bram Mylemans
- School
of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | | | - Andrew Herman
- Flow
Cytometry Facility, School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, U.K.
| | - Helen M. Rice
- Flow
Cytometry Facility, School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, U.K.
| | | | - Natalie Tigue
- BioPharmaceuticals
R&D, AstraZeneca, Cambridge CB4 0WG, U.K.
| | - Derek N. Woolfson
- School
of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K.
- School
of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Nigel J. Savery
- School
of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K.
- BrisEngBio,
School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
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9
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Dai Y, You L, Chilkoti A. Engineering synthetic biomolecular condensates. NATURE REVIEWS BIOENGINEERING 2023; 1:1-15. [PMID: 37359769 PMCID: PMC10107566 DOI: 10.1038/s44222-023-00052-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 03/06/2023] [Indexed: 06/28/2023]
Abstract
The concept of phase-separation-mediated formation of biomolecular condensates provides a new framework to understand cellular organization and cooperativity-dependent cellular functions. With growing understanding of how biological systems drive phase separation and how cellular functions are encoded by biomolecular condensates, opportunities have emerged for cellular control through engineering of synthetic biomolecular condensates. In this Review, we discuss how to construct synthetic biomolecular condensates and how they can regulate cellular functions. We first describe the fundamental principles by which biomolecular components can drive phase separation. Next, we discuss the relationship between the properties of condensates and their cellular functions, which informs the design of components to create programmable synthetic condensates. Finally, we describe recent applications of synthetic biomolecular condensates for cellular control and discuss some of the design considerations and prospective applications.
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Affiliation(s)
- Yifan Dai
- Department of Biomedical Engineering, Duke University, Durham, NC USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC USA
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10
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Wu K, Bai H, Chang YT, Redler R, McNally KE, Sheffler W, Brunette TJ, Hicks DR, Morgan TE, Stevens TJ, Broerman A, Goreshnik I, DeWitt M, Chow CM, Shen Y, Stewart L, Derivery E, Silva DA, Bhabha G, Ekiert DC, Baker D. De novo design of modular peptide-binding proteins by superhelical matching. Nature 2023; 616:581-589. [PMID: 37020023 PMCID: PMC10115654 DOI: 10.1038/s41586-023-05909-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 03/01/2023] [Indexed: 04/07/2023]
Abstract
General approaches for designing sequence-specific peptide-binding proteins would have wide utility in proteomics and synthetic biology. However, designing peptide-binding proteins is challenging, as most peptides do not have defined structures in isolation, and hydrogen bonds must be made to the buried polar groups in the peptide backbone1-3. Here, inspired by natural and re-engineered protein-peptide systems4-11, we set out to design proteins made out of repeating units that bind peptides with repeating sequences, with a one-to-one correspondence between the repeat units of the protein and those of the peptide. We use geometric hashing to identify protein backbones and peptide-docking arrangements that are compatible with bidentate hydrogen bonds between the side chains of the protein and the peptide backbone12. The remainder of the protein sequence is then optimized for folding and peptide binding. We design repeat proteins to bind to six different tripeptide-repeat sequences in polyproline II conformations. The proteins are hyperstable and bind to four to six tandem repeats of their tripeptide targets with nanomolar to picomolar affinities in vitro and in living cells. Crystal structures reveal repeating interactions between protein and peptide interactions as designed, including ladders of hydrogen bonds from protein side chains to peptide backbones. By redesigning the binding interfaces of individual repeat units, specificity can be achieved for non-repeating peptide sequences and for disordered regions of native proteins.
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Affiliation(s)
- Kejia Wu
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Biological Physics, Structure and Design Graduate Program, University of Washington, Seattle, WA, USA
| | - Hua Bai
- 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
| | - Ya-Ting Chang
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Rachel Redler
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | | | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - T J Brunette
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Derrick R Hicks
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | | | - Adam Broerman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Inna Goreshnik
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Michelle DeWitt
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Cameron M Chow
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Yihang Shen
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - Daniel Adriano Silva
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong.
- Monod Bio, Seattle, WA, USA.
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Damian C Ekiert
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - 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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11
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Hakata Y, Yamashita K, Hashimoto S, Ohtsuki T, Miyazawa M, Kitamatsu M. Adjusting Heterodimeric Coiled-Coils (K/E Zipper) to Connect Autophagy-Inducing Peptide with Cell-Penetrating Peptide. Pharmaceutics 2023; 15:pharmaceutics15041048. [PMID: 37111533 PMCID: PMC10141234 DOI: 10.3390/pharmaceutics15041048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/16/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
A connection of a functional peptide with a cell-penetrating peptide (CPP) used a heterodimeric coiled-coil as a molecular zipper can improve the intracellular delivery and activity of the functional peptide. However, the chain length of the coiled coil required for functioning as the molecular zipper is unknown at present. To solve the problem, we prepared an autophagy-inducing peptide (AIP) that conjugates with the CPP via heterodimeric coiled-coils consisting of 1 to 4 repeating units (K/E zipper; AIP-Kn and En-CPP), and we investigated the optimum length of the K/E zipper for effective intracellular delivery and autophagy induction. Fluorescence spectroscopy showed that K/E zippers with n = 3 and 4 formed a stable 1:1 hybrid (AIP-K3/E3-CPP and AIP-K4/E4-CPP, respectively). Both AIP-K3 and AIP-K4 were successfully delivered into cells by the corresponding hybrid formation with K3-CPP and K4-CPP, respectively. Interestingly, autophagy was also induced by the K/E zippers with n = 3 and 4, more intensively by the former than by the latter. The peptides and K/E zippers used in this study did not show significant cytotoxicity. These results indicate that the effective induction of autophagy occurs via an exquisite balance of the association and dissociation of the K/E zipper in this system.
