1
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Nourani L, Lotfi A, Vand-Rajabpour H, Pourhashem Z, Nemati F, Mehrizi AA. Optimized Refolding Buffers Oriented Humoral Immune Responses Versus PfGCS1 Self-Assembled Peptide Nanoparticle. Mol Biotechnol 2024; 66:2648-2664. [PMID: 38267696 DOI: 10.1007/s12033-023-01044-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/15/2023] [Indexed: 01/26/2024]
Abstract
Developing a novel class of vaccine is pivotal for eliminating and eradicating malaria. Preceding investigations demonstrated partial blocking activity in malaria transmission against recombinant vaccine PfHAP2-GCS1 and conserved region of the cd loop. The effectiveness of immune response varies with the size and shape of the self-assembly of peptide nanoparticles (SAPNs) displaying antigen, affected by different components in refolding buffers. Plasmodium falciparum Generative Cell Specific 1 (PfGCS1), a promising malaria transmission-blocking vaccine (TBV) candidate, was expressed, purified, and followed by a four-step refolding process to form nanoparticles (PfGCS1-SAPNs). The influence of buffer components on the size and shape of SAPNs was investigated by DLS and FESEM. Furthermore, the immunogenicity of nanostructures was assessed in different mouse groups. The results showed that PfGCS1-SAPN was immunogenic and its administration with Poly (I:C), stimulated humoral and cellular responses in the mouse model. In the immunized mice groups, the level of IgG antibodies against PfGCS1-SAPN was significantly increased in different time points (second and third boost) and heterogeneous boosters. The various IgG-subclasses profile shifted to Th1, Th2, or Th1/Th2 mix responses in mice immunized with PfGCS1-SAPN refolded in different buffers, indicating a prerequisite for further investigations to optimize vaccine formulation to enhance and modulate Th1/cellular responses. Such studies pave the way to improve biophysical features related to the nanoparticles' size, shape, and conformational epitopes of candidate antigens and T- and B-cells presented on the superficial structure to elicit robust immune responses.
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Affiliation(s)
- Leila Nourani
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, P.O. Box: 1316943551, Tehran, Iran
| | - Anita Lotfi
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, P.O. Box: 1316943551, Tehran, Iran
- Department of Biotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Hediye Vand-Rajabpour
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, P.O. Box: 1316943551, Tehran, Iran
| | - Zeinab Pourhashem
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, P.O. Box: 1316943551, Tehran, Iran
| | - Fahimeh Nemati
- Department of Biotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Akram Abouie Mehrizi
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, P.O. Box: 1316943551, Tehran, Iran.
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2
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El Bissati K, Krishack PA, Zhou Y, Weber CR, Lykins J, Jankovic D, Edelblum KL, Fraczek L, Grover H, Chentoufi AA, Singh G, Reardon C, Dubey JP, Reed S, Alexander J, Sidney J, Sette A, Shastri N, McLeod R. CD4 + T Cell Responses to Toxoplasma gondii Are a Double-Edged Sword. Vaccines (Basel) 2023; 11:1485. [PMID: 37766162 PMCID: PMC10535856 DOI: 10.3390/vaccines11091485] [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: 07/17/2023] [Revised: 08/26/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
CD4+ T cells have been found to play critical roles in the control of both acute and chronic Toxoplasma infection. Previous studies identified a protective role for the Toxoplasma CD4+ T cell-eliciting peptide AS15 (AVEIHRPVPGTAPPS) in C57BL/6J mice. Herein, we found that immunizing mice with AS15 combined with GLA-SE, a TLR-4 agonist in emulsion adjuvant, can be either helpful in protecting male and female mice at early stages against Type I and Type II Toxoplasma parasites or harmful (lethal with intestinal, hepatic, and spleen pathology associated with a storm of IL6). Introducing the universal CD4+ T cell epitope PADRE abrogates the harmful phenotype of AS15. Our findings demonstrate quantitative and qualitative features of an effective Toxoplasma-specific CD4+ T cell response that should be considered in testing next-generation vaccines against toxoplasmosis. Our results also are cautionary that individual vaccine constituents can cause severe harm depending on the company they keep.
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Affiliation(s)
- Kamal El Bissati
- Institute of Molecular Engineering, University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Paulette A. Krishack
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA; (P.A.K.); (C.R.W.); (G.S.); (C.R.)
| | - Ying Zhou
- Department of Ophthalmology and Visual Sciences, University of Chicago, Chicago, IL 60637, USA; (Y.Z.); (J.L.); (L.F.); (R.M.)
| | - Christopher R. Weber
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA; (P.A.K.); (C.R.W.); (G.S.); (C.R.)
| | - Joseph Lykins
- Department of Ophthalmology and Visual Sciences, University of Chicago, Chicago, IL 60637, USA; (Y.Z.); (J.L.); (L.F.); (R.M.)
