Engineering topics
Publications and source records attributed to Shaw, Jared B..
Methods are described for using a combination of mass spectroscopic and proteomic approaches for identifying the specific pairing of heavy and light chains for an intact antibody, an antibody fragment, a mixture of intact antibodies, or a mixture of antibody fragments.
Pseudoenzymes have emerged as key regulatory elements in all kingdoms of life despite being catalytically nonactive. Yet many factors defining why one protein is active while its homologue is inactive remain uncertain. For pseudoenzyme–enzyme pairs, the similarity of both subunits can often hinder conventional characterization approaches. In plants, a pseudoenzyme, PDX1.2, positively regulates vitamin B 6 production by association with its active catalytic homologues such as PDX1.3 through an unknown assembly mechanism. Here we used an integrative experimental approach to learn that such pseudoenzyme–enzyme pair associations result in heterocomplexes of variable stoichiometry, which are unexpectedly tunable. We also present the atomic structure of the PDX1.2 pseudoenzyme as well as the population averaged PDX1.2–PDX1.3 pseudoenzyme–enzyme pair. Finally, we dissected hetero-dodecamers of each stoichiometry to understand the arrangement of monomers in the heterocomplexes and identified symmetry-imposed preferences in PDX1.2–PDX1.3 interactions. In this work, our results provide a new model of pseudoenzyme–enzyme interactions and their native heterogeneity.
Three clinically relevant ebolaviruses – Ebola (EBOV), Bundibugyo (BDBV), and Sudan (SUDV) viruses, are responsible for severe disease and occasional deadly outbreaks in Africa. The largest Ebola virus disease (EVD) epidemic to date in 2013-2016 in West Africa highlighted the urgent need for countermeasures, leading to the development and FDA approval of the Ebola virus vaccine rVSV-ZEBOV (Ervebo ® ) in 2020 and two monoclonal antibody (mAb)-based therapeutics (Inmazeb ® [atoltivimab, maftivimab, and odesivimab-ebgn] and Ebanga ® (ansuvimab-zykl) in 2020. The humoral response plays an indispensable role in ebolavirus immunity, based on studies of mAbs isolated from the antibody genes in peripheral blood circulating ebolavirus-specific human memory B cells. However, antibodies in the body are not secreted by circulating memory B cells in the blood but rather principally by plasma cells in the bone marrow. Little is known about the protective polyclonal antibody responses in convalescent plasma. Here we exploited both single-cell antibody gene sequencing and proteomic sequencing approaches to assess the composition of the ebolavirus glycoprotein (GP)-reactive antibody repertoire in the plasma of an EVD survivor. We first identified 1,512 GP-specific mAb variable gene sequences from single cells in the memory B cell compartment. Using mass spectrometric analysis of the corresponding GP-specific plasma IgG, we found that only a portion of the large B cell antibody repertoire was represented in the plasma. Molecular and functional analysis of proteomics-identified mAbs revealed recognition of epitopes in three major antigenic sites - the GP head domain, the glycan cap, and the base region, with a high prevalence of neutralizing and protective mAb specificities that targeted the base and glycan cap regions on the GP. Polyclonal plasma antibodies from the survivor reacted broadly to EBOV, BDBV, and SUDV GP, while reactivity of the potently neutralizing mAbs we identified was limited mostly to the homologous EBOV GP. Together these results reveal a restricted diversity of neutralizing humoral response in which mAbs targeting two antigenic sites on GP – glycan cap and base – play a principal role in plasma-antibody-mediated protective immunity against EVD.
