1
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Miller LM, Hawkins L, Jarrold MF. Compaction, Relaxation, and Linearization of Megadalton-Sized DNA Plasmids: DNA Structures Probed by CD-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39013154 DOI: 10.1021/jasms.4c00222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
High purity plasmid DNA is a raw material for recombinant protein production as well as an active ingredient in DNA vaccines. There are four primary plasmid structures that can be observed in a typical plasmid formulation: supercoiled, relaxed (circular), linearized, and condensed. Determining what structures are present in a sample is important, as the structure can affect activity; the supercoiled structure has the highest activity, and >90% supercoiled is desired for industry standards. Recently, charge detection mass spectrometry (CD-MS) was used to distinguish two of the structures, supercoiled and condensed, by measuring the charge deposited on the ions by positive mode electrospray. Here, CD-MS is used to probe the structures of DNA plasmids during compaction with polycations, and through enzymatic treatment to relax and linearize plasmids. We find that all four structural types for plasmid DNA have unique charging profiles that can be distinguished using CD-MS. The extent of mechanical shearing of the DNA plasmids during electrospray is strongly influenced by the structural type.
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Affiliation(s)
- Lohra M Miller
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Luke Hawkins
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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2
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Song J, Zhang D, Dai X, Huang Z, Fang X, Tian D, Jiang Y. Numerical Analysis and Quantification of Transfer Efficiency Coupled with Capillary and Quadrupole Ion Guide in an API-MS System. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1497-1506. [PMID: 38828990 DOI: 10.1021/jasms.4c00097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Ion trajectory simulation is a significant and useful tool for understanding ion transfer mechanisms within the first vacuum region of the atmospheric pressure ionization mass spectrometer (API-MS). However, the complex dynamic gas field and wide pressure range lead to inaccurate simulation and huge computational costs. In this work, a novel electrohydrodynamic simulation called the statistical diffusion-hard-sphere (SDHS) mixed collision model was developed for characterizing the ion trajectories. For the first time, the influence of the dynamic pressure on the ion trajectory is considered for simulation, which helps to avoid an intolerable computational cost. Comparing with the conventional Monte Carlo collision model, the SDHS method helps to improve the calculation accuracy of ion trajectories under the first vacuum region and reduce the computational cost for at least 12-folds. Simulation results showed that the maximum ion loss came from the gap of the electrodes. The distance of the capillary-quadrupole ion guide was also a non-negligible factor. The trend of quantitative experimental results matches the SDHS simulation results. The maximum ion transfer efficiencies of quantitative experiment and simulation were 55% and 52%, respectively. Moreover, three ions, caffeine, reserpine, and Ultramark 1621, were measured for evaluating the applicability of SDHS in real API-MS. The trend of experimental results showed good agreement with that of computation. And the results of caffeine further illustrated the reason that the small mass ion transfer efficiency decreased with increasing radio frequency voltage. SDHS method is expected to be useful in the design of ion guides for further improvement of the sensitivity of API-MS.
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Affiliation(s)
- Jiafeng Song
- College of Instrumentation & Electrical Engineering, Jilin University, Changchun 130012, China
| | - Di Zhang
- Technology Innovation Center of Mass Spectrometry for Stata Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China
| | - Xinhua Dai
- Technology Innovation Center of Mass Spectrometry for Stata Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China
| | - Zejian Huang
- Technology Innovation Center of Mass Spectrometry for Stata Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China
| | - Xiang Fang
- Technology Innovation Center of Mass Spectrometry for Stata Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China
| | - Di Tian
- College of Instrumentation & Electrical Engineering, Jilin University, Changchun 130012, China
| | - You Jiang
- Technology Innovation Center of Mass Spectrometry for Stata Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China
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3
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Szyszka TN, Andreas MP, Lie F, Miller LM, Adamson LSR, Fatehi F, Twarock R, Draper BE, Jarrold MF, Giessen TW, Lau YH. Point mutation in a virus-like capsid drives symmetry reduction to form tetrahedral cages. Proc Natl Acad Sci U S A 2024; 121:e2321260121. [PMID: 38722807 PMCID: PMC11098114 DOI: 10.1073/pnas.2321260121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/25/2024] [Indexed: 05/18/2024] Open
Abstract
Protein capsids are a widespread form of compartmentalization in nature. Icosahedral symmetry is ubiquitous in capsids derived from spherical viruses, as this geometry maximizes the internal volume that can be enclosed within. Despite the strong preference for icosahedral symmetry, we show that simple point mutations in a virus-like capsid can drive the assembly of unique symmetry-reduced structures. Starting with the encapsulin from Myxococcus xanthus, a 180-mer bacterial capsid that adopts the well-studied viral HK97 fold, we use mass photometry and native charge detection mass spectrometry to identify a triple histidine point mutant that forms smaller dimorphic assemblies. Using cryoelectron microscopy, we determine the structures of a precedented 60-mer icosahedral assembly and an unexpected 36-mer tetrahedron that features significant geometric rearrangements around a new interaction surface between capsid protomers. We subsequently find that the tetrahedral assembly can be generated by triple-point mutation to various amino acids and that even a single histidine point mutation is sufficient to form tetrahedra. These findings represent a unique example of tetrahedral geometry when surveying all characterized encapsulins, HK97-like capsids, or indeed any virus-derived capsids reported in the Protein Data Bank, revealing the surprising plasticity of capsid self-assembly that can be accessed through minimal changes in the protein sequence.
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Affiliation(s)
- Taylor N. Szyszka
- School of Chemistry, The University of Sydney, Camperdown, NSW2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW2006, Australia
| | - Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI48109
| | - Felicia Lie
- School of Chemistry, The University of Sydney, Camperdown, NSW2006, Australia
| | - Lohra M. Miller
- Chemistry Department, Indiana University, Bloomington, IN47405
| | | | - Farzad Fatehi
- Department of Mathematics, University of York, YorkYO10 5DD, United Kingdom
- York Cross-Disciplinary Centre for Systems Analysis, University of York, YorkYO10 5DD, United Kingdom
| | - Reidun Twarock
- Department of Mathematics, University of York, YorkYO10 5DD, United Kingdom
- York Cross-Disciplinary Centre for Systems Analysis, University of York, YorkYO10 5DD, United Kingdom
- Department of Biology, University of York, YorkYO10 5DD, United Kingdom
| | | | | | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI48109
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW2006, Australia
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4
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Zhang J, Frabutt DA, Chrzanowski M, Li N, Miller LM, Tian J, Mulcrone PL, Lam AK, Draper BE, Jarrold MF, Herzog RW, Xiao W. A novel class of self-complementary AAV vectors with multiple advantages based on cceAAV lacking mutant ITR. Mol Ther Methods Clin Dev 2024; 32:101206. [PMID: 38390555 PMCID: PMC10881427 DOI: 10.1016/j.omtm.2024.101206] [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: 09/30/2023] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
Self-complementary AAV vectors (scAAV) use a mutant inverted terminal repeat (mITR) for efficient packaging of complementary stranded DNA, enabling rapid transgene expression. However, inefficient resolution at the mITR leads to the packaging of monomeric or subgenomic AAV genomes. These noncanonical particles reduce transgene expression and may affect the safety of gene transfer. To address these issues, we have developed a novel class of scAAV vectors called covalently closed-end double-stranded AAV (cceAAV) that eliminate the mITR resolution step during production. Instead of using a mutant ITR, we used a 56-bp recognition sequence of protelomerase (TelN) to covalently join the top and bottom strands, allowing the vector to be generated with just a single ITR. To produce cceAAV vectors, the vector plasmid is initially digested with TelN, purified, and then subjected to a standard triple-plasmid transfection protocol followed by traditional AAV vector purification procedures. Such cceAAV vectors demonstrate yields comparable to scAAV vectors. Notably, we observed enhanced transgene expression as compared to traditional scAAV vectors. The treatment of mice with hemophilia B with cceAAV-FIX resulted in significantly enhanced long-term FIX expression. The cceAAV vectors hold several advantages over scAAV vectors, potentially leading to the development of improved human gene therapy drugs.