- Department of Emergency Medicine, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02215, USA
| | - Dragana Jankovic
- Immunoparasitology Unit, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Karen L. Edelblum
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- Center for Immunity and Inflammation, Laboratory Medicine, Department of Pathology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Laura Fraczek
- Department of Ophthalmology and Visual Sciences, University of Chicago, Chicago, IL 60637, USA; (Y.Z.); (J.L.); (L.F.); (R.M.)
| | - Harshita Grover
- Division of Immunology and Pathogenesis, Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA; (H.G.); (N.S.)
| | - Aziz A. Chentoufi
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria 0028, South Africa;
| | - Gurminder Singh
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA; (P.A.K.); (C.R.W.); (G.S.); (C.R.)
| | - Catherine Reardon
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA; (P.A.K.); (C.R.W.); (G.S.); (C.R.)
| | - J. P. Dubey
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
| | - Steve Reed
- Infectious Diseases Research Institute, 1616 Eastlake Ave E #400, Seattle, WA 98102, USA;
| | - Jeff Alexander
- PaxVax, 3985-A Sorrento Valley Blvd, San Diego, CA 92121, USA;
| | - John Sidney
- La Jolla Institute of Allergy and Immunology, 9420 Athena Cir, La Jolla, CA 92037, USA; (J.S.); (A.S.)
| | - Alessandro Sette
- La Jolla Institute of Allergy and Immunology, 9420 Athena Cir, La Jolla, CA 92037, USA; (J.S.); (A.S.)
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA; (H.G.); (N.S.)
| | - Rima McLeod
- Department of Ophthalmology and Visual Sciences, University of Chicago, Chicago, IL 60637, USA; (Y.Z.); (J.L.); (L.F.); (R.M.)
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3
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Mallik BB, Stanislaw J, Alawathurage TM, Khmelinskaia A. De Novo Design of Polyhedral Protein Assemblies: Before and After the AI Revolution. Chembiochem 2023; 24:e202300117. [PMID: 37014094 DOI: 10.1002/cbic.202300117] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 04/05/2023]
Abstract
Self-assembling polyhedral protein biomaterials have gained attention as engineering targets owing to their naturally evolved sophisticated functions, ranging from protecting macromolecules from the environment to spatially controlling biochemical reactions. Precise computational design of de novo protein polyhedra is possible through two main types of approaches: methods from first principles, using physical and geometrical rules, and more recent data-driven methods based on artificial intelligence (AI), including deep learning (DL). Here, we retrospect first principle- and AI-based approaches for designing finite polyhedral protein assemblies, as well as advances in the structure prediction of such assemblies. We further highlight the possible applications of these materials and explore how the presented approaches can be combined to overcome current challenges and to advance the design of functional protein-based biomaterials.
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Affiliation(s)
- Bhoomika Basu Mallik
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
| | - Jenna Stanislaw
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
| | - Tharindu Madhusankha Alawathurage
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
| | - Alena Khmelinskaia
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
- Current address: Department of Chemistry, Ludwig Maximillian University, 80539, Munich, Germany
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4
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Design and development of a self-assembling protein nanoparticle displaying PfHAP2 antigenic determinants recognized by natural acquired antibodies. PLoS One 2022; 17:e0274275. [PMID: 36094917 PMCID: PMC9467374 DOI: 10.1371/journal.pone.0274275] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/24/2022] [Indexed: 11/19/2022] Open
Abstract
Backgrounds In order to move towards the elimination and eradication of malaria in the world, the development of vaccines is inevitable. Many modern vaccines are based on recombinant technology; however, they may not provide a fully protective, long-lasting immune response. One of the strategies to improve recombinant vaccines is designing the nanovaccines such as self-assembling protein nanoparticles (SAPNs). Hence, the presentation of epitopes in a repeat array and correct conformation should be considered. P. falciparum generative cell-specific 1 (PfGCS1) is a main transmission-blocking vaccine candidate with two highly conserved fragments, HAP2-GCS1 and cd loop, inducing partial malaria transmission inhibitory antibodies. Therefore, to design an effective malaria vaccine, we used cd loop and HAP2-GCS1 fragments at the amino and carboxy terminuses of the SAPN-forming amino acid sequence, respectively. Methodology/Principal findings The SAPN monomer (PfGCS1-SAPN) sequence was designed, and the three-dimensional (3D) structure was predicted. The result of this prediction ensured the presence of antigens on the SAPN surface. Then the accuracy of the predicted 3D structure and its stability were confirmed by 100 ns molecular dynamics (MD) simulation. The designed SAPN substructure sequence was synthesized, cloned, and expressed in Escherichia coli. With a gradual decrease in urea concentration in dialysis solutions, the purified proteins progressed to the final desired structure of the SAPN, which then was confirmed by Dynamic Light Scattering (DLS) and Field Emission Scanning Electron Microscopy (FESEM) tests. According to the Enzyme-Linked Immunosorbent Assay (ELISA), antigenic determinants were presented on the SAPN surface and interacted with antibodies in the serum of malaria patients. Conclusions/Significance Our results show that the SAPN formed by PfGCS1-SAPN has produced the correct shape and size, and the antigenic determinants are presented on the surface of the SAPN, which indicates that the designed SAPN has great potential to be used in the future as a malaria vaccine.