The Consortium for Top-Down Proteomics (www.topdownproteomics.org) launched the present study to assess the state of top-down mass spectrometry (TD MS) and middle-down mass spectrometry (MD MS) for characterizing monoclonal antibody (mAb) primary structures, including their modifications. To meet the needs of the rapidly growing therapeutic antibody market, it is important to develop analytical strategies to characterize the heterogeneity of a therapeutic product’s primary structure reliably and reproducibly. The major objective of the present study was to determine whether current TD/MD MS technologies and protocols can add value to the more commonly employed bottom-up approaches, such as confirming protein integrity, sequencing variable domains, ruling out artefacts, and revealing modifications and their locations. A panel of three mAbs was selected and centrally provided to twenty laboratories worldwide for the analysis: Sigma mAb standard (SiLuLite), NIST mAb standard, and the therapeutic mAb Herceptin (trastuzumab). A variety of different MS instrument platforms and ion dissociation techniques were employed. Overall, the present study confirms that MD/TD MS strategies are valuable and readily available tools in laboratories worldwide. They provide complementary information to the bottom-up approach and can add unique information, which may be crucial for comprehensive mAb characterization. The current limitations, as well as possible solutions to overcome them, are also outlined. One of the limitations revealed by the results of the present study is that the expert knowledge in both experiment and data analysis is indispensable to practice TD/MD MS, but the number of TD/MD MS experts is still very low.
In the indeterminate nodules of a model legume Medicago truncatula, ~700 nodule-specific cysteine-rich (NCR) peptides with conserved cysteine signature are expressed. NCR peptides are highly diverse in sequence, and some of these cationic peptides exhibit antimicrobial activity in vitro and in vivo. However, there is a lack of knowledge regarding their structural architecture, antifungal activity, and modes of action against plant fungal pathogens. Here, the three-dimensional NMR structure of the 36-amino acid NCR044 peptide was solved. This unique structure was largely disordered and highly dynamic with one four-residue α-helix and one three-residue antiparallel β-sheet stabilized by two disulfide bonds. NCR044 peptide also exhibited potent fungicidal activity against multiple plant fungal pathogens, including Botrytis cinerea and three Fusarium spp. It inhibited germination in quiescent spores of B. cinerea. In germlings, it breached the fungal plasma membrane and induced reactive oxygen species. It bound to multiple bioactive phosphoinositides in vitro. Time-lapse confocal and superresolution microscopy revealed strong fungal cell wall binding, penetration of the cell membrane at discrete foci, followed by gradual loss of turgor, subsequent accumulation in the cytoplasm, and elevated levels in nucleoli of germlings. Spray-applied NCR044 significantly reduced gray mold disease symptoms caused by the fungal pathogen B. cinerea in tomato and tobacco plants, and postharvest products. Our work illustrates the antifungal activity of a structurally unique NCR peptide against plant fungal pathogens and paves the way for future development of this class of peptides as a spray-on fungistat/fungicide.
Characterization of the metabolic heterogeneity in cell populations requires the analysis of single cells. Most current methods in single-cell analysis rely on cell manipulation, potentially altering the abundance of metabolites in individual cells. Small sample volume and the chemical diversity of metabolites are additional challenges in single-cell metabolomics. Here, we describe the combination of fiber-based laser ablation electrospray ionization (f-LAESI) with 21 tesla Fourier transform ion cyclotron resonance mass spectrometry (21TFTICR-MS) for in situ single-cell metabolic profiling in plant tissue. Single plant cells infected by bacteria were selected and sampled directly from the tissue without cell manipulation through mid-infrared ablation with a fine optical fiber tip for ionization by f-LAESI. Finally, ultrahigh performance 21T-FTICR-MS enabled the simultaneous capture of isotopic fine structures (IFSs) for 47 known and 11 unknown compounds, thus elucidating their elemental compositions from single cells, and providing information on metabolic heterogeneity in the cell population.
