1
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Meador K, Castells-Graells R, Aguirre R, Sawaya MR, Arbing MA, Sherman T, Senarathne C, Yeates TO. A suite of designed protein cages using machine learning and protein fragment-based protocols. Structure 2024; 32:751-765.e11. [PMID: 38513658 PMCID: PMC11162342 DOI: 10.1016/j.str.2024.02.017] [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: 10/19/2023] [Revised: 01/22/2024] [Accepted: 02/23/2024] [Indexed: 03/23/2024]
Abstract
Designed protein cages and related materials provide unique opportunities for applications in biotechnology and medicine, but their creation remains challenging. Here, we apply computational approaches to design a suite of tetrahedrally symmetric, self-assembling protein cages. For the generation of docked conformations, we emphasize a protein fragment-based approach, while for sequence design of the de novo interface, a comparison of knowledge-based and machine learning protocols highlights the power and increased experimental success achieved using ProteinMPNN. An analysis of design outcomes provides insights for improving interface design protocols, including prioritizing fragment-based motifs, balancing interface hydrophobicity and polarity, and identifying preferred polar contact patterns. In all, we report five structures for seven protein cages, along with two structures of intermediate assemblies, with the highest resolution reaching 2.0 Å using cryo-EM. This set of designed cages adds substantially to the body of available protein nanoparticles, and to methodologies for their creation.
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Affiliation(s)
- Kyle Meador
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | | | - Roman Aguirre
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Michael R Sawaya
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Mark A Arbing
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Trent Sherman
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Chethaka Senarathne
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA.
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2
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Szyszka TN, Andreas MP, Lie F, Miller LM, Adamson LSR, Fatehi F, Twarock R, Draper BE, Jarrold MF, Giessen TW, Lau YH. Point mutation in a virus-like capsid drives symmetry reduction to form tetrahedral cages. Proc Natl Acad Sci U S A 2024; 121:e2321260121. [PMID: 38722807 PMCID: PMC11098114 DOI: 10.1073/pnas.2321260121] [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: 12/06/2023] [Accepted: 03/25/2024] [Indexed: 05/18/2024] Open
Abstract
Protein capsids are a widespread form of compartmentalization in nature. Icosahedral symmetry is ubiquitous in capsids derived from spherical viruses, as this geometry maximizes the internal volume that can be enclosed within. Despite the strong preference for icosahedral symmetry, we show that simple point mutations in a virus-like capsid can drive the assembly of unique symmetry-reduced structures. Starting with the encapsulin from Myxococcus xanthus, a 180-mer bacterial capsid that adopts the well-studied viral HK97 fold, we use mass photometry and native charge detection mass spectrometry to identify a triple histidine point mutant that forms smaller dimorphic assemblies. Using cryoelectron microscopy, we determine the structures of a precedented 60-mer icosahedral assembly and an unexpected 36-mer tetrahedron that features significant geometric rearrangements around a new interaction surface between capsid protomers. We subsequently find that the tetrahedral assembly can be generated by triple-point mutation to various amino acids and that even a single histidine point mutation is sufficient to form tetrahedra. These findings represent a unique example of tetrahedral geometry when surveying all characterized encapsulins, HK97-like capsids, or indeed any virus-derived capsids reported in the Protein Data Bank, revealing the surprising plasticity of capsid self-assembly that can be accessed through minimal changes in the protein sequence.
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Affiliation(s)
- Taylor N. Szyszka
- School of Chemistry, The University of Sydney, Camperdown, NSW2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW2006, Australia
| | - Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI48109
| | - Felicia Lie
- School of Chemistry, The University of Sydney, Camperdown, NSW2006, Australia
| | - Lohra M. Miller
- Chemistry Department, Indiana University, Bloomington, IN47405
| | | | - Farzad Fatehi
- Department of Mathematics, University of York, YorkYO10 5DD, United Kingdom
- York Cross-Disciplinary Centre for Systems Analysis, University of York, YorkYO10 5DD, United Kingdom
| | - Reidun Twarock
- Department of Mathematics, University of York, YorkYO10 5DD, United Kingdom
- York Cross-Disciplinary Centre for Systems Analysis, University of York, YorkYO10 5DD, United Kingdom
- Department of Biology, University of York, YorkYO10 5DD, United Kingdom
| | | | | | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI48109
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW2006, Australia
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3
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Azuma Y, Gaweł S, Pasternak M, Woźnicka O, Pyza E, Heddle JG. Reengineering of an Artificial Protein Cage for Efficient Packaging of Active Enzymes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2312286. [PMID: 38738740 DOI: 10.1002/smll.202312286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 04/01/2024] [Indexed: 05/14/2024]
Abstract
Protein cages that readily encapsulate active enzymes of interest present useful nanotools for delivery and catalysis, wherein those with programmable disassembly characteristics serve as particularly attractive platforms. Here, a general guest packaging system based on an artificial protein cage, TRAP-cage, the disassembly of which can be induced by the addition of reducing agents, is established. In this system, TRAP-cage with SpyCatcher moieties in the lumen is prepared using genetic modification of the protein building block and assembled into a cage structure with either monovalent gold ions or molecular crosslinkers. The resulting protein cage can efficiently capture guest proteins equipped with a SpyTag by simply mixing them in an aqueous solution. This post-assembly loading system, which circumvents the exposure of guests to thiol-reactive crosslinkers, enables the packaging of enzymes possessing a catalytic cysteine or a metal cofactor while retaining their catalytic activity.
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Affiliation(s)
- Yusuke Azuma
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, Krakow, 30-387, Poland
| | - Szymon Gaweł
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, Krakow, 30-387, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. S. Łojasiewicza 11, Krakow, 30-348, Poland
| | - Monika Pasternak
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, Krakow, 30-387, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. S. Łojasiewicza 11, Krakow, 30-348, Poland
| | - Olga Woźnicka
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa 9, Krakow, 30-387, Poland
| | - Elżbieta Pyza
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa 9, Krakow, 30-387, Poland
| | - Jonathan G Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, Krakow, 30-387, Poland
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4
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Yang EC, Divine R, Miranda MC, Borst AJ, Sheffler W, Zhang JZ, Decarreau J, Saragovi A, Abedi M, Goldbach N, Ahlrichs M, Dobbins C, Hand A, Cheng S, Lamb M, Levine PM, Chan S, Skotheim R, Fallas J, Ueda G, Lubner J, Somiya M, Khmelinskaia A, King NP, Baker D. Computational design of non-porous pH-responsive antibody nanoparticles. Nat Struct Mol Biol 2024:10.1038/s41594-024-01288-5. [PMID: 38724718 DOI: 10.1038/s41594-024-01288-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/22/2024] [Indexed: 05/21/2024]
Abstract
Programming protein nanomaterials to respond to changes in environmental conditions is a current challenge for protein design and is important for targeted delivery of biologics. Here we describe the design of octahedral non-porous nanoparticles with a targeting antibody on the two-fold symmetry axis, a designed trimer programmed to disassemble below a tunable pH transition point on the three-fold axis, and a designed tetramer on the four-fold symmetry axis. Designed non-covalent interfaces guide cooperative nanoparticle assembly from independently purified components, and a cryo-EM density map closely matches the computational design model. The designed nanoparticles can package protein and nucleic acid payloads, are endocytosed following antibody-mediated targeting of cell surface receptors, and undergo tunable pH-dependent disassembly at pH values ranging between 5.9 and 6.7. The ability to incorporate almost any antibody into a non-porous pH-dependent nanoparticle opens up new routes to antibody-directed targeted delivery.
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Affiliation(s)
- Erin C Yang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure & Design, University of Washington, Seattle, WA, USA
| | - Robby Divine
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Graduate Program in Biochemistry, University of Washington, Seattle, WA, USA
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Marcos C Miranda
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Andrew J Borst
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Will Sheffler
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jason Z Zhang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Justin Decarreau
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Amijai Saragovi
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Mohamad Abedi
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Nicolas Goldbach
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Technical University of Munich, Munich, Germany
| | - Maggie Ahlrichs
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Craig Dobbins
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alexis Hand
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Suna Cheng
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Mila Lamb
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Paul M Levine
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Sidney Chan
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rebecca Skotheim
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jorge Fallas
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - George Ueda
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Joshua Lubner
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Masaharu Somiya
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- SANKEN, Osaka University, Osaka, Japan
| | - Alena Khmelinskaia
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Transdisciplinary Research Area 'Building Blocks of Matter and Fundamental Interactions (TRA Matter)', University of Bonn, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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5
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Agdanowski MP, Castells-Graells R, Sawaya MR, Cascio D, Yeates TO, Arbing MA. X-ray crystal structure of a designed rigidified imaging scaffold in the ligand-free conformation. Acta Crystallogr F Struct Biol Commun 2024; 80:107-115. [PMID: 38767964 PMCID: PMC11134730 DOI: 10.1107/s2053230x2400414x] [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: 02/22/2024] [Accepted: 05/06/2024] [Indexed: 05/22/2024] Open
Abstract
Imaging scaffolds composed of designed protein cages fused to designed ankyrin repeat proteins (DARPins) have enabled the structure determination of small proteins by cryogenic electron microscopy (cryo-EM). One particularly well characterized scaffold type is a symmetric tetrahedral assembly composed of 24 subunits, 12 A and 12 B, which has three cargo-binding DARPins positioned on each vertex. Here, the X-ray crystal structure of a representative tetrahedral scaffold in the apo state is reported at 3.8 Å resolution. The X-ray crystal structure complements recent cryo-EM findings on a closely related scaffold, while also suggesting potential utility for crystallographic investigations. As observed in this crystal structure, one of the three DARPins, which serve as modular adaptors for binding diverse `cargo' proteins, present on each of the vertices is oriented towards a large solvent channel. The crystal lattice is unusually porous, suggesting that it may be possible to soak crystals of the scaffold with small (≤30 kDa) protein cargo ligands and subsequently determine cage-cargo structures via X-ray crystallography. The results suggest the possibility that cryo-EM scaffolds may be repurposed for structure determination by X-ray crystallography, thus extending the utility of electron-microscopy scaffold designs for alternative structural biology applications.
