1
|
Bhattacharya S, Jenkins MC, Keshavarz-Joud P, Bourque AR, White K, Alvarez Barkane AM, Bryksin AV, Hernandez C, Kopylov M, Finn M. Heterologous Prime-Boost with Immunologically Orthogonal Protein Nanoparticles for Peptide Immunofocusing. ACS NANO 2024; 18:20083-20100. [PMID: 39041587 PMCID: PMC11308774 DOI: 10.1021/acsnano.4c00949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/24/2024]
Abstract
Protein nanoparticles are effective platforms for antigen presentation and targeting effector immune cells in vaccine development. Encapsulins are a class of protein-based microbial nanocompartments that self-assemble into icosahedral structures with external diameters ranging from 24 to 42 nm. Encapsulins from Myxococcus xanthus were designed to package bacterial RNA when produced in E. coli and were shown to have immunogenic and self-adjuvanting properties enhanced by this RNA. We genetically incorporated a 20-mer peptide derived from a mutant strain of the SARS-CoV-2 receptor binding domain (RBD) into the encapsulin protomeric coat protein for presentation on the exterior surface of the particle, inducing the formation of several nonicosahedral structures that were characterized by cryogenic electron microscopy. This immunogen elicited conformationally relevant humoral responses to the SARS-CoV-2 RBD. Immunological recognition was enhanced when the same peptide was presented in a heterologous prime/boost vaccination strategy using the engineered encapsulin and a previously reported variant of the PP7 virus-like particle, leading to the development of a selective antibody response against a SARS-CoV-2 RBD point mutant. While generating epitope-focused antibody responses is an interplay between inherent vaccine properties and B/T cells, here we demonstrate the use of orthogonal nanoparticles to fine-tune the control of epitope focusing.
Collapse
Affiliation(s)
- Sonia Bhattacharya
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Matthew C. Jenkins
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Parisa Keshavarz-Joud
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Alisyn Retos Bourque
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Keiyana White
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Amina Maria Alvarez Barkane
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anton V. Bryksin
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Carolina Hernandez
- New
York Structural Biology Center, New York, New York 10027, United States
| | - Mykhailo Kopylov
- New
York Structural Biology Center, New York, New York 10027, United States
| | - M.G. Finn
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
- School
of Biological Sciences, Georgia Institute
of Technology, Atlanta, Georgia 30332, United
States
| |
Collapse
|
2
|
Van de Steen A, Wilkinson HC, Dalby PA, Frank S. Encapsulation of Transketolase into In Vitro-Assembled Protein Nanocompartments Improves Thermal Stability. ACS APPLIED BIO MATERIALS 2024; 7:3660-3674. [PMID: 38835217 PMCID: PMC11190991 DOI: 10.1021/acsabm.3c01153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/06/2024]
Abstract
Protein compartments offer definitive structures with a large potential design space that are of particular interest for green chemistry and therapeutic applications. One family of protein compartments, encapsulins, are simple prokaryotic nanocompartments that self-assemble from a single monomer into selectively permeable cages of between 18 and 42 nm. Over the past decade, encapsulins have been developed for a diverse application portfolio utilizing their defined cargo loading mechanisms and repetitive surface display. Although it has been demonstrated that encapsulation of non-native cargo proteins provides protection from protease activity, the thermal effects arising from enclosing cargo within encapsulins remain poorly understood. This study aimed to establish a methodology for loading a reporter protein into thermostable encapsulins to determine the resulting stability change of the cargo. Building on previous in vitro reassembly studies, we first investigated the effectiveness of in vitro reassembly and cargo-loading of two size classes of encapsulins Thermotoga maritima T = 1 and Myxococcus xanthus T = 3, using superfolder Green Fluorescent Protein. We show that the empty T. maritima capsid reassembles with higher yield than the M. xanthus capsid and that in vitro loading promotes the formation of the M. xanthus T = 3 capsid form over the T = 1 form, while overloading with cargo results in malformed T. maritima T = 1 encapsulins. For the stability study, a Förster resonance energy transfer (FRET)-probed industrially relevant enzyme cargo, transketolase, was then loaded into the T. maritima encapsulin. Our results show that site-specific orthogonal FRET labels can reveal changes in thermal unfolding of encapsulated cargo, suggesting that in vitro loading of transketolase into the T. maritima T = 1 encapsulin shell increases the thermal stability of the enzyme. This work supports the move toward fully harnessing structural, spatial, and functional control of in vitro assembled encapsulins with applications in cargo stabilization.