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Affiliation(s)
- Junping Zhang
- Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Dylan A. Frabutt
- Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - Ning Li
- Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - Jiahe Tian
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Patrick L. Mulcrone
- Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Anh K. Lam
- Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - Martin F. Jarrold
- Chemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Roland W. Herzog
- Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Weidong Xiao
- Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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5
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Ibreljic N, Draper BE, Lawton CW. Recombinant AAV genome size effect on viral vector production, purification, and thermostability. Mol Ther Methods Clin Dev 2024; 32:101188. [PMID: 38327806 PMCID: PMC10847916 DOI: 10.1016/j.omtm.2024.101188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024]
Abstract
Adeno-associated virus (AAV) has shown great promise as a viral vector for gene therapy in clinical applications. The present work studied the effect of genome size on AAV production, purification, and thermostability by producing AAV2-GFP using suspension-adapted HEK293 cells via triple transfection using AAV plasmids containing the same GFP transgene with DNA stuffers for variable-size AAV genomes consisting of 1.9, 3.4, and 4.9 kb (ITR to ITR). Production was performed at the small and large shake flask scales and the results showed that the 4.9 kb GFP genome had significantly reduced encapsidation compared to other genomes. The large shake flask productions were purified by AEX chromatography, and the results suggest that the triple transfection condition significantly affects the AEX retention time and resolution between the full and empty capsid peaks. Charge detection-mass spectrometry was performed on all AEX full-capsid peak samples showing a wide distribution of empty, partial, full length, and copackaged DNA in the capsids. The AEX-purified samples were then analyzed by differential scanning fluorimetry, and the results suggest that sample formulation may improve the thermostability of AAV genome ejection melting temperature regardless of the packaged genome content.
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Affiliation(s)
- Nermin Ibreljic
- Department of Chemical Engineering, University of Massachusetts Lowell, One University Avenue, Lowell, MA 01854, USA
- Sarepta Therapeutics, 55 Blue Sky Drive, Burlington, MA 01803, USA
| | | | - Carl W. Lawton
- Department of Chemical Engineering, University of Massachusetts Lowell, One University Avenue, Lowell, MA 01854, USA
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6
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Parikh RA, Draper BE, Jarrold MF. Multiple Ion Charge Extraction (MICE) for High-Throughput Charge Detection Mass Spectrometry. Anal Chem 2024. [PMID: 38329825 DOI: 10.1021/acs.analchem.3c05087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Charge detection mass spectrometry (CD-MS) is a single-particle technique, where the masses of individual ions are determined from simultaneous measurements of their mass-to-charge ratio (m/z) and charge. The ions are trapped in an electrostatic linear ion trap (ELIT) and oscillate back and forth through a conducting cylinder connected to a charge-sensitive amplifier. The oscillating ions generate a periodic signal that is processed with fast Fourier transforms (FFTs) to obtain the oscillation frequency (which is related to m/z) and magnitude (which is proportional to the charge). The simultaneous trapping of two or more ions is a way to increase throughput. However, when multiple ions are trapped, it is possible that some of them have overlapping oscillation frequencies, which can lead to an error in the charge determination. To avoid this error, results from overlapping ions are usually discarded. When measurements are performed with many trapped ions, the most abundant m/z species are discarded at a higher rate, which affects the relative abundances in the mass distribution. Here, we report the development of a post-processing method called multiple ion charge extraction (MICE) that uses a statistical approach to assign charges to ions with overlapping frequencies. MICE recovers single-ion information from high signal measurements and makes the relative abundances more resilient to the signal intensity. This approach corrects for high signal m/z biasing, allowing analysis to be faster and more reliable. Using MICE, CD-MS measurements were made at rates of 120 ions/s with little m/z biasing.
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Affiliation(s)
- Raj A Parikh
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington, Indiana 47405, United States
| | - Benjamin E Draper
- Megadalton Solutions Inc., 3750 E Bluebird Ln, Bloomington, Indiana 47401, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington, Indiana 47405, United States
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7
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Szyszka TN, Andreas MP, Lie F, Miller LM, Adamson LSR, Fatehi F, Twarock R, Draper BE, Jarrold MF, Giessen TW, Lau YH. Point mutation in a virus-like capsid drives symmetry reduction to form tetrahedral cages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.579038. [PMID: 38370832 PMCID: PMC10871247 DOI: 10.1101/2024.02.05.579038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Protein capsids are a widespread form of compartmentalisation in nature. Icosahedral symmetry is ubiquitous in capsids derived from spherical viruses, as this geometry maximises the internal volume that can be enclosed within. Despite the strong preference for icosahedral symmetry, we show that simple point mutations in a virus-like capsid can drive the assembly of novel symmetry-reduced structures. Starting with the encapsulin from Myxococcus xanthus, a 180-mer bacterial capsid that adopts the well-studied viral HK97 fold, we use mass photometry and native charge detection mass spectrometry to identify a triple histidine point mutant that forms smaller dimorphic assemblies. Using cryo-EM, we determine the structures of a precedented 60-mer icosahedral assembly and an unprecedented 36-mer tetrahedron that features significant geometric rearrangements around a novel interaction surface between capsid protomers. We subsequently find that the tetrahedral assembly can be generated by triple point mutation to various amino acids, and that even a single histidine point mutation is sufficient to form tetrahedra. These findings represent the first example of tetrahedral geometry across all characterised encapsulins, HK97-like capsids, or indeed any virus-derived capsids reported in the Protein Data Bank, revealing the surprising plasticity of capsid self-assembly that can be accessed through minimal changes in protein sequence.
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Affiliation(s)
- Taylor N Szyszka
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Michael P Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Felicia Lie
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Lohra M Miller
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Lachlan S R Adamson
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Farzad Fatehi
- Department of Mathematics, University of York, York, UK
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Reidun Twarock
- Department of Mathematics, University of York, York, UK
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - Benjamin E Draper
- Megadalton Solutions Inc., 3750 E Bluebird Ln, Bloomington, IN 47401, USA
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW 2006, Australia
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8
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Prokhorov NS, Davis C, Maruthi K, Yang Q, Sherman M, Woodson M, White M, Miller LM, Jarrold M, Catalano C, Morais M. Biophysical and structural characterization of a multifunctional viral genome packaging motor. Nucleic Acids Res 2024; 52:831-843. [PMID: 38084901 PMCID: PMC10810279 DOI: 10.1093/nar/gkad1135] [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: 07/03/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 01/26/2024] Open
Abstract
The large dsDNA viruses replicate their DNA as concatemers consisting of multiple covalently linked genomes. Genome packaging is catalyzed by a terminase enzyme that excises individual genomes from concatemers and packages them into preassembled procapsids. These disparate tasks are catalyzed by terminase alternating between two distinct states-a stable nuclease that excises individual genomes and a dynamic motor that translocates DNA into the procapsid. It was proposed that bacteriophage λ terminase assembles as an anti-parallel dimer-of-dimers nuclease complex at the packaging initiation site. In contrast, all characterized packaging motors are composed of five terminase subunits bound to the procapsid in a parallel orientation. Here, we describe biophysical and structural characterization of the λ holoenzyme complex assembled in solution. Analytical ultracentrifugation, small angle X-ray scattering, and native mass spectrometry indicate that 5 subunits assemble a cone-shaped terminase complex. Classification of cryoEM images reveals starfish-like rings with skewed pentameric symmetry and one special subunit. We propose a model wherein nuclease domains of two subunits alternate between a dimeric head-to-head arrangement for genome maturation and a fully parallel arrangement during genome packaging. Given that genome packaging is strongly conserved in both prokaryotic and eukaryotic viruses, the results have broad biological implications.
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Affiliation(s)
- Nikolai S Prokhorov
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Christal R Davis
- Program in Structural Biology and Biochemistry, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kashyap Maruthi
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Qin Yang
- Department of Pharmaceutical Chemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Campus, Aurora, CO 80045, USA
| | - Michael B Sherman
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Michael Woodson
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Mark A White
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Lohra M Miller
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Martin F Jarrold
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Carlos E Catalano
- Program in Structural Biology and Biochemistry, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pharmaceutical Chemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Campus, Aurora, CO 80045, USA
| | - Marc C Morais
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
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9
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Li X, Miller LM, Chrzanowski M, Tian J, Jarrold MF, Herzog RW, Xiao W, Draper B, Zhang J. Quantitative analysis of preferential utilization of AAV ITR as the packaging terminal signal. Front Bioeng Biotechnol 2023; 11:1327433. [PMID: 38173872 PMCID: PMC10761532 DOI: 10.3389/fbioe.2023.1327433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
Genetic engineering advances have led to recombinant adeno-associated virus (rAAV) becoming an invaluable tool for the development of effective gene therapies. The production of rAAV is susceptible to off-target heterogeneous packaging, the effects of which are still being understood. Here, rAAV vectors with four-genome lengths were produced using both adherent and suspension HEK293 cells to understand the 5'ITR termination. AAV8 vectors were produced from the human FVIII plasmid for a full-length cargo of 4,707 nucleotides with specific truncations, creating smaller genomes. Conventionally, rAAV is characterized by differentiating empty capsids from full capsids, but for this work, that description is incomplete. The small genomes in this study were characterized by charge detection-mass spectrometry (CD-MS). Using CD-MS, packaged genomes in the range conventionally attributed to partials were resolved and quantified. In addition, alkaline gels and qPCR were used to assess the identity of the packaged genomes. Together, these results showed a propensity for unit-length genomes to be encapsidated. Packaged genomes occurred as replication intermediates emanating from the 5'ITR, indicating that HEK293 cells prefer unit-length genomes as opposed to the 5'ITR termination and heterogeneous DNA packaging observed previously from Sf9 cell systems. As both manufacturing processes are used and continually assessed to produce clinical material, such an understanding will benefit rAAV design for basic research and gene therapy.
