1
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Stover L, Bahramimoghaddam H, Wang L, Schrecke S, Yadav GP, Zhou M, Laganowsky A. Grafting the ALFA tag for structural studies of aquaporin Z. J Struct Biol X 2024; 9:100097. [PMID: 38361954 PMCID: PMC10867769 DOI: 10.1016/j.yjsbx.2024.100097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Aquaporin Z (AqpZ), a bacterial water channel, forms a tetrameric complex and, like many other membrane proteins, activity is regulated by lipids. Various methods have been developed to facilitate structure determination of membrane proteins, such as the use of antibodies. Here, we graft onto AqpZ the ALFA tag (AqpZ-ALFA), an alpha helical epitope, to make use of the high-affinity anti-ALFA nanobody (nB). Native mass spectrometry reveals the AqpZ-ALFA fusion forms a stable, 1:1 complex with nB. Single-particle cryogenic electron microscopy studies reveal the octameric (AqpZ-ALFA)4(nB)4 complex forms a dimeric assembly and the structure was determined to 1.9 Å resolution. Dimerization of the octamer is mediated through stacking of the symmetrically bound nBs. Tube-like density is also observed, revealing a potential cardiolipin binding site. Grafting of the ALFA tag, or other epitope, along with binding and association of nBs to promote larger complexes will have applications in structural studies and protein engineering.
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Affiliation(s)
- Lauren Stover
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States
| | | | - Lie Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Samantha Schrecke
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States
| | - Gaya P. Yadav
- Laboratory for Biomolecular Structure and Dynamics (LBSD), Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States
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2
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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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3
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Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. A computational toolbox for the assembly yield of complex and heterogeneous structures. Nat Commun 2023; 14:8328. [PMID: 38097568 PMCID: PMC10721878 DOI: 10.1038/s41467-023-43168-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 11/02/2023] [Indexed: 12/17/2023] Open
Abstract
The self-assembly of complex structures from a set of non-identical building blocks is a hallmark of soft matter and biological systems, including protein complexes, colloidal clusters, and DNA-based assemblies. Predicting the dependence of the equilibrium assembly yield on the concentrations and interaction energies of building blocks is highly challenging, owing to the difficulty of computing the entropic contributions to the free energy of the many structures that compete with the ground state configuration. While these calculations yield well known results for spherically symmetric building blocks, they do not hold when the building blocks have internal rotational degrees of freedom. Here we present an approach for solving this problem that works with arbitrary building blocks, including proteins with known structure and complex colloidal building blocks. Our algorithm combines classical statistical mechanics with recently developed computational tools for automatic differentiation. Automatic differentiation allows efficient evaluation of equilibrium averages over configurations that would otherwise be intractable. We demonstrate the validity of our framework by comparison to molecular dynamics simulations of simple examples, and apply it to calculate the yield curves for known protein complexes and for the assembly of colloidal shells.
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Affiliation(s)
- Agnese I Curatolo
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Ofer Kimchi
- Lewis-Sigler Institute, Princeton University, Princeton, NJ, 08544, USA
| | - Carl P Goodrich
- Institute of Science and Technology Austria, A-3400, Klosterneuburg, Austria
| | - Ryan K Krueger
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Michael P Brenner
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA.
- Department of Physics, Harvard University, Cambridge, MA, 02138, USA.
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4
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A simple self-assembling system of melittin for hepatoma treatment. Cancer Nanotechnol 2023. [DOI: 10.1186/s12645-022-00154-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Abstract
Background
Hepatoma is a serious public health concern. New attempts are urgently needed to solve this problem. Melittin, a host defense peptide derived from the venom of honeybees, has noteworthy hemolysis and non-specific cytotoxicity in clinical applications. Here, the self-assembly of melittin and vitamin E-succinic acid-(glutamate)12 (VG) was fabricated via noncovalent π-stacking and hydrogen bonding interactions using an environment-friendly method without “toxic” solvents.
Results
As expected, the designed self-assembly (denoted as M/VG nanoparticles) exhibits a uniform morphology with a particle size of approximately 60 nm and a zeta potential of approximately − 26.8 mV. Furthermore, added VG significantly decreased hemolytic activity, increased tumor-targeted effects, and accelerated apoptosis.
Conclusion
Our research provides a promising strategy for the development of natural self-assembled biological peptides for clinical application, particularly for transforming toxic peptides into safe therapeutic systems.
Graphical Abstract
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5
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João J, Prazeres DMF. Manufacturing of non-viral protein nanocages for biotechnological and biomedical applications. Front Bioeng Biotechnol 2023; 11:1200729. [PMID: 37520292 PMCID: PMC10374429 DOI: 10.3389/fbioe.2023.1200729] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023] Open
Abstract
Protein nanocages are highly ordered nanometer scale architectures, which are typically formed by homo- or hetero-self-assembly of multiple monomers into symmetric structures of different size and shape. The intrinsic characteristics of protein nanocages make them very attractive and promising as a biological nanomaterial. These include, among others, a high surface/volume ratio, multi-functionality, ease to modify or manipulate genetically or chemically, high stability, mono-dispersity, and biocompatibility. Since the beginning of the investigation into protein nanocages, several applications were conceived in a variety of areas such as drug delivery, vaccine development, bioimaging, biomineralization, nanomaterial synthesis and biocatalysis. The ability to generate large amounts of pure and well-folded protein assemblies is one of the keys to transform nanocages into clinically valuable products and move biomedical applications forward. This calls for the development of more efficient biomanufacturing processes and for the setting up of analytical techniques adequate for the quality control and characterization of the biological function and structure of nanocages. This review concisely covers and overviews the progress made since the emergence of protein nanocages as a new, next-generation class of biologics. A brief outline of non-viral protein nanocages is followed by a presentation of their main applications in the areas of bioengineering, biotechnology, and biomedicine. Afterwards, we focus on a description of the current processes used in the manufacturing of protein nanocages with particular emphasis on the most relevant aspects of production and purification. The state-of-the-art on current characterization techniques is then described and future alternative or complementary approaches in development are also discussed. Finally, a critical analysis of the limitations and drawbacks of the current manufacturing strategies is presented, alongside with the identification of the major challenges and bottlenecks.
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Affiliation(s)
- Jorge João
- iBB–Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB–Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Duarte Miguel F. Prazeres
- iBB–Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB–Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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6
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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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7
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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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8
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Zhou S, Wei Y. Kaleidoscope megamolecules synthesis and application using self-assembly technology. Biotechnol Adv 2023; 65:108147. [PMID: 37023967 DOI: 10.1016/j.biotechadv.2023.108147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 02/20/2023] [Accepted: 04/02/2023] [Indexed: 04/08/2023]
Abstract
The megamolecules with high ordered structures play an important role in chemical biology and biomedical engineering. Self-assembly, a long-discovered but very appealing technique, could induce many reactions between biomacromolecules and organic linking molecules, such as an enzyme domain and its covalent inhibitors. Enzyme and its small-molecule inhibitors have achieved many successes in medical application, which realize the catalysis process and theranostic function. By employing the protein engineering technology, the building blocks of enzyme fusion protein and small molecule linker can be assembled into a novel architecture with the specified organization and conformation. Molecular level recognition of enzyme domain could provide both covalent reaction sites and structural skeleton for the functional fusion protein. In this review, we will discuss the range of tools available to combine functional domains by using the recombinant protein technology, which can assemble them into precisely specified architectures/valences and develop the kaleidoscope megamolecules for catalytic and medical application.