Collapse
Affiliation(s)
| | | | - Paul A. Dalby
- Department of Biochemical
Engineering, University College London, Bernard Katz Building, Gower Street, London WC1E 6BT, U.K.
| | - Stefanie Frank
- Department of Biochemical
Engineering, University College London, Bernard Katz Building, Gower Street, London WC1E 6BT, U.K.
| |
Collapse
|
3
|
Bhattacharya S, Jenkins MC, Keshavarz-Joud P, Bourque AR, White K, Alvarez Barkane AM, Bryksin AV, Hernandez C, Kopylov M, Finn MG. Heterologous Prime-Boost with Immunologically Orthogonal Protein Nanoparticles for Peptide Immunofocusing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.24.581861. [PMID: 38464232 PMCID: PMC10925081 DOI: 10.1101/2024.02.24.581861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Protein nanoparticles are effective platforms for antigen presentation and targeting effector immune cells in vaccine development. Encapsulins are a class of protein-based microbial nanocompartments that self-assemble into icosahedral structures with external diameters ranging from 24 to 42 nm. Encapsulins from Mxyococcus xanthus were designed to package bacterial RNA when produced in E. coli and were shown to have immunogenic and self-adjuvanting properties enhanced by this RNA. We genetically incorporated a 20-mer peptide derived from a mutant strain of the SARS-CoV-2 receptor binding domain (RBD) into the encapsulin protomeric coat protein for presentation on the exterior surface of the particle. This immunogen elicited conformationally-relevant humoral responses to the SARS-CoV-2 RBD. Immunological recognition was enhanced when the same peptide was presented in a heterologous prime/boost vaccination strategy using the engineered encapsulin and a previously reported variant of the PP7 virus-like particle, leading to the development of a selective antibody response against a SARS-CoV-2 RBD point mutant. While generating epitope-focused antibody responses is an interplay between inherent vaccine properties and B/T cells, here we demonstrate the use of orthogonal nanoparticles to fine-tune the control of epitope focusing.
Collapse
Affiliation(s)
- Sonia Bhattacharya
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Matthew C Jenkins
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Parisa Keshavarz-Joud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alisyn Retos Bourque
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Keiyana White
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Amina M Alvarez Barkane
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Anton V Bryksin
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | | | - Mykhailo Kopylov
- New York Structural Biology Center, New York, New York, 10027, USA
| | - M G Finn
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| |
Collapse
|
4
|
Kim KJ, Kim G, Bae JH, Song JJ, Kim HS. A pH-Responsive Virus-Like Particle as a Protein Cage for a Targeted Delivery. Adv Healthc Mater 2024; 13:e2302656. [PMID: 37966427 DOI: 10.1002/adhm.202302656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 11/05/2023] [Indexed: 11/16/2023]
Abstract
A stimuli-responsive protein self-assembly offers promising utility as a protein nanocage for biotechnological and medical applications. Herein, the development of a virus-like particle (VLP) that undergoes a transition between assembly and disassembly under a neutral and acidic pH, respectively, for a targeted delivery is reported. The structure of the bacteriophage P22 coat protein is used for the computational design of coat subunits that self-assemble into a pH-responsive VLP. Subunit designs are generated through iterative computational cycles of histidine substitutions and evaluation of the interaction energies among the subunits under an acidic and neutral pH. The top subunit designs are tested and one that is assembled into a VLP showing the highest pH-dependent structural transition is selected. The cryo-EM structure of the VLP is determined, and the structural basis of a pH-triggered disassembly is delineated. The utility of the designed VLP is exemplified through the targeted delivery of a cytotoxic protein cargo into tumor cells in a pH-dependent manner. These results provide strategies for the development of self-assembling protein architectures with new functionality for diverse applications.