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Affiliation(s)
- Matthew P. Agdanowski
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Roger Castells-Graells
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Michael R. Sawaya
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Duilio Cascio
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Todd O. Yeates
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Mark A. Arbing
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA
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6
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Jeon H, Han AR, Oh S, Park JG, Namkoong M, Bang KM, Kim HM, Kim NK, Hwang KY, Hur K, Lee BJ, Heo J, Kim S, Song HK, Cho H, Lee IG. Polymorphic Self-Assembly with Procedural Flexibility for Monodisperse Quaternary Protein Structures of DegQ Enzymes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2308837. [PMID: 38351715 DOI: 10.1002/adma.202308837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/08/2024] [Indexed: 02/29/2024]
Abstract
As large molecular tertiary structures, some proteins can act as small robots that find, bind, and chaperone target protein clients, showing the potential to serve as smart building blocks in self-assembly fields. Instead of using such intrinsic functions, most self-assembly methodologies for proteins aim for de novo-designed structures with accurate geometric assemblies, which can limit procedural flexibility. Here, a strategy enabling polymorphic clustering of quaternary proteins, exhibiting simplicity and flexibility of self-assembling paths for proteins in forming monodisperse quaternary cage particles is presented. It is proposed that the enzyme protomer DegQ, previously solved at low resolution, may potentially be usable as a threefold symmetric building block, which can form polyhedral cages incorporated by the chaperone action of DegQ in the presence of protein clients. To obtain highly monodisperse cage particles, soft, and hence, less resistive client proteins, which can program the inherent chaperone activity of DegQ to efficient formations of polymorphic cages, depending on the size of clients are utilized. By reconstructing the atomic resolution cryogenic electron microscopy DegQ structures using obtained 12- and 24-meric clusters, the polymorphic clustering of DegQ enzymes is validated in terms of soft and rigid domains, which will provide effective routes for protein self-assemblies with procedural flexibility.
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Affiliation(s)
- Hanul Jeon
- Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
- Department of Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Ah-Reum Han
- Center for Biomolecular and Cellular Structure, Life Science Cluster, Institute for Basic Science (IBS), 55, Expo-ro, Daejeon, 34126, Republic of Korea
| | - Sangmin Oh
- Extreme Materials Research Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Jin-Gyeong Park
- Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
- Department of Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Myeong Namkoong
- Extreme Materials Research Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Kyeong-Mi Bang
- Advanced Analysis Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
- Department of Life Science, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Ho Min Kim
- Center for Biomolecular and Cellular Structure, Life Science Cluster, Institute for Basic Science (IBS), 55, Expo-ro, Daejeon, 34126, Republic of Korea
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291, Daehak-ro, Daejeon, 34126, Republic of Korea
| | - Nak-Kyoon Kim
- Advanced Analysis Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Kwang Yeon Hwang
- Department of Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Kahyun Hur
- Extreme Materials Research Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Science, Seoul National University, 599, Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
- College of Pharmacy, Ajou University, 206, Worldcup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea
| | - Jeongyun Heo
- Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Sehoon Kim
- Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Hyun Kyu Song
- Department of Life Science, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Hyesung Cho
- Extreme Materials Research Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - In-Gyun Lee
- Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
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7
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Ohara N, Kawakami N, Arai R, Adachi N, Ikeda A, Senda T, Miyamoto K. Fusion then fission: splitting and reassembly of an artificial fusion-protein nanocage. Chem Commun (Camb) 2024; 60:4605-4608. [PMID: 38586927 DOI: 10.1039/d4cc00115j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
A split-protein system is a simple approach to introduce new termini which are useful as modification sites in protein engineering, but has been adapted mainly for monomeric proteins. Here we demonstrate the design of split subunits of the 60-mer artificial fusion-protein nanocage TIP60. The subunit fragments successfully reformed the cage structure in the same manner as prior to splitting. One of the newly introduced terminals at the interior surface can be modified using a tag peptide and green fluorescent protein. Therefore, the termini could serve as a versatile modification site for incorporating a wide variety of functional peptides and proteins.
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Affiliation(s)
- Naoya Ohara
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan.
| | - Norifumi Kawakami
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan.
| | - Ryoichi Arai
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Ueda, Nagano 386-8567, Japan
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Naruhiko Adachi
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Akihito Ikeda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
| | - Kenji Miyamoto
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan.
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8
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Gladkov N, Scott EA, Meador K, Lee EJ, Laganowsky AD, Yeates TO, Castells‐Graells R. Design of a symmetry-broken tetrahedral protein cage by a method of internal steric occlusion. Protein Sci 2024; 33:e4973. [PMID: 38533546 PMCID: PMC10966355 DOI: 10.1002/pro.4973] [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: 11/15/2023] [Revised: 03/05/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
Methods in protein design have made it possible to create large and complex, self-assembling protein cages with diverse applications. These have largely been based on highly symmetric forms exemplified by the Platonic solids. Prospective applications of protein cages would be expanded by strategies for breaking the designed symmetry, for example, so that only one or a few (instead of many) copies of an exterior domain or motif might be displayed on their surfaces. Here we demonstrate a straightforward design approach for creating symmetry-broken protein cages able to display singular copies of outward-facing domains. We modify the subunit of an otherwise symmetric protein cage through fusion to a small inward-facing domain, only one copy of which can be accommodated in the cage interior. Using biochemical methods and native mass spectrometry, we show that co-expression of the original subunit and the modified subunit, which is further fused to an outward-facing anti-GFP DARPin domain, leads to self-assembly of a protein cage presenting just one copy of the DARPin protein on its exterior. This strategy of designed occlusion provides a facile route for creating new types of protein cages with unique properties.
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Affiliation(s)
- Nika Gladkov
- Department of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Elena A. Scott
- Department of ChemistryTexas A&M UniversityCollege StationTexasUSA
| | - Kyle Meador
- Department of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Eric J. Lee
- Department of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCaliforniaUSA
| | | | - Todd O. Yeates
- Department of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCaliforniaUSA
- Molecular Biology InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
- UCLA‐DOE Institute for Genomics and ProteomicsLos AngelesCaliforniaUSA
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9
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Gee M, Atai K, Coller HA, Yeates TO, Castells-Graells R. Designed fluorescent protein cages as fiducial markers for targeted cell imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582585. [PMID: 38464160 PMCID: PMC10925312 DOI: 10.1101/2024.02.28.582585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Understanding how proteins function within their cellular environments is essential for cellular biology and biomedical research. However, current imaging techniques exhibit limitations, particularly in the study of small complexes and individual proteins within cells. Previously, protein cages have been employed as imaging scaffolds to study purified small proteins using cryo-electron microscopy (cryo-EM). Here we demonstrate an approach to deliver designed protein cages - endowed with fluorescence and targeted binding properties - into cells, thereby serving as fiducial markers for cellular imaging. We used protein cages with anti-GFP DARPin domains to target a mitochondrial protein (MFN1) expressed in mammalian cells, which was genetically fused to GFP. We demonstrate that the protein cages can penetrate cells, are directed to specific subcellular locations, and are detectable with confocal microscopy. This innovation represents a milestone in developing tools for in-depth cellular exploration, especially in conjunction with methods such as cryo-correlative light and electron microscopy (cryo-CLEM).
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Affiliation(s)
- Morgan Gee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA 90095
| | - Kaiser Atai
- Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, CA, USA 90095
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA 90095
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA 90095
| | - Hilary A Coller
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA 90095
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA 90095
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA 90095
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA 90095
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA 90095
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA 90095
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10
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Huddy TF, Hsia Y, Kibler RD, Xu J, Bethel N, Nagarajan D, Redler R, Leung PJY, Weidle C, Courbet A, Yang EC, Bera AK, Coudray N, Calise SJ, Davila-Hernandez FA, Han HL, Carr KD, Li Z, McHugh R, Reggiano G, Kang A, Sankaran B, Dickinson MS, Coventry B, Brunette TJ, Liu Y, Dauparas J, Borst AJ, Ekiert D, Kollman JM, Bhabha G, Baker D. Blueprinting extendable nanomaterials with standardized protein blocks. Nature 2024; 627:898-904. [PMID: 38480887 PMCID: PMC10972742 DOI: 10.1038/s41586-024-07188-4] [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: 06/06/2023] [Accepted: 02/09/2024] [Indexed: 03/26/2024]
Abstract
A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies, in comparison, has been much more complex, largely owing to the irregular shapes of protein structures1. Here we describe extendable linear, curved and angled protein building blocks, as well as inter-block interactions, that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight 'train track' assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence-structure relationships, it has not previously been possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank three-dimensional canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to 'back of an envelope' architectural blueprints.
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Affiliation(s)
- Timothy F Huddy
- 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
| | - Ryan D Kibler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jinwei Xu
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Neville Bethel
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - Rachel Redler
- Department of Cell Biology, NYU School of Medicine, New York, NY, USA
| | - Philip J Y Leung
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular Engineering and Sciences Institute, 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
| | - 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
| | - Erin C Yang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Biological Physics, Structure and 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
| | - Nicolas Coudray
- Department of Cell Biology, NYU School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY, USA
- Division of Precision Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - S John Calise
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Fatima A Davila-Hernandez
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hannah L Han
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Kenneth D Carr
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, 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
| | - Ryan McHugh
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Gabriella Reggiano
- 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
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Miles S Dickinson
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Brian Coventry
- 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
| | - Yulai Liu
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Justas Dauparas
- 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
| | - Damian Ekiert
- Department of Cell Biology, NYU School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY, USA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Gira Bhabha
- Applied Bioinformatics Laboratories, NYU 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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Lu Q, Xu Y, Poppleton E, Zhou K, Sulc P, Stephanopoulos N, Ke Y. DNA-Nanostructure-Guided Assembly of Proteins into Programmable Shapes. NANO LETTERS 2024; 24:1703-1709. [PMID: 38278134 PMCID: PMC10853956 DOI: 10.1021/acs.nanolett.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 01/28/2024]
Abstract
The development of methods to synthesize artificial protein complexes with precisely controlled configurations will enable diverse biological and medical applications. Using DNA to link proteins provides programmability that can be difficult to achieve with other methods. Here, we use DNA origami as an "assembler" to guide the linking of protein-DNA conjugates using a series of oligonucleotide hybridization and displacement operations. We constructed several isomeric protein nanostructures, including a dimer, two types of trimer structures, and three types of tetramer assemblies, on a DNA origami platform by using a C3-symmetric building block composed of a protein trimer modified with DNA handles. Our approach expands the scope for the precise assembly of protein-based nanostructures and will enable the formulation of functional protein complexes with stoichiometric and geometric control.