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5
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Villegas JA, Sinha NJ, Teramoto N, Von Bargen CD, Pochan DJ, Saven JG. Computational Design of Single-Peptide Nanocages with Nanoparticle Templating. Molecules 2022; 27:1237. [PMID: 35209027 PMCID: PMC8874777 DOI: 10.3390/molecules27041237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 01/25/2023] Open
Abstract
Protein complexes perform a diversity of functions in natural biological systems. While computational protein design has enabled the development of symmetric protein complexes with spherical shapes and hollow interiors, the individual subunits often comprise large proteins. Peptides have also been applied to self-assembly, and it is of interest to explore such short sequences as building blocks of large, designed complexes. Coiled-coil peptides are promising subunits as they have a symmetric structure that can undergo further assembly. Here, an α-helical 29-residue peptide that forms a tetrameric coiled coil was computationally designed to assemble into a spherical cage that is approximately 9 nm in diameter and presents an interior cavity. The assembly comprises 48 copies of the designed peptide sequence. The design strategy allowed breaking the side chain conformational symmetry within the peptide dimer that formed the building block (asymmetric unit) of the cage. Dynamic light scattering (DLS) and transmission electron microscopy (TEM) techniques showed that one of the seven designed peptide candidates assembled into individual nanocages of the size and shape. The stability of assembled nanocages was found to be sensitive to the assembly pathway and final solution conditions (pH and ionic strength). The nanocages templated the growth of size-specific Au nanoparticles. The computational design serves to illustrate the possibility of designing target assemblies with pre-determined specific dimensions using short, modular coiled-coil forming peptide sequences.
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Affiliation(s)
- José A. Villegas
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA; (J.A.V.); (C.D.V.B.)
| | - Nairiti J. Sinha
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA; (N.J.S.); (N.T.)
| | - Naozumi Teramoto
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA; (N.J.S.); (N.T.)
| | - Christopher D. Von Bargen
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA; (J.A.V.); (C.D.V.B.)
| | - Darrin J. Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA; (N.J.S.); (N.T.)
| | - Jeffery G. Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA; (J.A.V.); (C.D.V.B.)
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6
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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: 93] [Impact Index Per Article: 31.0] [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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7
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Meleties M, Katyal P, Lin B, Britton D, Montclare JK. Self-assembly of stimuli-responsive coiled-coil fibrous hydrogels. SOFT MATTER 2021; 17:6470-6476. [PMID: 34137426 DOI: 10.1039/d1sm00780g] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Owing to their tunable properties, hydrogels comprised of stimuli-sensitive polymers are one of the most appealing scaffolds with applications in tissue engineering, drug delivery and other biomedical fields. We previously reported a thermoresponsive hydrogel formed using a coiled-coil protein, Q. Here, we expand our studies to identify the gelation of Q protein at distinct pH conditions, creating a protein hydrogel system that is sensitive to temperature and pH. Through secondary structure analysis, transmission electron microscopy, and rheology, we observed that Q self-assembles and forms fiber-based hydrogels exhibiting upper critical solution temperature behavior with increased elastic properties at pH 7.4 and pH 10. At pH 6, however, Q forms polydisperse nanoparticles, which do not further self-assemble and undergo gelation. The high net positive charge of Q at pH 6 creates significant electrostatic repulsion, preventing its gelation. This study will potentially guide the development of novel scaffolds and functional biomaterials that are sensitive towards biologically relevant stimuli.
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Affiliation(s)
- Michael Meleties
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, USA.
| | - Priya Katyal
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, USA.
| | - Bonnie Lin
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, USA.
| | - Dustin Britton
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, USA.
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, USA. and Department of Radiology, New York University Langone Health, New York, New York 10016, USA and Department of Biomaterials, New York University College of Dentistry, New York, New York 10010, USA and Department of Chemistry, New York University, New York, New York 10003, USA
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8
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Khmelinskaia A, Wargacki A, King NP. Structure-based design of novel polyhedral protein nanomaterials. Curr Opin Microbiol 2021; 61:51-57. [PMID: 33784513 DOI: 10.1016/j.mib.2021.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/05/2021] [Accepted: 03/11/2021] [Indexed: 02/06/2023]
Abstract
Organizing matter at the atomic scale is a central goal of nanotechnology. Bottom-up approaches, in which molecular building blocks are programmed to assemble via supramolecular interactions, are a proven and versatile route to new and useful nanomaterials. Although a wide variety of molecules have been used as building blocks, proteins have several intrinsic features that present unique opportunities for designing nanomaterials with sophisticated functions. There has been tremendous recent progress in designing proteins to fold and assemble to highly ordered structures. Here we review the leading approaches to the design of closed polyhedral protein assemblies, highlight the importance of considering the assembly process itself, and discuss various applications and future directions for the field. We emphasize throughout the exciting opportunities presented by recent advances as well as challenges that remain.
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Affiliation(s)
- Alena Khmelinskaia
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Adam Wargacki
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Neil P King
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA.
