Disassembly Intermediates of the Brome Mosaic Virus Identified by Charge Detection Mass Spectrometry

Dissecting the Heterogeneous Glycan Profiles of Recombinant Coronavirus Spike Proteins with Individual Ion Mass Spectrometry

Surface-embedded glycoproteins, such as the spike protein trimers of coronaviruses MERS, SARS-CoV, and SARS-CoV-2, play a key role in viral function and are the target antigen for many vaccines. However, their significant glycan heterogeneity poses an analytical challenge. Here, we utilized individual ion mass spectrometry (I2MS), a multiplexed charge detection measurement with similarities to charge detection mass spectrometry (CDMS), in which a commercially available Orbitrap analyzer is used to directly produce mass profiles of these heterogeneous coronavirus spike protein trimers under native-like conditions. Analysis by I2MS shows that glycosylation contributes to the molecular mass of each protein trimer more significantly than expected by bottom-up techniques, highlighting the importance of obtaining complementary intact mass information when characterizing glycosylation of such heterogeneous proteins. Enzymatic dissection to remove sialic acid or N-linked glycans demonstrates that I2MS can be used to better understand the glycan profile from a native viewpoint. Deglycosylation of N-glycans followed by I2MS analysis indicates that the SARS-CoV-2 spike protein trimer contains glycans that are more difficult to remove than its MERS and SARS-CoV counterparts, and these differences are correlated with solvent accessibility. I2MS technology enables characterization of protein mass and intact glycan profile and is orthogonal to traditional mass analysis methods such as size exclusion chromatography-multiangle light scattering (SEC-MALS) and field flow fractionation-multiangle light scattering (FFF-MALS). An added advantage of I2MS is low sample use, requiring 100-fold less than other methodologies. This work highlights how I2MS technology can enable efficient development of vaccines and therapeutics for pharmaceutical development.

pyCapsid: identifying dominant dynamics and quasi-rigid mechanical units in protein shells

SUMMARY

pyCapsid is a Python package developed to facilitate the characterization of the dynamics and quasi-rigid mechanical units of protein shells and other protein complexes. The package was developed in response to the rapid increase of high-resolution structures, particularly capsids of viruses, requiring multiscale biophysical analyses. Given a protein shell, pyCapsid generates the collective vibrations of its amino-acid residues, identifies quasi-rigid mechanical regions associated with the disassembly of the structure, and maps the results back to the input proteins for interpretation. pyCapsid summarizes the main results in a report that includes publication-quality figures.

AVAILABILITY AND IMPLEMENTATION

pyCapsid's source code is available under MIT License on GitHub. It is compatible with Python 3.8-3.10 and has been deployed in two leading Python package-management systems, PIP and Conda. Installation instructions and tutorials are available in the online documentation and in the pyCapsid's YouTube playlist. In addition, a cloud-based implementation of pyCapsid is available as a Google Colab notebook. pyCapsid Colab does not require installation and generates the same report and outputs as the installable version. Users can post issues regarding pyCapsid in the repository's issues section.

Fluorescence, Circular Dichroism and Mass Spectrometry as Tools to Study Virus Structure

Fluorescence and circular dichroism, as analytical spectroscopic techniques, and mass spectrometry, as an analytical tool to determine molecular mass, are important biophysical methods in structural virology. Although they do not provide atomic or near-atomic details as cryogenic electron microscopy, X-ray crystallography or nuclear magnetic resonance spectroscopy can, they do deliver important insights into virus particle composition, structure, conformational stability and dynamics, assembly and maturation and interactions with other viral and cellular biomolecules. They can also be used to investigate the molecular determinants of virus particle structure and properties and the changes induced in them by external factors. In this chapter, the physical foundations of these three techniques will be described, alongside examples demonstrating their contribution in understanding the structure and physicochemical properties of virus particles.

Charge detection mass spectrometry for the analysis of viruses and virus-like particles

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.

The diversity of protein-protein interaction interfaces within T=3 icosahedral viral capsids

Some non-enveloped virus capsids assemble from multiple copies of a single type of coat-protein (CP). The comparative energetics of the diverse CP-CP interfaces present in such capsids likely govern virus assembly-disassembly mechanisms. The T = 3 icosahedral capsids comprise 180 CP copies arranged about two-, three-, five- and six-fold axes of (quasi-)rotation symmetry. Structurally diverse CPs can assemble into T = 3 capsids. Specifically, the Leviviridae CPs are structurally distinct from the Bromoviridae, Tombusviridae and Tymoviridae CPs which fold into the classic “jelly-roll” fold. However, capsids from across the four families are known to disassemble into dimers. To understand whether the overall symmetry of the capsid or the structural details of the CP determine virus assembly-disassembly mechanisms, we analyze the different CP-CP interfaces that occur in the four virus families. Previous work studied protein homodimer interfaces using interface size (relative to the monomer) and hydrophobicity. Here, we analyze all CP-CP interfaces using these two parameters and find that the dimerization interface (present between two CPs congruent through a two-fold axis of rotation) has a larger relative size in the Leviviridae than in the other viruses. The relative sizes of the other Leviviridae interfaces and all the jelly-roll interfaces are similar. However, the dimerization interfaces across families have slightly higher hydrophobicity, potentially making them stronger than other interfaces. Finally, although the CP-monomers of the jelly-roll viruses are structurally similar, differences in their dimerization interfaces leads to varied dimer flexibility. Overall, differences in CP-structures may induce different modes of swelling and assembly-disassembly in the T = 3 viruses.

Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes

Progress in structural biology research has led to a high demand for powerful and yet complementary analytical tools for structural characterization of proteins and protein complexes. This demand has significantly increased interest in native mass spectrometry (nMS), particularly native top-down mass spectrometry (nTDMS) in the past decade. This review highlights recent advances in nTDMS for structural research of biological assemblies, with a particular focus on the extra multi-layers of information enabled by TDMS. We include a short introduction of sample preparation and ionization to nMS, tandem fragmentation techniques as well as mass analyzers and software/analysis pipelines used for nTDMS. We highlight unique structural information offered by nTDMS and examples of its broad range of applications in proteins, protein-ligand interactions (metal, cofactor/drug, DNA/RNA, and protein), therapeutic antibodies and antigen-antibody complexes, membrane proteins, macromolecular machineries (ribosome, nucleosome, proteosome, and viruses), to endogenous protein complexes. The challenges, potential, along with perspectives of nTDMS methods for the analysis of proteins and protein assemblies in recombinant and biological samples are discussed.

Native Mass Spectrometry: Recent Progress and Remaining Challenges

Native mass spectrometry (nMS) has emerged as an important tool in studying the structure and function of macromolecules and their complexes in the gas phase. In this review, we cover recent advances in nMS and related techniques including sample preparation, instrumentation, activation methods, and data analysis software. These advances have enabled nMS-based techniques to address a variety of challenging questions in structural biology. The second half of this review highlights recent applications of these technologies and surveys the classes of complexes that can be studied with nMS. Complementarity of nMS to existing structural biology techniques and current challenges in nMS are also addressed.

Applications of Charge Detection Mass Spectrometry in Molecular Biology and Biotechnology

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.

High Speed Mass Measurement of a Single Metal-Organic Framework Nanocrystal in a Paul Trap

Mass spectrometry (MS) has emerged as an excellent tool for the characterization of metal-organic frameworks (MOFs) based on the characteristic metal ions and organic ligands. Mass measurement of intact MOF nanocrystals, however, remains a challenge for MS technology. Here, we reported the development of a probe particles based charge detection-quadrupole ion trap mass spectrometry (probe CD-QIT MS) method, where charge detection and mass measurement of a single MOF nanocrystal were achieved under the assistance of probe particles of micrometer size. As a validation of the method, the masses of a series of polystyrene (PS) size standards from 493 nm to 1.6 μm were measured with 3 μm PS particles as probes, and the measured masses were found to match well with their certified masses. Then, charge detections and mass analysis of single ZIF-8 and GOx@ZIF-8 with a size around 600 nm were achieved successfully. The method presented here demonstrates simplicity, high speed, and accuracy. Notably, it allows quantitative measurement of the amount of immobilized GOx enzyme by using the mass difference between ZIF-8 and GOx@ZIF-8. In addition, based on the determined mass, the size analysis of these MOF particles with irregular shape was carried out and demonstrated to be complementary to transmission electron microscopy (TEM).

Analysis of Recombinant Adenovirus Vectors by Ion Trap Charge Detection Mass Spectrometry: Accurate Molecular Weight Measurements beyond 150 MDa

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.

The viral capsid as novel nanomaterials for drug delivery

The purpose of this review is to highlight recent scientific developments and provide an overview of virus self-assembly and viral particle dynamics. Viruses are organized supramolecular structures with distinct yet related features and functions. Plant viruses are extensively used in biotechnology, and virus-like particulate matter is generated by genetic modification. Both provide a material-based means for selective distribution and delivery of drug molecules. Through surface engineering of their capsids, virus-derived nanomaterials facilitate various potential applications for selective drug delivery. Viruses have significant implications in chemotherapy, gene transfer, vaccine production, immunotherapy and molecular imaging.

Characterization of Classical Vaccines by Charge Detection Mass Spectrometry

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.

Top-Down and Bottom-Up Proteomics Methods to Study RNA Virus Biology

RNA viruses cause a wide range of human diseases that are associated with high mortality and morbidity. In the past decades, the rise of genetic-based screening methods and high-throughput sequencing approaches allowed the uncovering of unique and elusive aspects of RNA virus replication and pathogenesis at an unprecedented scale. However, viruses often hijack critical host functions or trigger pathological dysfunctions, perturbing cellular proteostasis, macromolecular complex organization or stoichiometry, and post-translational modifications. Such effects require the monitoring of proteins and proteoforms both on a global scale and at the structural level. Mass spectrometry (MS) has recently emerged as an important component of the RNA virus biology toolbox, with its potential to shed light on critical aspects of virus-host perturbations and streamline the identification of antiviral targets. Moreover, multiple novel MS tools are available to study the structure of large protein complexes, providing detailed information on the exact stoichiometry of cellular and viral protein complexes and critical mechanistic insights into their functions. Here, we review top-down and bottom-up mass spectrometry-based approaches in RNA virus biology with a special focus on the most recent developments in characterizing host responses, and their translational implications to identify novel tractable antiviral targets.