1
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Pham Q, Glicksman J, Chatterjee A. Chemical approaches to probe and engineer AAV vectors. NANOSCALE 2024; 16:13820-13833. [PMID: 38978480 PMCID: PMC11271820 DOI: 10.1039/d4nr01300j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 06/14/2024] [Indexed: 07/10/2024]
Abstract
Adeno-associated virus (AAV) has emerged as the most promising vector for in vivo human gene therapy, with several therapeutic approvals in the last few years and countless more under development. Underlying this remarkable success are several attractive features that AAV offers, including lack of pathogenicity, low immunogenicity, long-term gene expression without genomic integration, the ability to infect both dividing and non-dividing cells, etc. However, the commonly used wild-type AAV capsids in therapeutic development present significant challenges, including inadequate tissue specificity and the need for large doses to attain therapeutic effectiveness, raising safety concerns. Additionally, significant preexisting adaptive immunity against most natural capsids, and the development of such anti-capsid immunity after the first treatment, represent major challenges. Strategies to engineer the AAV capsid are critically needed to address these challenges and unlock the full promise of AAV gene therapy. Chemical modification of the AAV capsid has recently emerged as a powerful new approach to engineer its properties. Unlike genetic strategies, which can be more disruptive to the delicate capsid assembly and packaging processes, "late-stage" chemical modification of the assembled capsid-whether at natural amino acid residues or site-specifically installed noncanonical amino acid residues-often enables a versatile approach to introducing new properties to the capsid. This review summarizes the significant recent progress in AAV capsid engineering strategies, with a particular focus on chemical modifications in advancing the next generation of AAV-based gene therapies.
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Affiliation(s)
- Quan Pham
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
| | - Jake Glicksman
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
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2
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Hoffmann M, Gallant J, LeBeau A, Schmidt D. Unlocking precision gene therapy: harnessing AAV tropism with nanobody swapping at capsid hotspots. NAR MOLECULAR MEDICINE 2024; 1:ugae008. [PMID: 39022346 PMCID: PMC11250487 DOI: 10.1093/narmme/ugae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/20/2024]
Abstract
Adeno-associated virus (AAV) has been remarkably successful in the clinic, but its broad tropism is a practical limitation of precision gene therapy. A promising path to engineer AAV tropism is the addition of binding domains to the AAV capsid that recognize cell surface markers present on a targeted cell type. We have recently identified two previously unexplored capsid regions near the 2/5-fold wall and 5-fold pore of the AAV capsid that are amenable to insertion of larger protein domains, including nanobodies. Here, we demonstrate that these hotspots facilitate AAV tropism switching through simple nanobody replacement without extensive optimization in both VP1 and VP2. Our data suggest that engineering VP2 is the preferred path for maintaining both virus production yield and infectivity. We demonstrate highly specific targeting of human cancer cells expressing fibroblast activating protein (FAP). Furthermore, we found that the combination of FAP nanobody insertion plus ablation of the heparin binding domain can reduce off-target infection to a minimum, while maintaining a strong infection of FAP receptor-positive cells. Taken together, our study shows that nanobody swapping at multiple capsid locations is a viable strategy for nanobody-directed cell-specific AAV targeting.
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Affiliation(s)
- Mareike D Hoffmann
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Joseph P Gallant
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Aaron M LeBeau
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Daniel Schmidt
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
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3
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Hoffmann MD, Gallant JP, LeBeau AM, Schmidt D. Unlocking Precision Gene Therapy: Harnessing AAV Tropism with Nanobody Swapping at Capsid Hotspots. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587049. [PMID: 38585985 PMCID: PMC10996663 DOI: 10.1101/2024.03.27.587049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Adeno-associated virus has been remarkably successful in the clinic, but its broad tropism is a practical limitation of precision gene therapy. A promising path to engineer AAV tropism is the addition of binding domains to the AAV capsid that recognize cell surface markers present on a targeted cell type. We have recently identified two previously unexplored capsid regions near the 2-fold valley and 5-fold pore of the AAV capsid that are amenable to insertion of larger protein domains including nanobodies. Here, we demonstrate that these hotspots facilitate AAV tropism switching through simple nanobody replacement without extensive optimization in both VP1 and VP2. We demonstrate highly specific targeting of human cancer cells expressing fibroblast activating protein (FAP). Our data suggest that engineering VP2 is the preferred path for maintaining both virus production yield and infectivity. Our study shows that nanobody swapping at multiple capsid location is a viable strategy for nanobody-directed cell-specific AAV targeting.