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9
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Schneider CG, Taylor JA, Sibilo MQ, Miura K, Mallory KL, Mann C, Karch C, Beck Z, Matyas GR, Long CA, Bergmann-Leitner E, Burkhard P, Angov E. Orientation of Antigen Display on Self-Assembling Protein Nanoparticles Influences Immunogenicity. Vaccines (Basel) 2021; 9:vaccines9020103. [PMID: 33572803 PMCID: PMC7911071 DOI: 10.3390/vaccines9020103] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 11/16/2022] Open
Abstract
Self-assembling protein nanoparticles (SAPN) serve as a repetitive antigen delivery platform with high-density epitope display; however, antigen characteristics such as size and epitope presentation can influence the immunogenicity of the assembled particle and are aspects to consider for a rationally designed effective vaccine. Here, we characterize the folding and immunogenicity of heterogeneous antigen display by integrating (a) dual-stage antigen SAPN presenting the P. falciparum (Pf) merozoite surface protein 1 subunit, PfMSP119, and Pf cell-traversal protein for ookinetes and sporozoites, PfCelTOS, in addition to (b) a homogenous antigen SAPN displaying two copies of PfCelTOS. Mice and rabbits were utilized to evaluate antigen-specific humoral and cellular induction as well as functional antibodies via growth inhibition of the blood-stage parasite. We demonstrate that antigen orientation and folding influence the elicited immune response, and when appropriately designed, SAPN can serve as an adaptable platform for an effective multi-antigen display.
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Affiliation(s)
- Cosette G. Schneider
- Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (C.G.S.); (J.A.T.); (M.Q.S.); (K.L.M.); (C.M.); (E.B.-L.)
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37831, USA
| | - Justin A. Taylor
- Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (C.G.S.); (J.A.T.); (M.Q.S.); (K.L.M.); (C.M.); (E.B.-L.)
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37831, USA
| | - Michael Q. Sibilo
- Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (C.G.S.); (J.A.T.); (M.Q.S.); (K.L.M.); (C.M.); (E.B.-L.)
- Parsons Corporation, Centreville, VA 20120, USA
| | - Kazutoyo Miura
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD 20892, USA; (K.M.); (C.A.L.)
| | - Katherine L. Mallory
- Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (C.G.S.); (J.A.T.); (M.Q.S.); (K.L.M.); (C.M.); (E.B.-L.)
- Parsons Corporation, Centreville, VA 20120, USA
| | - Christopher Mann
- Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (C.G.S.); (J.A.T.); (M.Q.S.); (K.L.M.); (C.M.); (E.B.-L.)
- Parsons Corporation, Centreville, VA 20120, USA
| | - Christopher Karch
- Laboratory of Antigen and Adjuvants, US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (C.K.); (Z.B.); (G.R.M.)
- Henry Jackson Foundation, Bethesda, MD 20817, USA
| | - Zoltan Beck
- Laboratory of Antigen and Adjuvants, US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (C.K.); (Z.B.); (G.R.M.)
- Henry Jackson Foundation, Bethesda, MD 20817, USA
| | - Gary R. Matyas
- Laboratory of Antigen and Adjuvants, US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (C.K.); (Z.B.); (G.R.M.)
| | - Carole A. Long
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD 20892, USA; (K.M.); (C.A.L.)
| | - Elke Bergmann-Leitner
- Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (C.G.S.); (J.A.T.); (M.Q.S.); (K.L.M.); (C.M.); (E.B.-L.)
| | | | - Evelina Angov
- Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (C.G.S.); (J.A.T.); (M.Q.S.); (K.L.M.); (C.M.); (E.B.-L.)
- Correspondence: ; Tel.: +1-301-319-9614
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10
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Linghu C, Johnson SL, Valdes PA, Shemesh OA, Park WM, Park D, Piatkevich KD, Wassie AT, Liu Y, An B, Barnes SA, Celiker OT, Yao CC, Yu CCJ, Wang R, Adamala KP, Bear MF, Keating AE, Boyden ES. Spatial Multiplexing of Fluorescent Reporters for Imaging Signaling Network Dynamics. Cell 2020; 183:1682-1698.e24. [PMID: 33232692 DOI: 10.1016/j.cell.2020.10.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 10/05/2020] [Accepted: 10/21/2020] [Indexed: 12/23/2022]
Abstract
In order to analyze how a signal transduction network converts cellular inputs into cellular outputs, ideally one would measure the dynamics of many signals within the network simultaneously. We found that, by fusing a fluorescent reporter to a pair of self-assembling peptides, it could be stably clustered within cells at random points, distant enough to be resolved by a microscope but close enough to spatially sample the relevant biology. Because such clusters, which we call signaling reporter islands (SiRIs), can be modularly designed, they permit a set of fluorescent reporters to be efficiently adapted for simultaneous measurement of multiple nodes of a signal transduction network within single cells. We created SiRIs for indicators of second messengers and kinases and used them, in hippocampal neurons in culture and intact brain slices, to discover relationships between the speed of calcium signaling, and the amplitude of PKA signaling, upon receiving a cAMP-driving stimulus.