Antibody-drug conjugates (ADCs) have recently gained traction in the biomedical community due to their promise for human therapeutics and an alternative to chemotherapy for cancer. Crucial metrics for ADC efficacy, safety, and selectivity are their drug-antibody ratios (DARs). However, DAR characterization (i.e., determining the average number of conjugated drugs on the antibody) through analytical methods remains challenging due to the heterogeneity of drug conjugation as well as the numerous post-translational modifications possible in the monoclonal antibody. In this work, we report on the use of high-resolution ion mobility spectrometry separations in our structures for lossless ion manipulations coupled to mass spectrometry (SLIM IMS-MS) platform for the rapid and simultaneous characterization of the drug load profile (i.e., stoichiometric distribution of the number of conjugated drugs present on the mAb), determination of the weighted average DAR in both the heavy and light chains of a model antibody-drug conjugate, and calculation of the overall DAR of the ADC. After chemical reduction of the ADC and a subsequent 31.5 meter SLIM IMS separation the various drug bound antibody species could be well resolved for both chains. Furthermore, we also show that higher resolution separations were possible with SLIM IMS as compared to ones performed on a commercially available (~1 meter) drift tube IMS-MS platform. Interestingly, additional gas-phase substructures become evident with longer path length SLIM IMS, potentially providing insight related to how drug conjugation may alter the structural properties of a monoclonal antibody and thus affect its overall potency and/or selectivity for a given antigen. We expect high-resolution SLIM IMS separations will augment the existing toolbox for ADC characterization, particularly for structural confirmation to enable the rapid optimization of DAR for a given ADC and thus better understand its potential toxicity and potency.
The extent to which noncovalent protein complexes retain native structure in the gas phase is highly dependent on experimental conditions. Energetic collisions with background gas can cause structural changes ranging from unfolding to subunit dissociation. Additionally, recent studies have highlighted the role of charge in such structural changes, but the mechanism is not completely understood. In this study, native top down (native TD) mass spectrometry was used to probe gas-phase structural changes of alcohol dehydrogenase (ADH, 4mer) under varying degrees of in-source activation. Changes in covalent backbone fragments produced by electron capture dissociation (ECD) or 193 nm ultraviolet photodissociation (UVPD) were correlated to structural changes of the ADH 4mer. ECD fragments indicated unfolding started at the N-terminus, and the charge states of UVPD fragments enabled monitoring of charge migration to the unfolded regions. Interestingly, UVPD fragments also indicated that the charge at the “unfolding” N-terminus of ADH decreased at high in-source activation energies after the initial increase. We proposed a possible “refolding-after-unfolding” mechanism, as further supported by monitoring hydrogen elimination from radical a-ions produced by UVPD at the N-terminus of ADH. However, “refolding-after-unfolding” with increasing in-source activation was not observed for charge-reduced ADH, which likely adopted compact structures that are resistant to both charge migration and unfolding. Combined, these results support a charge-directed unfolding mechanism for protein complexes. Overall, an experimental framework was outlined for utilizing native TD to generate structure-informative mass spectral signatures for protein complexes that complement other structure characterization techniques, such as ion mobility spectrometry and computational modeling.
Vitamin B 6 (also called pyridoxine) is a central cofactor for over a hundred enzymatic processes and plays a critical role in the defense mechanism against oxidative stress. While plants are able to synthesize vitamin B 6 de novo, humans lack this ability and fully rely on external food nutrition for its intake. In plants, vitamin B6 is synthesized by a PDX1 dodecamer, complexed with a variable number of PDX2 subunits (up to 12). Arabidopsis thaliana has three homologs of PDX1, designated as PDX1.1, PDX1.2 and PDX1.3, along with one homolog of PDX2. While PDX1.1, PDX1.3 and PDX2 are all active enzymes, PDX1.2 is inactive but still essential for plant development and also the regulation of PDX1.1 and PDX1.3 catalytic activity in vivo. In addition, while the structure of PDX1.3 has been solved by X-ray crystallography, the homomeric PDX1.2 pseudoenzyme and PDX1.2/PDX1.3 heterocomplexes remain uncharacterized at the molecular level. To address these gaps, we combined cell-free expression, functional assays, native mass spectrometry, single particle cryo-electron microscopy and other biochemical approaches to evaluate the structure and kinetics of PDX1.2 and its interaction with PDX1.3. Here, we highlight the newly solved structure of homomeric PDX1.2, its assembly into heteromeric complexes with PDX1.3 and propose a new mechanism for how PDX1.2 regulates overall vitamin B6 biosynthesis in the plant. We show that all PDX1.2/PDX1.3 heterocomplexes were found to exist as a population of dodecameric assemblies rather than a single species of one defined stoichiometry. In all co-expression conditions tested, we detected populationa of 6-8 complexes of variable stoichiometry, driven by availability of each protein. A higher ratio of PDX1.2 DNA template fed into the cell-free reaction resulted in a higher number of PDX1.2 subunits present in the heterocomplexes and correlated to a decrease in overall kinetics for PLP synthesis despite improving the stability of the entire complex. Overall, this study highlights a powerful and highly integrated biochemical, mass spectrometry and imaging approach to dissect heteromeric complexes and their association mechanisms.