Collapse
Affiliation(s)
- Kwan-Jip Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejon, 34141, South Korea
| | - Gijeong Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejon, 34141, South Korea
| | - Jin-Ho Bae
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejon, 34141, South Korea
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejon, 34141, South Korea
| | - Hak-Sung Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejon, 34141, South Korea
| |
Collapse
|
5
|
Kwon S, Andreas MP, Giessen TW. Structure and heterogeneity of a highly cargo-loaded encapsulin shell. J Struct Biol 2023; 215:108022. [PMID: 37657675 DOI: 10.1016/j.jsb.2023.108022] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/26/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023]
Abstract
Encapsulins are self-assembling protein nanocompartments able to selectively encapsulate dedicated cargo enzymes. Encapsulins are widespread across bacterial and archaeal phyla and are involved in oxidative stress resistance, iron storage, and sulfur metabolism. Encapsulin shells exhibit icosahedral geometry and consist of 60, 180, or 240 identical protein subunits. Cargo encapsulation is mediated by the specific interaction of targeting peptides or domains, found in all cargo proteins, with the interior surface of the encapsulin shell during shell self-assembly. Here, we report the 2.53 Å cryo-EM structure of a heterologously produced and highly cargo-loaded T3 encapsulin shell from Myxococcus xanthus and explore the systems' structural heterogeneity. We find that exceedingly high cargo loading results in the formation of substantial amounts of distorted and aberrant shells, likely caused by a combination of unfavorable steric clashes of cargo proteins and shell conformational changes. Based on our cryo-EM structure, we determine and analyze the targeting peptide-shell binding mode. We find that both ionic and hydrophobic interactions mediate targeting peptide binding. Our results will guide future attempts at rationally engineering encapsulins for biomedical and biotechnological applications.
Collapse
Affiliation(s)
- Seokmu Kwon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael P Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| |
Collapse
|
6
|
Quinton AR, McDowell HB, Hoiczyk E. Encapsulins: Nanotechnology's future in a shell. ADVANCES IN APPLIED MICROBIOLOGY 2023; 125:1-48. [PMID: 38783722 DOI: 10.1016/bs.aambs.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Encapsulins, virus capsid-like bacterial nanocompartments have emerged as promising tools in medicine, imaging, and material sciences. Recent work has shown that these protein-bound icosahedral 'organelles' possess distinct properties that make them exceptionally usable for nanotechnology applications. A key factor contributing to their appeal is their ability to self-assemble, coupled with their capacity to encapsulate a wide range of cargos. Their genetic manipulability, stability, biocompatibility, and nano-size further enhance their utility, offering outstanding possibilities for practical biotechnology applications. In particular, their amenability to engineering has led to their extensive modification, including the packaging of non-native cargos and the utilization of the shell surface for displaying immunogenic or targeting proteins and peptides. This inherent versatility, combined with the ease of expressing encapsulins in heterologous hosts, promises to provide broad usability. Although mostly not yet commercialized, encapsulins have started to demonstrate their vast potential for biotechnology, from drug delivery to biofuel production and the synthesis of valuable inorganic materials. In this review, we will initially discuss the structure, function and diversity of encapsulins, which form the basis for these emerging applications, before reviewing ongoing practical uses and highlighting promising applications in medicine, engineering and environmental sciences.
Collapse
Affiliation(s)
- Amy Ruth Quinton
- School of Biosciences, The Krebs Institute, The University of Sheffield, Sheffield, United Kingdom
| | - Harry Benjamin McDowell
- School of Biosciences, The Krebs Institute, The University of Sheffield, Sheffield, United Kingdom
| | - Egbert Hoiczyk
- School of Biosciences, The Krebs Institute, The University of Sheffield, Sheffield, United Kingdom.