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Affiliation(s)
- Yoshiyuki Hakata
- Department of Immunology, Faculty of Medicine, Kindai University, 377-2 Ohno-Higashi, Osakasayama 589-8511, Japan
- Department of Arts and Sciences, Faculty of Medicine, Kindai University, 377-2 Ohno-Higashi, Osakasayama 589-8511, Japan
| | - Kazuma Yamashita
- Department of Applied Chemistry, Faculty of Science and Engineering, Kindai University, 3-4-1 Kowakae, Higashiosaka 577-8502, Japan
| | - Sonoko Hashimoto
- Department of Applied Chemistry, Faculty of Science and Engineering, Kindai University, 3-4-1 Kowakae, Higashiosaka 577-8502, Japan
| | - Takashi Ohtsuki
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan
| | - Masaaki Miyazawa
- Department of Immunology, Faculty of Medicine, Kindai University, 377-2 Ohno-Higashi, Osakasayama 589-8511, Japan
| | - Mizuki Kitamatsu
- Department of Applied Chemistry, Faculty of Science and Engineering, Kindai University, 3-4-1 Kowakae, Higashiosaka 577-8502, Japan
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12
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Menke FS, Wicher B, Maurizot V, Huc I. Homochiral versus Heterochiral Dimeric Helical Foldamer Bundles: Chlorinated-Solvent-Dependent Self-Sorting. Angew Chem Int Ed Engl 2023; 62:e202217325. [PMID: 36625790 DOI: 10.1002/anie.202217325] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/11/2023]
Abstract
Aromatic oligoamide sequences programmed to fold into stable helical conformations were designed to display a linear array of hydrogen-bond donors and acceptors at their surface. Sequences were prepared by solid-phase synthesis. Solution 1 H NMR spectroscopic studies and solid-state crystallographic structures demonstrated the formation of stable hydrogen-bond-mediated dimeric helix bundles that could be either heterochiral (with a P and an M helix) or homochiral (with two P or two M helices). Formation of the hetero- or homochiral dimers could be driven quantitatively using different chlorinated solvents-exemplifying a remarkable case of either social or narcissistic chiral self-sorting or upon imposing absolute handedness to the helices to forbid PM species.
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Affiliation(s)
- Friedericke S Menke
- Department of Pharmacy, Ludwig-Maximilians-University of Munich, Butenandtstr. 5-13, 81377, München, Germany
| | - Barbara Wicher
- Department of Chemical Technology of Drugs, Poznan University of Medical Sciences, 6 Grunwaldzka St., 60-780, Poznan, Poland
| | - Victor Maurizot
- CBMN (UMR 5248), Univ. Bordeaux, CNRS, Bordeaux INP, 2, Rue Robert Escarpit, 33600, Pessac, France
| | - Ivan Huc
- Department of Pharmacy, Ludwig-Maximilians-University of Munich, Butenandtstr. 5-13, 81377, München, Germany
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13
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Woolfson DN. Understanding a protein fold: the physics, chemistry, and biology of α-helical coiled coils. J Biol Chem 2023; 299:104579. [PMID: 36871758 PMCID: PMC10124910 DOI: 10.1016/j.jbc.2023.104579] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 03/07/2023] Open
Abstract
Protein science is being transformed by powerful computational methods for structure prediction and design: AlphaFold2 can predict many natural protein structures from sequence, and other AI methods are enabling the de novo design of new structures. This raises a question: how much do we understand the underlying sequence-to-structure/function relationships being captured by these methods? This perspective presents our current understanding of one class of protein assembly, the α-helical coiled coils. At first sight, these are straightforward: sequence repeats of hydrophobic (h) and polar (p) residues, (hpphppp)n, direct the folding and assembly of amphipathic α helices into bundles. However, many different bundles are possible: they can have two or more helices (different oligomers); the helices can have parallel, antiparallel or mixed arrangements (different topologies); and the helical sequences can be the same (homomers) or different (heteromers). Thus, sequence-to-structure relationships must be present within the hpphppp repeats to distinguish these states. I discuss the current understanding of this problem at three levels: First, physics gives a parametric framework to generate the many possible coiled-coil backbone structures. Second, chemistry provides a means to explore and deliver sequence-to-structure relationships. Third, biology shows how coiled coils are adapted and functionalized in nature, inspiring applications of coiled coils in synthetic biology. I argue that the chemistry is largely understood; the physics is partly solved, though the considerable challenge of predicting even relative stabilities of different coiled-coil states remains; but there is much more to explore in the biology and synthetic biology of coiled coils.