Mass spectrometry (MS) has been an indispensable analytical tool in capturing the complexity and array of biomolecules within biological systems. However, conventional MS-based analytical workflows are limited in both throughput and measuring the native molecular state these systems, due in large part to sample handling and preparation. The development of ambient ionization methods capable of sampling directly from tissues circumvent many of these issues but requires the use of high-performance MS to resolve the molecular complexity within these samples. Herein, we demonstrate the unique combination of laser ablation electrospray ionization (LAESI) coupled with a 21 Tesla Fourier transform ion cyclotron resonance (21T-FTICR-MS) for MS imaging applications. This analytical platform provides isotopic fine structure information directly from native tissues, delivering a higher degree of confidence for molecular identification. The ability to capture and visualize the complex metabolic behavior of living organisms in situ is a bioanalytical grand challenge that has yet to be fully realized. Due to their excellent sensitivity and selectivity, mass spectrometry (MS)-based platforms offer a unique opportunity to characterize an array of biomolecules from a variety of biological samples.[1] One method in particular, MS imaging (MSI), has demonstrated the ability to simultaneously determine the spatial distributions for hundreds of biomolecules, e. g., metabolites, lipids, peptides, and xenobiotics, within complex biological systems simultaneously.[2-3] Matrix-assisted laser desorption/ionization (MALDI)-MSI remains the most common of these methods.[4] However, the application of an exogenous matrix, and the limited availability of commercial sources that operate under atmospheric pressure,[5] has significantly prohibited the ability of MALDI to be useful for biomolecular mapping of living systems. Ambient ionization methods that require minimal to no sample preparation, like desorption electrospray ionization (DESI and nano-DESI) and laser ablation electrospray ionization (LAESI), demonstrated the ability to spatially map biomolecule distributions within live organisms.
The chemical structure of organic molecules profoundly impacts their interactions with metal ions and mineral phases in soils. Understanding the sources and cycling of metal-chelating compounds is therefore essential for predicting the bioavailability and transport of metals throughout terrestrial environments. We investigate the molecular speciation of organic molecules that solubilize trace metals in calcareous soils from Eastern Washington. Ultra-high performance Fourier transform ion cyclotron resonance mass spectrometry at 21 Tesla enabled fast and confident detection and identification of metal chelators that are produced by microbes that inhabit these soils based on screening for features that match diagnostic metal isotope patterns. We compared two approaches, one based on direct infusion using the incorporation of a rare isotope to validate true iron-binding features, and another based on separation with liquid chromatography and detection of isotopologues with coherent elution profiles. While the isotopic exchange method requires significantly shorter analysis time, nearly twice as many features were observed with liquid chromatography mass spectrometry (LCMS), mostly due to the reduction in ion suppression where major features limit the sensitivity of minor features. In addition, LCMS enabled the collection of higher quality fragmentation spectra and facilitated feature identification. Siderophores belonging to four major classes were identified, including ferrioxamines, pseudobactins, enterobactins, and arthrobactins. Each of these siderophores likely derives from a unique member of the microbial community, and each possesses different chemical characteristics and uptake pathways, likely contributing to fierce competition for iron within these soils. Our results provide insight into the metabolic pathways by which microbes that co-inhabit calcareous soils compete for this essential micronutrient.