| |
Collapse
|
7
|
Kwon S, Andreas MP, Giessen TW. Structure and heterogeneity of a highly cargo-loaded encapsulin shell. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.26.550694. [PMID: 37546724 PMCID: PMC10402063 DOI: 10.1101/2023.07.26.550694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Encapsulins are self-assembling protein nanocompartments able to selectively encapsulate dedicated cargo enzymes. Encapsulins are widespread across bacterial and archaeal phyla and are involved in oxidative stress resistance, iron storage, and sulfur metabolism. Encapsulin shells exhibit icosahedral geometry and consist of 60, 180, or 240 identical protein subunits. Cargo encapsulation is mediated by the specific interaction of targeting peptides or domains, found in all cargo proteins, with the interior surface of the encapsulin shell during shell self-assembly. Here, we report the 2.53 Å cryo-EM structure of a heterologously produced and highly cargo-loaded T3 encapsulin shell from Myxococcus xanthus and explore the systems' structural heterogeneity. We find that exceedingly high cargo loading results in the formation of substantial amounts of distorted and aberrant shells, likely caused by a combination of unfavorable steric clashes of cargo proteins and shell conformational changes. Based on our cryo-EM structure, we determine and analyze the targeting peptide-shell binding mode. We find that both ionic and hydrophobic interactions mediate targeting peptide binding. Our results will guide future attempts at rationally engineering encapsulins for biomedical and biotechnological applications.
Collapse
Affiliation(s)
- Seokmu Kwon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| |
Collapse
|
8
|
Abstract
Encapsulins are a recently discovered class of prokaryotic self-assembling icosahedral protein nanocompartments measuring between 24 and 42 nm in diameter, capable of selectively encapsulating dedicated cargo proteins in vivo. They have been classified into four families based on sequence identity and operon structure, and thousands of encapsulin systems have recently been computationally identified across a wide range of bacterial and archaeal phyla. Cargo encapsulation is mediated by the presence of specific targeting motifs found in all native cargo proteins that interact with the interior surface of the encapsulin shell during self-assembly. Short C-terminal targeting peptides (TPs) are well documented in Family 1 encapsulins, while more recently, larger N-terminal targeting domains (TDs) have been discovered in Family 2. The modular nature of TPs and their facile genetic fusion to non-native cargo proteins of interest has made cargo encapsulation, both in vivo and in vitro, readily exploitable and has therefore resulted in a range of rationally engineered nano-compartmentalization systems. This review summarizes current knowledge on cargo protein encapsulation within encapsulins and highlights select studies that utilize TP fusions to non-native cargo in creative and useful ways.
Collapse
Affiliation(s)
- Jesse A Jones
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Robert Benisch
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
9
|
Jones JA, Andreas MP, Giessen TW. Exploring the Extreme Acid Tolerance of a Dynamic Protein Nanocage. Biomacromolecules 2023; 24:1388-1399. [PMID: 36796007 DOI: 10.1021/acs.biomac.2c01424] [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] [Indexed: 02/18/2023]
Abstract
Encapsulins are microbial protein nanocages capable of efficient self-assembly and cargo enzyme encapsulation. Due to their favorable properties, including high thermostability, protease resistance, and robust heterologous expression, encapsulins have become popular bioengineering tools for applications in medicine, catalysis, and nanotechnology. Resistance against physicochemical extremes like high temperature and low pH is a highly desirable feature for many biotechnological applications. However, no systematic search for acid-stable encapsulins has been carried out, while the influence of pH on encapsulin shells has so far not been thoroughly explored. Here, we report on a newly identified encapsulin nanocage from the acid-tolerant bacterium Acidipropionibacterium acidipropionici. Using transmission electron microscopy, dynamic light scattering, and proteolytic assays, we demonstrate its extreme acid tolerance and resilience against proteases. We structurally characterize the novel nanocage using cryo-electron microscopy, revealing a dynamic five-fold pore that displays distinct "closed" and "open" states at neutral pH but only a singular "closed" state under strongly acidic conditions. Further, the "open" state exhibits the largest pore in an encapsulin shell reported to date. Non-native protein encapsulation capabilities are demonstrated, and the influence of external pH on internalized cargo is explored. Our results expand the biotechnological application range of encapsulin nanocages toward potential uses under strongly acidic conditions and highlight pH-responsive encapsulin pore dynamics.