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Affiliation(s)
- Mareike D. Hoffmann
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Joseph P. Gallant
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, United States
| | - Aaron M. LeBeau
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, United States
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, United States
| | - Daniel Schmidt
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN, 55455, USA
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4
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Gidwani SV, Brahmbhatt D, Zomback A, Bassie M, Martinez J, Zhuang J, Schulze J, McLellan JS, Mariani R, Alff P, Frasca D, Blomberg BB, Marshall CP, Yondola MA. Engineered dityrosine-bonding of the RSV prefusion F protein imparts stability and potency advantages. Nat Commun 2024; 15:2202. [PMID: 38485927 PMCID: PMC10940300 DOI: 10.1038/s41467-024-46295-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 02/21/2024] [Indexed: 03/18/2024] Open
Abstract
Viral fusion proteins facilitate cellular infection by fusing viral and cellular membranes, which involves dramatic transitions from their pre- to postfusion conformations. These proteins are among the most protective viral immunogens, but they are metastable which often makes them intractable as subunit vaccine targets. Adapting a natural enzymatic reaction, we harness the structural rigidity that targeted dityrosine crosslinks impart to covalently stabilize fusion proteins in their native conformations. We show that the prefusion conformation of respiratory syncytial virus fusion protein can be stabilized with two engineered dityrosine crosslinks (DT-preF), markedly improving its stability and shelf-life. Furthermore, it has 11X greater potency as compared with the DS-Cav1 stabilized prefusion F protein in immunogenicity studies and overcomes immunosenescence in mice with simply a high-dose formulation on alum.
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Affiliation(s)
- Sonal V Gidwani
- Calder Biosciences Inc., Brooklyn Army Terminal, Brooklyn, NY, USA
| | | | - Aaron Zomback
- Calder Biosciences Inc., Brooklyn Army Terminal, Brooklyn, NY, USA
| | - Mamie Bassie
- Calder Biosciences Inc., Brooklyn Army Terminal, Brooklyn, NY, USA
| | | | - Jian Zhuang
- Calder Biosciences Inc., Brooklyn Army Terminal, Brooklyn, NY, USA
- Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA
| | - John Schulze
- Molecular Structure Facility, University of California, Davis, Davis, CA, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, University of Texas at Austin, College of Natural Sciences, Austin, TX, USA
| | - Roberto Mariani
- Calder Biosciences Inc., Brooklyn Army Terminal, Brooklyn, NY, USA
- CUNY Kingsborough Community College, Brooklyn, NY, USA
| | - Peter Alff
- Calder Biosciences Inc., Brooklyn Army Terminal, Brooklyn, NY, USA
| | - Daniela Frasca
- Department of Microbiology and Immunology, University of Miami, Miami, FL, USA
| | - Bonnie B Blomberg
- Department of Microbiology and Immunology, University of Miami, Miami, FL, USA
| | | | - Mark A Yondola
- Calder Biosciences Inc., Brooklyn Army Terminal, Brooklyn, NY, USA.
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5
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Hoffmann MD, Zdechlik AC, He Y, Nedrud D, Aslanidi G, Gordon W, Schmidt D. Multiparametric domain insertional profiling of adeno-associated virus VP1. Mol Ther Methods Clin Dev 2023; 31:101143. [PMID: 38027057 PMCID: PMC10661864 DOI: 10.1016/j.omtm.2023.101143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 10/21/2023] [Indexed: 12/01/2023]
Abstract
Several evolved properties of adeno-associated virus (AAV), such as broad tropism and immunogenicity in humans, are barriers to AAV-based gene therapy. Most efforts to re-engineer these properties have focused on variable regions near AAV's 3-fold protrusions and capsid protein termini. To comprehensively survey AAV capsids for engineerable hotspots, we determined multiple AAV fitness phenotypes upon insertion of six structured protein domains into the entire AAV-DJ capsid protein VP1. This is the largest and most comprehensive AAV domain insertion dataset to date. Our data revealed a surprising robustness of AAV capsids to accommodate large domain insertions. Insertion permissibility depended strongly on insertion position, domain type, and measured fitness phenotype, which clustered into contiguous structural units that we could link to distinct roles in AAV assembly, stability, and infectivity. We also identified engineerable hotspots of AAV that facilitate the covalent attachment of binding scaffolds, which may represent an alternative approach to re-direct AAV tropism.
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Affiliation(s)
- Mareike D. Hoffmann
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Alina C. Zdechlik
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yungui He
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Nedrud
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Wendy Gordon
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel Schmidt
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
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6
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Gonzalez TJ, Mitchell-Dick A, Blondel LO, Fanous MM, Hull JA, Oh DK, Moller-Tank S, Castellanos Rivera RM, Piedrahita JA, Asokan A. Structure-guided AAV capsid evolution strategies for enhanced CNS gene delivery. Nat Protoc 2023; 18:3413-3459. [PMID: 37735235 DOI: 10.1038/s41596-023-00875-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 06/13/2023] [Indexed: 09/23/2023]
Abstract
Over the past 5 years, our laboratory has systematically developed a structure-guided library approach to evolve new adeno-associated virus (AAV) capsids with altered tissue tropism, higher transduction efficiency and the ability to evade pre-existing humoral immunity. Here, we provide a detailed protocol describing two distinct evolution strategies using structurally divergent AAV serotypes as templates, exemplified by improving CNS gene transfer efficiency in vivo. We outline four major components of our strategy: (i) structure-guided design of AAV capsid libraries, (ii) AAV library production, (iii) library cycling in single versus multiple animal models, followed by (iv) evaluation of lead AAV vector candidates in vivo. The protocol spans ~95 d, excluding gene expression analysis in vivo, and can vary depending on user experience, resources and experimental design. A distinguishing attribute of the current protocol is the focus on providing biomedical researchers with 3D structural information to guide evolution of precise 'hotspots' on AAV capsids. Furthermore, the protocol outlines two distinct methods for AAV library evolution consisting of adenovirus-enabled infectious cycling in a single species and noninfectious cycling in a cross-species manner. Notably, our workflow can be seamlessly merged with other RNA transcript-based library strategies and tailored for tissue-specific capsid selection. Overall, the procedures outlined herein can be adapted to expand the AAV vector toolkit for genetic manipulation of animal models and development of human gene therapies.