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Affiliation(s)
- Shengwang Zhou
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China.
| | - Yuan Wei
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China
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9
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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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10
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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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11
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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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12
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Multifunctional building elements for the construction of peptide drug conjugates. ENGINEERED REGENERATION 2022. [DOI: 10.1016/j.engreg.2022.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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13
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Jeong R, Eom JH, Gong J, Kang M, Kim J, Lee HS. Programmed hierarchical radial association of anisotropic foldamer assemblies. NANOSCALE 2022; 14:1700-1705. [PMID: 35050287 DOI: 10.1039/d1nr05135k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Herein, we report the first example of a programmed radial assembly of anisotropic microparticles derived from a helical foldamer with a C-terminal cysteine residue. Surface-exposed thiols played a crucial role in facilitating the interparticle hydrogen bonding to form higher-order structures in an aqueous solution.
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Affiliation(s)
- Rokam Jeong
- Department of Chemistry and Center for Multiscale Chiral Architectures, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Jae-Hoon Eom
- Department of Chemistry and Center for Multiscale Chiral Architectures, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Jintaek Gong
- Department of Chemistry and Center for Multiscale Chiral Architectures, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Minsang Kang
- Department of Chemistry and Center for Multiscale Chiral Architectures, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Jaewook Kim
- Department of Chemistry and Center for Multiscale Chiral Architectures, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Hee-Seung Lee
- Department of Chemistry and Center for Multiscale Chiral Architectures, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon 34141, Republic of Korea.
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14
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Sinha NJ, Langenstein MG, Pochan DJ, Kloxin CJ, Saven JG. Peptide Design and Self-assembly into Targeted Nanostructure and Functional Materials. Chem Rev 2021; 121:13915-13935. [PMID: 34709798 DOI: 10.1021/acs.chemrev.1c00712] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peptides have been extensively utilized to construct nanomaterials that display targeted structure through hierarchical assembly. The self-assembly of both rationally designed peptides derived from naturally occurring domains in proteins as well as intuitively or computationally designed peptides that form β-sheets and helical secondary structures have been widely successful in constructing nanoscale morphologies with well-defined 1-d, 2-d, and 3-d architectures. In this review, we discuss these successes of peptide self-assembly, especially in the context of designing hierarchical materials. In particular, we emphasize the differences in the level of peptide design as an indicator of complexity within the targeted self-assembled materials and highlight future avenues for scientific and technological advances in this field.
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Affiliation(s)
- Nairiti J Sinha
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Matthew G Langenstein
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Darrin J Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Christopher J Kloxin
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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15
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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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16
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Cheng R, Li J, Ríos de Anda I, Taylor TWC, Faers MA, Anderson JLR, Seddon AM, Royall CP. Protein-polymer mixtures in the colloid limit: Aggregation, sedimentation, and crystallization. J Chem Phys 2021; 155:114901. [PMID: 34551522 DOI: 10.1063/5.0052122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
While proteins have been treated as particles with a spherically symmetric interaction, of course in reality, the situation is rather more complex. A simple step toward higher complexity is to treat the proteins as non-spherical particles and that is the approach we pursue here. We investigate the phase behavior of the enhanced green fluorescent protein (eGFP) under the addition of a non-adsorbing polymer, polyethylene glycol. From small angle x-ray scattering, we infer that the eGFP undergoes dimerization and we treat the dimers as spherocylinders with aspect ratio L/D - 1 = 1.05. Despite the complex nature of the proteins, we find that the phase behavior is similar to that of hard spherocylinders with an ideal polymer depletant, exhibiting aggregation and, in a small region of the phase diagram, crystallization. By comparing our measurements of the onset of aggregation with predictions for hard colloids and ideal polymers [S. V. Savenko and M. Dijkstra, J. Chem. Phys. 124, 234902 (2006) and Lo Verso et al., Phys. Rev. E 73, 061407 (2006)], we find good agreement, which suggests that the behavior of the eGFP is consistent with that of hard spherocylinders and ideal polymers.
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Affiliation(s)
- Rui Cheng
- HH Wills Physics Laboratory, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
| | - Jingwen Li
- HH Wills Physics Laboratory, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
| | | | - Thomas W C Taylor
- HH Wills Physics Laboratory, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
| | | | - J L Ross Anderson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Annela M Seddon
- HH Wills Physics Laboratory, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
| | - C Patrick Royall
- HH Wills Physics Laboratory, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
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17
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Molecular Biology Methods to Construct Recombinant Fibrous Protein. Methods Mol Biol 2021. [PMID: 34472061 DOI: 10.1007/978-1-0716-1574-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Recombinant technologies are often used to synthesize fibrous proteins that are difficult to separate and extract in nature, such as spider silks and elastin. Although the recombination techniques can be diverse, PCR, gel electrophoresis, and seamless cloning, as the basic methods of molecular biology, have been widely used for constructing fibrous proteins' homologous recombinant plasmids. Considering that some readers of this book may not have a molecular biology background, in this chapter, we will introduce these three most used and effective recombination techniques. For PCR, we primarily introduce colony PCR, high-fidelity PCR, and overlap PCR, which are three kinds of the most used methods. In terms of seamless cloning, the detailed protocols of Gibson Assembly and Golden Gate Assembly are introduced. The introduction of this chapter is expected to provide a comprehensive methodological reference for the following chapters to introduce the recombination of specific fibroin proteins.
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18
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Gómez-González J, Bouzada D, Pérez-Márquez LA, Sciortino G, Maréchal JD, Vázquez López M, Vázquez ME. Stereoselective Self-Assembly of DNA Binding Helicates Directed by the Viral β-Annulus Trimeric Peptide Motif. Bioconjug Chem 2021; 32:1564-1569. [PMID: 34320309 PMCID: PMC8485332 DOI: 10.1021/acs.bioconjchem.1c00312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
Combining
coordination chemistry and peptide engineering offers
extraordinary opportunities for developing novel molecular (supra)structures.
Here, we demonstrate that the β-annulus motif is capable of
directing the stereoselective assembly of designed peptides containing
2,2′-bipyridine ligands into parallel three-stranded chiral
peptide helicates, and that these helicates selectively bind with
high affinity to three-way DNA junctions.