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Affiliation(s)
- Xin Li
- Herman B Wells Center for Pediatric Research, Indiana University IUSM, Indianapolis, IN, United States
| | | | | | - Jiahe Tian
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - Martin F. Jarrold
- Chemistry Department, Indiana University, Bloomington, IN, United States
| | - Roland W. Herzog
- Herman B Wells Center for Pediatric Research, Indiana University IUSM, Indianapolis, IN, United States
| | - Weidong Xiao
- Herman B Wells Center for Pediatric Research, Indiana University IUSM, Indianapolis, IN, United States
| | | | - Junping Zhang
- Herman B Wells Center for Pediatric Research, Indiana University IUSM, Indianapolis, IN, United States
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10
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Troxell B, Jaslow SL, Tsai IW, Sullivan C, Draper BE, Jarrold MF, Lindsey K, Blue L. Partial genome content within rAAVs impacts performance in a cell assay-dependent manner. Mol Ther Methods Clin Dev 2023; 30:288-302. [PMID: 37583716 PMCID: PMC10423999 DOI: 10.1016/j.omtm.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/17/2023] [Indexed: 08/17/2023]
Abstract
Recombinant adeno-associated viruses (rAAVs) deliver DNA to numerous cell types. However, packaging of partial genomes into the rAAV capsid is of concern. Although empty rAAV capsids are studied, there is little information regarding the impact of partial DNA content on rAAV performance in controlled studies. To address this, we tested vectors containing varying levels of partial, self-complementary EGFP genomes. Density gradient cesium chloride ultracentrifugation was used to isolate three distinct rAAV populations: (1) a lighter fraction, (2) a moderate fraction, and (3) a heavy fraction. Alkaline gels, Illumina Mi-Seq, size exclusion chromatography with multi-angle light scattering (SEC-MALS), and charge detection mass spectrometry (CD-MS) were used to characterize the genome of each population and ddPCR to quantify residual DNA molecules. Live-cell imaging and EGFP ELISA assays demonstrated reduced expression following transduction with the light fraction compared with the moderate and heavy fractions. However, PCR-based assays showed that the light density delivered EGFP DNA to cells as efficiently as the moderate and heavy fractions. Mi-Seq data revealed an underrepresentation of the promoter region for EGFP, suggesting that expression of EGFP was reduced because of lack of regulatory control. This work demonstrates that rAAVs containing partial genomes contribute to the DNA signal but have reduced vector performance.
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Affiliation(s)
- Bryan Troxell
- StrideBio Analytical Development and Quality Control, 5 Laboratory Drive, Suite 1200, Research Triangle Park, NC 27709, USA
- AjaxBio, LLC, Holly Springs, NC 27540, USA
| | - Sarah L. Jaslow
- StrideBio Analytical Development and Quality Control, 5 Laboratory Drive, Suite 1200, Research Triangle Park, NC 27709, USA
| | - I-Wei Tsai
- StrideBio Analytical Development and Quality Control, 5 Laboratory Drive, Suite 1200, Research Triangle Park, NC 27709, USA
| | - Chelsea Sullivan
- StrideBio Analytical Development and Quality Control, 5 Laboratory Drive, Suite 1200, Research Triangle Park, NC 27709, 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
| | - Kate Lindsey
- StrideBio Analytical Development and Quality Control, 5 Laboratory Drive, Suite 1200, Research Triangle Park, NC 27709, USA
| | - Levi Blue
- StrideBio Analytical Development and Quality Control, 5 Laboratory Drive, Suite 1200, Research Triangle Park, NC 27709, USA
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11
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Miller LM, Draper BE, Barnes LF, Ofoegbu PC, Jarrold MF. Analysis of Megadalton-Sized DNA by Charge Detection Mass Spectrometry: Entropic Trapping and Shearing in Nanoelectrospray. Anal Chem 2023. [PMID: 37267126 DOI: 10.1021/acs.analchem.3c01027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The analysis of nucleic acids by conventional mass spectrometry is complicated by counter ions which cause mass heterogeneity and limit the size of the DNA that can be analyzed. In this work, we overcome this limitation using charge detection mass spectrometry to analyze megadalton-sized DNA. Using positive mode electrospray, we find two dramatically different charge distributions for DNA plasmids. A low charge population that charges like compact DNA origami and a much higher charge population, with charges that extend over a broad range. For the high-charge population, the deviation between the measured mass and mass expected from the DNA sequence is consistently around 1%. For the low-charge population, the deviation is larger and more variable. The high-charge population is attributed to the supercoiled plasmid in a random coil configuration, with the broad charge distribution resulting from the rich variety of geometries the random coil can adopt. High-resolution measurements show that the mass distribution shifts to slightly lower mass with increasing charge. The low-charge population is attributed to a condensed form of the plasmid. We suggest that the condensed form results from entropic trapping where the random coil must undergo a geometry change to squeeze through the Taylor cone and enter an electrospray droplet. For the larger plasmids, shearing (mechanical breakup) occurs during electrospray or in the electrospray interface. Shearing is reduced by lowering the salt concentration.
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Affiliation(s)
- Lohra M Miller
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington, Indiana 47405, United States
| | - Benjamin E Draper
- Megadalton Solutions Inc, 3750 E Bluebird Ln, Bloomington, Indiana 47401, United States
| | - Lauren F Barnes
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington, Indiana 47405, United States
| | - Polycarp C Ofoegbu
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington, Indiana 47405, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington, Indiana 47405, United States
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12
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Miller LM, Jarrold MF. Charge detection mass spectrometry for the analysis of viruses and virus-like particles. Essays Biochem 2023; 67:315-323. [PMID: 36062529 PMCID: PMC10842916 DOI: 10.1042/ebc20220101] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022]
Abstract
Heterogeneity usually restricts conventional mass spectrometry to molecular weights less than around a megadalton. As a single-particle technique, charge detection mass spectrometry (CDMS) overcomes this limitation. In CDMS, the mass-to-charge (m/z) ratio and charge are measured simultaneously for individual ions, giving a direct mass measurement for each ion. Recent applications include the analysis of viruses, virus-like particles, vaccines, heavily glycosylated proteins, and gene therapy vectors.
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Affiliation(s)
- Lohra M Miller
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington 47401, Indiana
| | - Martin F Jarrold
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington 47401, Indiana
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13
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Barnes LF, Draper BE, Kurian J, Chen YT, Shapkina T, Powers TW, Jarrold MF. Analysis of AAV-Extracted DNA by Charge Detection Mass Spectrometry Reveals Genome Truncations. Anal Chem 2023; 95:4310-4316. [PMID: 36880264 DOI: 10.1021/acs.analchem.2c04234] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Adeno-associated virus (AAV) is a widely used gene therapy vector. The intact packaged genome is a critical quality attribute and necessary for an effective therapeutic. In this work, charge detection mass spectrometry (CDMS) was used to measure the molecular weight (MW) distribution for the genome of interest (GOI) extracted from recombinant AAV (rAAV) vectors. The measured MWs were compared to sequence masses for a range of rAAV vectors with different GOIs, serotypes, and production methods (Sf9 and HEK293 cell lines). In most cases, the measured MWs were slightly larger than the sequence masses, a result attributed to counterions. However, in a few cases, the measured MWs were significantly smaller than the sequence masses. In these cases, genome truncation is the only reasonable explanation for the discrepancy. These results suggest that direct analysis of the extracted GOI by CDMS provides a rapid and powerful tool to evaluate genome integrity in gene therapy products.