Collapse
Affiliation(s)
- Jesse A Jones
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0624, United States
| | - Michael P Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0624, United States
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0624, United States
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, Michigan 48109-1382, United States
| |
Collapse
|
10
|
Kwon S, Giessen TW. Engineered Protein Nanocages for Concurrent RNA and Protein Packaging In Vivo. ACS Synth Biol 2022; 11:3504-3515. [PMID: 36170610 PMCID: PMC9944510 DOI: 10.1021/acssynbio.2c00391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Protein nanocages have emerged as an important engineering platform for biotechnological and biomedical applications. Among naturally occurring protein cages, encapsulin nanocompartments have recently gained prominence due to their favorable physico-chemical properties, ease of shell modification, and highly efficient and selective intrinsic protein packaging capabilities. Here, we expand encapsulin function by designing and characterizing encapsulins for concurrent RNA and protein encapsulation in vivo. Our strategy is based on modifying encapsulin shells with nucleic acid-binding peptides without disrupting the native protein packaging mechanism. We show that our engineered encapsulins reliably self-assemble in vivo, are capable of efficient size-selective in vivo RNA packaging, can simultaneously load multiple functional RNAs, and can be used for concurrent in vivo packaging of RNA and protein. Our engineered encapsulation platform has potential for codelivery of therapeutic RNAs and proteins to elicit synergistic effects and as a modular tool for other biotechnological applications.
Collapse
Affiliation(s)
- Seokmu Kwon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tobias W. Giessen
- Department of Biological Chemistry and Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
11
|
Miller JE, Srinivasan Y, Dharmaraj NP, Liu A, Nguyen PL, Taylor SD, Yeates TO. Designing Protease-Triggered Protein Cages. J Am Chem Soc 2022; 144:12681-12689. [PMID: 35802879 DOI: 10.1021/jacs.2c02165] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteins that self-assemble into enclosed polyhedral cages, both naturally and by design, are garnering attention for their prospective utility in the fields of medicine and biotechnology. Notably, their potential for encapsulation and surface display are attractive for experiments that require protection and targeted delivery of cargo. The ability to control their opening or disassembly would greatly advance the development of protein nanocages into widespread molecular tools. Toward the development of protein cages that disassemble in a systematic manner and in response to biologically relevant stimuli, here we demonstrate a modular protein cage system that is opened by highly sequence-specific proteases, based on sequence insertions at strategically chosen loop positions in the protein cage subunits. We probed the generality of the approach in the context of protein cages built using the two prevailing methods of construction: genetic fusion between oligomeric components and (non-covalent) computational interface design between oligomeric components. Our results suggest that the former type of cage may be more amenable than the latter for endowing proteolytically controlled disassembly. We show that a successfully designed cage system, based on oligomeric fusion, is modular with regard to its triggering protease. One version of the cage is targeted by an asparagine protease implicated in cancer and Alzheimer's disease, whereas the second version is responsive to the blood-clotting protease, thrombin. The approach demonstrated here should guide future efforts to develop therapeutic vectors to treat disease states where protease induction or mis-regulation occurs.
Collapse
Affiliation(s)
- Justin E Miller
- UCLA Molecular Biology Institute, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States.,UCLA-DOE Institute for Genomics and Proteomics, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States
| | - Yashes Srinivasan
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Nithin P Dharmaraj
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Andrew Liu
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Phillip L Nguyen
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Scott D Taylor
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Todd O Yeates
- UCLA Molecular Biology Institute, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States.,UCLA-DOE Institute for Genomics and Proteomics, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States.,UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| |
Collapse
|
12
|
Tasneem N, Szyszka TN, Jenner EN, Lau YH. How Pore Architecture Regulates the Function of Nanoscale Protein Compartments. ACS NANO 2022; 16:8540-8556. [PMID: 35583458 DOI: 10.1021/acsnano.2c02178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Self-assembling proteins can form porous compartments that adopt well-defined architectures at the nanoscale. In nature, protein compartments act as semipermeable barriers to enable spatial separation and organization of complex biochemical processes. The compartment pores play a key role in their overall function by selectively controlling the influx and efflux of important biomolecular species. By engineering the pores, the functionality of compartments can be tuned to facilitate non-native applications, such as artificial nanoreactors for catalysis. In this review, we analyze how protein structure determines the porosity and impacts the function of both native and engineered compartments, highlighting the wealth of structural data recently obtained by cryo-EM and X-ray crystallography. Through this analysis, we offer perspectives on how current structural insights can inform future studies into the design of artificial protein compartments as nanoreactors with tunable porosity and function.