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Affiliation(s)
- Jacobo Gómez-González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - David Bouzada
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Lidia A Pérez-Márquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Giuseppe Sciortino
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola, Spain
| | - Jean-Didier Maréchal
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola, Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - M Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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19
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Mishra NK, Østergaard M, Midtgaard SR, Strindberg SS, Winkler S, Wu S, Sørensen TJ, Hassenkam T, Poulsen JCN, Lo Leggio L, Nielsen HM, Arleth L, Christensen NJ, Thulstrup PW, Jensen KJ. Controlling the fractal dimension in self-assembly of terpyridine modified insulin by Fe 2+ and Eu 3+ to direct in vivo effects. NANOSCALE 2021; 13:8467-8473. [PMID: 33984105 DOI: 10.1039/d1nr00414j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Metal ion-induced self-assembly (SA) of proteins into higher-order structures can provide new, dynamic nano-assemblies. Here, the synthesis and characterization of a human insulin (HI) analog modified at LysB29 with the tridentate chelator 2,2':6',2''-terpyridine (Tpy) is described. SA of this new insulin analog (LysB29Tpy-HI) in the presence of the metal ions Fe2+ and Eu3+ at different concentrations was studied in solution by fluorescence luminescence and CD spectroscopy, dynamic light scattering, and small-angle X-ray scattering, while surface assembly was probed by AFM. Unique oligomerization was observed in solution, as Fe2+ yielded small magenta-colored discrete non-native assemblies, while Eu3+ caused the formation of large fractal assemblies. Binding of both metal ions to Tpy was demonstrated spectroscopically, and emission lifetime experiments revealed a distinct Eu3+ coordination geometry that included two water molecules. SAXS suggested that LysB29Tpy-HI with Fe2+ oligomerized to a discrete, roughly octameric species, while LysB29Tpy-HI with Eu3+ gave very large assemblies that could be modelled as fractals. The fractal dimensionality increased with the Eu3+ concentration. We propose that this is a consequence of Eu3+ binding to both Tpy and to free carboxylic acid groups on the insulin surface. LysB29Tpy-HI maintained insulin receptor affinity, and showed extended blood glucose lowering and plasma concentration after subcutaneous injection in rats. The combination of metal ion directed SA and native SA provides control of nano-scale fractal dimensionality and points towards use in therapeutics.
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Affiliation(s)
- Narendra Kumar Mishra
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery and Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark.
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20
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Schoeder C, Schmitz S, Adolf-Bryfogle J, Sevy AM, Finn JA, Sauer MF, Bozhanova NG, Mueller BK, Sangha AK, Bonet J, Sheehan JH, Kuenze G, Marlow B, Smith ST, Woods H, Bender BJ, Martina CE, del Alamo D, Kodali P, Gulsevin A, Schief WR, Correia BE, Crowe JE, Meiler J, Moretti R. Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design. Biochemistry 2021; 60:825-846. [PMID: 33705117 PMCID: PMC7992133 DOI: 10.1021/acs.biochem.0c00912] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/02/2021] [Indexed: 01/16/2023]
Abstract
Structure-based antibody and antigen design has advanced greatly in recent years, due not only to the increasing availability of experimentally determined structures but also to improved computational methods for both prediction and design. Constant improvements in performance within the Rosetta software suite for biomolecular modeling have given rise to a greater breadth of structure prediction, including docking and design application cases for antibody and antigen modeling. Here, we present an overview of current protocols for antibody and antigen modeling using Rosetta and exemplify those by detailed tutorials originally developed for a Rosetta workshop at Vanderbilt University. These tutorials cover antibody structure prediction, docking, and design and antigen design strategies, including the addition of glycans in Rosetta. We expect that these materials will allow novice users to apply Rosetta in their own projects for modeling antibodies and antigens.
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Affiliation(s)
- Clara
T. Schoeder
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Samuel Schmitz
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Jared Adolf-Bryfogle
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
| | - Alexander M. Sevy
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
- Chemical
and Physical Biology Program, Vanderbilt
University, Nashville, Tennessee 37232-0301, United States
- Vanderbilt
Vaccine Center, Vanderbilt University Medical
Center, Nashville, Tennessee 37232-0417, United States
| | - Jessica A. Finn
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
- Vanderbilt
Vaccine Center, Vanderbilt University Medical
Center, Nashville, Tennessee 37232-0417, United States
- Department
of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Marion F. Sauer
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
- Chemical
and Physical Biology Program, Vanderbilt
University, Nashville, Tennessee 37232-0301, United States
- Vanderbilt
Vaccine Center, Vanderbilt University Medical
Center, Nashville, Tennessee 37232-0417, United States
| | - Nina G. Bozhanova
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Benjamin K. Mueller
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Amandeep K. Sangha
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Jaume Bonet
- Institute
of Bioengineering, École Polytechnique
Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Jonathan H. Sheehan
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Georg Kuenze
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
- Institute
for Drug Discovery, University Leipzig Medical
School, 04103 Leipzig, Germany
| | - Brennica Marlow
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
- Chemical
and Physical Biology Program, Vanderbilt
University, Nashville, Tennessee 37232-0301, United States
| | - Shannon T. Smith
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
- Chemical
and Physical Biology Program, Vanderbilt
University, Nashville, Tennessee 37232-0301, United States
| | - Hope Woods
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
- Chemical
and Physical Biology Program, Vanderbilt
University, Nashville, Tennessee 37232-0301, United States
| | - Brian J. Bender
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
- Department
of Pharmacology, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Cristina E. Martina
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Diego del Alamo
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
- Chemical
and Physical Biology Program, Vanderbilt
University, Nashville, Tennessee 37232-0301, United States
| | - Pranav Kodali
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Alican Gulsevin
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - William R. Schief
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
| | - Bruno E. Correia
- Institute
of Bioengineering, École Polytechnique
Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - James E. Crowe
- Vanderbilt
Vaccine Center, Vanderbilt University Medical
Center, Nashville, Tennessee 37232-0417, United States
- Department
of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department
of Pediatrics, Vanderbilt University Medical
Center, Nashville, Tennessee 37232, United States
| | - Jens Meiler
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
- Institute
for Drug Discovery, University Leipzig Medical
School, 04103 Leipzig, Germany
| | - Rocco Moretti
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
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21
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Zhang W, Mo S, Liu M, Liu L, Yu L, Wang C. Rationally Designed Protein Building Blocks for Programmable Hierarchical Architectures. Front Chem 2020; 8:587975. [PMID: 33195088 PMCID: PMC7658299 DOI: 10.3389/fchem.2020.587975] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/05/2020] [Indexed: 01/23/2023] Open
Abstract
Diverse natural/artificial proteins have been used as building blocks to construct a variety of well-ordered nanoscale structures over the past couple of decades. Sophisticated protein self-assemblies have attracted great scientific interests due to their potential applications in disease diagnosis, illness treatment, biomechanics, bio-optics and bio-electronics, etc. This review outlines recent efforts directed to the creation of structurally defined protein assemblies including one-dimensional (1D) strings/rings/tubules, two-dimensional (2D) planar sheets and three-dimensional (3D) polyhedral scaffolds. We elucidate various innovative strategies for manipulating proteins to self-assemble into desired architectures. The emergent applications of protein assemblies as versatile platforms in medicine and material science with improved performances have also been discussed.