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Affiliation(s)
- Qinyi Lu
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Yang Xu
- Biodesign
Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Erik Poppleton
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Kun Zhou
- Department
of Biomedical Engineering, Georgia Institute
of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Petr Sulc
- Biodesign
Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Nicholas Stephanopoulos
- Biodesign
Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Yonggang Ke
- Department
of Biomedical Engineering, Georgia Institute
of Technology and Emory University, Atlanta, Georgia 30322, United States
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12
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Szyszka TN, Andreas MP, Lie F, Miller LM, Adamson LSR, Fatehi F, Twarock R, Draper BE, Jarrold MF, Giessen TW, Lau YH. Point mutation in a virus-like capsid drives symmetry reduction to form tetrahedral cages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.579038. [PMID: 38370832 PMCID: PMC10871247 DOI: 10.1101/2024.02.05.579038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Protein capsids are a widespread form of compartmentalisation in nature. Icosahedral symmetry is ubiquitous in capsids derived from spherical viruses, as this geometry maximises the internal volume that can be enclosed within. Despite the strong preference for icosahedral symmetry, we show that simple point mutations in a virus-like capsid can drive the assembly of novel symmetry-reduced structures. Starting with the encapsulin from Myxococcus xanthus, a 180-mer bacterial capsid that adopts the well-studied viral HK97 fold, we use mass photometry and native charge detection mass spectrometry to identify a triple histidine point mutant that forms smaller dimorphic assemblies. Using cryo-EM, we determine the structures of a precedented 60-mer icosahedral assembly and an unprecedented 36-mer tetrahedron that features significant geometric rearrangements around a novel interaction surface between capsid protomers. We subsequently find that the tetrahedral assembly can be generated by triple point mutation to various amino acids, and that even a single histidine point mutation is sufficient to form tetrahedra. These findings represent the first example of tetrahedral geometry across all characterised encapsulins, HK97-like capsids, or indeed any virus-derived capsids reported in the Protein Data Bank, revealing the surprising plasticity of capsid self-assembly that can be accessed through minimal changes in protein sequence.
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Affiliation(s)
- Taylor N Szyszka
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Michael P Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Felicia Lie
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Lohra M Miller
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Lachlan S R Adamson
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Farzad Fatehi
- Department of Mathematics, University of York, York, UK
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Reidun Twarock
- Department of Mathematics, University of York, York, UK
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - Benjamin E Draper
- Megadalton Solutions Inc., 3750 E Bluebird Ln, Bloomington, IN 47401, USA
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW 2006, Australia
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13
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Lee EJ, Gladkov N, Miller JE, Yeates TO. Design of Ligand-Operable Protein-Cages That Open Upon Specific Protein Binding. ACS Synth Biol 2024; 13:157-167. [PMID: 38133598 DOI: 10.1021/acssynbio.3c00383] [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] [Indexed: 12/23/2023]
Abstract
Protein nanocages have diverse applications in medicine and biotechnology, including molecular delivery. However, although numerous studies have demonstrated the ability of protein nanocages to encapsulate various molecular species, limited methods are available for subsequently opening a nanocage for cargo release under specific conditions. A modular platform with a specific protein-target-based mechanism of nanocage opening is notably lacking. To address this important technology gap, we present a new class of designed protein cages, the Ligand-Operable Cage (LOC). LOCs primarily comprise a protein nanocage core and a fused surface binding adaptor. The geometry of the LOC is designed so that binding of a target protein ligand (or multiple copies thereof) to the surface binder is sterically incompatible with retention of the assembled state of the cage. Therefore, the tight binding of a target ligand drives cage disassembly by mass action, subsequently exposing the encapsulated cargo. LOCs are modular; direct substitution of the surface binder sequence can reprogram the nanocage to open in response to any target protein ligand of interest. We demonstrate these design principles using both a natural and a designed protein cage as the core, with different proteins acting as the triggering ligand and with different reporter readouts─fluorescence unquenching and luminescence─for cage disassembly. These developments advance the critical problem of targeted molecular delivery and detection.
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Affiliation(s)
- Eric J Lee
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Nika Gladkov
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Justin E Miller
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, United States
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, United States
- UCLA-DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095, United States
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14
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Kim H, Yang I, Lim SI. Streamlined construction of robust heteroprotein complexes by self-induced in-cell disulfide pairing. Int J Biol Macromol 2024; 254:127965. [PMID: 37944724 DOI: 10.1016/j.ijbiomac.2023.127965] [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: 09/11/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
Biomolecules and their functional subdomains are essential building blocks in the creation of multifunctional nanocomplexes. Methyl-binding domain protein 2 (MBD2) and p66α stand out as small α-helical motifs with an ability to self-assemble into a heterodimeric coiled-coil, making them promising building units. Yet, their practical use is hindered by rapid dissociation upon dilution. In this study, novel fusion tags, MBD2 and p66α variants, were developed to covalently link during co-expression in E. coli SHuffle. Through strategic placement of cysteine at each α-helix's terminus, intracellular crosslinking occurred with high specificity and yield, facilitated by preserved α-helical interactions. This instant disulfide bonding in the oxidative cytoplasm of E. coli SHuffle efficiently overcame the need for inefficient in vitro oxidation and protein extraction prone to creating non-specific adducts and suboptimal bioprocesses. In contrast to their wild-type counterparts, the GFP-mCherry protein complex cross-linked by the fusion tags maintained the heterodimeric state even under extensive dilution. The fusion tags, when combined with the E. coli SHuffle system, allowed for the streamlined co-expression of a stable protein complex through self-induced intracellular cysteine coupling. The approach demonstrated herein holds great promise for producing multifunctional and robust heteroprotein complexes.
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Affiliation(s)
- Hyunji Kim
- Department of Chemical Engineering, Pukyong National University, Yongso-ro 45, Nam-gu, Busan, Republic of Korea
| | - Iji Yang
- Department of Chemical Engineering, Pukyong National University, Yongso-ro 45, Nam-gu, Busan, Republic of Korea
| | - Sung In Lim
- Department of Chemical Engineering, Pukyong National University, Yongso-ro 45, Nam-gu, Busan, Republic of Korea.
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15
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Romero-Romero ML, Garcia-Seisdedos H. Agglomeration: when folded proteins clump together. Biophys Rev 2023; 15:1987-2003. [PMID: 38192350 PMCID: PMC10771401 DOI: 10.1007/s12551-023-01172-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/25/2023] [Indexed: 01/10/2024] Open
Abstract
Protein self-association is a widespread phenomenon that results in the formation of multimeric protein structures with critical roles in cellular processes. Protein self-association can lead to finite protein complexes or open-ended, and potentially, infinite structures. This review explores the concept of protein agglomeration, a process that results from the infinite self-assembly of folded proteins. We highlight its differences from other better-described processes with similar macroscopic features, such as aggregation and liquid-liquid phase separation. We review the sequence, structural, and biophysical factors influencing protein agglomeration. Lastly, we briefly discuss the implications of agglomeration in evolution, disease, and aging. Overall, this review highlights the need to study protein agglomeration for a better understanding of cellular processes.
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Affiliation(s)
- M. L. Romero-Romero
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology, Dresden, Germany
| | - H. Garcia-Seisdedos
- Department of Structural and Molecular Biology, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
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16
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Gladkov N, Scott EA, Meador K, Lee EJ, Laganowsky AD, Yeates TO, Castells-Graells R. Design of a symmetry-broken tetrahedral protein cage by a method of internal steric occlusion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566319. [PMID: 37986890 PMCID: PMC10659388 DOI: 10.1101/2023.11.08.566319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Methods in protein design have made it possible to create large and complex, self-assembling protein cages with diverse applications. These have largely been based on highly symmetric forms exemplified by the Platonic solids. Prospective applications of protein cages would be expanded by strategies for breaking the designed symmetry, e.g., so that only one or a few (instead of many) copies of an exterior domain or motif might be displayed on their surfaces. Here we demonstrate a straightforward design approach for creating symmetry-broken protein cages able to display singular copies of outward-facing domains. We modify the subunit of an otherwise symmetric protein cage through fusion to a small inward-facing domain, only one copy of which can be accommodated in the cage interior. Using biochemical methods and native mass spectrometry, we show that co-expression of the original subunit and the modified subunit, which is further fused to an outward-facing anti-GFP DARPin domain, leads to self-assembly of a protein cage presenting just one copy of the DARPin protein on its exterior. This strategy of designed occlusion provides a facile route for creating new types of protein cages with unique properties.