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Affiliation(s)
- Lauren F Barnes
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Benjamin E Draper
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Justin Kurian
- Analytical Research and Development, Pfizer Inc., 875 Chesterfield Pkwy. West, Chesterfield, Missouri 63017, United States
| | - Yu-Ting Chen
- Analytical Research and Development, Pfizer Inc., 875 Chesterfield Pkwy. West, Chesterfield, Missouri 63017, United States
| | - Tatiana Shapkina
- Analytical Research and Development, Pfizer Inc., 875 Chesterfield Pkwy. West, Chesterfield, Missouri 63017, United States
| | - Thomas W Powers
- Analytical Research and Development, Pfizer Inc., 875 Chesterfield Pkwy. West, Chesterfield, Missouri 63017, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
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14
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Du S, Jia H, Xu W, Zhai Y. Field-Gradient-Focusing Ion Guide for Enhanced Transfer Efficiency of Low-Mass Ions. Anal Chem 2023; 95:2079-2086. [PMID: 36632644 DOI: 10.1021/acs.analchem.2c05014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Efficient transmission of low-mass ions in a rough vacuum pressure region has always been a challenging issue in mass spectrometry (MS). In this study, a novel ion guide, namely, field-gradient-focusing ion guide (FGF-IG), was proposed to improve the transfer efficiency of ions, especially low-mass ions in a rough vacuum region. The FGF-IG has 12 electrodes whose surfaces gradually narrowed and tilted inward, and its electric field gradually varies from dodecapole (or multipole) to quadrupole along the ion transfer route. The field radius was gradually decreased from 6 to 2 mm in the multipole region (65 mm in length) and finally remained unchanged as 2 mm in the quadrupole region (20 mm in length). By integrating into a miniature mass spectrometer (mini-MS) with a continuous atmospheric pressure interface, this ion guide was optimized in terms of inlet capillary position, radio frequency amplitude, and direct current voltage applied on it. Results showed that a reduced low-mass discrimination effect and improved efficiency of simultaneously transferring mid and low m/z ions were achieved for FGF-IG compared with a conventional ion funnel. Under optimized conditions, a limit of detection of 1 ng/mL was obtained for both reserpine (m/z 609) and arginine (m/z 175) ions by integrating FGF-IG into the mini-MS. The sensitivity of smaller arginine ions using FGF-IG was enhanced by ∼10 times than that obtained using the conventional ion funnel (10 ng/mL) in comparative experiments. The idea of smooth transfer from dodecapole to quadrupole fields could be extended to other multipole fields, as well as in lab-scale MS instruments.
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Affiliation(s)
- Shiyu Du
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Heyuan Jia
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Wei Xu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
- Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, China
| | - Yanbing Zhai
- Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, China
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
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15
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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: 13] [Impact Index Per Article: 6.5] [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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16
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Brown BA, Guda PR, Zeng X, Anthony A, Couse A, Barnes LF, Sharon EM, Trinidad JC, Sen CK, Jarrold MF, Ghatak S, Clemmer DE. Analysis of Keratinocytic Exosomes from Diabetic and Nondiabetic Mice by Charge Detection Mass Spectrometry. Anal Chem 2022; 94:8909-8918. [PMID: 35699514 PMCID: PMC9450994 DOI: 10.1021/acs.analchem.2c00453] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Unresolved inflammation compromises diabetic wound healing. Recently, we reported that inadequate RNA packaging in murine wound-edge keratinocyte-originated exosomes (Exoκ) leads to persistent inflammation [Zhou, X. ACS Nano 2020, 14(10), 12732-12748]. Herein, we use charge detection mass spectrometry (CDMS) to analyze intact Exoκ isolated from a 5 day old wound-edge tissue of diabetic mice and a heterozygous nondiabetic littermate control group. In CDMS, the charge (z) and mass-to-charge ratio (m/z) of individual exosome particles are measured simultaneously, enabling the direct analysis of masses in the 1-200 MDa range anticipated for exosomes. These measurements reveal a broad mass range for Exoκ from ∼10 to >100 MDa. The m and z values for these exosomes appear to fall into families (subpopulations); a statistical modeling analysis partially resolves ∼10-20 Exoκ subpopulations. Complementary proteomics, immunofluorescence, and electron microscopy studies support the CDMS results that Exoκ from diabetic and nondiabetic mice vary substantially. Subpopulations having high z (>650) and high m (>44 MDa) are more abundant in nondiabetic animals. We propose that these high m and z particles may arise from differences in cargo packaging. The veracity of this idea is discussed in light of other recent CDMS results involving genome packaging in vaccines, as well as exosome imaging experiments. Characterization of intact exosome particles based on the physical properties of m and z provides a new means of investigating wound healing and suggests that CDMS may be useful for other pathologies.
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Affiliation(s)
- Brooke A Brown
- Department of Chemistry, Indiana University, Bloomington, Indiana 47505, United States
| | - Poornachander R Guda
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Xuyao Zeng
- Department of Chemistry, Indiana University, Bloomington, Indiana 47505, United States
| | - Adam Anthony
- Department of Chemistry, Indiana University, Bloomington, Indiana 47505, United States
| | - Andrew Couse
- Department of Chemistry, Indiana University, Bloomington, Indiana 47505, United States
| | - Lauren F Barnes
- Department of Chemistry, Indiana University, Bloomington, Indiana 47505, United States
| | - Edie M Sharon
- Department of Chemistry, Indiana University, Bloomington, Indiana 47505, United States
| | - Jonathan C Trinidad
- Department of Chemistry, Indiana University, Bloomington, Indiana 47505, United States
| | - Chandan K Sen
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Martin F Jarrold
- Department of Chemistry, Indiana University, Bloomington, Indiana 47505, United States
| | - Subhadip Ghatak
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47505, United States
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17
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Woodbury BM, Motwani T, Leroux MN, Barnes LF, Lyktey NA, Banerjee S, Dedeo CL, Jarrold MF, Teschke CM. Tryptophan Residues Are Critical for Portal Protein Assembly and Incorporation in Bacteriophage P22. Viruses 2022; 14:1400. [PMID: 35891382 PMCID: PMC9320234 DOI: 10.3390/v14071400] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/13/2022] [Accepted: 06/23/2022] [Indexed: 11/16/2022] Open
Abstract
The oligomerization and incorporation of the bacteriophage P22 portal protein complex into procapsids (PCs) depends upon an interaction with scaffolding protein, but the region of the portal protein that interacts with scaffolding protein has not been defined. In herpes simplex virus 1 (HSV-1), conserved tryptophan residues located in the wing domain are required for portal-scaffolding protein interactions. In this study, tryptophan residues (W) present at positions 41, 44, 207 and 211 within the wing domain of the bacteriophage P22 portal protein were mutated to both conserved and non-conserved amino acids. Substitutions at each of these positions were shown to impair portal function in vivo, resulting in a lethal phenotype by complementation. The alanine substitutions caused the most severe defects and were thus further characterized. An analysis of infected cell lysates for the W to A mutants revealed that all the portal protein variants except W211A, which has a temperature-sensitive incorporation defect, were successfully recruited into procapsids. By charge detection mass spectrometry, all W to A mutant portal proteins were shown to form stable dodecameric rings except the variant W41A, which dissociated readily to monomers. Together, these results suggest that for P22 conserved tryptophan, residues in the wing domain of the portal protein play key roles in portal protein oligomerization and incorporation into procapsids, ultimately affecting the functionality of the portal protein at specific stages of virus assembly.
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Affiliation(s)
- Brianna M. Woodbury
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (B.M.W.); (T.M.); (M.N.L.); (S.B.); (C.L.D.)
| | - Tina Motwani
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (B.M.W.); (T.M.); (M.N.L.); (S.B.); (C.L.D.)
| | - Makayla N. Leroux
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (B.M.W.); (T.M.); (M.N.L.); (S.B.); (C.L.D.)
| | - Lauren F. Barnes
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA; (L.F.B.); (N.A.L.); (M.F.J.)
| | - Nicholas A. Lyktey
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA; (L.F.B.); (N.A.L.); (M.F.J.)
| | - Sanchari Banerjee
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (B.M.W.); (T.M.); (M.N.L.); (S.B.); (C.L.D.)
| | - Corynne L. Dedeo
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (B.M.W.); (T.M.); (M.N.L.); (S.B.); (C.L.D.)
| | - Martin F. Jarrold
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA; (L.F.B.); (N.A.L.); (M.F.J.)
| | - Carolyn M. Teschke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (B.M.W.); (T.M.); (M.N.L.); (S.B.); (C.L.D.)