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Affiliation(s)
- Wenbo Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shanshan Mo
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mingwei Liu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Liu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Lanlan Yu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chenxuan Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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22
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Abstract
Recently an artificial protein named Pizza6 was reported, which possesses six identical tandem repeats and adopts a monomeric β -propeller fold with sixfold structural symmetry. Pizza2, a truncated form that consists of a double tandem repeat, self-assembles into a trimer reconstructing the same propeller architecture as Pizza6. The ability of pizza proteins to self-assemble to form complete propellers makes them interesting building blocks to engineer larger symmetrical protein complexes such as symmetric nanoparticles. Here we have explored the self-assembly of Pizza2 fused to homo-oligomerizing peptides. In total, we engineered five different fusion proteins, of which three appeared to assemble successfully into larger complexes. Further characterization of these proteins showed one monodisperse designer protein with a structure close to the intended design. This protein was further fused to eGFP to investigate functionalization of the nanoparticle. The fusion protein was stable and could be expressed in high yield, showing that Pizza-based nanoparticles may be further decorated with functional domains.
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23
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Majsterkiewicz K, Azuma Y, Heddle JG. Connectability of protein cages. NANOSCALE ADVANCES 2020; 2:2255-2264. [PMID: 36133365 PMCID: PMC9416917 DOI: 10.1039/d0na00227e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 04/27/2020] [Indexed: 06/14/2023]
Abstract
Regular, hollow proteinaceous nanoparticles are widespread in nature. The well-defined structures as well as diverse functions of naturally existing protein cages have inspired the development of new nanoarchitectures with desired capabilities. In such approaches, a key functionality is "connectability". Engineering of interfaces between cage building blocks to modulate intra-cage connectability leads to protein cages with new morphologies and assembly-disassembly properties. Modification of protein cage surfaces to control inter-cage connectability enables their arrangement into lattice-like nanomaterials. Here, we review the current progress in control of intra- and inter-cage connectability for protein cage-based nanotechnology development.
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Affiliation(s)
- Karolina Majsterkiewicz
- Małopolska Centre of Biotechnology, Jagiellonian University Gronostajowa 7A 30-387 Krakow Poland
- Postgraduate School of Molecular Medicine Trojdena 2a 02-091 Warsaw Poland
| | - Yusuke Azuma
- Małopolska Centre of Biotechnology, Jagiellonian University Gronostajowa 7A 30-387 Krakow Poland
| | - Jonathan G Heddle
- Małopolska Centre of Biotechnology, Jagiellonian University Gronostajowa 7A 30-387 Krakow Poland
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24
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Lapenta F, Jerala R. Design of novel protein building modules and modular architectures. Curr Opin Struct Biol 2020; 63:90-96. [PMID: 32505942 DOI: 10.1016/j.sbi.2020.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/31/2022]
Abstract
Nature uses only a limited number of protein topologies and while several folds have evolved independently over time, there are clearly many possible topologies that have not been explored by evolution. With recent advances of protein design concepts, computational modeling tools, high resolution and high-throughput experimental methods it is now possible to design new protein architectures. The collection of building blocks and design principles widened both in size and complexity, offering an expanded toolset for building new modular folds and functional protein structures. Here we review and discuss recent achievements of protein design, focusing in particular on the use and prospects of modular approaches for assembling new protein folds.
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Affiliation(s)
- Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia; EN-FIST Centre of Excellence, Ljubljana, Slovenia.
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25
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Su Z, Zhang R, Yan XY, Guo QY, Huang J, Shan W, Liu Y, Liu T, Huang M, Cheng SZ. The role of architectural engineering in macromolecular self-assemblies via non-covalent interactions: A molecular LEGO approach. Prog Polym Sci 2020. [DOI: 10.1016/j.progpolymsci.2020.101230] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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26
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Cannon KA, Nguyen VN, Morgan C, Yeates TO. Design and Characterization of an Icosahedral Protein Cage Formed by a Double-Fusion Protein Containing Three Distinct Symmetry Elements. ACS Synth Biol 2020; 9:517-524. [PMID: 32050070 DOI: 10.1021/acssynbio.9b00392] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Exploiting simple types of symmetry common to many natural protein oligomers as a starting point, several recent studies have succeeded in engineering complex self-assembling protein architectures reminiscent but distinct from those evolved in the natural world. Designing symmetric protein cages with a wide range of properties has been of particular interest for potential applications in the fields of medicine, energy, imaging, and more. In this study we genetically fused three naturally symmetric protein components together-a pentamer, trimer, and dimer-in a fashion designed to create a self-assembling icosahedral protein cage built from 60 copies of the protein subunit. The connection between the pentamer and dimer was based on a continuous shared α helix in order to control the relative orientation of those components. Following selection of suitable components by computational methods, a construct with favorable design properties was tested experimentally. Negative stain electron microscopy and solution-state methods indicated successful formation of a 60-subunit icosahedral cage, 2.5 MDa in mass and 30 nm in diameter. Diverse experimental studies also suggested substantial degrees of flexibility and asymmetric deformation of the assembled particle in solution. The results add further examples of successes and challenges in designing atomically precise protein materials.
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Affiliation(s)
- Kevin A. Cannon
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, United States
- UCLA Department of Chemistry and Biochemistry, Los Angeles, California 90095, United States
| | - Vy N. Nguyen
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, United States
- UCLA Department of Chemistry and Biochemistry, Los Angeles, California 90095, United States
| | - Christian Morgan
- UCLA Department of Ecology and Evolutionary Biology, Los Angeles, California 90095, United States
| | - Todd O. Yeates
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, United States
- UCLA Department of Chemistry and Biochemistry, Los Angeles, California 90095, United States
- UCLA Molecular Biology Institute, 611 Charles E Young Drive East, Los Angeles, California 90095, United States
- California Nanosystems Institute, Los Angeles, California 90095, United States
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27
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Sinha NJ, Wu D, Kloxin CJ, Saven JG, Jensen GV, Pochan DJ. Polyelectrolyte character of rigid rod peptide bundlemer chains constructed via hierarchical self-assembly. SOFT MATTER 2019; 15:9858-9870. [PMID: 31738361 DOI: 10.1039/c9sm01894h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Short α-helical peptides were computationally designed to self-assemble into robust coiled coils that are antiparallel, homotetrameric bundles. These peptide bundle units, or 'bundlemers', have been utilized as anisotropic building blocks to construct bundlemer-based polymers via a hierarchical, hybrid physical-covalent assembly pathway. The bundlemer chains were constructed using short linker connections via 'click' chemistry reactions between the N-termini of bundlemer constituent peptides. The resulting bundlemer chains appear as extremely rigid, cylindrical rods in transmission electron microscopy (TEM) images. Small angle neutron scattering (SANS) shows that these bundlemer chains exist as individual rods in solution with a cross-section that is equal to that of a single coiled coil bundlemer building block of ≈20 Å. SANS further confirms that the interparticle solution structure of the rigid rod bundlemer chains is heterogeneous and responsive to solution conditions, such as ionic-strength and pH. Due to their peptidic constitution, the bundlemer assemblies behave like polyelectrolytes that carry an average charge density of approximately 3 charges per bundlemer as determined from SANS structure factor data fitting, which describes the repulsion between charged rods in solution. This repulsion manifests as a correlation hole in the scattering profile that is suppressed by dilution or addition of salt. Presence of rod cluster aggregates with a mass fractal dimension of ≈2.5 is also confirmed across all samples. The formation of such dense, fractal-like cluster aggregates in a solution of net repulsive rods is a unique example of the subtle balance between short-range attraction and long-rage repulsion interactions in proteins and other biomaterials. With computational control of constituent peptide sequences, it is further possible to deconvolute the underlying sequence driven structure-property relationships in the modular bundlemer chains.