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Affiliation(s)
- Nika Gladkov
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, United States of America
| | - Elena A. Scott
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States of America
| | - Kyle Meador
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, United States of America
| | - Eric J. Lee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, United States of America
| | - Arthur D. Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States of America
| | - Todd O. Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, United States of America
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, United States of America
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, United States of America
| | - Roger Castells-Graells
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, United States of America
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17
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Khmelinskaia A, Bethel NP, Fatehi F, Antanasijevic A, Borst AJ, Lai SH, Wang JYJ, Mallik BB, Miranda MC, Watkins AM, Ogohara C, Caldwell S, Wu M, Heck AJR, Veesler D, Ward AB, Baker D, Twarock R, King NP. Local structural flexibility drives oligomorphism in computationally designed protein assemblies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.18.562842. [PMID: 37905007 PMCID: PMC10614843 DOI: 10.1101/2023.10.18.562842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Many naturally occurring protein assemblies have dynamic structures that allow them to perform specialized functions. For example, clathrin coats adopt a wide variety of architectures to adapt to vesicular cargos of various sizes. Although computational methods for designing novel self-assembling proteins have advanced substantially over the past decade, most existing methods focus on designing static structures with high accuracy. Here we characterize the structures of three distinct computationally designed protein assemblies that each form multiple unanticipated architectures, and identify flexibility in specific regions of the subunits of each assembly as the source of structural diversity. Cryo-EM single-particle reconstructions and native mass spectrometry showed that only two distinct architectures were observed in two of the three cases, while we obtained six cryo-EM reconstructions that likely represent a subset of the architectures present in solution in the third case. Structural modeling and molecular dynamics simulations indicated that the surprising observation of a defined range of architectures, instead of non-specific aggregation, can be explained by constrained flexibility within the building blocks. Our results suggest that deliberate use of structural flexibility as a design principle will allow exploration of previously inaccessible structural and functional space in designed protein assemblies.
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18
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Meador K, Castells-Graells R, Aguirre R, Sawaya MR, Arbing MA, Sherman T, Senarathne C, Yeates TO. A Suite of Designed Protein Cages Using Machine Learning Algorithms and Protein Fragment-Based Protocols. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561468. [PMID: 37873110 PMCID: PMC10592684 DOI: 10.1101/2023.10.09.561468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Designed protein cages and related materials provide unique opportunities for applications in biotechnology and medicine, while methods for their creation remain challenging and unpredictable. In the present study, we apply new computational approaches to design a suite of new tetrahedrally symmetric, self-assembling protein cages. For the generation of docked poses, we emphasize a protein fragment-based approach, while for de novo interface design, a comparison of computational protocols highlights the power and increased experimental success achieved using the machine learning program ProteinMPNN. In relating information from docking and design, we observe that agreement between fragment-based sequence preferences and ProteinMPNN sequence inference correlates with experimental success. Additional insights for designing polar interactions are highlighted by experimentally testing larger and more polar interfaces. In all, using X-ray crystallography and cryo-EM, we report five structures for seven protein cages, with atomic resolution in the best case reaching 2.0 Å. We also report structures of two incompletely assembled protein cages, providing unique insights into one type of assembly failure. The new set of designed cages and their structures add substantially to the body of available protein nanoparticles, and to methodologies for their creation.
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Affiliation(s)
- Kyle Meador
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA 90095
| | | | - Roman Aguirre
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA 90095
| | - Michael R. Sawaya
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA 90095
| | - Mark A. Arbing
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA 90095
| | - Trent Sherman
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA 90095
| | - Chethaka Senarathne
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA 90095
| | - Todd O. Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA 90095
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA 90095
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19
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Li L, Li Z, Wang Z, Chen S, Liu R, Xu X, Zhang Z, Ye L, Ding Y, Luo Q, Cao S, Zhang L, Imberty A, Chen G. Spatiotemporal Landscape for the Sophisticated Transformation of Protein Assemblies Defined by Multiple Supramolecular Interactions. ACS NANO 2023; 17:15001-15011. [PMID: 37459282 DOI: 10.1021/acsnano.3c04029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Precise protein assemblies not only constitute a series of living machineries but also provide an advanced class of biomaterials. Previously, we developed the inducing ligand strategy to generate various fixed protein assemblies, without the formation of noncovalent interactions between proteins. Here, we demonstrated that controlling the symmetry and number of supramolecular interactions introduced on protein surfaces could direct the formation of unspecific interactions between proteins and induce various nanoscale assemblies, including coiling nanowires, nanotubes, and nanosheets, without manipulation of the protein's native surfaces. More importantly, these nanoscale assemblies could spontaneously evolve into more ordered architectures, crystals. We further showed that the transformation from the introduced supramolecular interactions to the interactions formed between proteins was crucial for pathway selection and outcomes of evolution. These findings reveal a transformation mechanism of protein self-assembly that has not been exploited before and may provide an approach to generate complex and transformable biomacromolecular self-assemblies.
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Affiliation(s)
- Long Li
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Zhen Li
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Ziying Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shuyu Chen
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi'an Jiaotong University, Xi'an 710049, China
| | - Rongying Liu
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Xuyang Xu
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Zhi Zhang
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Linfei Ye
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Yu Ding
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Quan Luo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
- Key Laboratory of Emergency and Trauma, Ministry of Education, College of Emergency and Trauma, Hainan Medical University, Haikou 571199, China
| | - Sheng Cao
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi'an Jiaotong University, Xi'an 710049, China
| | - Anne Imberty
- Université Grenoble Alpes, CNRS, CERMAV, Grenoble 38000, France
| | - Guosong Chen
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Multiscale Research Institute for Complex Systems, Fudan University, Shanghai 200433, China
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20
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Mallik BB, Stanislaw J, Alawathurage TM, Khmelinskaia A. De Novo Design of Polyhedral Protein Assemblies: Before and After the AI Revolution. Chembiochem 2023; 24:e202300117. [PMID: 37014094 DOI: 10.1002/cbic.202300117] [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: 02/15/2023] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 04/05/2023]
Abstract
Self-assembling polyhedral protein biomaterials have gained attention as engineering targets owing to their naturally evolved sophisticated functions, ranging from protecting macromolecules from the environment to spatially controlling biochemical reactions. Precise computational design of de novo protein polyhedra is possible through two main types of approaches: methods from first principles, using physical and geometrical rules, and more recent data-driven methods based on artificial intelligence (AI), including deep learning (DL). Here, we retrospect first principle- and AI-based approaches for designing finite polyhedral protein assemblies, as well as advances in the structure prediction of such assemblies. We further highlight the possible applications of these materials and explore how the presented approaches can be combined to overcome current challenges and to advance the design of functional protein-based biomaterials.
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Affiliation(s)
- Bhoomika Basu Mallik
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
| | - Jenna Stanislaw
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
| | - Tharindu Madhusankha Alawathurage
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
| | - Alena Khmelinskaia
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
- Current address: Department of Chemistry, Ludwig Maximillian University, 80539, Munich, Germany
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21
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Dowling QM, Park YJ, Gerstenmaier N, Yang EC, Wargacki A, Hsia Y, Fries CN, Ravichandran R, Walkey C, Burrell A, Veesler D, Baker D, King NP. Hierarchical design of pseudosymmetric protein nanoparticles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545393. [PMID: 37398374 PMCID: PMC10312784 DOI: 10.1101/2023.06.16.545393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Discrete protein assemblies ranging from hundreds of kilodaltons to hundreds of megadaltons in size are a ubiquitous feature of biological systems and perform highly specialized functions 1-3. Despite remarkable recent progress in accurately designing new self-assembling proteins, the size and complexity of these assemblies has been limited by a reliance on strict symmetry 4,5. Inspired by the pseudosymmetry observed in bacterial microcompartments and viral capsids, we developed a hierarchical computational method for designing large pseudosymmetric self-assembling protein nanomaterials. We computationally designed pseudosymmetric heterooligomeric components and used them to create discrete, cage-like protein assemblies with icosahedral symmetry containing 240, 540, and 960 subunits. At 49, 71, and 96 nm diameter, these nanoparticles are the largest bounded computationally designed protein assemblies generated to date. More broadly, by moving beyond strict symmetry, our work represents an important step towards the accurate design of arbitrary self-assembling nanoscale protein objects.
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Affiliation(s)
- Quinton M Dowling
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Neil Gerstenmaier
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Erin C Yang
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Adam Wargacki
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Yang Hsia
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Chelsea N Fries
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Ravichandran
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Carl Walkey
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Anika Burrell
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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22
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Pan C, Ye J, Zhang S, Li X, Shi Y, Guo Y, Wang K, Sun P, Wu J, Wang H, Zhu L. Production of a promising modular proteinaceous self-assembled delivery system for vaccination. NANOSCALE 2023. [PMID: 37326289 DOI: 10.1039/d2nr06718h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Recently, there have been enormous advances in nano-delivery materials, especially safer and more biocompatible protein-based nanoparticles. Generally, proteinaceous nanoparticles (such as ferritin and virus-like particles) are self-assembled from some natural protein monomers. However, to ensure their capability of assembly, it is difficult to upgrade the protein structure through major modifications. Here, we have developed an efficient orthogonal modular proteinaceous self-assembly delivery system that could load antigens with an attractive coupling strategy. In brief, we constructed a nanocarrier by fusing two orthogonal domains-a pentameric cholera toxin B subunit and a trimer forming peptide-and an engineered streptavidin monomer for binding biotinylated antigens. After successfully preparing the nanoparticles, the receptor-binding domain of SARS-CoV-2 spike protein and influenza virus haemagglutination antigen are used as model antigens for further evaluation. We found that the biotinylated antigen is able to bind to the nanoparticles with high affinity and achieve efficient lymph node drainage when loaded on the nanoparticles. Then, T cells are greatly activated and the formation of germinal centers is observed. Experiments of two mouse models demonstrate the strong antibody responses and prophylactic effects of these nanovaccines. Thus, we establish a proof-of-concept for the delivery system with the potential to load diverse antigen cargos to generate high-performance nanovaccines, thereby offering an attractive platform technology for nanovaccine preparation.
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Affiliation(s)
- Chao Pan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, PR China.
| | - Jingqin Ye
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, PR China.
| | - Sen Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Millitary Medical Sciences, Beijing, 100071, PR China
| | - Xiang Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, PR China.
| | - Yixin Shi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, PR China.
| | - Yan Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, PR China.
| | - Kangfeng Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, PR China.