Top-down proteomics is an emerging analytical strategy to characterize combinatorial protein post-translational modifications (PTMs). However, sample complexity and small mass differences between chemically closely related proteoforms often limit the resolution attainable by separations employing a single liquid chromatographic (LC) principle. In particular, for ultra-modified proteins like histones, extensive and time-consuming fractionation is needed to achieve deep proteoform coverage. Herein, we present the first online nano-flow comprehensive two-dimensional liquid chromatography (nLC×LC) platform top-down mass spectrometry analysis of histone proteoforms. The described two-dimensional LC system combines weak cation exchange chromatography under hydrophilic interaction LC conditions (i.e. charge- and hydrophilicity-based separation) with reversed phase liquid chromatography (i.e. hydrophobicity-based separation). The two independent chemical selectivities were run at nanoflows (300 nL/min) and coupled online with high-resolution mass spectrometry employing ultraviolet photodissociation (UVPD-HRMS). The nLC×LC workflow increased the number of intact protein masses observable relative to one-dimensional approaches and allowed characterization of hundreds of proteforms starting from limited sample quantities (~1.5 µg).
Correction to: Nature Methods 14, 909–914, https://doi.org/10.1038/nmeth.4388 (2017), published online 7 August 2017. In the version of this article initially published, the authors erroneously reported the search mode that was used for ProSightPC 3.0 in the Online Methods and in Supplementary Table 3. The results presented in Fig. 5 were obtained with ‘absolute mass’ search mode, not ‘biomarker discovery’ search mode. The ‘biomarker discovery’ search mode of ProSightPC 3.0 looks for subsequences of those contained in the annotated proteoform database (e.g., truncated forms from degradation and/or cleavage). This search mode is expected to generate similar numbers of identifications as Informed-Proteomics, but is also expected to take dramatically longer (~480 CPU hours). Unfortunately, because of these heavy computational requirements, the authors were unable to complete an analysis using this search mode. They chose to use ‘absolute mass’ mode to illustrate the effect of search mode and database choice on the results. ‘Absolute mass’ mode is the most restrictive of the search modes illustrated in Fig. 5, as it searches only for proteoforms explicitly listed in the proteoform database within a user-defined mass tolerance. In addition, in the supplementary information originally published online, Supplementary Table 3 incorrectly stated that ProSightPC v3.0 was used in ‘biomarker discovery’ mode. ‘Absolute mass’ mode was the mode actually used in this comparison. These errors have been corrected in the HTML and PDF versions of this article and in the associated supplementary information.
Many elements are scarcely soluble in aqueous conditions found in high pH environments, such as calcareous grassland soils, unless complexed to strong binding organic ligands. To overcome this limitation, some plants and microbes produce chelators that solubilize micronutrient metals such as Fe, Ni, Cu, and Zn from mineral phases. These complexes are taken up by organisms via specific membrane receptors, thereby differentially impacting the bioavailability of these metals to the plant and microbial community. Although the importance of these chelation strategies for individual organisms has been well established, little is known about which pathways coexist within rhizosphere microbiomes or how they interact and compete for metal binding. Identifying these metallo-organic species within natural ecosystems has remained a formidable analytical challenge due to the vast diversity of compounds and poorly defined metabolic processes in complex soil matrix. Herein, we employed recently developed liquid chromatography (LC) mass spectrometry (MS) methods to characterize the speciation of water-soluble dissolved trace elements (Fe, Ni, Cu, and Zn) from Kansas Prairie soil. Both plant and fungal chelators were identified, revealing compound-specific patterns of chelation to biologically essential metals. Numerous metabolites typically implicated in plant iron acquisition and homeostasis, including mugineic acids, deoxymugineic acid, nicotianamine, and hydroxynicotianamine, dominated the speciation of divalent metals such as Ni, Cu, and Zn (2-57 pmol / g soil). In contrast, the fungal siderophore ferricrocine bound comparatively more trivalent Fe (9pmol / g soil). These results define biochemical pathways that underpin the regulation of metals in the grassland rhizosphere. They also raise new questions about the competition of these compounds for metal binding and their bioavailability to different members of the rhizosphere population. Even small structural differences result in significant differences in their environmental metal speciation, and likely impact metal uptake within the rhizosphere of calcareous soils.