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Affiliation(s)
- Trevor J Gonzalez
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | | | - Leo O Blondel
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Marco M Fanous
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Joshua A Hull
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Daniel K Oh
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Sven Moller-Tank
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Jorge A Piedrahita
- North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
| | - Aravind Asokan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA.
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
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7
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Hoffmann MD, Zdechlik AC, He Y, Nedrud D, Aslanidi G, Gordon W, Schmidt D. Multiparametric domain insertional profiling of Adeno-Associated Virus VP1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537549. [PMID: 37131661 PMCID: PMC10153220 DOI: 10.1101/2023.04.19.537549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Evolved properties of Adeno-Associated Virus (AAV), such as broad tropism and immunogenicity in humans, are barriers to AAV-based gene therapy. Previous efforts to re-engineer these properties have focused on variable regions near AAV’s 3-fold protrusions and capsid protein termini. To comprehensively survey AAV capsids for engineerable hotspots, we determined multiple AAV fitness phenotypes upon insertion of large, structured protein domains into the entire AAV-DJ capsid protein VP1. This is the largest and most comprehensive AAV domain insertion dataset to date. Our data revealed a surprising robustness of AAV capsids to accommodate large domain insertions. There was strong positional, domain-type, and fitness phenotype dependence of insertion permissibility, which clustered into correlated structural units that we could link to distinct roles in AAV assembly, stability, and infectivity. We also identified new engineerable hotspots of AAV that facilitate the covalent attachment of binding scaffolds, which may represent an alternative approach to re-direct AAV tropism.
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8
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Assembly of Protein Cages for Drug Delivery. Pharmaceutics 2022; 14:pharmaceutics14122609. [PMID: 36559102 PMCID: PMC9785872 DOI: 10.3390/pharmaceutics14122609] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Nanoparticles (NPs) have been widely used as target delivery vehicles for therapeutic goods; however, compared with inorganic and organic nanomaterials, protein nanomaterials have better biocompatibility and can self-assemble into highly ordered cage-like structures, which are more favorable for applications in targeted drug delivery. In this review, we concentrate on the typical protein cage nanoparticles drugs encapsulation processes, such as drug fusion expression, diffusion, electrostatic contact, covalent binding, and protein cage disassembly/recombination. The usage of protein cage nanoparticles in biomedicine is also briefly discussed. These materials can be utilized to transport small molecules, peptides, siRNA, and other medications for anti-tumor, contrast, etc.
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9
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Barnes LF, Draper BE, Jarrold MF. Analysis of thermally driven structural changes, genome release, disassembly, and aggregation of recombinant AAV by CDMS. Mol Ther Methods Clin Dev 2022; 27:327-336. [PMID: 36381304 PMCID: PMC9630626 DOI: 10.1016/j.omtm.2022.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/12/2022] [Indexed: 12/13/2022]
Abstract
Charge detection mass spectrometry (CDMS) was used to analyze recombinant adeno-associated virus serotype 8 (rAAV8) vectors after incubation at elevated temperatures. rAAV8 vectors with a range of genomes of interest (GOIs) from 2.22 to 4.84 kb were investigated. For the shorter GOIs, GOI release occurred at surprisingly low temperatures (15 min at 45°C for cytomegalovirus [CMV]-GFP). The released DNA and intermediates with the GOI extruded from the capsid were detected. The temperature required to release the short GOIs is well below the 65°C incubation temperature required to disassemble the empty rAAV8 capsid. The temperature for GOI release increased with its GOI length. With the longer GOIs, the GOI stabilized the capsid so that it remained intact under conditions that would disassemble the empty particle. After incubation at 65°C, the main species in the CDMS mass distributions for the longer GOIs was the vector with the GOI. However, for GOIs longer than the wild-type genome (∼4.7 kb), the stability diminished, and genome release occurred at a lower temperature. Heterogeneous DNA fragments from the host cells or plasmids is released at a lower temperature than the longer GOIs, suggesting that the GOIs have a feature that resists early release.
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Affiliation(s)
- Lauren F. Barnes
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Benjamin E. Draper
- Megadalton Solutions, Inc., 3750 E Bluebird Ln, Bloomington, IN 47401, USA
| | - Martin F. Jarrold
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, IN 47405, USA,Corresponding author Martin F. Jarrold, Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, IN 47405, USA.