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
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18
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Abstract
Charge detection mass spectrometry (CDMS) is a single-particle technique where the masses of individual ions are determined from simultaneous measurement of their mass-to-charge ratio (m/z) and charge. Masses are determined for thousands of individual ions, and then the results are binned to give a mass spectrum. Using this approach, accurate mass distributions can be measured for heterogeneous and high-molecular-weight samples that are usually not amenable to analysis by conventional mass spectrometry. Recent applications include heavily glycosylated proteins, protein complexes, protein aggregates such as amyloid fibers, infectious viruses, gene therapies, vaccines, and vesicles such as exosomes.
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Affiliation(s)
- Martin F Jarrold
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47404, United States
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19
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Starr CA, Barnes LF, Jarrold MF, Zlotnick A. Hysteresis in Hepatitis B Virus (HBV) Requires Assembly of Near-Perfect Capsids. Biochemistry 2022; 61:505-513. [PMID: 35258283 PMCID: PMC9443786 DOI: 10.1021/acs.biochem.1c00810] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The hepatitis B virus (HBV) must release its contents to initiate infection, making capsid disassembly critical to the viral life cycle. Capsid assembly proceeds through a cascade of weak interactions between copies of capsid protein (Cp) to yield uniform particles. However, there is a hysteresis to capsid dissociation that allows capsids to persist under conditions where they could not assemble. In this study, we have sought to define the basis of hysteresis by examining urea-induced dissociation of in vitro-assembled HBV capsids. In general, capsid samples show a mixture of two pools, differentiated by stability. Labile capsid dissociation corresponds to an ∼5 μM pseudocritical concentration of assembly (pcc), the same as that observed in assembly reactions. Dissociation of the stable pool corresponds to a subfemtomolar pcc, indicative of hysteresis. The fraction of stable capsids in an assembly reaction increases with the integrity of the Cp preparation and when association is performed at a higher ionic strength, which modifies the Cp conformation. Labile complexes are more prevalent when assembly conditions yield many kinetically trapped (incomplete and overgrown) products. Cp isolated from stable capsids reassembles into a mixture of stable and labile capsids. These results suggest that hysteresis arises from an ideal capsid lattice, even when some of the substituents in that lattice have defects. Consistent with structural studies that show a subtle difference between Cp dimers and Cp in capsid, we propose that hysteresis arises when HBV capsids undergo a lattice-dependent structural transition.
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Affiliation(s)
- Caleb A. Starr
- – Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405
| | - Lauren F. Barnes
- – Chemistry Department, Indiana University, Bloomington, IN 47405
| | | | - Adam Zlotnick
- – Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405
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20
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Barnes LF, Draper BE, Jarrold MF. Analysis of Recombinant Adenovirus Vectors by Ion Trap Charge Detection Mass Spectrometry: Accurate Molecular Weight Measurements beyond 150 MDa. Anal Chem 2022; 94:1543-1551. [PMID: 35023731 DOI: 10.1021/acs.analchem.1c02439] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adenovirus is one of the largest nonenveloped, double-stranded DNA viruses. It is widely used as a gene therapy vector and has recently received a lot of attention as a novel vaccine platform for SARS-CoV-2. Human adenovirus 5 (HAdV5) contains over 2500 protein molecules and has a 36 kbp genome. Adenovirus is well beyond the range of conventional mass spectrometry, and it was unclear how well such a large complex could be desolvated. Here, we report molecular weight (MW) distributions measured for HAdV5 and for 11 recombinant AdV vectors with genomes of varying lengths. The MW distributions were recorded using ion trap charge detection mass spectrometry (CDMS), a single-particle technique where m/z and charge are measured for individual ions. The results show that ions as large as 150 MDa can be effectively desolvated and accurate MW distributions obtained. The MW distribution for HAdV5 contains a narrow peak at 156.1 MDa, assigned to the infectious virus. A smaller peak at 129.6 MDa is attributed to incomplete particles that have not packaged a genome. The ions in the 129.6 MDa peak have a much lower average charge than those in the peak at 156.1 MDa. This is attributed to the empty particles missing some or all of the fibers that decorate the surface of the virion. The MW measured for the mature virus (156.1 MDa) is much larger than that predicted from sequence masses and copy numbers of the constituents (142.5 MDa). Measurements performed for recombinant AdV as a function of genome length show that for every 1 MDa increase in the genome MW, the MW of the mature virus increases by around 2.3 MDa. The additional 1.3 MDa is attributed to core proteins that are copackaged with the DNA. This observation suggests that the discrepancy between the measured and expected MWs for mature HAdV5 is due to an underestimate in the copy numbers of the core proteins.
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Affiliation(s)
- Lauren F Barnes
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Benjamin E Draper
- Megadalton Solutions, Inc., 3750 E Bluebird Lane, Bloomington, Indiana 47401, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
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21
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Barnes LF, Draper BE, Chen YT, Powers TW, Jarrold MF. Quantitative analysis of genome packaging in recombinant AAV vectors by charge detection mass spectrometry. Mol Ther Methods Clin Dev 2021; 23:87-97. [PMID: 34631929 PMCID: PMC8476707 DOI: 10.1016/j.omtm.2021.08.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/16/2021] [Indexed: 12/13/2022]
Abstract
Recombinant adeno-associated virus (rAAV) has emerged as an important gene therapy vector with many clinical trials currently in progress. Analytical characterization and quantitation of particle content remain challenges in both the development and production of rAAV vectors. In this study, charge detection mass spectrometry (CDMS) and gel electrophoresis are used to characterize the DNA content of recombinant AAV8 (rAAV8) vectors with a wide range of target genome sizes. We show that the differences between the masses of empty particles and particles with the genome of interest (GOI) are correlated with the expected genome mass. A small systematic deviation (around 2%) is attributed to the packaging of counterions along with the DNA. In addition to the GOI, a broad distribution of heterogeneous DNA is packaged. The distribution peaks are close to the packaging capacity of the rAAV8 vectors. There is also evidence for the co-packaging of small DNA fragments along with the GOI. Finally, we present evidence that incubation at an elevated temperature can reduce the heterogeneity of the packaged DNA. Taken together, these results show that CDMS is a viable tool for characterization of the packaged genome.
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Affiliation(s)
- Lauren F Barnes
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Benjamin E Draper
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Yu-Ting Chen
- Pfizer, Inc., BioTherapeutics Pharmaceutical Sciences, Analytical R&D, 875 Chesterfield Parkway West, Chesterfield, MO 63017, USA
| | - Thomas W Powers
- Pfizer, Inc., BioTherapeutics Pharmaceutical Sciences, Analytical R&D, 875 Chesterfield Parkway West, Chesterfield, MO 63017, USA
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA
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22
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Mullins EK, Powers TW, Zobel J, Clawson KM, Barnes LF, Draper BE, Zou Q, Binder JJ, Dai S, Zhang K, Friese O, Runnels HA, Jarrold MF, Thompson LC. Characterization of Recombinant Chimpanzee Adenovirus C68 Low and High-Density Particles: Impact on Determination of Viral Particle Titer. Front Bioeng Biotechnol 2021; 9:753480. [PMID: 34805110 PMCID: PMC8599148 DOI: 10.3389/fbioe.2021.753480] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/20/2021] [Indexed: 12/03/2022] Open
Abstract
We observed differential infectivity and product yield between two recombinant chimpanzee adenovirus C68 constructs whose primary difference was genome length. To determine a possible reason for this outcome, we characterized the proportion and composition of the empty and packaged capsids. Both analytical ultracentrifugation (AUC) and differential centrifugation sedimentation (DCS, a rapid and quantitative method for measuring adenoviral packaging variants) were employed for an initial assessment of genome packaging and showed multiple species whose abundance deviated between the virus builds but not manufacturing campaigns. Identity of the packaging variants was confirmed by charge detection mass spectrometry (CDMS), the first known application of this technique to analyze adenovirus. The empty and packaged capsid populations were separated via preparative ultracentrifugation and then combined into a series of mixtures. These mixtures showed the oft-utilized denaturing A260 adenoviral particle titer method will underestimate the actual particle titer by as much as three-fold depending on the empty/full ratio. In contrast, liquid chromatography with fluorescence detection proves to be a superior viral particle titer methodology.