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Affiliation(s)
- Changyang Linghu
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - Shannon L Johnson
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA
| | - Pablo A Valdes
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Neurosurgery, Harvard Medical School, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Or A Shemesh
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA; Department of Neurobiology and Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Won Min Park
- Tim Taylor Department of Chemical Engineering, Kansas State University, Manhattan, KS 66506, USA
| | - Demian Park
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA
| | - Kiryl D Piatkevich
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Asmamaw T Wassie
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA
| | - Yixi Liu
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA
| | - Bobae An
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | - Stephanie A Barnes
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA; Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
| | - Orhan T Celiker
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - Chun-Chen Yao
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | - Chih-Chieh Jay Yu
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA
| | - Ru Wang
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA
| | - Katarzyna P Adamala
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mark F Bear
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA; Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
| | - Amy E Keating
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Edward S Boyden
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA; Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA; Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA.
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11
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Park WM. Coiled-Coils: the Molecular Zippers that Self-Assemble Protein Nanostructures. Int J Mol Sci 2020; 21:E3584. [PMID: 32438665 PMCID: PMC7278914 DOI: 10.3390/ijms21103584] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023] Open
Abstract
Coiled-coils, the bundles of intertwined helical protein motifs, have drawn much attention as versatile molecular toolkits. Because of programmable interaction specificity and affinity as well as well-established sequence-to-structure relationships, coiled-coils have been used as subunits that self-assemble various molecular complexes in a range of fields. In this review, I describe recent advances in the field of protein nanotechnology, with a focus on programming assembly of protein nanostructures using coiled-coil modules. Modular design approaches to converting the helical motifs into self-assembling building blocks are described, followed by a discussion on the molecular basis and principles underlying the modular designs. This review also provides a summary of recently developed nanostructures with a variety of structural features, which are in categories of unbounded nanostructures, discrete nanoparticles, and well-defined origami nanostructures. Challenges existing in current design strategies, as well as desired improvements for controls over material properties and functionalities for applications, are also provided.
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Affiliation(s)
- Won Min Park
- Tim Taylor Department of Chemical Engineering, Kansas State University, Manhattan, KS 66506, USA
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12
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Liang J, Mazur F, Tang C, Ning X, Chandrawati R, Liang K. Peptide-induced super-assembly of biocatalytic metal-organic frameworks for programmed enzyme cascades. Chem Sci 2019; 10:7852-7858. [PMID: 31853344 PMCID: PMC6839597 DOI: 10.1039/c9sc02021g] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/20/2019] [Indexed: 01/03/2023] Open
Abstract
Despite the promise of metal-organic frameworks (MOFs) as functional matrices for enzyme stabilization, the development of a stimulus-responsive approach to induce a multi-enzyme cascade reaction in MOFs remains a critical challenge. Here, a novel method using peptide-induced super-assembly of MOFs is developed for programmed enzyme cascade reactions on demand. The super-assembled MOF particles containing different enzymes show remarkable 7.3-fold and 4.4-fold catalytic activity enhancements for the two-enzyme and three-enzyme cascade reactions, respectively, as compared with the unassembled MOF nanoparticles. Further digestion of the coiled-coil forming peptides on the MOF surfaces leads to the MOF superstructure disassembly and the programmed enzyme cascade reaction being "switched-off". Research on these stimuli-responsive materials with controllable and predictable biocatalytic functions/properties provide a concept to facilitate the fabrication of next-generation smart materials based on precision chemistry.
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Affiliation(s)
- Jieying Liang
- School of Chemical Engineering , The University of New South Wales , Sydney , NSW 2052 , Australia . ;
- School of Environmental Science and Engineering , Guangdong University of Technology , Guangzhou 510006 , China .
| | - Federico Mazur
- School of Chemical Engineering , The University of New South Wales , Sydney , NSW 2052 , Australia . ;
| | - Chuyang Tang
- School of Chemical Engineering , The University of New South Wales , Sydney , NSW 2052 , Australia . ;
| | - Xunan Ning
- School of Environmental Science and Engineering , Guangdong University of Technology , Guangzhou 510006 , China .
| | - Rona Chandrawati
- School of Chemical Engineering , The University of New South Wales , Sydney , NSW 2052 , Australia . ;
| | - Kang Liang
- School of Chemical Engineering , The University of New South Wales , Sydney , NSW 2052 , Australia . ;
- Graduate School of Biomedical Engineering , The University of New South Wales , Sydney , NSW 2052 , Australia
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13
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Katyal P, Meleties M, Montclare JK. Self-Assembled Protein- and Peptide-Based Nanomaterials. ACS Biomater Sci Eng 2019; 5:4132-4147. [PMID: 33417774 DOI: 10.1021/acsbiomaterials.9b00408] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Considerable effort has been devoted to generating novel protein- and peptide-based nanomaterials with their applications in a wide range of fields. Specifically, the unique property of proteins to self-assemble has been utilized to create a variety of nanoassemblies, which offer significant possibilities for next-generation biomaterials. In this minireview, we describe self-assembled protein- and peptide-based nanomaterials with focus on nanofibers and nanoparticles. Their applications in delivering therapeutic drugs and genes are discussed.