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10
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Kostelic MM, Ryan JP, Brown LS, Jackson TW, Hsieh CC, Zak CK, Sanders HM, Liu Y, Chen VS, Byrne M, Aspinwall CA, Baker ES, Marty MT. Stability and Dissociation of Adeno-Associated Viral Capsids by Variable Temperature-Charge Detection-Mass Spectrometry. Anal Chem 2022; 94:11723-11727. [PMID: 35981215 DOI: 10.1021/acs.analchem.2c02378] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Adeno-associated viral (AAV) vectors have emerged as gene therapy and vaccine delivery systems. Differential scanning fluorimetry or differential scanning calorimetry is commonly used to measure the thermal stability of AAVs, but these global methods are unable to distinguish the stabilities of different AAV subpopulations in the same sample. To address this challenge, we combined charge detection-mass spectrometry (CD-MS) with a variable temperature (VT) electrospray source that controls the temperature of the solution prior to electrospray. Using VT-CD-MS, we measured the thermal stabilities of empty and filled capsids. We found that filled AAVs ejected their cargo first and formed intermediate empty capsids before completely dissociating. Finally, we observed that pH stress caused a major decrease in thermal stability. This new approach better characterizes the thermal dissociation of AAVs, providing the simultaneous measurement of the stabilities and dissociation pathways of different subpopulations.
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Affiliation(s)
- Marius M Kostelic
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Jack P Ryan
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Levi S Brown
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Tyler W Jackson
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Chih-Chieh Hsieh
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Ciara K Zak
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Henry M Sanders
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Yang Liu
- REGENXBIO Inc., 9804 Medical Center Dr., Rockville, Maryland 20850, United States
| | - Victor Shugui Chen
- REGENXBIO Inc., 9804 Medical Center Dr., Rockville, Maryland 20850, United States
| | - Michael Byrne
- REGENXBIO Inc., 9804 Medical Center Dr., Rockville, Maryland 20850, United States
| | - Craig A Aspinwall
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
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11
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Maiti BK, Govil N, Kundu T, Moura JJ. Designed Metal-ATCUN Derivatives: Redox- and Non-redox-Based Applications Relevant for Chemistry, Biology, and Medicine. iScience 2020; 23:101792. [PMID: 33294799 PMCID: PMC7701195 DOI: 10.1016/j.isci.2020.101792] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
The designed "ATCUN" motif (amino-terminal copper and nickel binding site) is a replica of naturally occurring ATCUN site found in many proteins/peptides, and an attractive platform for multiple applications, which include nucleases, proteases, spectroscopic probes, imaging, and small molecule activation. ATCUN motifs are engineered at periphery by conjugation to recombinant proteins, peptides, fluorophores, or recognition domains through chemically or genetically, fulfilling the needs of various biological relevance and a wide range of practical usages. This chemistry has witnessed significant growth over the last few decades and several interesting ATCUN derivatives have been described. The redox role of the ATCUN moieties is also an important aspect to be considered. The redox potential of designed M-ATCUN derivatives is modulated by judicious choice of amino acid (including stereochemistry, charge, and position) that ultimately leads to the catalytic efficiency. In this context, a wide range of M-ATCUN derivatives have been designed purposefully for various redox- and non-redox-based applications, including spectroscopic probes, target-based catalytic metallodrugs, inhibition of amyloid-β toxicity, and telomere shortening, enzyme inactivation, biomolecules stitching or modification, next-generation antibiotic, and small molecule activation.
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Affiliation(s)
- Biplab K. Maiti
- National Institute of Technology Sikkim, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India
| | - Nidhi Govil
- National Institute of Technology Sikkim, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India
| | - Taraknath Kundu
- National Institute of Technology Sikkim, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India
| | - José J.G. Moura
- LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
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12
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The Golgi Calcium ATPase Pump Plays an Essential Role in Adeno-associated Virus Trafficking and Transduction. J Virol 2020; 94:JVI.01604-20. [PMID: 32817219 PMCID: PMC7565633 DOI: 10.1128/jvi.01604-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 08/10/2020] [Indexed: 01/08/2023] Open
Abstract
Adeno-associated viruses (AAVs) have proven to be effective gene transfer vectors. However, our understanding of how the host cell environment influences AAV transduction is still evolving. In the present study, we investigated the role of ATP2C1, which encodes a membrane calcium transport pump, SPCA1, essential for maintaining cellular calcium homeostasis on AAV transduction. Our results indicate that cellular calcium is essential for efficient intracellular trafficking and conformational changes in the AAV capsid that support efficient genome transcription. Further, we show that pharmacological modulation of cellular calcium levels can potentially be applied to improve the AAV gene transfer efficiency. Adeno-associated viruses (AAVs) are dependoparvoviruses that have proven useful for therapeutic gene transfer; however, our understanding of host factors that influence AAV trafficking and transduction is still evolving. Here, we investigated the role of cellular calcium in the AAV infectious pathway. First, we demonstrated a critical role for the host Golgi compartment-resident ATP-powered calcium pump (secretory pathway calcium ATPase 1 [SPCA1]) encoded by the ATP2C1 gene in AAV infection. CRISPR-based knockout (KO) of ATP2C1 decreases transduction by different AAV serotypes. ATP2C1 KO does not appear to inhibit AAV binding, cellular uptake, or nuclear entry; however, capsids within ATP2C1 KO cells demonstrate dispersed and punctate trafficking distinct from the perinuclear, trans-Golgi pattern observed in normal cells. In addition, we observed a defect in the ability of AAV capsids to undergo conformational changes and support efficient vector genome transcription in ATP2C1 KO cells. The calcium chelator BAPTA-AM, which reduces cytosolic calcium, rescues the defective ATP2C1 KO phenotype and AAV transduction in vitro. Conversely, the calcium ionophore ionomycin, which disrupts calcium gradients, blocks AAV transduction. Further, we demonstrated that modulating calcium in the murine brain using BAPTA-AM augments AAV gene expression in vivo. Taking these data together, we postulate that the maintenance of an intracellular calcium gradient by the calcium ATPase and processing within the Golgi compartment are essential for priming the capsid to support efficient AAV genome transcription. IMPORTANCE Adeno-associated viruses (AAVs) have proven to be effective gene transfer vectors. However, our understanding of how the host cell environment influences AAV transduction is still evolving. In the present study, we investigated the role of ATP2C1, which encodes a membrane calcium transport pump, SPCA1, essential for maintaining cellular calcium homeostasis on AAV transduction. Our results indicate that cellular calcium is essential for efficient intracellular trafficking and conformational changes in the AAV capsid that support efficient genome transcription. Further, we show that pharmacological modulation of cellular calcium levels can potentially be applied to improve the AAV gene transfer efficiency.