- College of Life Science, Hebei University, Baoding, 071002, PR China
| | - Peng Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, PR China.
- School of Medicine, Tsinghua University, Beijing, 100084, PR China
| | - Jun Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, PR China.
| | - Hengliang Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, PR China.
| | - Li Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, PR China.
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23
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Huddy TF, Hsia Y, Kibler RD, Xu J, Bethel N, Nagarajan D, Redler R, Leung PJY, Courbet A, Yang EC, Bera AK, Coudray N, Calise SJ, Davila-Hernandez FA, Weidle C, Han HL, Li Z, McHugh R, Reggiano G, Kang A, Sankaran B, Dickinson MS, Coventry B, Brunette TJ, Liu Y, Dauparas J, Borst AJ, Ekiert D, Kollman JM, Bhabha G, Baker D. Blueprinting expandable nanomaterials with standardized protein building blocks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544258. [PMID: 37333359 PMCID: PMC10274926 DOI: 10.1101/2023.06.09.544258] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies in comparison has been much more complex, largely due to the irregular shapes of protein structures 1 . Here we describe extendable linear, curved, and angled protein building blocks, as well as inter-block interactions that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight "train track" assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence-structure relationships, it has not been previously possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank 3D canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to "back of an envelope" architectural blueprints.
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24
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Sheffler W, Yang EC, Dowling Q, Hsia Y, Fries CN, Stanislaw J, Langowski MD, Brandys M, Li Z, Skotheim R, Borst AJ, Khmelinskaia A, King NP, Baker D. Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock. PLoS Comput Biol 2023; 19:e1010680. [PMID: 37216343 PMCID: PMC10237659 DOI: 10.1371/journal.pcbi.1010680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 06/02/2023] [Accepted: 04/09/2023] [Indexed: 05/24/2023] Open
Abstract
Computationally designed multi-subunit assemblies have shown considerable promise for a variety of applications, including a new generation of potent vaccines. One of the major routes to such materials is rigid body sequence-independent docking of cyclic oligomers into architectures with point group or lattice symmetries. Current methods for docking and designing such assemblies are tailored to specific classes of symmetry and are difficult to modify for novel applications. Here we describe RPXDock, a fast, flexible, and modular software package for sequence-independent rigid-body protein docking across a wide range of symmetric architectures that is easily customizable for further development. RPXDock uses an efficient hierarchical search and a residue-pair transform (RPX) scoring method to rapidly search through multidimensional docking space. We describe the structure of the software, provide practical guidelines for its use, and describe the available functionalities including a variety of score functions and filtering tools that can be used to guide and refine docking results towards desired configurations.
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Affiliation(s)
- William Sheffler
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Erin C. Yang
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Graduate Program in Biological Physics, Structure & Design, University of Washington, Seattle, Washington, United States of America
| | - Quinton Dowling
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Yang Hsia
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Chelsea N. Fries
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Jenna Stanislaw
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Transdisciplinary Research Area “Building Blocks of Matter and Fundamental Interactions (TRA Matter)”, University of Bonn, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Mark D. Langowski
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, Washington, United States of America
| | - Marisa Brandys
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Zhe Li
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Rebecca Skotheim
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Andrew J. Borst
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Alena Khmelinskaia
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Transdisciplinary Research Area “Building Blocks of Matter and Fundamental Interactions (TRA Matter)”, University of Bonn, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Neil P. King
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, United States of America
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25
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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: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [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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26
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Yang EC, Divine R, Miranda MC, Borst AJ, Sheffler W, Zhang JZ, Decarreau J, Saragovi A, Abedi M, Goldbach N, Ahlrichs M, Dobbins C, Hand A, Cheng S, Lamb M, Levine PM, Chan S, Skotheim R, Fallas J, Ueda G, Lubner J, Somiya M, Khmelinskaia A, King NP, Baker D. Computational design of non-porous, pH-responsive antibody nanoparticles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.537263. [PMID: 37131615 PMCID: PMC10153164 DOI: 10.1101/2023.04.17.537263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Programming protein nanomaterials to respond to changes in environmental conditions is a current challenge for protein design and important for targeted delivery of biologics. We describe the design of octahedral non-porous nanoparticles with the three symmetry axes (four-fold, three-fold, and two-fold) occupied by three distinct protein homooligomers: a de novo designed tetramer, an antibody of interest, and a designed trimer programmed to disassemble below a tunable pH transition point. The nanoparticles assemble cooperatively from independently purified components, and a cryo-EM density map reveals that the structure is very close to the computational design model. The designed nanoparticles can package a variety of molecular payloads, are endocytosed following antibody-mediated targeting of cell surface receptors, and undergo tunable pH-dependent disassembly at pH values ranging between to 5.9-6.7. To our knowledge, these are the first designed nanoparticles with more than two structural components and with finely tunable environmental sensitivity, and they provide new routes to antibody-directed targeted delivery.
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Affiliation(s)
- Erin C Yang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure & Design, University of Washington, Seattle, WA, USA
| | - Robby Divine
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Graduate Program in Biochemistry, University of Washington, Seattle, WA, USA
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Marcos C Miranda
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Andrew J Borst
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Will Sheffler
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jason Z Zhang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Justin Decarreau
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Amijai Saragovi
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Mohamad Abedi
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Nicolas Goldbach
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Technical University of Munich, Munich, Germany
| | - Maggie Ahlrichs
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Craig Dobbins
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alexis Hand
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Suna Cheng
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Mila Lamb
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Paul M Levine
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Sidney Chan
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rebecca Skotheim
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jorge Fallas
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - George Ueda
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Joshua Lubner
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Masaharu Somiya
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- SANKEN, Osaka University, Osaka, Japan
| | - Alena Khmelinskaia
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Transdisciplinary Research Area "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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27
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Wang JY(J, Khmelinskaia A, Sheffler W, Miranda MC, Antanasijevic A, Borst AJ, Torres SV, Shu C, Hsia Y, Nattermann U, Ellis D, Walkey C, Ahlrichs M, Chan S, Kang A, Nguyen H, Sydeman C, Sankaran B, Wu M, Bera AK, Carter L, Fiala B, Murphy M, Baker D, Ward AB, King NP. Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains. Proc Natl Acad Sci U S A 2023; 120:e2214556120. [PMID: 36888664 PMCID: PMC10089191 DOI: 10.1073/pnas.2214556120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 02/03/2023] [Indexed: 03/09/2023] Open
Abstract
Computationally designed protein nanoparticles have recently emerged as a promising platform for the development of new vaccines and biologics. For many applications, secretion of designed nanoparticles from eukaryotic cells would be advantageous, but in practice, they often secrete poorly. Here we show that designed hydrophobic interfaces that drive nanoparticle assembly are often predicted to form cryptic transmembrane domains, suggesting that interaction with the membrane insertion machinery could limit efficient secretion. We develop a general computational protocol, the Degreaser, to design away cryptic transmembrane domains without sacrificing protein stability. The retroactive application of the Degreaser to previously designed nanoparticle components and nanoparticles considerably improves secretion, and modular integration of the Degreaser into design pipelines results in new nanoparticles that secrete as robustly as naturally occurring protein assemblies. Both the Degreaser protocol and the nanoparticles we describe may be broadly useful in biotechnological applications.
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Affiliation(s)
- Jing Yang (John) Wang
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA98195
| | - Alena Khmelinskaia
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Transdisciplinary Research Area “Building Blocks of Matter and Fundamental Interactions”, University of Bonn, 53113Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53121Bonn, Germany
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Marcos C. Miranda
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Aleksandar Antanasijevic
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA92037
| | - Andrew J. Borst
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Susana V. Torres
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Chelsea Shu
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Yang Hsia
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Una Nattermann
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA98195
| | - Daniel Ellis
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA98195
| | - Carl Walkey
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Maggie Ahlrichs
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Sidney Chan
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Claire Sydeman
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, CA94720
- Berkeley Center for Structural Biology, Lawrence Berkeley Laboratory, Berkeley, CA94720
| | - Mengyu Wu
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Asim K. Bera
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Brooke Fiala
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Michael Murphy
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Andrew B. Ward
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA92037
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
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28
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Su Z, Wu Y. Dissecting the general mechanisms of protein cage self-assembly by coarse-grained simulations. Protein Sci 2023; 32:e4552. [PMID: 36541820 PMCID: PMC9854185 DOI: 10.1002/pro.4552] [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: 07/05/2022] [Revised: 12/15/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
The development of artificial protein cages has recently gained massive attention due to their promising application prospect as novel delivery vehicles for therapeutics. These nanoparticles are formed through a process called self-assembly, in which individual subunits spontaneously arrange into highly ordered patterns via non-covalent but specific interactions. Therefore, the first step toward the design of novel engineered protein cages is to understand the general mechanisms of their self-assembling dynamics. Here we have developed a new computational method to tackle this problem. Our method is based on a coarse-grained model and a diffusion-reaction simulation algorithm. Using a tetrahedral cage as test model, we showed that self-assembly of protein cage requires of a seeding process in which specific configurations of kinetic intermediate states are identified. We further found that there is a critical concentration to trigger self-assembly of protein cages. This critical concentration allows that cages can only be successfully assembled under a persistently high concentration. Additionally, phase diagram of self-assembly has been constructed by systematically testing the model across a wide range of binding parameters. Finally, our simulations demonstrated the importance of protein's structural flexibility in regulating the dynamics of cage assembly. In summary, this study throws lights on the general principles underlying self-assembly of large cage-like protein complexes and thus provides insights to design new nanomaterials.