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Affiliation(s)
- Priya Katyal
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, Brooklyn, New York 11201, United States
| | - Michael Meleties
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, Brooklyn, New York 11201, United States
| | - Jin K Montclare
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, Brooklyn, New York 11201, United States.,Department of Radiology, New York University Langone Health, New York, New York 10016, United States.,Department of Biomaterials, College of Dentistry, New York University, New York, New York 10010, United States.,Department of Chemistry, New York University, New York, New York 10003, United States
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14
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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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15
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Karch CP, Bai H, Torres OB, Tucker CA, Michael NL, Matyas GR, Rolland M, Burkhard P, Beck Z. Design and characterization of a self-assembling protein nanoparticle displaying HIV-1 Env V1V2 loop in a native-like trimeric conformation as vaccine antigen. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2019; 16:206-216. [DOI: 10.1016/j.nano.2018.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 11/27/2018] [Accepted: 12/10/2018] [Indexed: 01/08/2023]
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16
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Katyal P, Montclare JK. Design and Characterization of Fibers and Bionanocomposites Using the Coiled-Coil Domain of Cartilage Oligomeric Matrix Protein. Methods Mol Biol 2018; 1798:239-263. [PMID: 29868965 DOI: 10.1007/978-1-4939-7893-9_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tremendous effort has been dedicated to the design and assembly of bioinspired protein-based architectures with potential applications in drug delivery, tissue engineering, biosensing, and bioimaging. Here, we describe our strategy to generate fibers and bionanocomposites using the coiled-coil domain of cartilage oligomeric matrix protein (COMPcc). Our construct, Q, engineered by swapping particular regions of COMPcc to optimize surface charge, self-assembles to form nanofibers. The Q protein nanofibers can efficiently bind curcumin to form robust mesofibers that can be potentially used for drug delivery and biomedical applications. In addition, using the same Q protein, we describe the biotemplation of gold nanoparticles (AuNP) in the presence and absence of the hexahistidine tag (His-tag). The Q bearing His-tag·AuNP (Q·AuNP) readily deposits on electrode surfaces, while Q without His-tag·AuNP (Qx·AuNP) stabilizes the soluble protein·gold bionanocomposites for several days without aggregating.
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Affiliation(s)
- Priya Katyal
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, Brooklyn, NY, USA
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, Brooklyn, NY, USA.
- Department of Biochemistry, SUNY Downstate Medical Center, Brooklyn, NY, USA.
- Department of Biomaterials, New York University College of Dentistry, New York, NY, USA.
- Department of Chemistry, New York University, New York, NY, USA.
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17
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Jiang L, Yang S, Lund R, Dong H. Shape-specific nanostructured protein mimics from de novo designed chimeric peptides. Biomater Sci 2018; 6:272-279. [DOI: 10.1039/c7bm00906b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We experimentally and theoretically demonstrated the formation of well-defined trigonal-bipyramidal protein-mimics through self-assembly of “simple” de novo designed chimeric peptides.
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Affiliation(s)
- Linhai Jiang
- Department of Chemistry & Biomolecular Science
- Clarkson University
- Potsdam
- USA
| | - Su Yang
- Department of Chemistry & Biomolecular Science
- Clarkson University
- Potsdam
- USA
| | - Reidar Lund
- Department of Chemistry
- University of Oslo
- Oslo 0315
- Norway
| | - He Dong
- Department of Chemistry & Biomolecular Science
- Clarkson University
- Potsdam
- USA
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18
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Karch CP, Doll TAPF, Paulillo SM, Nebie I, Lanar DE, Corradin G, Burkhard P. The use of a P. falciparum specific coiled-coil domain to construct a self-assembling protein nanoparticle vaccine to prevent malaria. J Nanobiotechnology 2017; 15:62. [PMID: 28877692 PMCID: PMC5588597 DOI: 10.1186/s12951-017-0295-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 08/29/2017] [Indexed: 11/10/2022] Open
Abstract
Background The parasitic disease malaria remains a major global public health concern and no truly effective vaccine exists. One approach to the development of a malaria vaccine is to target the asexual blood stage that results in clinical symptoms. Most attempts have failed. New antigens such as P27A and P27 have emerged as potential new vaccine candidates. Multiple studies have demonstrated that antigens are more immunogenic and are better correlated with protection when presented on particulate delivery systems. One such particulate delivery system is the self-assembling protein nanoparticle (SAPN) that relies on coiled-coil domains of proteins to form stable nanoparticles. In the past we have used de novo designed amino acid domains to drive the formation of the coiled-coil scaffolds which present the antigenic epitopes on the particle surface. Results Here we use naturally occurring domains found in the tex1 protein to form the coiled-coil scaffolding of the nanoparticle. Thus, by engineering P27A and a new extended form of the coiled-coil domain P27 onto the N and C terminus of the SAPN protein monomer we have developed a particulate delivery system that effectively displays both antigens on a single particle that uses malaria tex1 sequences to form the nanoparticle scaffold. These particles are immunogenic in a murine model and induce immune responses similar to the ones observed in seropositive individuals in malaria endemic regions. Conclusions We demonstrate that our P27/P27A-SAPNs induce an immune response akin to the one in seropositive individuals in Burkina Faso. Since P27 is highly conserved among different Plasmodium species, these novel SAPNs may even provide cross-protection between Plasmodium falciparum and Plasmodium vivax the two major human malaria pathogens. As the SAPNs are also easy to manufacture and store they can be delivered to the population in need without complication thus providing a low cost malaria vaccine.