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Affiliation(s)
- Nairiti J Sinha
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA.
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28
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Diverse protein assembly driven by metal and chelating amino acids with selectivity and tunability. Nat Commun 2019; 10:5545. [PMID: 31804480 PMCID: PMC6895169 DOI: 10.1038/s41467-019-13491-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 11/08/2019] [Indexed: 01/01/2023] Open
Abstract
Proteins are versatile natural building blocks with highly complex and multifunctional architectures, and self-assembled protein structures have been created by the introduction of covalent, noncovalent, or metal-coordination bonding. Here, we report the robust, selective, and reversible metal coordination properties of unnatural chelating amino acids as the sufficient and dominant driving force for diverse protein self-assembly. Bipyridine-alanine is genetically incorporated into a D3 homohexamer. Depending on the position of the unnatural amino acid, 1-directional, crystalline and noncrystalline 2-directional, combinatory, and hierarchical architectures are effectively created upon the addition of metal ions. The length and shape of the structures is tunable by altering conditions related to thermodynamics and kinetics of metal-coordination and subsequent reactions. The crystalline 1-directional and 2-directional biomaterials retain their native enzymatic activities with increased thermal stability, suggesting that introducing chelating ligands provides a specific chemical basis to synthesize diverse protein-based functional materials while retaining their native structures and functions. Precise manipulation of protein self-assembly in vitro is challenging. Here, the authors developed an approach for driving metal-mediated reversible protein assembly by genetically installing a bipyridine residue into an oligomeric (D3) protein.
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29
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Affiliation(s)
- Aleksei Solomonov
- Department of Materials and Interfaces Weizmann Institute of Science 7610001 Rehovot Israel
| | - Ulyana Shimanovich
- Department of Materials and Interfaces Weizmann Institute of Science 7610001 Rehovot Israel
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30
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Cristie-David AS, Chen J, Nowak DB, Bondy AL, Sun K, Park SI, Banaszak Holl MM, Su M, Marsh ENG. Coiled-Coil-Mediated Assembly of an Icosahedral Protein Cage with Extremely High Thermal and Chemical Stability. J Am Chem Soc 2019; 141:9207-9216. [PMID: 31117640 DOI: 10.1021/jacs.8b13604] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The organization of protein molecules into higher-order nanoscale architectures is ubiquitous in Nature and represents an important goal in synthetic biology. Furthermore, the stabilization of enzyme activity has many practical applications in biotechnology and medicine. Here we describe the symmetry-directed design of an extremely stable, enzymatically active, hollow protein cage of Mr ≈ 2.1 MDa with dimensions similar to those of a small icosahedral virus. The cage was constructed based on icosahedral symmetry by genetically fusing a trimeric protein (TriEst) to a small pentameric de novo-designed coiled coil domain, separated by a flexible oligo-glycine linker sequence. Screening a small library of designs in which the linker length varied from 2 to 12 residues identified a construct containing 8 glycine residues (Ico8) that formed well-defined cages. Characterization by dynamic light scattering, negative stain, and cryo-EM and by atomic force and IR-photoinduced force microscopy established that Ico8 assembles into a flexible hollow cage comprising 20 copies of the esterase trimer, 60 protein subunits in total, with overall icosahedral geometry. Notably, the cages formed by Ico8 proved to be extremely stable toward thermal and chemical denaturation: whereas TriEst was unfolded by heating ( Tm ≈ 75 °C) or denatured by 1.5 M guanidine hydrochloride, the Ico8 cages remained folded even at 120 °C or in 8 M guanidine hydrochloride. The increased stability of the cages is a new property that emerges from the higher-order structure of the protein cage, rather than being intrinsic to the components from which it is constructed.
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Affiliation(s)
- Ajitha S Cristie-David
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Junjie Chen
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Derek B Nowak
- Molecular Vista Inc , Via Del Oro Suite 110 , San Jose , California 95119 , United States
| | - Amy L Bondy
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Kai Sun
- Michigan Center for Materials Characterization , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Sung I Park
- Molecular Vista Inc , Via Del Oro Suite 110 , San Jose , California 95119 , United States
| | - Mark M Banaszak Holl
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Min Su
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - E Neil G Marsh
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
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31
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Garcia‐Seisdedos H, Villegas JA, Levy ED. Infinite Ansammlungen gefalteter Proteine im Kontext von Evolution, Krankheiten und Proteinentwicklung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201806092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - José A. Villegas
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
| | - Emmanuel D. Levy
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
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32
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Garcia‐Seisdedos H, Villegas JA, Levy ED. Infinite Assembly of Folded Proteins in Evolution, Disease, and Engineering. Angew Chem Int Ed Engl 2019; 58:5514-5531. [PMID: 30133878 PMCID: PMC6471489 DOI: 10.1002/anie.201806092] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/06/2018] [Indexed: 12/14/2022]
Abstract
Mutations and changes in a protein's environment are well known for their potential to induce misfolding and aggregation, including amyloid formation. Alternatively, such perturbations can trigger new interactions that lead to the polymerization of folded proteins. In contrast to aggregation, this process does not require misfolding and, to highlight this difference, we refer to it as agglomeration. This term encompasses the amorphous assembly of folded proteins as well as the polymerization in one, two, or three dimensions. We stress the remarkable potential of symmetric homo-oligomers to agglomerate even by single surface point mutations, and we review the double-edged nature of this potential: how aberrant assemblies resulting from agglomeration can lead to disease, but also how agglomeration can serve in cellular adaptation and be exploited for the rational design of novel biomaterials.
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Affiliation(s)
| | - José A. Villegas
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
| | - Emmanuel D. Levy
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
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33
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Abstract
![]()
Ordered
protein assemblies are attracting interest as next-generation
biomaterials with a remarkable range of structural and functional
properties, leading to potential applications in biocatalysis, materials
templating, drug delivery and vaccine development. This Review covers
ordered protein assemblies including protein nanowires/nanofibrils,
nanorings, nanotubes, designed two- and three-dimensional ordered
protein lattices and protein-like cages including polyhedral virus-like
cage structures. The main focus is on designed ordered protein assemblies,
in which the spatial organization of the proteins is controlled by
tailored noncovalent interactions (including metal ion binding interactions,
electrostatic interactions and ligand–receptor interactions
among others) or by careful design of modified (mutant) proteins or de novo constructs. The modification of natural protein
assemblies including bacterial S-layers and cage-like and rod-like
viruses to impart novel function, e.g. enzymatic activity, is also
considered. A diversity of structures have been created using distinct
approaches, and this Review provides a summary of the state-of-the-art
in the development of these systems, which have exceptional potential
as advanced bionanomaterials for a diversity of applications.