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13
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Chen MY, Butler SS, Chen W, Suh J. Physical, chemical, and synthetic virology: Reprogramming viruses as controllable nanodevices. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 11:e1545. [PMID: 30411529 PMCID: PMC6461522 DOI: 10.1002/wnan.1545] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/03/2018] [Accepted: 10/04/2018] [Indexed: 01/24/2023]
Abstract
The fields of physical, chemical, and synthetic virology work in partnership to reprogram viruses as controllable nanodevices. Physical virology provides the fundamental biophysical understanding of how virus capsids assemble, disassemble, display metastability, and assume various configurations. Chemical virology considers the virus capsid as a chemically addressable structure, providing chemical pathways to modify the capsid exterior, interior, and subunit interfaces. Synthetic virology takes an engineering approach, modifying the virus capsid through rational, combinatorial, and bioinformatics-driven design strategies. Advances in these three subfields of virology aim to develop virus-based materials and tools that can be applied to solve critical problems in biomedicine and biotechnology, including applications in gene therapy and drug delivery, diagnostics, and immunotherapy. Examples discussed include mammalian viruses, such as adeno-associated virus (AAV), plant viruses, such as cowpea mosaic virus (CPMV), and bacterial viruses, such as Qβ bacteriophage. Importantly, research efforts in physical, chemical, and synthetic virology have further unraveled the design principles foundational to the form and function of viruses. This article is categorized under: Diagnostic Tools > Diagnostic Nanodevices Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
| | - Susan S Butler
- Department of Bioengineering, Rice University, Houston, Texas
| | - Weitong Chen
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas
| | - Junghae Suh
- Department of Bioengineering, Rice University, Houston, Texas
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, Texas
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14
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Thadani NN, Dempsey C, Zhao J, Vasquez SM, Suh J. Reprogramming the Activatable Peptide Display Function of Adeno-Associated Virus Nanoparticles. ACS NANO 2018; 12:1445-1454. [PMID: 29278489 DOI: 10.1021/acsnano.7b07804] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We harnessed an intrinsic activatable peptide display behavior shared by several parvoviruses, including the adeno-associated virus (AAV), in order to design protein-based nanodevices that can carry out an exogenous functional output in response to stimulus detection. Specifically, we generated truncated viral capsid subunits that, when combined with native capsid components into mosaic capsids, can perform robust activatable peptide display. By modulating the ratio of subunits in the mosaic capsid, properties of the activatable peptide display function can be optimized. Interestingly, the truncated subunits can form homomeric capsids not observed in nature, but at the price of losing the ability to carry out activatable peptide display. Collectively, our results demonstrate the importance of capsid mosaicism when activatable peptide display is desired and help explain why the wild-type AAV capsid exists as a mosaic of different subunits. This proof-of-concept study illustrates a strategy for reprogramming a particular conformational output behavior of AAV in pursuit of the long-term vision of creating stimulus-responsive nanodevices.