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Affiliation(s)
- Christopher P Karch
- Institute of Materials Science, University of Connecticut, Storrs, CT, 06269-3136, USA
| | - Tais A P F Doll
- Institute of Materials Science, University of Connecticut, Storrs, CT, 06269-3136, USA
| | | | - Issa Nebie
- Centre National de Recherche et de Formation sur le Paludisme, 01 BP 2208, Ouagadougou, West Africa, Burkina Faso
| | - David E Lanar
- Malaria Vaccine Branch, USMMRP-WRAIR, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Giampietro Corradin
- Biochemistry Department, University of Lausanne, 1066, Epalinges, Switzerland.
| | - Peter Burkhard
- Institute of Materials Science, University of Connecticut, Storrs, CT, 06269-3136, USA. .,Alpha-O Peptides AG, 4125, Riehen, Switzerland. .,Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269-3125, USA.
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19
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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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20
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Beyond icosahedral symmetry in packings of proteins in spherical shells. Proc Natl Acad Sci U S A 2017; 114:9014-9019. [PMID: 28790186 DOI: 10.1073/pnas.1706825114] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The formation of quasi-spherical cages from protein building blocks is a remarkable self-assembly process in many natural systems, where a small number of elementary building blocks are assembled to build a highly symmetric icosahedral cage. In turn, this has inspired synthetic biologists to design de novo protein cages. We use simple models, on multiple scales, to investigate the self-assembly of a spherical cage, focusing on the regularity of the packing of protein-like objects on the surface. Using building blocks, which are able to pack with icosahedral symmetry, we examine how stable these highly symmetric structures are to perturbations that may arise from the interplay between flexibility of the interacting blocks and entropic effects. We find that, in the presence of those perturbations, icosahedral packing is not the most stable arrangement for a wide range of parameters; rather disordered structures are found to be the most stable. Our results suggest that (i) many designed, or even natural, protein cages may not be regular in the presence of those perturbations and (ii) optimizing those flexibilities can be a possible design strategy to obtain regular synthetic cages with full control over their surface properties.
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21
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Indelicato G, Burkhard P, Twarock R. Classification of self-assembling protein nanoparticle architectures for applications in vaccine design. ROYAL SOCIETY OPEN SCIENCE 2017; 4:161092. [PMID: 28484626 PMCID: PMC5414263 DOI: 10.1098/rsos.161092] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/30/2017] [Indexed: 06/07/2023]
Abstract
We introduce here a mathematical procedure for the structural classification of a specific class of self-assembling protein nanoparticles (SAPNs) that are used as a platform for repetitive antigen display systems. These SAPNs have distinctive geometries as a consequence of the fact that their peptide building blocks are formed from two linked coiled coils that are designed to assemble into trimeric and pentameric clusters. This allows a mathematical description of particle architectures in terms of bipartite (3,5)-regular graphs. Exploiting the relation with fullerene graphs, we provide a complete atlas of SAPN morphologies. The classification enables a detailed understanding of the spectrum of possible particle geometries that can arise in the self-assembly process. Moreover, it provides a toolkit for a systematic exploitation of SAPNs in bioengineering in the context of vaccine design, predicting the density of B-cell epitopes on the SAPN surface, which is critical for a strong humoral immune response.
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Affiliation(s)
- G. Indelicato
- Dipartimento di Matematica, Università di Torino, Via Carlo Alberto 10, 10123 Torino, Italy
| | - P. Burkhard
- The Institute of Materials Science, University of Connecticut, 97 North Eagleville Road, Storrs, CT 06269, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269-3125, USA
| | - R. Twarock
- Departments of Mathematics and Biology, University of York, York YO10 5DD, UK
- York Centre for Complex Systems Analysis, University of York, York YO10 5GE, UK
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22
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Sciore A, Marsh ENG. Symmetry-Directed Design of Protein Cages and Protein Lattices and Their Applications. Subcell Biochem 2017; 83:195-224. [PMID: 28271478 DOI: 10.1007/978-3-319-46503-6_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The assembly of individual protein subunits into large-scale structures is important in many biological contexts. Proteins may assemble into geometrical cages or extended lattices that are characterized by a high degree of symmetry; examples include viral capsids and bacterial S-layers. The precisely defined higher order structure exhibited by these assemblies has inspired efforts to design such structures de novo by applying the principles of symmetry evident in natural protein assemblies. Here we discuss progress towards this goal and also examples of natural protein cages and lattices that have been engineered to repurpose them towards a diverse range of applications in materials science and nano-medicine.