Collapse
Affiliation(s)
- Nuren Tasneem
- School of Chemistry, The University of Sydney, Eastern Avenue, Camperdown, New South Wales 2006, Australia
| | - Taylor N Szyszka
- School of Chemistry, The University of Sydney, Eastern Avenue, Camperdown, New South Wales 2006, Australia
- University of Sydney Nano Institute, Camperdown, New South Wales 2006, Australia
| | - Eric N Jenner
- School of Chemistry, The University of Sydney, Eastern Avenue, Camperdown, New South Wales 2006, Australia
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Eastern Avenue, Camperdown, New South Wales 2006, Australia
- University of Sydney Nano Institute, Camperdown, New South Wales 2006, Australia
| |
Collapse
|
13
|
Boyton I, Goodchild SC, Diaz D, Elbourne A, Collins-Praino LE, Care A. Characterizing the Dynamic Disassembly/Reassembly Mechanisms of Encapsulin Protein Nanocages. ACS OMEGA 2022; 7:823-836. [PMID: 35036749 PMCID: PMC8757444 DOI: 10.1021/acsomega.1c05472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/19/2021] [Indexed: 05/22/2023]
Abstract
Encapsulins, self-assembling icosahedral protein nanocages derived from prokaryotes, represent a versatile set of tools for nanobiotechnology. However, a comprehensive understanding of the mechanisms underlying encapsulin self-assembly, disassembly, and reassembly is lacking. Here, we characterize the disassembly/reassembly properties of three encapsulin nanocages that possess different structural architectures: T = 1 (24 nm), T = 3 (32 nm), and T = 4 (42 nm). Using spectroscopic techniques and electron microscopy, encapsulin architectures were found to exhibit varying sensitivities to the denaturant guanidine hydrochloride (GuHCl), extreme pH, and elevated temperature. While all three encapsulins showed the capacity to reassemble following GuHCl-induced disassembly (within 75 min), only the smallest T = 1 nanocage reassembled after disassembly in basic pH (within 15 min). Furthermore, atomic force microscopy revealed that all encapsulins showed a significant loss of structural integrity after undergoing sequential disassembly/reassembly steps. These findings provide insights into encapsulins' disassembly/reassembly dynamics, thus informing their future design, modification, and application.
Collapse
Affiliation(s)
- India Boyton
- School
of Life Sciences, University of Technology
Sydney, Ultimo, New South Wales 2007, Australia
- ARC
Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Macquarie
Park, New South Wales 2109, Australia
| | - Sophia C. Goodchild
- Department
of Molecular Sciences, Macquarie University, Macquarie Park, New South
Wales 2109, Australia
| | - Dennis Diaz
- Department
of Molecular Sciences, Macquarie University, Macquarie Park, New South
Wales 2109, Australia
| | - Aaron Elbourne
- School
of Science, College of Science, Engineering and Health, RMIT University, Melbourne, Victoria 3000, Australia
| | - Lyndsey E. Collins-Praino
- Adelaide
Medical School, The University of Adelaide, Adelaide, South Australia 5005, Australia
- ARC
Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Macquarie
Park, New South Wales 2109, Australia
| | - Andrew Care
- School
of Life Sciences, University of Technology
Sydney, Ultimo, New South Wales 2007, Australia
- ARC
Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Macquarie
Park, New South Wales 2109, Australia
- ARC Centre
of Excellence in Synthetic Biology, Macquarie
University, Macquarie Park, New South Wales 2109, Australia
| |
Collapse
|