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Affiliation(s)
- Zhaoqian Su
- Department of Systems and Computational BiologyAlbert Einstein College of MedicineBronxNew YorkUSA
| | - Yinghao Wu
- Department of Systems and Computational BiologyAlbert Einstein College of MedicineBronxNew YorkUSA
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29
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Lu H, Cheng Z, Hu Y, Tang LV. What Can De Novo Protein Design Bring to the Treatment of Hematological Disorders? BIOLOGY 2023; 12:biology12020166. [PMID: 36829445 PMCID: PMC9952452 DOI: 10.3390/biology12020166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Protein therapeutics have been widely used to treat hematological disorders. With the advent of de novo protein design, protein therapeutics are not limited to ameliorating natural proteins but also produce novel protein sequences, folds, and functions with shapes and functions customized to bind to the therapeutic targets. De novo protein techniques have been widely used biomedically to design novel diagnostic and therapeutic drugs, novel vaccines, and novel biological materials. In addition, de novo protein design has provided new options for treating hematological disorders. Scientists have designed protein switches called Colocalization-dependent Latching Orthogonal Cage-Key pRoteins (Co-LOCKR) that perform computations on the surface of cells. De novo designed molecules exhibit a better capacity than the currently available tyrosine kinase inhibitors in chronic myeloid leukemia therapy. De novo designed protein neoleukin-2/15 enhances chimeric antigen receptor T-cell activity. This new technique has great biomedical potential, especially in exploring new treatment methods for hematological disorders. This review discusses the development of de novo protein design and its biological applications, with emphasis on the treatment of hematological disorders.
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30
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Ohara N, Kawakami N, Arai R, Adachi N, Moriya T, Kawasaki M, Miyamoto K. Reversible Assembly of an Artificial Protein Nanocage Using Alkaline Earth Metal Ions. J Am Chem Soc 2023; 145:216-223. [PMID: 36541447 DOI: 10.1021/jacs.2c09537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein nanocages are of increasing interest for use as drug capsules, but the encapsulation and release of drug molecules at appropriate times require the reversible association and dissociation of the nanocages. One promising approach to addressing this challenge is the design of metal-dependent associating proteins. Such designed proteins typically have Cys or His residues at the protein surface for connecting the associating proteins through metal-ion coordination. However, Cys and His residues favor interactions with soft and borderline metal ions, such as Au+ and Zn2+, classified by the hard and soft acids and bases concept, restricting the types of metal ions available to drive association. Here, we show the alkaline earth (AE) metal-dependent association of the recently designed artificial protein nanocage TIP60, which is composed of 60-mer fusion proteins. The introduction of a Glu (hard base) mutation to the fusion protein (K67E mutant) prevented the formation of the 60-mer but formed the expected cage structure in the presence of Ca, Sr, or Ba ions (hard acids). Cryogenic electron microscopy (cryo-EM) analysis indicated a Ba ion at the interface of the subunits. Furthermore, we demonstrated the encapsulation and release of single-stranded DNA molecules using this system. Our results provide insights into the design of AE metal-dependent association and dissociation mechanisms for proteins.
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Affiliation(s)
- Naoya Ohara
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Norifumi Kawakami
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Ryoichi Arai
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Ueda, Nagano 386-8567, Japan.,Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Naruhiko Adachi
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
| | - Toshio Moriya
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
| | - Masato Kawasaki
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
| | - Kenji Miyamoto
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
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31
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Kobayashi N, Arai R. Protein Cages and Nanostructures Constructed from Protein Nanobuilding Blocks. Methods Mol Biol 2023; 2671:79-94. [PMID: 37308639 DOI: 10.1007/978-1-0716-3222-2_4] [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] [Indexed: 06/14/2023]
Abstract
Protein cages and nanostructures are promising biocompatible medical materials, such as vaccines and drug carriers. Recent advances in designed protein nanocages and nanostructures have opened up cutting-edge applications in the fields of synthetic biology and biopharmaceuticals. A simple approach for constructing self-assembling protein nanocages and nanostructures is the design of a fusion protein composed of two different proteins forming symmetric oligomers. In this chapter, we describe the design and methods of protein nanobuilding blocks (PN-Blocks) using a dimeric de novo protein WA20 to construct self-assembling protein cages and nanostructures. A protein nanobuilding block (PN-Block), WA20-foldon, was developed by fusing an intermolecularly folded dimeric de novo protein WA20 and a trimeric foldon domain from bacteriophage T4 fibritin. The WA20-foldon self-assembled into several oligomeric nanoarchitectures in multiples of 6-mer. De novo extender protein nanobuilding blocks (ePN-Blocks) were also developed by fusing tandemly two WA20 with various linkers, to construct self-assembling cyclized and extended chain-like nanostructures. These PN-Blocks would be useful for the construction of self-assembling protein cages and nanostructures and their potential applications in the future.
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Affiliation(s)
- Naoya Kobayashi
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Ryoichi Arai
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Ueda, Nagano, Japan.
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano, Japan.
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32
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Olshefsky A, Richardson C, Pun SH, King NP. Engineering Self-Assembling Protein Nanoparticles for Therapeutic Delivery. Bioconjug Chem 2022; 33:2018-2034. [PMID: 35487503 PMCID: PMC9673152 DOI: 10.1021/acs.bioconjchem.2c00030] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Despite remarkable advances over the past several decades, many therapeutic nanomaterials fail to overcome major in vivo delivery barriers. Controlling immunogenicity, optimizing biodistribution, and engineering environmental responsiveness are key outstanding delivery problems for most nanotherapeutics. However, notable exceptions exist including some lipid and polymeric nanoparticles, some virus-based nanoparticles, and nanoparticle vaccines where immunogenicity is desired. Self-assembling protein nanoparticles offer a powerful blend of modularity and precise designability to the field, and have the potential to solve many of the major barriers to delivery. In this review, we provide a brief overview of key designable features of protein nanoparticles and their implications for therapeutic delivery applications. We anticipate that protein nanoparticles will rapidly grow in their prevalence and impact as clinically relevant delivery platforms.
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Affiliation(s)
- Audrey Olshefsky
- Department
of Bioengineering, University of Washington, Seattle, Washington 98195, United States
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Christian Richardson
- Department
of Bioengineering, University of Washington, Seattle, Washington 98195, United States
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Suzie H. Pun
- Department
of Bioengineering, University of Washington, Seattle, Washington 98195, United States
- Molecular
Engineering and Sciences Institute, University
of Washington, Seattle, Washington 98195, United States
| | - Neil P. King
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
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33
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Murray DT, Shin DS, Classen S, Brosey CA, Hura GL. Visualizing and accessing correlated SAXS data sets with Similarity Maps and Simple Scattering web resources. Methods Enzymol 2022; 678:411-440. [PMID: 36641216 DOI: 10.1016/bs.mie.2022.09.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Constructing a comprehensive understanding of macromolecular behavior from a set of correlated small angle scattering (SAS) data is aided by tools that analyze all scattering curves together. SAS experiments on biological systems can be performed on specimens that are more easily prepared, modified, and formatted relative to those of most other techniques. An X-ray SAS measurement (SAXS) can be performed in less than a milli-second in-line with treatment steps such as purification or exposure to modifiers. These capabilities are valuable since biological macromolecules (proteins, polynucleotides, lipids, and carbohydrates) change conformation or assembly under specific conditions that often define their biological role. Furthermore, mutation or post-translational modification change their behavior and provides an avenue to tailor their mechanics. Here, we describe tools to combine multiple correlated SAS measurements for analysis and review their application to biological systems. The SAXS Similarity Map (SSM) compares a set of scattering curves and quantifies the similarity between them for display as a color on a grid. Visualizing an entire correlated data set with SSMs helps identify patterns that reveal biological functions. The SSM analysis is available as a web-based tool at https://sibyls.als.lbl.gov/saxs-similarity/. To make data available and promote tool development, we have also deployed a repository of correlated SAS data sets called Simple Scattering (available at https://simplescattering.com). The correlated data sets used to demonstrate the SSM are available on the Simple Scattering website. We expect increased utilization of correlated SAS measurements to characterize the tightly controlled mechanistic properties of biological systems and fine-tune engineered macromolecules for nanotechnology-based applications.
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Affiliation(s)
- Daniel T Murray
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - David S Shin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Scott Classen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Chris A Brosey
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Greg L Hura
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, United States.
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34
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Li Y, Champion JA. Self-assembling nanocarriers from engineered proteins: Design, functionalization, and application for drug delivery. Adv Drug Deliv Rev 2022; 189:114462. [PMID: 35934126 DOI: 10.1016/j.addr.2022.114462] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/09/2022] [Accepted: 07/15/2022] [Indexed: 01/24/2023]
Abstract
Self-assembling proteins are valuable building blocks for constructing drug nanocarriers due to their self-assembly behavior, monodispersity, biocompatibility, and biodegradability. Genetic and chemical modifications allow for modular design of protein nanocarriers with effective drug encapsulation, targetability, stimuli responsiveness, and in vivo half-life. Protein nanocarriers have been developed to deliver various therapeutic molecules including small molecules, proteins, and nucleic acids with proven in vitro and in vivo efficacy. This article reviews recent advances in protein nanocarriers that are not derived from natural protein nanostructures, such as protein cages or virus like particles. The protein nanocarriers described here are self-assembled from rationally or de novo designed recombinant proteins, as well as recombinant proteins complexed with other biomolecules, presenting properties that are unique from those of natural protein carriers. Design, functionalization, and therapeutic application of protein nanocarriers will be discussed.
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Affiliation(s)
- Yirui Li
- BioEngineering Program, Georgia Institute of Technology, United States
| | - Julie A Champion
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 950 Atlantic Drive NW, Atlanta, GA 30332, United States; BioEngineering Program, Georgia Institute of Technology, United States.