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Affiliation(s)
- Ian W Hamley
- Department of Chemistry , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
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34
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Kuan SL, Bergamini FRG, Weil T. Functional protein nanostructures: a chemical toolbox. Chem Soc Rev 2018; 47:9069-9105. [PMID: 30452046 PMCID: PMC6289173 DOI: 10.1039/c8cs00590g] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Indexed: 01/08/2023]
Abstract
Nature has evolved an optimal synthetic factory in the form of translational and posttranslational processes by which millions of proteins with defined primary sequences and 3D structures can be built. Nature's toolkit gives rise to protein building blocks, which dictates their spatial arrangement to form functional protein nanostructures that serve a myriad of functions in cells, ranging from biocatalysis, formation of structural networks, and regulation of biochemical processes, to sensing. With the advent of chemical tools for site-selective protein modifications and recombinant engineering, there is a rapid development to develop and apply synthetic methods for creating structurally defined, functional protein nanostructures for a broad range of applications in the fields of catalysis, materials and biomedical sciences. In this review, design principles and structural features for achieving and characterizing functional protein nanostructures by synthetic approaches are summarized. The synthetic customization of protein building blocks, the design and introduction of recognition units and linkers and subsequent assembly into structurally defined protein architectures are discussed herein. Key examples of these supramolecular protein nanostructures, their unique functions and resultant impact for biomedical applications are highlighted.
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Affiliation(s)
- Seah Ling Kuan
- Max-Planck Institute for Polymer Research
,
Ackermannweg 10
, 55128 Mainz
, Germany
.
;
- Institute of Inorganic Chemistry I – Ulm University
,
Albert-Einstein-Allee 11
, 89081 Ulm
, Germany
| | - Fernando R. G. Bergamini
- Institute of Chemistry
, Federal University of Uberlândia – UFU
,
38400-902 Uberlândia
, MG
, Brazil
| | - Tanja Weil
- Max-Planck Institute for Polymer Research
,
Ackermannweg 10
, 55128 Mainz
, Germany
.
;
- Institute of Inorganic Chemistry I – Ulm University
,
Albert-Einstein-Allee 11
, 89081 Ulm
, Germany
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35
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Gómez-González J, Peña DG, Barka G, Sciortino G, Maréchal JD, Vázquez López M, Vázquez ME. Directed Self-Assembly of Trimeric DNA-Bindingchiral Miniprotein Helicates. Front Chem 2018; 6:520. [PMID: 30425980 PMCID: PMC6218460 DOI: 10.3389/fchem.2018.00520] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/09/2018] [Indexed: 01/19/2023] Open
Abstract
We propose that peptides are highly versatile platforms for the precise design of supramolecular metal architectures, and particularly, for the controlled assembly of helicates. In this context, we show that the bacteriophage T4 Fibritin foldon (T4Ff) can been engineered on its N-terminus with metal-chelating 2,2'-bipyridine units that stereoselectively assemble in the presence of Fe(II) into parallel, three-stranded peptide helicates with preferred helical orientation. Modeling studies support the proposed self-assembly and the stability of the final helicate. Furthermore, we show that these designed mini-metalloproteins selectively recognize three-way DNA junctions over double-stranded DNA.
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Affiliation(s)
- Jacobo Gómez-González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Diego G Peña
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ghofrane Barka
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Giuseppe Sciortino
- Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola, Spain.,Dipartimento di Chimica e Farmacia, Università di Sassari, Sassari, Italy
| | | | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - M Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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36
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Li P, Sun M, Xu Z, Liu X, Zhao W, Gao W. Site-Selective in Situ Growth-Induced Self-Assembly of Protein–Polymer Conjugates into pH-Responsive Micelles for Tumor Microenvironment Triggered Fluorescence Imaging. Biomacromolecules 2018; 19:4472-4479. [DOI: 10.1021/acs.biomac.8b01368] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pengyong Li
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Mengmeng Sun
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Zhikun Xu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xinyu Liu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Wenguo Zhao
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Weiping Gao
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
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37
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Tian Y, Polzer FB, Zhang HV, Kiick KL, Saven JG, Pochan DJ. Nanotubes, Plates, and Needles: Pathway-Dependent Self-Assembly of Computationally Designed Peptides. Biomacromolecules 2018; 19:4286-4298. [DOI: 10.1021/acs.biomac.8b01163] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Yu Tian
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
| | - Frank B. Polzer
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
| | - Huixi Violet Zhang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Kristi L. Kiick
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffery G. Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Darrin J. Pochan
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
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38
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Alcala-Torano R, Walther M, Sommer DJ, Park CK, Ghirlanda G. Rational design of a hexameric protein assembly stabilized by metal chelation. Biopolymers 2018; 109:e23233. [PMID: 30191549 DOI: 10.1002/bip.23233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 06/15/2018] [Accepted: 07/05/2018] [Indexed: 12/27/2022]
Abstract
Protein-based self-assembled nanostructures hold tremendous promise as smart materials. One strategy to control the assembly of individual protein modules takes advantage of the directionality and high affinity bonding afforded by metal chelation. Here, we describe the use of 2,2'-bipyridine units (Bpy) as side chains to template the assembly of large structures (MW approx. 35 000 Da) in a metal-dependent manner. The structures are trimers of independently folded 3-helix bundles, and are held together by 2 Me(Bpy)3 complexes. The assemblies are stable to thermal denaturation, and are more than 90% helical at 90°C. Circular dichroism spectroscopy shows that one of the 2 possible (Bpy)3 enantiomers is favored over the other. Because of the sequence pliability of the starting peptides, these constructs could find use to organize functional groups at controlled positions within a supramolecular assembly.
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Affiliation(s)
| | - Mathieu Walther
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
| | - Dayn J Sommer
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
| | - Chad K Park
- Department of Biochemistry, University of Arizona, Tucson, Arizona
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39
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Diaz D, Care A, Sunna A. Bioengineering Strategies for Protein-Based Nanoparticles. Genes (Basel) 2018; 9:E370. [PMID: 30041491 PMCID: PMC6071185 DOI: 10.3390/genes9070370] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/16/2018] [Accepted: 07/17/2018] [Indexed: 12/16/2022] Open
Abstract
In recent years, the practical application of protein-based nanoparticles (PNPs) has expanded rapidly into areas like drug delivery, vaccine development, and biocatalysis. PNPs possess unique features that make them attractive as potential platforms for a variety of nanobiotechnological applications. They self-assemble from multiple protein subunits into hollow monodisperse structures; they are highly stable, biocompatible, and biodegradable; and their external components and encapsulation properties can be readily manipulated by chemical or genetic strategies. Moreover, their complex and perfect symmetry have motivated researchers to mimic their properties in order to create de novo protein assemblies. This review focuses on recent advances in the bioengineering and bioconjugation of PNPs and the implementation of synthetic biology concepts to exploit and enhance PNP's intrinsic properties and to impart them with novel functionalities.