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Affiliation(s)
- Nicole N Thadani
- Department of Bioengineering, Rice University , Houston, Texas 77005, United States
| | - Christopher Dempsey
- Department of Bioengineering, Rice University , Houston, Texas 77005, United States
| | - Julia Zhao
- Department of Bioengineering, Rice University , Houston, Texas 77005, United States
| | - Sonya M Vasquez
- Department of Bioengineering, Rice University , Houston, Texas 77005, United States
| | - Junghae Suh
- Department of Bioengineering, Rice University , Houston, Texas 77005, United States
- Systems, Synthetic and Physical Biology, Rice University , Houston, Texas 77005, United States
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15
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Mohsen MO, Zha L, Cabral-Miranda G, Bachmann MF. Major findings and recent advances in virus-like particle (VLP)-based vaccines. Semin Immunol 2017; 34:123-132. [PMID: 28887001 DOI: 10.1016/j.smim.2017.08.014] [Citation(s) in RCA: 331] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/18/2017] [Accepted: 08/23/2017] [Indexed: 01/03/2023]
Abstract
Virus-like particles (VLPs) have made giant strides in the field of vaccinology over the last three decades. VLPs constitute versatile tools in vaccine development due to their favourable immunological characteristics such as their size, repetitive surface geometry, ability to induce both innate and adaptive immune responses as well as being safe templates with favourable economics. Several VLP-based vaccines are commercially available including vaccines against Human Papilloma Virus (HPV) such as Cervarix®, Gardasil® & Gardasil9® and Hepatitis B Virus (HBV) including the 3rd generation Sci-B-Vac™. In addition, the first licensed malaria-VLP-based vaccine Mosquirix™ has been recently approved by the European regulators. Several other VLP-based vaccines are currently undergoing preclinical and clinical development. This review summarizes some of the major findings and recent advances in VLP-based vaccine development and technologies and outlines general principles that may be harnessed for induction of targeted immune responses.
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Affiliation(s)
- Mona O Mohsen
- Jenner Institute, University of Oxford, Roosevelt Dr, Oxford OX3 7BN, UK; Qatar Foundation, Doha, State of Qatar
| | - Lisha Zha
- Inselspital, Universitatsklinik RIA, Immunologie, Sahlihaus 1, 3010 Bern, Switzerland
| | | | - Martin F Bachmann
- Jenner Institute, University of Oxford, Roosevelt Dr, Oxford OX3 7BN, UK; Inselspital, Universitatsklinik RIA, Immunologie, Sahlihaus 1, 3010 Bern, Switzerland.
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16
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Microglia-specific targeting by novel capsid-modified AAV6 vectors. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2016; 3:16026. [PMID: 27308302 PMCID: PMC4909093 DOI: 10.1038/mtm.2016.26] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 02/29/2016] [Accepted: 02/29/2016] [Indexed: 01/14/2023]
Abstract
Recombinant adeno-associated viruses (rAAV) have been widely used in gene therapy
applications for central nervous system diseases. Though rAAV can efficiently target
neurons and astrocytes in mouse brains, microglia, the immune cells of the brain, are
refractile to rAAV. To identify AAV capsids with microglia-specific transduction
properties, we initially screened the most commonly used serotypes, AAV1–9 and
rh10, on primary mouse microglia cultures. While these capsids were not permissive, we
then tested the microglial targeting properties of a newly characterized set of modified
rAAV6 capsid variants with high tropism for monocytes. Indeed, these newly characterized
rAAV6 capsid variants, specially a triply mutated Y731F/Y705F/T492V form, carrying a
self-complementary genome and microglia-specific promoters (F4/80 or CD68) could
efficiently and selectively transduce microglia in vitro. Delivery of these
constructs in mice brains resulted in microglia-specific expression of green fluorescent
protein, albeit at modest levels. We further show that CD68 promoter–driven
expression of the inflammatory cytokine, interleukin-6, using this capsid variant leads to
increased astrogliosis in the brains of wild-type mice. Our study describes the first
instance of AAV-targeted microglial gene expression leading to functional modulation of
the innate immune system in mice brains. This provides the rationale for utilizing these
unique capsid/promoter combinations for microglia-specific gene targeting for modeling or
functional studies.
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17
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Halder S, Van Vliet K, Smith JK, Duong TTP, McKenna R, Wilson JM, Agbandje-McKenna M. Structure of neurotropic adeno-associated virus AAVrh.8. J Struct Biol 2015; 192:21-36. [PMID: 26334681 PMCID: PMC4617535 DOI: 10.1016/j.jsb.2015.08.017] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 08/22/2015] [Accepted: 08/30/2015] [Indexed: 12/19/2022]
Abstract
Adeno-associated virus rhesus isolate 8 (AAVrh.8) is a leading vector for the treatment of neurological diseases due to its efficient transduction of neuronal cells and reduced peripheral tissue tropism. Toward identification of the capsid determinants for these properties, the structure of AAVrh.8 was determined by X-ray crystallography to 3.5 Å resolution and compared to those of other AAV isolates. The capsid viral protein (VP) structure consists of an αA helix and an eight-stranded anti-parallel β-barrel core conserved in parvoviruses, and large insertion loop regions between the β-strands form the capsid surface topology. The AAVrh.8 capsid exhibits the surface topology conserved in all AAVs: depressions at the icosahedral twofold axis and surrounding the cylindrical channel at the fivefold axis, and three protrusions around the threefold axis. A structural comparison to serotypes AAV2, AAV8, and AAV9, to which AAVrh.8 shares ∼ 84%, ∼ 91%, and ∼ 87% VP sequence identity, respectively, revealed differences in the surface loops known to affect receptor binding, transduction efficiency, and antigenicity. Consistent with this observation, biochemical assays showed that AAVrh.8 is unable to bind heparin and does not cross-react with conformational monoclonal antibodies and human donor serum directed against the other AAVs compared. This structure of AAVrh.8 thus identified capsid surface differences which can serve as template regions for rational design of vectors with enhanced transduction for specific tissues and escape pre-existing antibody recognition. These features are essential for the creation of an AAV vector toolkit that is amenable to personalized disease treatment.