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35
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Mahynski NA, Han B, Markiewitz D, Shen VK. Derivable genetic programming for two-dimensional colloidal materials. J Chem Phys 2022; 157:114112. [PMID: 36137809 DOI: 10.1063/5.0106131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We describe a method for deriving surface functionalization patterns for colloidal systems that can induce self-assembly into any chosen periodic symmetry at a planar interface. The result is a sequence of letters, s ∈ {A,T,C,G}, or a gene, that describes the perimeter of the colloidal object and programs its self-assembly. This represents a genome that is finite and can be exhaustively enumerated. These genes derive from symmetry, which may be topologically represented by two-dimensional parabolic orbifolds; since these orbifolds are surfaces that may be derived from first principles, this represents an ab initio route to colloid functionality. The genes are human readable and can be employed to easily design colloidal units. We employ a biological (genetic) analogy to demonstrate this and illustrate their connection to the designs of Maurits Cornelis (M. C.) Escher.
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Affiliation(s)
- Nathan A Mahynski
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Bliss Han
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Daniel Markiewitz
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Vincent K Shen
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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36
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Li L, Chen G. Precise Assembly of Proteins and Carbohydrates for Next-Generation Biomaterials. J Am Chem Soc 2022; 144:16232-16251. [PMID: 36044681 DOI: 10.1021/jacs.2c04418] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The complexity and diversity of biomacromolecules make them a unique class of building blocks for generating precise assemblies. They are particularly available to a new generation of biomaterials integrated with living systems due to their intrinsic properties such as accurate recognition, self-organization, and adaptability. Therefore, many excellent approaches have been developed, leading to a variety of quite practical outcomes. Here, we review recent advances in the fabrication and application of artificially precise assemblies by employing proteins and carbohydrates as building blocks, followed by our perspectives on some of new challenges, goals, and opportunities for the future research directions in this field.
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Affiliation(s)
- Long Li
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, People's Republic of China
| | - Guosong Chen
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, People's Republic of China.,Multiscale Research Institute for Complex Systems, Fudan University, Shanghai 200433, People's Republic of China
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37
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Miller JE, Srinivasan Y, Dharmaraj NP, Liu A, Nguyen PL, Taylor SD, Yeates TO. Designing Protease-Triggered Protein Cages. J Am Chem Soc 2022; 144:12681-12689. [PMID: 35802879 DOI: 10.1021/jacs.2c02165] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteins that self-assemble into enclosed polyhedral cages, both naturally and by design, are garnering attention for their prospective utility in the fields of medicine and biotechnology. Notably, their potential for encapsulation and surface display are attractive for experiments that require protection and targeted delivery of cargo. The ability to control their opening or disassembly would greatly advance the development of protein nanocages into widespread molecular tools. Toward the development of protein cages that disassemble in a systematic manner and in response to biologically relevant stimuli, here we demonstrate a modular protein cage system that is opened by highly sequence-specific proteases, based on sequence insertions at strategically chosen loop positions in the protein cage subunits. We probed the generality of the approach in the context of protein cages built using the two prevailing methods of construction: genetic fusion between oligomeric components and (non-covalent) computational interface design between oligomeric components. Our results suggest that the former type of cage may be more amenable than the latter for endowing proteolytically controlled disassembly. We show that a successfully designed cage system, based on oligomeric fusion, is modular with regard to its triggering protease. One version of the cage is targeted by an asparagine protease implicated in cancer and Alzheimer's disease, whereas the second version is responsive to the blood-clotting protease, thrombin. The approach demonstrated here should guide future efforts to develop therapeutic vectors to treat disease states where protease induction or mis-regulation occurs.
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Affiliation(s)
- Justin E Miller
- UCLA Molecular Biology Institute, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States.,UCLA-DOE Institute for Genomics and Proteomics, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States
| | - Yashes Srinivasan
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Nithin P Dharmaraj
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Andrew Liu
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Phillip L Nguyen
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Scott D Taylor
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Todd O Yeates
- UCLA Molecular Biology Institute, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States.,UCLA-DOE Institute for Genomics and Proteomics, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States.,UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
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38
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Precision materials: Computational design methods of accurate protein materials. Curr Opin Struct Biol 2022; 74:102367. [DOI: 10.1016/j.sbi.2022.102367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 02/22/2022] [Accepted: 02/28/2022] [Indexed: 11/23/2022]
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39
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Edwardson TGW, Levasseur MD, Tetter S, Steinauer A, Hori M, Hilvert D. Protein Cages: From Fundamentals to Advanced Applications. Chem Rev 2022; 122:9145-9197. [PMID: 35394752 DOI: 10.1021/acs.chemrev.1c00877] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins that self-assemble into polyhedral shell-like structures are useful molecular containers both in nature and in the laboratory. Here we review efforts to repurpose diverse protein cages, including viral capsids, ferritins, bacterial microcompartments, and designed capsules, as vaccines, drug delivery vehicles, targeted imaging agents, nanoreactors, templates for controlled materials synthesis, building blocks for higher-order architectures, and more. A deep understanding of the principles underlying the construction, function, and evolution of natural systems has been key to tailoring selective cargo encapsulation and interactions with both biological systems and synthetic materials through protein engineering and directed evolution. The ability to adapt and design increasingly sophisticated capsid structures and functions stands to benefit the fields of catalysis, materials science, and medicine.
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Affiliation(s)
| | | | - Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Angela Steinauer
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Mao Hori
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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40
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Liu Y, Zang J, Leng X, Zhao G. A short helix regulates conversion of dimeric and 24-meric ferritin architectures. Int J Biol Macromol 2022; 203:535-542. [PMID: 35120932 DOI: 10.1016/j.ijbiomac.2022.01.174] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 12/28/2022]
Abstract
The inter-subunit interaction at the protein interfaces plays a key role in protein self-assembly, through which enabling protein self-assembly controllable is of great importance for preparing the novel nanoscale protein materials with unexplored properties. Different from normal 24-meric ferritin, archaeal ferritin, Thermotoga maritima ferritin (TmFtn) naturally occurs as a dimer, which can assemble into a 24-mer nanocage induced by salts. However, the regulation mechanism of protein self-assembly underlying this phenomenon remains unclear. Here, a combination of the computational energy simulation and key interface reconstruction revealed that a short helix involved interactions at the C4 interface are mainly responsible for the existence of such dimer. Agreeing with this idea, deletion of such short helix of each subunit triggers it to be a stable dimer, which losses the ability to reassemble into 24-meric ferritin in the presence of salts in solution. Further support for this idea comes from the observation that grafting a small helix from human H ferritin onto archaeal subunit resulted in a stable 24-mer protein nanocage even in the absence of salts. Thus, these findings demonstrate that adjusting the interactions at the protein interfaces appears to be a facile, effective approach to control subunit assembly into different protein architectures.
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Affiliation(s)
- Yu Liu
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China
| | - Jiachen Zang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China
| | - Xiaojing Leng
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Guanghua Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
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Habibi N, Mauser A, Ko Y, Lahann J. Protein Nanoparticles: Uniting the Power of Proteins with Engineering Design Approaches. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104012. [PMID: 35077010 PMCID: PMC8922121 DOI: 10.1002/advs.202104012] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/12/2021] [Indexed: 05/16/2023]
Abstract
Protein nanoparticles, PNPs, have played a long-standing role in food and industrial applications. More recently, their potential in nanomedicine has been more widely pursued. This review summarizes recent trends related to the preparation, application, and chemical construction of nanoparticles that use proteins as major building blocks. A particular focus has been given to emerging trends related to applications in nanomedicine, an area of research where PNPs are poised for major breakthroughs as drug delivery carriers, particle-based therapeutics or for non-viral gene therapy.
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Affiliation(s)
- Nahal Habibi
- Biointerfaces InstituteDepartment of Chemical EngineeringUniversity of MichiganAnn ArborMI48109USA
| | - Ava Mauser
- Biointerfaces InstituteDepartment of Biomedical EngineeringUniversity of MichiganAnn ArborMI48109USA
| | - Yeongun Ko
- Biointerfaces InstituteDepartment of Chemical EngineeringUniversity of MichiganAnn ArborMI48109USA
| | - Joerg Lahann
- Biointerfaces InstituteDepartments of Chemical EngineeringMaterial Science and EngineeringBiomedical Engineeringand Macromolecular Science and EngineeringUniversity of MichiganAnn ArborMI48109USA
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Reddy MM, Bhandari P, Hati KC, Sandanaraj BS. Rational Design of Self-Assembling Artificial Proteins Utilizing a Micelle-Assisted Protein Labeling Technology (MAPLabTech): Testing the Scope. Chembiochem 2022; 23:e202100607. [PMID: 35181981 DOI: 10.1002/cbic.202100607] [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: 11/03/2021] [Revised: 02/03/2022] [Indexed: 11/07/2022]
Abstract
Self-assembling artificial proteins (SAPs) have gained enormous interest in recent years due to their applications in different fields. Synthesis of well-defined monodisperse SAPs is accomplished predominantly through genetic methods. However, the last decade has witnessed the use of a few chemical technologies for this purpose. In particular, micelle-assisted protein labeling technology (MAPLabTech) has made huge progress in this area. The first generation MAPLabTech focused on site-specific labeling of the active-site residue of serine proteases to make SAPs. Further, this methodology was exploited for labeling of N-terminal residue of a globular protein to make functional SAPs. In this study, we describe the synthesis of novel SAPs by developing a chemical method for site-specific labeling of a surface-exposed cysteine residue of globular proteins. In addition, we disclose the synthesis of redox-sensitive SAPs and their systematic self-assembly and disassembly studies using size-exclusion chromatography. Altogether these studies further expand the scope of MAPLabTech in different fields such as vaccine design, targeted drug delivery, diagnostic imaging, biomaterials, and tissue engineering.