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Affiliation(s)
- Dennis Diaz
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Andrew Care
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW 2109, Australia.
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW 2109, Australia.
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW 2109, Australia.
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40
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Abstract
A general formulation for constructing addressable atomic clusters is introduced, based on one or more reference structures. By modifying the well depths in a given interatomic potential in favour of nearest-neighbour interactions that are defined in the reference(s), the potential energy landscape can be biased to make a particular permutational isomer the global minimum. The magnitude of the bias changes the resulting potential energy landscape systematically, providing a framework to produce clusters that should self-organise efficiently into the target structure. These features are illustrated for small systems, where all the relevant local minima and transition states can be identified, and for the low-energy regions of the landscape for larger clusters. For a 55-particle cluster, it is possible to design a target structure from a transition state of the original potential and to retain this structure in a doubly addressable landscape. Disconnectivity graphs based on local minima that have no direct connections to a lower minimum provide a helpful way to visualise the larger databases. These minima correspond to the termini of monotonic sequences, which always proceed downhill in terms of potential energy, and we identify them as a class of biminimum. Multiple copies of the target cluster are treated by adding a repulsive term between particles with the same address to maintain distinguishable targets upon aggregation. By tuning the magnitude of this term, it is possible to create assemblies of the target cluster corresponding to a variety of structures, including rings and chains.
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Affiliation(s)
- David J Wales
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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41
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Abstract
Within the materials science community, proteins with cage-like architectures are being developed as versatile nanoscale platforms for use in protein nanotechnology. Much effort has been focused on the functionalization of protein cages with biological and non-biological moieties to bring about new properties of not only individual protein cages, but collective bulk-scale assemblies of protein cages. In this review, we report on the current understanding of protein cage assembly, both of the cages themselves from individual subunits, and the assembly of the individual protein cages into higher order structures. We start by discussing the key properties of natural protein cages (for example: size, shape and structure) followed by a review of some of the mechanisms of protein cage assembly and the factors that influence it. We then explore the current approaches for functionalizing protein cages, on the interior or exterior surfaces of the capsids. Lastly, we explore the emerging area of higher order assemblies created from individual protein cages and their potential for new and exciting collective properties.
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Affiliation(s)
- William M Aumiller
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
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42
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Lutomski CA, Lyktey NA, Pierson EE, Zhao Z, Zlotnick A, Jarrold MF. Multiple Pathways in Capsid Assembly. J Am Chem Soc 2018; 140:5784-5790. [PMID: 29672035 DOI: 10.1021/jacs.8b01804] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
For a three-dimensional structure to spontaneously self-assemble from many identical components, the steps on the pathway must be kinetically accessible. Many virus capsids are icosahedral and assembled from hundreds of identical proteins, but how they navigate the assembly process is poorly understood. Capsid assembly is thought to involve stepwise addition of subunits to a growing capsid fragment. Coarse-grained models suggest that the reaction occurs on a downhill energy landscape, so intermediates are expected to be fleeting. In this work, charge detection mass spectrometry (CDMS) has been used to track assembly of the hepatitis B virus (HBV) capsid in real time. The icosahedral T = 4 capsid of HBV is assembled from 120 capsid protein dimers. Our results indicate that there are multiple pathways for assembly. Under conditions that favor a modest association energy there is no accumulation of large intermediates, which indicates that available pathways include ones on a downhill energy surface. Under higher salt conditions, where subunit interactions are strengthened, around half of the products of the initial assembly reaction have masses close to the T = 4 capsid and the other half are stalled intermediates which emerge abruptly at around 90 dimers, indicating a bifurcation in the ensemble of assembly paths. When incubated at room temperature, the 90-dimer intermediates accumulate dimers and gradually shift to higher mass and merge with the capsid peak. Though free subunits are present in solution, the stalled intermediates indicate the presence of a local minima on the energy landscape. Some intermediates may result from hole closure, where the growing capsid distorts to close the hole due to the missing capsid proteins or from a species where subsequent additions are particularly labile.
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Zeng X, Li ZW, Zheng X, Zhu L, Sun ZY, Lu ZY, Huang X. Improving the productivity of monodisperse polyhedral cages by the rational design of kinetic self-assembly pathways. Phys Chem Chem Phys 2018; 20:10030-10037. [PMID: 29620122 DOI: 10.1039/c8cp00522b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Hollow polyhedral cages hold great potential for application in nanotechnological and biomedical fields. Understanding the formation mechanism of these self-assembled structures could provide guidance for the rational design of the desired polyhedral cages. Here, by constructing kinetic network models from extensive coarse-grained molecular dynamics simulations, we elucidated the formation mechanism of the dodecahedral cage, which is formed by the self-assembly of patchy particles. We found that the dodecahedral cage is formed through increasing the aggregate size followed by structure rearrangement. Based on this mechanistic understanding, we improved the productivity of the dodecahedral cage through the rational design of the patch arrangement of patchy particles, which promotes the structural rearrangement process. Our results demonstrate that it should be a feasible strategy to achieve the rational design of the desired nanostructures via the kinetic analysis. We anticipate that this methodology could be extended to other self-assembly systems for the fabrication of functional nanomaterials.
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Affiliation(s)
- Xiangze Zeng
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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Sanchez-deAlcazar D, Mejias SH, Erazo K, Sot B, Cortajarena AL. Self-assembly of repeat proteins: Concepts and design of new interfaces. J Struct Biol 2018; 201:118-129. [DOI: 10.1016/j.jsb.2017.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/09/2017] [Accepted: 09/02/2017] [Indexed: 11/25/2022]
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45
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Okesola BO, Mata A. Multicomponent self-assembly as a tool to harness new properties from peptides and proteins in material design. Chem Soc Rev 2018; 47:3721-3736. [DOI: 10.1039/c8cs00121a] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nature is enriched with a wide variety of complex, synergistic and highly functional protein-based multicomponent assemblies.
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Affiliation(s)
- Babatunde O. Okesola
- School of Engineering and Materials Science
- Institute of Bioengineering
- Queen Mary University of London
- UK
| | - Alvaro Mata
- School of Engineering and Materials Science
- Institute of Bioengineering
- Queen Mary University of London
- UK
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46
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Wołek K, Cieplak M. Self-assembly of model proteins into virus capsids. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:474003. [PMID: 29027904 PMCID: PMC7104874 DOI: 10.1088/1361-648x/aa9351] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/29/2017] [Accepted: 10/13/2017] [Indexed: 06/07/2023]
Abstract
We consider self-assembly of proteins into a virus capsid by the methods of molecular dynamics. The capsid corresponds either to SPMV or CCMV and is studied with and without the RNA molecule inside. The proteins are flexible and described by the structure-based coarse-grained model augmented by electrostatic interactions. Previous studies of the capsid self-assembly involved solid objects of a supramolecular scale, e.g. corresponding to capsomeres, with engineered couplings and stochastic movements. In our approach, a single capsid is dissociated by an application of a high temperature for a variable period and then the system is cooled down to allow for self-assembly. The restoration of the capsid proceeds to various extent, depending on the nature of the dissociated state, but is rarely complete because some proteins depart too far unless the process takes place in a confined space.