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Affiliation(s)
- Sujata Halder
- University of Florida, Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, Gainesville, FL 32610, USA
| | - Kim Van Vliet
- University of Florida, Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, Gainesville, FL 32610, USA
| | - J Kennon Smith
- University of Florida, Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, Gainesville, FL 32610, USA
| | - Thao Thi Phuong Duong
- University of Florida, Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, Gainesville, FL 32610, USA
| | - Robert McKenna
- University of Florida, Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, Gainesville, FL 32610, USA
| | - James M Wilson
- Gene Therapy Program, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mavis Agbandje-McKenna
- University of Florida, Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, Gainesville, FL 32610, USA.
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18
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Jones LH, Narayanan A, Hett EC. Understanding and applying tyrosine biochemical diversity. MOLECULAR BIOSYSTEMS 2014; 10:952-69. [PMID: 24623162 DOI: 10.1039/c4mb00018h] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This review highlights some of the recent advances made in our understanding of the diversity of tyrosine biochemistry and shows how this has inspired novel applications in numerous areas of molecular design and synthesis, including chemical biology and bioconjugation. The pathophysiological implications of tyrosine biochemistry will be presented from a molecular perspective and the opportunities for therapeutic intervention explored.
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Affiliation(s)
- Lyn H Jones
- Pfizer R&D, Chemical Biology Group, BioTherapeutics Chemistry, WorldWide Medicinal Chemistry, 200 Cambridge Park Drive, Cambridge, MA 02140, USA.
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19
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Metal-binding and redox properties of substituted linear and cyclic ATCUN motifs. J Inorg Biochem 2014; 139:65-76. [PMID: 24980953 DOI: 10.1016/j.jinorgbio.2014.06.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/29/2014] [Accepted: 06/02/2014] [Indexed: 01/13/2023]
Abstract
The amino-terminal copper and nickel binding (ATCUN) motif is a short peptide sequence found in human serum albumin and other proteins. Synthetic ATCUN-metal complexes have been used to oxidatively cleave proteins and DNA, cross-link proteins, and damage cancer cells. The ATCUN motif consists of a tripeptide that coordinates Cu(II) and Ni(II) ions in a square planar geometry, anchored by chelation sites at the N-terminal amine, histidine imidazole and two backbone amides. Many studies have shown that the histidine is required for tight binding and square planar geometry. Previously, we showed that macrocyclization of the ATCUN motif can lead to high-affinity binding with altered metal ion selectivity and enhanced Cu(II)/Cu(III) redox cycling (Inorg. Chem. 2013, 52, 2729-2735). In this work, we synthesize and characterize several linear and cyclic ATCUN variants to explore how substitutions at the histidine alter the metal-binding and catalytic properties. UV-visible spectroscopy, EPR spectroscopy and mass spectrometry indicate that cyclization can promote the formation of ATCUN-like complexes even in the absence of imidazole. We also report several novel ATCUN-like complexes and quantify their redox properties. These findings further demonstrate the effects of conformational constraints on short, metal-binding peptides, and also provide novel redox-active metallopeptides suitable for testing as catalysts for stereoselective or regioselective oxidation reactions.
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20
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Ravikiran B, Mahalakshmi R. Unusual post-translational protein modifications: the benefits of sophistication. RSC Adv 2014. [DOI: 10.1039/c4ra04694c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This review summarizes the “seemingly bizarre”, yet naturally occurring, covalent non-disulphide cross-links in enzymatic and scaffolding proteins and their functions.
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Affiliation(s)
- Boddepalli Ravikiran
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal, India
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21
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Systemic delivery of tyrosine-mutant AAV vectors results in robust transduction of neurons in adult mice. BIOMED RESEARCH INTERNATIONAL 2013; 2013:974819. [PMID: 23762870 PMCID: PMC3671507 DOI: 10.1155/2013/974819] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 04/19/2013] [Accepted: 04/21/2013] [Indexed: 12/20/2022]
Abstract
Recombinant adeno-associated virus (AAV) vectors are powerful tools for both basic neuroscience experiments and clinical gene therapies for neurological diseases. Intravascularly administered self-complementary AAV9 vectors can cross the blood-brain barrier. However, AAV9 vectors are of limited usefulness because they mainly transduce astrocytes in adult animal brains and have restrictions on foreign DNA package sizes. In this study, we show that intracardiac injections of tyrosine-mutant pseudotype AAV9/3 vectors resulted in extensive and widespread transgene expression in the brains and spinal cords of adult mice. Furthermore, the usage of neuron-specific promoters achieved selective transduction of neurons. These results suggest that tyrosine-mutant AAV9/3 vectors may be effective vehicles for delivery of therapeutic genes, including miRNAs, into the brain and for treating diseases that affect broad areas of the central nervous system.