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Affiliation(s)
- Aaron Sciore
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - E Neil G Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
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23
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Karch CP, Burkhard P. Vaccine technologies: From whole organisms to rationally designed protein assemblies. Biochem Pharmacol 2016; 120:1-14. [PMID: 27157411 PMCID: PMC5079805 DOI: 10.1016/j.bcp.2016.05.001] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/04/2016] [Indexed: 11/16/2022]
Abstract
Vaccines have been the single most significant advancement in public health, preventing morbidity and mortality in millions of people annually. Vaccine development has traditionally focused on whole organism vaccines, either live attenuated or inactivated vaccines. While successful for many different infectious diseases whole organisms are expensive to produce, require culture of the infectious agent, and have the potential to cause vaccine associated disease in hosts. With advancing technology and a desire to develop safe, cost effective vaccine candidates, the field began to focus on the development of recombinantly expressed antigens known as subunit vaccines. While more tolerable, subunit vaccines tend to be less immunogenic. Attempts have been made to increase immunogenicity with the addition of adjuvants, either immunostimulatory molecules or an antigen delivery system that increases immune responses to vaccines. An area of extreme interest has been the application of nanotechnology to vaccine development, which allows for antigens to be expressed on a particulate delivery system. One of the most exciting examples of nanovaccines are rationally designed protein nanoparticles. These nanoparticles use some of the basic tenants of structural biology, biophysical chemistry, and vaccinology to develop protective, safe, and easily manufactured vaccines. Rationally developed nanoparticle vaccines are one of the most promising candidates for the future of vaccine development.
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MESH Headings
- Adjuvants, Immunologic/adverse effects
- Adjuvants, Immunologic/chemistry
- Adjuvants, Immunologic/therapeutic use
- Allergy and Immunology/history
- Allergy and Immunology/trends
- Animals
- Antigens/adverse effects
- Antigens/chemistry
- Antigens/immunology
- Antigens/therapeutic use
- Biopharmaceutics/history
- Biopharmaceutics/methods
- Biopharmaceutics/trends
- Chemistry, Pharmaceutical/history
- Chemistry, Pharmaceutical/trends
- Communicable Disease Control/history
- Communicable Disease Control/trends
- Communicable Diseases/immunology
- Communicable Diseases/veterinary
- Drug Delivery Systems/adverse effects
- Drug Delivery Systems/trends
- Drug Delivery Systems/veterinary
- Drug Design
- History, 19th Century
- History, 20th Century
- History, 21st Century
- Humans
- Nanoparticles/adverse effects
- Nanoparticles/chemistry
- Nanoparticles/therapeutic use
- Protein Engineering/trends
- Protein Engineering/veterinary
- Protein Folding
- Recombinant Proteins/adverse effects
- Recombinant Proteins/chemistry
- Recombinant Proteins/immunology
- Recombinant Proteins/therapeutic use
- Vaccines/adverse effects
- Vaccines/chemistry
- Vaccines/immunology
- Vaccines/therapeutic use
- Vaccines, Subunit/adverse effects
- Vaccines, Subunit/chemistry
- Vaccines, Subunit/immunology
- Vaccines, Subunit/therapeutic use
- Vaccines, Synthetic/adverse effects
- Vaccines, Synthetic/chemistry
- Vaccines, Synthetic/immunology
- Vaccines, Synthetic/therapeutic use
- Veterinary Drugs/adverse effects
- Veterinary Drugs/chemistry
- Veterinary Drugs/immunology
- Veterinary Drugs/therapeutic use
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Affiliation(s)
- Christopher P Karch
- The Institute of Materials Science, 97 North Eagleville Road, Storrs, CT 06269, United States
| | - Peter Burkhard
- The Institute of Materials Science, 97 North Eagleville Road, Storrs, CT 06269, United States; Department of Molecular and Cell Biology, 93 North Eagleville Road, Storrs, CT 06269, United States.
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Abstract
Nanoparticles are getting a great deal of attention in the rapidly developing field of nanomedicine. For example they can be used as drug delivery systems, for imaging applications, or as carriers for synthetic vaccines. Protein-based nanoparticles offer the advantage of biocompatibility and biodegradability thus avoiding some of the major toxicity concerns with nanoparticle associated approaches. Our group has developed self-assembling peptide/protein nanopartices (SAPNs) that are built up from two coiled-coil oligomerization domains joined by a linker region and used them to design subunit vaccines. For drug delivery approaches the SAPNs need to be as small as possible to avoid strong immune responses that could possibly even lead to anaphylaxis. Here we used a computational and biophysical approach to minimize the size of the SAPNs for their use as drug delivery system. We tested different charge distributions on the pentameric and trimeric coiled-coils in silico with molecular dynamics simulations to down-select an optimal design. This design was then investigated in vitro by biophysical methods and we were able to engineer a minimal SAPN of only 11 nm in diameter. Such minimal-sized SAPNs offer new avenues for a safer development as drug delivery systems or other biomedical applications.
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Affiliation(s)
- Raja Dey
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269-3136, United States
| | - Yan Xia
- Department of Chemical & Biomolecular Engineering, University of Connecticut, Storrs, Connecticut 06269-3222, United States
| | - Mu-Ping Nieh
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269-3136, United States.,Department of Chemical & Biomolecular Engineering, University of Connecticut, Storrs, Connecticut 06269-3222, United States.,Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269-3247, United States
| | - Peter Burkhard
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269-3136, United States.,Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269-3125, United States
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