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Affiliation(s)
- Karol Wołek
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
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47
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Negahdaripour M, Golkar N, Hajighahramani N, Kianpour S, Nezafat N, Ghasemi Y. Harnessing self-assembled peptide nanoparticles in epitope vaccine design. Biotechnol Adv 2017; 35:575-596. [PMID: 28522213 PMCID: PMC7127164 DOI: 10.1016/j.biotechadv.2017.05.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/23/2017] [Accepted: 05/11/2017] [Indexed: 12/11/2022]
Abstract
Vaccination has been one of the most successful breakthroughs in medical history. In recent years, epitope-based subunit vaccines have been introduced as a safer alternative to traditional vaccines. However, they suffer from limited immunogenicity. Nanotechnology has shown value in solving this issue. Different kinds of nanovaccines have been employed, among which virus-like nanoparticles (VLPs) and self-assembled peptide nanoparticles (SAPNs) seem very promising. Recently, SAPNs have attracted special interest due to their unique properties, including molecular specificity, biodegradability, and biocompatibility. They also resemble pathogens in terms of their size. Their multivalency allows an orderly repetitive display of antigens on their surface, which induces a stronger immune response than single immunogens. In vaccine design, SAPN self-adjuvanticity is regarded an outstanding advantage, since the use of toxic adjuvants is no longer required. SAPNs are usually composed of helical or β-sheet secondary structures and are tailored from natural peptides or de novo structures. Flexibility in subunit selection opens the door to a wide variety of molecules with different characteristics. SAPN engineering is an emerging area, and more novel structures are expected to be generated in the future, particularly with the rapid progress in related computational tools. The aim of this review is to provide a state-of-the-art overview of self-assembled peptide nanoparticles and their use in vaccine design in recent studies. Additionally, principles for their design and the application of computational approaches to vaccine design are summarized.
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Affiliation(s)
- Manica Negahdaripour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nasim Golkar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutics Department, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nasim Hajighahramani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sedigheh Kianpour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran; Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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48
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Heddle JG, Chakraborti S, Iwasaki K. Natural and artificial protein cages: design, structure and therapeutic applications. Curr Opin Struct Biol 2017; 43:148-155. [DOI: 10.1016/j.sbi.2017.03.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 02/21/2017] [Accepted: 03/09/2017] [Indexed: 01/28/2023]
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49
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Yamanaka M, Hoshizumi M, Nagao S, Nakayama R, Shibata N, Higuchi Y, Hirota S. Formation and carbon monoxide-dependent dissociation of Allochromatium vinosum cytochrome c' oligomers using domain-swapped dimers. Protein Sci 2017; 26:464-474. [PMID: 27883268 PMCID: PMC5326568 DOI: 10.1002/pro.3090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/18/2016] [Accepted: 11/18/2016] [Indexed: 12/12/2022]
Abstract
The number of artificial protein supramolecules has been increasing; however, control of protein oligomer formation remains challenging. Cytochrome c' from Allochromatium vinosum (AVCP) is a homodimeric protein in its native form, where its protomer exhibits a four-helix bundle structure containing a covalently bound five-coordinate heme as a gas binding site. AVCP exhibits a unique reversible dimer-monomer transition according to the absence and presence of CO. Herein, domain-swapped dimeric AVCP was constructed and utilized to form a tetramer and high-order oligomers. The X-ray crystal structure of oxidized tetrameric AVCP consisted of two monomer subunits and one domain-swapped dimer subunit, which exchanged the region containing helices αA and αB between protomers. The active site structures of the domain-swapped dimer subunit and monomer subunits in the tetramer were similar to those of the monomer subunits in the native dimer. The subunit-subunit interactions at the interfaces of the domain-swapped dimer and monomer subunits in the tetramer were also similar to the subunit-subunit interaction in the native dimer. Reduced tetrameric AVCP dissociated to a domain-swapped dimer and two monomers upon CO binding. Without monomers, the domain-swapped dimers formed tetramers, hexamers, and higher-order oligomers in the absence of CO, whereas the oligomers dissociated to domain-swapped dimers in the presence of CO, demonstrating that the domain-swapped dimer maintains the CO-induced subunit dissociation behavior of native ACVP. These results suggest that protein oligomer formation may be controlled by utilizing domain swapping for a dimer-monomer transition protein.
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Affiliation(s)
- Masaru Yamanaka
- Graduate School of Materials ScienceNara Institute of Science and Technology8916‐5 Takayama, IkomaNara630‐0192Japan
| | - Makoto Hoshizumi
- Graduate School of Materials ScienceNara Institute of Science and Technology8916‐5 Takayama, IkomaNara630‐0192Japan
| | - Satoshi Nagao
- Graduate School of Materials ScienceNara Institute of Science and Technology8916‐5 Takayama, IkomaNara630‐0192Japan
| | - Ryoko Nakayama
- Graduate School of Materials ScienceNara Institute of Science and Technology8916‐5 Takayama, IkomaNara630‐0192Japan
| | - Naoki Shibata
- Department of Life ScienceGraduate School of Life Science, University of Hyogo3‐2‐1 Koto, Kamigori‐cho, Ako‐gunHyogo678‐1297Japan
- RIKEN SPring‐8 Center1‐1‐1 Koto, Sayo‐cho, Sayo‐gunHyogo679‐5148Japan
| | - Yoshiki Higuchi
- Department of Life ScienceGraduate School of Life Science, University of Hyogo3‐2‐1 Koto, Kamigori‐cho, Ako‐gunHyogo678‐1297Japan
- RIKEN SPring‐8 Center1‐1‐1 Koto, Sayo‐cho, Sayo‐gunHyogo679‐5148Japan
| | - Shun Hirota
- Graduate School of Materials ScienceNara Institute of Science and Technology8916‐5 Takayama, IkomaNara630‐0192Japan
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50
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Abstract
Emerging protein design strategies are enabling the creation of diverse, self-assembling supramolecular structures with precision on the atomic scale. The design possibilities include various types of architectures: finite cages or shells, essentially unbounded two-dimensional and three-dimensional arrays (i.e., crystals), and linear or tubular filaments. In nature, structures of those types are generally symmetric, and, accordingly, symmetry provides a powerful guide for developing new design approaches. Recent design studies have produced numerous protein assemblies in close agreement with geometric specifications. For certain design approaches, a complete list of allowable symmetry combinations that can be used for construction has been articulated, opening a path to a rich diversity of geometrically defined protein materials. Future challenges include improving and elaborating on current strategies and endowing designed protein nanomaterials with properties useful in nanomedicine and material science applications.
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Affiliation(s)
- Todd O Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095.,UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095;
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