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Affiliation(s)
- Elise K Mullins
- Analytical Research and Development, Biotherapeutic Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO, United States
| | - Thomas W Powers
- Analytical Research and Development, Biotherapeutic Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO, United States
| | - Jim Zobel
- Analytical Research and Development, Biotherapeutic Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO, United States
| | - Kory M Clawson
- Analytical Research and Development, Biotherapeutic Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO, United States
| | - Lauren F Barnes
- Chemistry Department, Indiana University, Bloomington, IN, United States
| | | | - Qin Zou
- Analytical Research and Development, Biotherapeutic Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO, United States
| | - Joseph J Binder
- Cancer Vaccines and Immunotherapies, Pfizer Inc., San Diego, CA, United States
| | - Stanley Dai
- Nektar Therapeutics, San Francisco, CA, United States
| | - Kun Zhang
- Analytical Research and Development, Biotherapeutic Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO, United States
| | - Olga Friese
- Analytical Research and Development, Biotherapeutic Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO, United States
| | - Herbert A Runnels
- Analytical Research and Development, Biotherapeutic Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, Bloomington, IN, United States
| | - Lawrence C Thompson
- Analytical Research and Development, Biotherapeutic Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO, United States
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23
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Core Protein-Directed Antivirals and Importin β Can Synergistically Disrupt HBV Capsids. J Virol 2021; 96:e0139521. [PMID: 34705562 DOI: 10.1128/jvi.01395-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viral structural proteins can have multiple activities. Antivirals that target structural proteins have potential to exhibit multiple antiviral mechanisms. Hepatitis B Virus (HBV) core protein (Cp) is involved in most stages of the viral lifecycle: it assembles into capsids, packages viral RNA, is a metabolic compartment for reverse transcription, interacts with nuclear trafficking machinery, and disassembles to release the viral genome into the nucleus. During nuclear localization, HBV capsids bind to host importins (e.g. Impβ) via Cp's C-terminal domain (CTD); the CTD is localized to the interior of the capsid and is transiently exposed on the exterior. We used HAP12 as a representative Cp Allosteric Modulators (CpAMs), a class of antivirals that inappropriately stimulates and misdirects HBV assembly and deforms capsids. CpAM impact on other aspects of the HBV lifecycle is poorly understood. We investigated how HAP12 influenced the interactions between empty or RNA-filled capsids with Impβ and trypsin in vitro. We showed that HAP12 can modulate CTD accessibility and capsid stability, depending on the saturation of HAP12-binding sites. We demonstrated that Impβ synergistically contributes to capsid disruption at high levels of HAP12 saturation, using electron microscopy to visualize disruption and rearrangement of Cp dimers into aberrant complexes. However, RNA-filled capsids resisted the destabilizing effects of HAP12 and Impβ. In summary, we show host protein-induced catalysis of capsid disruption, an unexpected additional mechanism of action for CpAMs. Potentially, untimely capsid disassembly can hamper the HBV lifecycle and also cause the virus to become vulnerable to host innate immune responses. IMPORTANCE The HBV core, an icosahedral complex of 120 copies of the homodimeric core (capsid) protein with or without packaged nucleic acid, is transported to the host nucleus by its interaction with host importin proteins. Importin-core interaction requires the core protein C-terminal domain, which is inside the capsid, to "flip" to the capsid exterior. Core-protein directed drugs that affect capsid assembly and stability have been developed recently. We show that these molecules can, synergistically with importins, disrupt capsids. This mechanism of action, synergism with host protein, has potential to disrupt the virus lifecycle and activate the innate immune system.
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Miller LM, Bond KM, Draper BE, Jarrold MF. Characterization of Classical Vaccines by Charge Detection Mass Spectrometry. Anal Chem 2021; 93:11965-11972. [PMID: 34435777 DOI: 10.1021/acs.analchem.1c01893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vaccines induce immunity by presenting disease antigens through several platforms ranging from individual protein subunits to whole viruses. Due to the large difference in antigen size, the analytical techniques employed for vaccine characterization are often platform-specific. A single, robust analytical technique capable of widespread, cross-platform use would be of great benefit and allow for comparisons across manufacturing processes. One method that spans the antigen mass range is charge detection mass spectrometry (CDMS). CDMS is a single-ion approach where the mass-to-charge ratio (m/z) and charge are measured simultaneously, allowing accurate mass distributions to be measured for heterogeneous analytes over a broad size range. In this work, CDMS was used to characterize the antigens from three classical multivalent vaccines, inactivated poliomyelitis vaccine (IPOL), RotaTeq, and Gardasil-9, directly from commercial samples. For each vaccine, the antigen purity was inspected, and in the whole virus vaccines, empty virus particles were detected. For IPOL, information on the extent of formaldehyde cross-linking was obtained. RotaTeq shows a narrow peak at 61.06 MDa. This is at a slightly lower mass than expected for the double-layer particle, suggesting that around 10 pentonal trimers are missing. For Gardasil-9, buffer exchange of the vaccine resulted in very broad mass distributions. However, removal of the virus-like particles from the aluminum adjuvant using a displacement reaction generated a spectrum with narrow peaks.
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Affiliation(s)
- Lohra M Miller
- Chemistry Department, Indiana University, 800 E Kirkwood Ave., Bloomington, Indiana 47405, United States
| | - Kevin M Bond
- Chemistry Department, Indiana University, 800 E Kirkwood Ave., Bloomington, Indiana 47405, United States
| | - Benjamin E Draper
- Megadalton Solutions, 3750 E Bluebird Lane, Bloomington, Indiana 47401, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E Kirkwood Ave., Bloomington, Indiana 47405, United States
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25
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Grajewski M, Hermann M, Oleschuk R, Verpoorte E, Salentijn G. Leveraging 3D printing to enhance mass spectrometry: A review. Anal Chim Acta 2021; 1166:338332. [DOI: 10.1016/j.aca.2021.338332] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/12/2021] [Accepted: 02/15/2021] [Indexed: 12/11/2022]
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26
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Miller LM, Barnes LF, Raab SA, Draper BE, El-Baba TJ, Lutomski CA, Robinson CV, Clemmer DE, Jarrold MF. Heterogeneity of Glycan Processing on Trimeric SARS-CoV-2 Spike Protein Revealed by Charge Detection Mass Spectrometry. J Am Chem Soc 2021; 143:3959-3966. [PMID: 33657316 PMCID: PMC8543487 DOI: 10.1021/jacs.1c00353] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The heterogeneity associated with glycosylation of the 66 N-glycan sites on the protein trimer making up the spike (S) region of the SARS-CoV-2 virus has been assessed by charge detection mass spectrometry (CDMS). CDMS allows simultaneous measurement of the mass-to-charge ratio and charge of individual ions, so that mass distributions can be determined for highly heterogeneous proteins such as the heavily glycosylated S protein trimer. The CDMS results are compared to recent glycoproteomics studies of the structure and abundance of glycans at specific sites. Interestingly, average glycan masses determined by "top-down" CDMS measurements are 35-47% larger than those obtained from the "bottom-up" glycoproteomics studies, suggesting that the glycoproteomic measurements underestimated the abundances of larger, more-complex glycans. Moreover, the distribution of glycan masses determined by CDMS is much broader than the distribution expected from the glycoproteomics studies, assuming that glycan processing on each trimer is not correlated. The breadth of the glycan mass distribution therefore indicates heterogeneity in the extent of glycan processing of the S protein trimers, with some trimers being much more heavily processed than others. This heterogeneity may have evolved as a way of further confounding the host's immune system.
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Affiliation(s)
- Lohra M Miller
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington Indiana 47405, United States
| | - Lauren F Barnes
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington Indiana 47405, United States
| | - Shannon A Raab
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington Indiana 47405, United States
| | - Benjamin E Draper
- Megadalton Solutions, 3520 E Bluebird Ln, Bloomington Indiana 47401, United States
| | - Tarick J El-Baba
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OXI 3QZ, U.K
| | - Corinne A Lutomski
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OXI 3QZ, U.K
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OXI 3QZ, U.K
| | - David E Clemmer
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington Indiana 47405, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington Indiana 47405, United States
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27
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Harper CC, Brauer DD, Francis MB, Williams ER. Direct observation of ion emission from charged aqueous nanodrops: effects on gaseous macromolecular charging. Chem Sci 2021; 12:5185-5195. [PMID: 34168773 PMCID: PMC8179642 DOI: 10.1039/d0sc05707j] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Mechanistic information about how gaseous ions are formed from charged droplets has been difficult to establish because direct observation of nanodrops in a size range relevant to gaseous macromolecular ion formation by optical or traditional mass spectrometry methods is challenging owing to their small size and heterogeneity. Here, the mass and charge of individual aqueous nanodrops between 1-10 MDa (15-32 nm diameter) with ∼50-300 charges are dynamically monitored for 1 s using charge detection mass spectrometry. Discrete losses of minimally solvated singly charged ions occur, marking the first direct observation of ion emission from aqueous nanodrops in late stages of droplet evaporation relevant to macromolecular ion formation in native mass spectrometry. Nanodrop charge depends on the identity of constituent ions, with pure water nanodrops charged slightly above the Rayleigh limit and aqueous solutions containing alkali metal ions charged progressively below the Rayleigh limit with increasing cation size. MS2 capsid ions (∼3.5 MDa; ∼27 nm diameter) are more highly charged from aqueous ammonium acetate than from its biochemically preferred, 100 mM NaCl/10 mM Na phosphate solution, consistent with ion emission reducing the nanodrop and resulting capsid charge. The extent of charging indicates that the capsid partially collapses inside the nanodrops prior to the charging and formation of the dehydrated gaseous ions. These results demonstrate that ion emission can affect macromolecular charging and that conformational changes to macromolecular structure can occur in nanodrops prior to the formation of naked gaseous ions.