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Affiliation(s)
- Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, United Kingdom; School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, United Kingdom; BrisEngBio, School of Chemistry, University of Bristol, Bristol, United Kingdom; Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, United Kingdom.
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14
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McDonald EF, Jones T, Plate L, Meiler J, Gulsevin A. Benchmarking AlphaFold2 on peptide structure prediction. Structure 2023; 31:111-119.e2. [PMID: 36525975 PMCID: PMC9883802 DOI: 10.1016/j.str.2022.11.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 10/15/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022]
Abstract
Recent advancements in computational tools have allowed protein structure prediction with high accuracy. Computational prediction methods have been used for modeling many soluble and membrane proteins, but the performance of these methods in modeling peptide structures has not yet been systematically investigated. We benchmarked the accuracy of AlphaFold2 in predicting 588 peptide structures between 10 and 40 amino acids using experimentally determined NMR structures as reference. Our results showed AlphaFold2 predicts α-helical, β-hairpin, and disulfide-rich peptides with high accuracy. AlphaFold2 performed at least as well if not better than alternative methods developed specifically for peptide structure prediction. AlphaFold2 showed several shortcomings in predicting Φ/Ψ angles, disulfide bond patterns, and the lowest RMSD structures failed to correlate with lowest pLDDT ranked structures. In summary, computation can be a powerful tool to predict peptide structures, but additional steps may be necessary to analyze and validate the results.
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Affiliation(s)
- Eli Fritz McDonald
- Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37212, USA
| | - Taylor Jones
- Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37212, USA
| | - Lars Plate
- Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN 37212, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37212, USA; Institute for Drug Discovery, Leipzig University Medical School, 04103 Leipzig, Germany.
| | - Alican Gulsevin
- Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37212, USA.
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15
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Naudin EA, Albanese KI, Smith AJ, Mylemans B, Baker EG, Weiner OD, Andrews DM, Tigue N, Savery NJ, Woolfson DN. From peptides to proteins: coiled-coil tetramers to single-chain 4-helix bundles. Chem Sci 2022; 13:11330-11340. [PMID: 36320580 PMCID: PMC9533478 DOI: 10.1039/d2sc04479j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/24/2022] [Indexed: 11/21/2022] Open
Abstract
The design of completely synthetic proteins from first principles—de novo protein design—is challenging. This is because, despite recent advances in computational protein–structure prediction and design, we do not understand fully the sequence-to-structure relationships for protein folding, assembly, and stabilization. Antiparallel 4-helix bundles are amongst the most studied scaffolds for de novo protein design. We set out to re-examine this target, and to determine clear sequence-to-structure relationships, or design rules, for the structure. Our aim was to determine a common and robust sequence background for designing multiple de novo 4-helix bundles. In turn, this could be used in chemical and synthetic biology to direct protein–protein interactions and as scaffolds for functional protein design. Our approach starts by analyzing known antiparallel 4-helix coiled-coil structures to deduce design rules. In terms of the heptad repeat, abcdefg—i.e., the sequence signature of many helical bundles—the key features that we identify are: a = Leu, d = Ile, e = Ala, g = Gln, and the use of complementary charged residues at b and c. Next, we implement these rules in the rational design of synthetic peptides to form antiparallel homo- and heterotetramers. Finally, we use the sequence of the homotetramer to derive in one step a single-chain 4-helix-bundle protein for recombinant production in E. coli. All of the assembled designs are confirmed in aqueous solution using biophysical methods, and ultimately by determining high-resolution X-ray crystal structures. Our route from peptides to proteins provides an understanding of the role of each residue in each design. Rules for designing 4-helix bundles are defined, tested, and used to generate de novo peptide assemblies and a single-chain protein.![]()
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Affiliation(s)
- Elise A. Naudin
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Katherine I. Albanese
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Abigail J. Smith
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK
| | - Bram Mylemans
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Emily G. Baker
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK
| | - Orion D. Weiner
- Cardiovascular Research Institute, Department of Biochemistry and Biophysics, University of California, 555 Mission Bay Blvd. South, San Francisco, CA 94158, USA
| | - David M. Andrews
- Oncology R&D, AstraZeneca, Cambridge Science Park, Darwin Building, Cambridge CB4 0WG, UK
| | - Natalie Tigue
- BioPharmaceuticals R&D, AstraZeneca, Granta Park, Cambridge CB21 6GH, UK
| | - Nigel J. Savery
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK
- BrisEngBio, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Derek N. Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK
- BrisEngBio, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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