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Affiliation(s)
- Mullapudi Mohan Reddy
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, India
| | - Pavankumar Bhandari
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, India
| | - Kshitish Chandra Hati
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, India
| | - Britto S Sandanaraj
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, India
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
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43
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Mutant libraries reveal negative design shielding proteins from supramolecular self-assembly and relocalization in cells. Proc Natl Acad Sci U S A 2022; 119:2101117119. [PMID: 35078932 PMCID: PMC8812688 DOI: 10.1073/pnas.2101117119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2021] [Indexed: 01/07/2023] Open
Abstract
Genetic mutations fuel organismal evolution but can also cause disease. As proteins are the cell’s workhorses, the ways in which mutations can disrupt their structure, stability, function, and interactions have been studied extensively. However, proteins evolve and function in a cellular context, and our ability to relate changes in protein sequence to cell-level phenotypes remains limited. In particular, the molecular mechanism underlying most disease-associated mutations is unknown. Here, we show that mutations changing a protein’s surface chemistry can dramatically impact its supramolecular self-assembly and localization in the cell. These results highlight the complex nature of genotype–phenotype relationships with a simple system. Understanding the molecular consequences of mutations in proteins is essential to map genotypes to phenotypes and interpret the increasing wealth of genomic data. While mutations are known to disrupt protein structure and function, their potential to create new structures and localization phenotypes has not yet been mapped to a sequence space. To map this relationship, we employed two homo-oligomeric protein complexes in which the internal symmetry exacerbates the impact of mutations. We mutagenized three surface residues of each complex and monitored the mutations’ effect on localization and assembly phenotypes in yeast cells. While surface mutations are classically viewed as benign, our analysis of several hundred mutants revealed they often trigger three main phenotypes in these proteins: nuclear localization, the formation of puncta, and fibers. Strikingly, more than 50% of random mutants induced one of these phenotypes in both complexes. Analyzing the mutant’s sequences showed that surface stickiness and net charge are two key physicochemical properties associated with these changes. In one complex, more than 60% of mutants self-assembled into fibers. Such a high frequency is explained by negative design: charged residues shield the complex from self-interacting with copies of itself, and the sole removal of the charges induces its supramolecular self-assembly. A subsequent analysis of several other complexes targeted with alanine mutations suggested that such negative design is common. These results highlight that minimal perturbations in protein surfaces’ physicochemical properties can frequently drive assembly and localization changes in a cellular context.
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Stupka I, Azuma Y, Biela AP, Imamura M, Scheuring S, Pyza E, Woźnicka O, Maskell DP, Heddle JG. Chemically induced protein cage assembly with programmable opening and cargo release. SCIENCE ADVANCES 2022; 8:eabj9424. [PMID: 34985943 PMCID: PMC8730398 DOI: 10.1126/sciadv.abj9424] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/16/2021] [Indexed: 06/14/2023]
Abstract
Engineered protein cages are promising tools that can be customized for applications in medicine and nanotechnology. A major challenge is developing a straightforward strategy for endowing cages with bespoke, inducible disassembly. Such cages would allow release of encapsulated cargoes at desired timing and location. Here, we achieve such programmable disassembly using protein cages, in which the subunits are held together by different molecular cross-linkers. This modular system enables cage disassembly to be controlled in a condition-dependent manner. Structural details of the resulting cages were determined using cryo–electron microscopy, which allowed observation of bridging cross-linkers at intended positions. Triggered disassembly was demonstrated by high-speed atomic force microscopy and subsequent cargo release using an encapsulated Förster resonance energy transfer pair whose signal depends on the quaternary structure of the cage.
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Affiliation(s)
- Izabela Stupka
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
- Postgraduate School of Molecular Medicine, 02-091 Warsaw, Poland
| | - Yusuke Azuma
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Artur P. Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Motonori Imamura
- Department of Anesthesiology, Weill Cornell Medicine, New York City, NY 10065, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York City, NY 10065, USA
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medicine, New York City, NY 10065, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York City, NY 10065, USA
| | - Elżbieta Pyza
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Olga Woźnicka
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Daniel P. Maskell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Jonathan G. Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
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45
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Soon JW, Oohora K, Hayashi T. A disulphide bond-mediated hetero-dimer of a hemoprotein and a fluorescent protein exhibiting efficient energy transfer †. RSC Adv 2022; 12:28519-28524. [PMID: 36320522 PMCID: PMC9535469 DOI: 10.1039/d2ra05249k] [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: 08/21/2022] [Accepted: 09/22/2022] [Indexed: 11/07/2022] Open
Abstract
Artificial protein hetero-dimerization is one of the promising strategies to construct protein-based chemical tools. In this work, cytochrome b562, an electron transfer hemoprotein, and green fluorescent protein (GFP) mutants with cysteine residues added to their surfaces were conjugated via a pyridyl disulphide-based thiol–disulfide exchange reaction. The eight hetero-dimers, which have cysteine residues at different positions to form the disulphide bonds, were obtained and characterized by gel-electrophoresis, mass spectrometry and size exclusion chromatography. The fluorescence properties of the hetero-dimers were evaluated by fluorescence spectroscopy and fluorescence lifetime measurements. Efficient photoinduced energy transfer from the GFP chromophore to the heme cofactor was observed in each of the hetero-dimers. The energy transfer efficiency is strongly dependent on the cross-linking residues, reaching 96%. Furthermore, the estimated Förster distance and the structure-based maximum possible distances of the donor and acceptor suggest that one of the hetero-dimers has a rigid protein–protein structure with favourable properties for energy transfer. The disulphide bond-mediated protein hetero-dimerization is useful for screening functional protein systems towards further developments. Hetero-dimerization of a hemoprotein and green fluorescent protein via a thiol–disulphide exchange reaction is achieved. The heterodimer has suitable cross-linking points and displays efficient energy transfer.![]()
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Affiliation(s)
- Julian Wong Soon
- Department of Applied Chemistry, Graduate School of Engineering, Osaka UniversitySuita565-0871Japan
| | - Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka UniversitySuita565-0871Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka UniversitySuita565-0871Japan
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Ioannou E, Labrou NE. Rational Design of Self-Assembling Supramolecular Protein Nanostructures Utilizing the Cucurbit[8]Uril Macrocyclic Host. Methods Mol Biol 2022; 2487:177-187. [PMID: 35687236 DOI: 10.1007/978-1-0716-2269-8_11] [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] [Indexed: 06/15/2023]
Abstract
Self-assembly is a phenomenon that governs molecular structural organization in nature, therefore raising research interest for the fabrication of novel nanomaterials with diverse applications in biocatalysis, biomedicine, material templating, and biosensor development. In this chapter we provide protocols for the development of supramolecular protein complexes based on host-guest interactions in the presence of the macrocyclic host, cucurbit[8]uril (CB[8]). CB[8] is reported to exhibit high binding affinity towards the tripeptide Phe-Gly-Gly (FGG), therefore it can be utilized as a selective adhesive of protein molecules, after fusion of FGG to an accessible protein surface.
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Affiliation(s)
- Elisavet Ioannou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece.
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47
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Artificial protein assemblies with well-defined supramolecular protein nanostructures. Biochem Soc Trans 2021; 49:2821-2830. [PMID: 34812854 DOI: 10.1042/bst20210808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022]
Abstract
Nature uses a wide range of well-defined biomolecular assemblies in diverse cellular processes, where proteins are major building blocks for these supramolecular assemblies. Inspired by their natural counterparts, artificial protein-based assemblies have attracted strong interest as new bio-nanostructures, and strategies to construct ordered protein assemblies have been rapidly expanding. In this review, we provide an overview of very recent studies in the field of artificial protein assemblies, with the particular aim of introducing major assembly methods and unique features of these assemblies. Computational de novo designs were used to build various assemblies with artificial protein building blocks, which are unrelated to natural proteins. Small chemical ligands and metal ions have also been extensively used for strong and bio-orthogonal protein linking. Here, in addition to protein assemblies with well-defined sizes, protein oligomeric and array structures with rather undefined sizes (but with definite repeat protein assembly units) also will be discussed in the context of well-defined protein nanostructures. Lastly, we will introduce multiple examples showing how protein assemblies can be effectively used in various fields such as therapeutics and vaccine development. We believe that structures and functions of artificial protein assemblies will be continuously evolved, particularly according to specific application goals.
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48
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The development of natural and designed protein nanocages for encapsulation and delivery of active compounds. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2021.107004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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49
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Zhu J, Avakyan N, Kakkis AA, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev 2021; 121:13701-13796. [PMID: 34405992 PMCID: PMC9148388 DOI: 10.1021/acs.chemrev.1c00308] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
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Affiliation(s)
| | | | - Albert A. Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chung-Jui Yu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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50
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Zeng R, Lv C, Wang C, Zhao G. Bionanomaterials based on protein self-assembly: Design and applications in biotechnology. Biotechnol Adv 2021; 52:107835. [PMID: 34520791 DOI: 10.1016/j.biotechadv.2021.107835] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 01/13/2023]
Abstract
Elegant protein assembly to generate new biomaterials undergoes extremely rapid development for wide extension of biotechnology applications, which can be a powerful tool not only for creating nanomaterials but also for advancing understanding of the structure of life. Unique biological properties of proteins bestow these artificial biomaterials diverse functions that can permit them to be applied in encapsulation, bioimaging, biocatalysis, biosensors, photosynthetic apparatus, electron transport, magnetogenetic applications, vaccine development and antibodies design. This review gives a perspective view of the latest advances in the construction of protein-based nanomaterials. We initially start with distinguishable, specific interactions to construct sundry nanomaterials through protein self-assembly and concisely expound the assembly mechanism from the design strategy. And then, the design and construction of 0D, 1D, 2D, 3D protein assembled nanomaterials are especially highlighted. Furthermore, the potential applications have been discussed in detail. Overall, this review will illustrate how to fabricate highly sophisticated nanomaterials oriented toward applications in biotechnology based on the rules of supramolecular chemistry.
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Affiliation(s)
- Ruiqi Zeng
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China
| | - Chenyan Lv
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China
| | - Chengtao Wang
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, No. 11 Fucheng Road, Haidian District, Beijing 100048, China
| | - Guanghua Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China.
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