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22
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Smith MT, Hawes AK, Bundy BC. Reengineering viruses and virus-like particles through chemical functionalization strategies. Curr Opin Biotechnol 2013; 24:620-6. [PMID: 23465756 DOI: 10.1016/j.copbio.2013.01.011] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 01/28/2013] [Accepted: 01/29/2013] [Indexed: 11/30/2022]
Abstract
Increasing demands from nanotechnology require increasingly more rigorous methods to control nanoparticle traits such as assembly, size, morphology, monodispersity, stability, and reactivity. Viruses are a compelling starting point for engineering nanoparticles, as eons of natural biological evolution have instilled diverse and desirable traits. The next step is to reengineer these viruses into something functional and useful. These reengineered particles, or virus-based nanoparticles (VNPs), are the foundation for many promising new technologies in drug delivery, targeted delivery, vaccines, imaging, and biocatalysis. To achieve these end goals, VNPs must often be manipulated genetically and post-translationally. We review prevailing strategies of genetic and noncovalent functionalization and focus on the covalent modifications using natural and unnatural amino acid residues.
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Affiliation(s)
- Mark Thomas Smith
- Department of Chemical Engineering, Brigham Young University, United States
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23
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Structure and dynamics of adeno-associated virus serotype 1 VP1-unique N-terminal domain and its role in capsid trafficking. J Virol 2013; 87:4974-84. [PMID: 23427155 DOI: 10.1128/jvi.02524-12] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The importance of the phospholipase A2 domain located within the unique N terminus of the capsid viral protein VP1 (VP1u) in parvovirus infection has been reported. This study used computational methods to characterize the VP1 sequence for adeno-associated virus (AAV) serotypes 1 to 12 and circular dichroism and electron microscopy to monitor conformational changes in the AAV1 capsid induced by temperature and the pHs encountered during trafficking through the endocytic pathway. Circular dichroism was also used to monitor conformational changes in AAV6 capsids assembled from VP2 and VP3 or VP1, VP2, and VP3 at pH 7.5. VP1u was predicted (computationally) and confirmed (in solution) to be structurally ordered. This VP domain was observed to undergo a reversible pH-induced unfolding/refolding process, a loss/gain of α-helical structure, which did not disrupt the capsid integrity and is likely facilitated by its difference in isoelectric point compared to the other VP sequences assembling the capsid. This study is the first to physically document conformational changes in the VP1u region that likely facilitate its externalization from the capsid interior during infection and establishes the order of events in the escape of the AAV capsid from the endosome en route to the nucleus.
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24
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Neupane KP, Aldous AR, Kritzer JA. Macrocyclization of the ATCUN motif controls metal binding and catalysis. Inorg Chem 2013; 52:2729-35. [PMID: 23421754 DOI: 10.1021/ic302820z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the design, synthesis, and characterization of macrocyclic analogues of the amino-terminal copper and nickel binding (ATCUN) motif. These macrocycles have altered pH transitions for metal binding, and unlike linear ATCUN motifs, the optimal cyclic peptide 1 binds Cu(II) selectively over Ni(II) at physiological pH. UV-vis and EPR spectroscopy showed that cyclic peptide 1 can coordinate Cu(II) or Ni(II) in a square planar geometry. Metal binding titration and ESI-MS data revealed a 1:1 binding stoichiometry. Macrocyclization allows for coordination of Cu(II) or Ni(II) as in linear ATCUN motifs, but with enhanced DNA cleavage by the Cu(II)-1 complex relative to linear analogues. The Cu(II)-1 complex was also capable of producing diffusible hydroxyl radicals, which is unique among ATCUN motifs and most other common copper(II) chelators.
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Affiliation(s)
- Kosh P Neupane
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
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25
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Biophysical and ultrastructural characterization of adeno-associated virus capsid uncoating and genome release. J Virol 2012; 87:2994-3002. [PMID: 23269804 DOI: 10.1128/jvi.03017-12] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We describe biophysical and ultrastructural differences in genome release from adeno-associated virus (AAV) capsids packaging wild-type DNA, recombinant single-stranded DNA (ssDNA), or dimeric, self-complementary DNA (scDNA) genomes. Atomic force microscopy and electron microscopy (EM) revealed that AAV particles release packaged genomes and undergo marked changes in capsid morphology upon heating in physiological buffer (pH 7.2). When different AAV capsids packaging ss/scDNA varying in length from 72 to 123% of wild-type DNA (3.4 to 5.8 kb) were incrementally heated, the proportion of uncoated AAV capsids decreased with genome length as observed by EM. Genome release was further characterized by a fluorimetric assay, which demonstrated that acidic pH and high osmotic pressure suppress genome release from AAV particles. In addition, fluorimetric analysis corroborated an inverse correlation between packaged genome length and the temperature needed to induce uncoating. Surprisingly, scAAV vectors required significantly higher temperatures to uncoat than their ssDNA-packaging counterparts. However, externalization of VP1 N termini appears to be unaffected by packaged genome length or self-complementarity. Further analysis by tungsten-shadowing EM revealed striking differences in the morphologies of ssDNA and scDNA genomes upon release from intact capsids. Computational modeling and molecular dynamics simulations suggest that the unusual thermal stability of scAAV vectors might arise from partial base pairing and optimal organization of packaged scDNA. Our work further defines the biophysical mechanisms underlying adeno-associated virus uncoating and genome release.
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