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Affiliation(s)
- Conner C Harper
- Department of Chemistry, University of California Berkeley California 94720-1460 USA
| | - Daniel D Brauer
- Department of Chemistry, University of California Berkeley California 94720-1460 USA
| | - Matthew B Francis
- Department of Chemistry, University of California Berkeley California 94720-1460 USA
| | - Evan R Williams
- Department of Chemistry, University of California Berkeley California 94720-1460 USA
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28
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Asymmetrizing an icosahedral virus capsid by hierarchical assembly of subunits with designed asymmetry. Nat Commun 2021; 12:589. [PMID: 33500404 PMCID: PMC7838286 DOI: 10.1038/s41467-020-20862-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 12/07/2020] [Indexed: 11/08/2022] Open
Abstract
Symmetrical protein complexes are ubiquitous in biology. Many have been re-engineered for chemical and medical applications. Viral capsids and their assembly are frequent platforms for these investigations. A means to create asymmetric capsids may expand applications. Here, starting with homodimeric Hepatitis B Virus capsid protein, we develop a heterodimer, design a hierarchical assembly pathway, and produce asymmetric capsids. In the heterodimer, the two halves have different growth potentials and assemble into hexamers. These preformed hexamers can nucleate co-assembly with other dimers, leading to Janus-like capsids with a small discrete hexamer patch. We can remove the patch specifically and observe asymmetric holey capsids by cryo-EM reconstruction. The resulting hole in the surface can be refilled with fluorescently labeled dimers to regenerate an intact capsid. In this study, we show how an asymmetric subunit can be used to generate an asymmetric particle, creating the potential for a capsid with different surface chemistries.
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29
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Ahmed E, Xiao D, Kabir KMM, Fletcher J, Donald WA. Ambient Pressure Ion Funnel: Concepts, Simulations, and Analytical Performance. Anal Chem 2020; 92:15811-15817. [DOI: 10.1021/acs.analchem.0c02938] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ezaz Ahmed
- School of Chemistry, University of New South Wales, Sydney, NSW 2052 Australia
| | - Dan Xiao
- School of Electrical Engineering and Telecommunications, University of New South Wales, Sydney, NSW 2052 Australia
| | - K. M. Mohibul Kabir
- School of Chemistry, University of New South Wales, Sydney, NSW 2052 Australia
| | - John Fletcher
- School of Electrical Engineering and Telecommunications, University of New South Wales, Sydney, NSW 2052 Australia
| | - William A. Donald
- School of Chemistry, University of New South Wales, Sydney, NSW 2052 Australia
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30
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Todd AR, Barnes LF, Young K, Zlotnick A, Jarrold MF. Higher Resolution Charge Detection Mass Spectrometry. Anal Chem 2020; 92:11357-11364. [PMID: 32806905 PMCID: PMC8587657 DOI: 10.1021/acs.analchem.0c02133] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Charge detection mass spectrometry is a single particle technique where the masses of individual ions are determined from simultaneous measurements of each ion's m/z ratio and charge. The ions pass through a conducting cylinder, and the charge induced on the cylinder is detected. The cylinder is usually placed inside an electrostatic linear ion trap so that the ions oscillate back and forth through the cylinder. The resulting time domain signal is analyzed by fast Fourier transformation; the oscillation frequency yields the m/z, and the charge is determined from the magnitudes. The mass resolving power depends on the uncertainties in both quantities. In previous work, the mass resolving power was modest, around 30-40. In this work we report around an order of magnitude improvement. The improvement was achieved by coupling high-accuracy charge measurements (obtained with dynamic calibration) with higher resolution m/z measurements. The performance was benchmarked by monitoring the assembly of the hepatitis B virus (HBV) capsid. The HBV capsid assembly reaction can result in a heterogeneous mixture of intermediates extending from the capsid protein dimer to the icosahedral T = 4 capsid with 120 dimers. Intermediates of all possible sizes were resolved, as well as some overgrown species. Despite the improved mass resolving power, the measured peak widths are still dominated by instrumental resolution. Heterogeneity makes only a small contribution. Resonances were observed in some of the m/z spectra. They result from ions with different masses and charges having similar m/z values. Analogous resonances are expected whenever the sample is a heterogeneous mixture assembled from a common building block.
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31
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Antoine R. Weighing synthetic polymers of ultra-high molar mass and polymeric nanomaterials: What can we learn from charge detection mass spectrometry? RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34 Suppl 2:e8539. [PMID: 31353622 DOI: 10.1002/rcm.8539] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/19/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
Advances in soft ionization techniques for mass spectrometry (MS) of polymeric materials make it possible to determine the masses of intact molecular ions exceeding megadaltons. Interfacing MS with separation and fragmentation methods has additionally led to impressive advances in the ability to structurally characterize polymers. Even if the gap to the megadalton range has been bridged by MS for polymers standards, the MS-based analysis for more complex polymeric materials is still challenging. Charge detection mass spectrometry (CDMS) is a single-molecule method where the mass and the charge of each ion are directly determined from individual measurements. The entire molecular mass distribution of a polymer sample can be thus accurately measured. Described in this perspective paper is how molecular weight distribution as well as charge distribution can provide new insights into the structural and compositional studies of synthetic polymers and polymeric nanomaterials in the megadalton to gigadalton range of molecular weight. The recent multidimensional CDMS studies involving couplings with separation and dissociation techniques will be presented. And, finally, an outlook for the future avenues of the CDMS technique in the field of synthetic polymers of ultra-high molar mass and polymeric nanomaterials will be provided.
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Affiliation(s)
- Rodolphe Antoine
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR 5306, F-69622, Lyon, France
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32
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Todd AR, Jarrold MF. Dynamic Calibration Enables High-Accuracy Charge Measurements on Individual Ions for Charge Detection Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1241-1248. [PMID: 32353231 DOI: 10.1021/jasms.0c00081] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Charge detection mass spectrometry (CDMS) depends on the measurement of the charge induced on a cylinder by individual ions by means of a charge-sensitive amplifier. For high-accuracy charge measurements, the detection cylinder is embedded in an electrostatic linear ion trap (ELIT), and the ions oscillate back and forth through the cylinder so that multiple measurements are made. To assign the charge state with a low error rate, the charge of each ion must be determined with an uncertainty (root-mean-square deviation) of around 0.2 elementary charges. We show here that high-accuracy charge measurements can be achieved for large ions by dynamic calibration of the charge measurement using an internal standard. The internal standard is generated by irradiating the detection cylinder, by means of a small antenna, with a radiofrequency signal. Using this approach, we have obtained a relative charge uncertainty of around 5 × 10-4, allowing charge-state resolution to be achieved for single ions with up to 500 charges. In another application of this approach, the detection cylinder is irradiated with a signal that counteracts the transients generated when the potentials on the ELIT end-caps are switched to trapping mode. Using this approach, the dead time after switching (during which the signal cannot be analyzed) has been reduced by more than an order of magnitude. With charge-state resolution for ions with up to 500 charges, we were able to calibrate the charges precisely. The results show that the response of the charge-sensitive amplifier with dynamic calibration is linear to within a small fraction of an elementary charge.