Mass spectrometric characterization of large biomolecules, such as intact proteins, requires the specificity afforded by ultra-high resolution mass measurements performed at both the intact mass and product ion levels. Although the performance of time-of-flight mass analyzers is steadily increasing, the choice of mass analyzer for large biomolecules (e.g. proteins >50 kDa) is generally limited to the Fourier transform family of mass analyzers, such as Orbitrap and ion cyclotron resonance (FTICR-MS) with the latter providing unmatched mass resolving power and measurement accuracy. Yet, protein analyses using FTMS are largely hindered by the low acquisition rates of ultra-high resolution spectra. Frequency multiple detection schemes enable FTICR-MS to overcome this fundamental barrier and achieve resolving powers and acquisition speeds 4X greater than the limits imposed by magnetic field strength. Here we expand upon earlier work on the implementation of this technique for biomolecular characterization. We report the coupling of 21T FTICR-MS, 4X frequency multiplication, ion trapping field harmonization technology, and spectral data processing methods to achieve unprecedented acquisition rates and resolving power in mass spectrometry of large intact proteins. Isotopically resolved spectra of multiply charged ubiquitin ions were acquired using detection periods as short as 12 ms. Large proteins such as apo-transferrin (MW=78 kDa) and monoclonal antibody (MW=150 kDa) were isotopically resolved with detection periods of 384 ms and 768 ms, respectively. These results illustrate the future capability of accurate characterization of large proteins on time-scales compatible with online separations.
The Consortium for Top-Down Proteomics (CTDP) proposes a standardized notation, ProForma, for writing the sequence of fully characterized proteoforms. ProForma provides a means to communicate any proteoform by writing the amino acid sequence using standard one-letter notation and specifying modifications or unidentified mass shifts within brackets following certain amino acids. The notation is unambiguous, human readable, and can easily be parsed and written by bioinformatic tools. This system uses seven rules and supports a wide range of possible use cases, ensuring compatibility and reproducibility of proteoform annotations. Standardizing proteoform sequences will simplify storage, comparison, and reanalysis of proteomic studies, and the Consortium welcomes input and contributions from the research community on the continued design and maintenance of this standard.
Top-down proteomics involves the analysis of intact proteins. This approach is very attractive as it allows for analyzing proteins in their endogenous form without proteolysis, preserving valuable information about post-translation modifications, isoforms, proteolytic processing or their combinations collectively called proteoforms. Moreover, the quality of the top-down LC-MS/MS datasets is rapidly increasing due to advances in the liquid chromatography and mass spectrometry instrumentation and sample processing protocols. However, the top-down mass spectra are substantially more complex compare to the more conventional bottom-up data. To take full advantage of the increasing quality of the top-down LC-MS/MS datasets there is an urgent need to develop algorithms and software tools for confident proteoform identification and quantification. In this study we present a new open source software suite for top-down proteomics analysis consisting of an LC-MS feature finding algorithm, a database search algorithm, and an interactive results viewer. The presented tool along with several other popular tools were evaluated using human-in-mouse xenograft luminal and basal breast tumor samples that are known to have significant differences in protein abundance based on bottom-up analysis.