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Affiliation(s)
- Aaron R Todd
- Chemistry Department, Indiana University, Bloomington, Indiana 47405 United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, Bloomington, Indiana 47405 United States
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33
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Brown BA, Zeng X, Todd AR, Barnes LF, Winstone JMA, Trinidad JC, Novotny MV, Jarrold MF, Clemmer DE. Charge Detection Mass Spectrometry Measurements of Exosomes and other Extracellular Particles Enriched from Bovine Milk. Anal Chem 2020; 92:3285-3292. [PMID: 31989813 PMCID: PMC7236431 DOI: 10.1021/acs.analchem.9b05173] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The masses of particles in a bovine milk extracellular vesicle (EV) preparation enriched for exosomes were directly determined for the first time by charge detection mass spectrometry (CDMS). In CDMS, both the mass-to-charge ratio (m/z) and z are determined simultaneously for individual particles, enabling mass determinations for particles that are far beyond the mass limit (∼1.0 MDa) of conventional mass spectrometry (MS). Particle masses and charges span a wide range from m ∼ 2 to ∼90 MDa and z ∼ 50 to ∼1300 e (elementary charges) and are highly dependent upon the conditions used to extract and isolate the EVs. EV particles span a continuum of masses, reflecting the highly heterogeneous nature of these samples. However, evidence for unique populations of particles is obtained from correlation of the charges and masses. An analysis that uses a two-dimensional Gaussian model, provides evidence for six families of particles, four of which having masses in the range expected for exosomes. Complementary proteomics measurements and electron microscopy (EM) imaging are used to further characterize the EVs and confirm that these samples have been enriched in exosomes. The ability to characterize such extremely heterogeneous mixtures of large particles with rapid, sensitive, and high-resolution MS techniques is critical to ongoing analytical efforts to separate and purify exosomes and exosome subpopulations. Direct measurement of each particle's mass and charge is a new means of characterizing the physical and chemical properties of exosomes and other EVs.
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Affiliation(s)
- Brooke A Brown
- Department of Chemistry , Indiana University , Bloomington , Indiana 47505 , United States
| | - Xuyao Zeng
- Department of Chemistry , Indiana University , Bloomington , Indiana 47505 , United States
| | - Aaron R Todd
- Department of Chemistry , Indiana University , Bloomington , Indiana 47505 , United States
| | - Lauren F Barnes
- Department of Chemistry , Indiana University , Bloomington , Indiana 47505 , United States
| | - Jonathan M A Winstone
- Department of Chemistry , Indiana University , Bloomington , Indiana 47505 , United States
| | - Jonathan C Trinidad
- Department of Chemistry , Indiana University , Bloomington , Indiana 47505 , United States
| | - Milos V Novotny
- Department of Chemistry , Indiana University , Bloomington , Indiana 47505 , United States
| | - Martin F Jarrold
- Department of Chemistry , Indiana University , Bloomington , Indiana 47505 , United States
| | - David E Clemmer
- Department of Chemistry , Indiana University , Bloomington , Indiana 47505 , United States
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34
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Todd AR, Alexander AW, Jarrold MF. Implementation of a Charge-Sensitive Amplifier without a Feedback Resistor for Charge Detection Mass Spectrometry Reduces Noise and Enables Detection of Individual Ions Carrying a Single Charge. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:146-154. [PMID: 32881508 DOI: 10.1021/jasms.9b00010] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Charge detection mass spectrometry (CDMS) depends on the measurement of the charge induced on a cylinder by individual ions by means of a charge-sensitive amplifier. Electrical noise limits the accuracy of the charge measurement and the smallest charge that can be detected. Thermal noise in the feedback resistor is a major source of electrical noise. We describe the implementation of a charge-sensitive amplifier without a feedback resistor. The design has significantly reduced 1/f noise facilitating the detection of high m/z ions and substantially reducing the measurement time required to achieve almost perfect charge accuracy. With the new design we have been able to detect individual ions carrying a single charge. This is an important milestone in the development of CDMS.
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Affiliation(s)
- Aaron R Todd
- Chemistry Department, Indiana University, Bloomington, Indiana 47405, United States
| | - Andrew W Alexander
- Chemistry Department, Indiana University, Bloomington, Indiana 47405, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, Bloomington, Indiana 47405, United States
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35
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Botamanenko DY, Jarrold MF. Ion-Ion Interactions in Charge Detection Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2741-2749. [PMID: 31677069 PMCID: PMC7487123 DOI: 10.1007/s13361-019-02343-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/16/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
Charge detection mass spectrometry (CDMS) is a single-particle technique where the masses of individual ions are determined by simultaneously measuring their mass-to-charge ratio (m/z) and charge. Ions are usually trapped inside an electrostatic linear ion trap (ELIT) where they oscillate back and forth through a detection cylinder, generating a periodic signal that is analyzed by fast Fourier transforms. The oscillation frequency is related to the ion's m/z, and the magnitude is related to the ion's charge. In early work, multiple ion trapping events were discarded because there was a question about whether ion-ion interactions affected the results. Here, we report trajectory calculations performed to assess the influence of ion-ion interactions when multiple highly charged ions are simultaneously trapped in an ELIT. Ion-ion interactions cause trajectory and energy fluctuations that lead to variations in the oscillation frequencies that in turn degrade the precision and accuracy of the m/z measurements. The peak shapes acquire substantial high and low m/z tails, and the average m/z shifts to a higher value as the number of trapped ions increases. The effects of the ion-ion interactions are proportional to the product of the charges and the square root of the number of trapped ions and depend on the ions' m/z distribution. For the ELIT design examined here, ion-ion interactions limit the m/z resolving power to several hundred for a typical homogeneous ion population.
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Affiliation(s)
- Daniel Y Botamanenko
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405, USA
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405, USA.
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36
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Todd AR, Jarrold MF. Dramatic Improvement in Sensitivity with Pulsed Mode Charge Detection Mass Spectrometry. Anal Chem 2019; 91:14002-14008. [PMID: 31589418 PMCID: PMC6834878 DOI: 10.1021/acs.analchem.9b03586] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Charge detection mass spectrometry (CDMS) is emerging as a valuable tool to determine mass distributions for heterogeneous and high-mass samples. It is a single-particle technique where masses are determined for individual ions from simultaneous measurements of their mass-to-charge ratio (m/z) and charge. Ions are trapped in an electrostatic linear ion trap (ELIT) and oscillate back and forth through a detection cylinder. The trap is open and able to trap ions for a small fraction of the total measurement time so most of the ions (>99.8%) in a continuous ion beam are lost. Here, we implement an ion storage scheme where ions are accumulated and stored in a hexapole and then injected into the ELIT at the right time for them to be trapped. This pulsed mode of operation increases the sensitivity of CDMS by more than 2 orders of magnitude, which allows much lower titer samples to be analyzed. A limit of detection of 3.3 × 108 particles/mL was obtained for hepatitis B virus T = 4 capsids with a 1.3 μL sample. The hexapole where the ions are accumulated and stored is a significant distance from the ion trap so ions are dispersed in time by their m/z values as they travel between the hexapole and the ELIT. By varying the delay time between ion release and trapping, different windows of m/z values can be trapped.
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Affiliation(s)
- Aaron R. Todd
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Martin F. Jarrold
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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Dülfer J, Kadek A, Kopicki JD, Krichel B, Uetrecht C. Structural mass spectrometry goes viral. Adv Virus Res 2019; 105:189-238. [PMID: 31522705 DOI: 10.1016/bs.aivir.2019.07.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Over the last 20 years, mass spectrometry (MS), with its ability to analyze small sample amounts with high speed and sensitivity, has more and more entered the field of structural virology, aiming to investigate the structure and dynamics of viral proteins as close to their native environment as possible. The use of non-perturbing labels in hydrogen-deuterium exchange MS allows for the analysis of interactions between viral proteins and host cell factors as well as their dynamic responses to the environment. Cross-linking MS, on the other hand, can analyze interactions in viral protein complexes and identify virus-host interactions in cells. Native MS allows transferring viral proteins, complexes and capsids into the gas phase and has broken boundaries to overcome size limitations, so that now even the analysis of intact virions is possible. Different MS approaches not only inform about size, stability, interactions and dynamics of virus assemblies, but also bridge the gap to other biophysical techniques, providing valuable constraints for integrative structural modeling of viral complex assemblies that are often inaccessible by single technique approaches. In this review, recent advances are highlighted, clearly showing that structural MS approaches in virology are moving towards systems biology and ever more experiments are performed on cellular level.
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Affiliation(s)
- Jasmin Dülfer
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Alan Kadek
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany; European XFEL GmbH, Schenefeld, Germany
| | - Janine-Denise Kopicki
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany; European XFEL GmbH, Schenefeld, Germany.
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