The Global Phosphorylation Landscape of SARS-CoV-2 Infection.

The causative agent of the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected millions and killed hundreds of thousands of people worldwide, highlighting an urgent need to develop antiviral therapies. Here we present a quantitative mass spectrometry-based phosphoproteomics survey of SARS-CoV-2 infection in Vero E6 cells, revealing dramatic rewiring of phosphorylation on host and viral proteins. SARS-CoV-2 infection promoted casein kinase II (CK2) and p38 MAPK activation, production of diverse cytokines, and shutdown of mitotic kinases, resulting in cell cycle arrest. Infection also stimulated a marked induction of CK2-containing filopodial protrusions possessing budding viral particles. Eighty-seven drugs and compounds were identified by mapping global phosphorylation profiles to dysregulated kinases and pathways. We found pharmacologic inhibition of the p38, CK2, CDK, AXL, and PIKFYVE kinases to possess antiviral efficacy, representing potential COVID-19 therapies.

Structural insights into the human PA28-20S proteasome enabled by efficient tagging and purification of endogenous proteins.

The ability to produce folded and functional proteins is a necessity for structural biology and many other biological sciences. This task is particularly challenging for numerous biomedically important targets in human cells, including membrane proteins and large macromolecular assemblies, hampering mechanistic studies and drug development efforts. Here we describe a method combining CRISPR-Cas gene editing and fluorescence-activated cell sorting to rapidly tag and purify endogenous proteins in HEK cells for structural characterization. We applied this approach to study the human proteasome from HEK cells and rapidly determined cryogenic electron microscopy structures of major proteasomal complexes, including a high-resolution structure of intact human PA28αß-20S. Our structures reveal that PA28 with a subunit stoichiometry of 3α/4ß engages tightly with the 20S proteasome. Addition of a hydrophilic peptide shows that polypeptides entering through PA28 are held in the antechamber of 20S prior to degradation in the proteolytic chamber. This study provides critical insights into an important proteasome complex and demonstrates key methodologies for the tagging of proteins from endogenous sources.

Proteomic Approaches to Study SARS-CoV-2 Biology and COVID-19 Pathology.

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), was declared a pandemic infection in March 2020. As of December 2020, two COVID-19 vaccines have been authorized for emergency use by the U.S. Food and Drug Administration, but there are no effective drugs to treat COVID-19, and pandemic mitigation efforts like physical distancing have had acute social and economic consequences. In this perspective, we discuss how the proteomic research community can leverage technologies and expertise to address the pandemic by investigating four key areas of study in SARS-CoV-2 biology. Specifically, we discuss how (1) mass spectrometry-based structural techniques can overcome limitations and complement traditional structural approaches to inform the dynamic structure of SARS-CoV-2 proteins, complexes, and virions; (2) virus-host protein-protein interaction mapping can identify the cellular machinery required for SARS-CoV-2 replication; (3) global protein abundance and post-translational modification profiling can characterize signaling pathways that are rewired during infection; and (4) proteomic technologies can aid in biomarker identification, diagnostics, and drug development in order to monitor COVID-19 pathology and investigate treatment strategies. Systems-level high-throughput capabilities of proteomic technologies can yield important insights into SARS-CoV-2 biology that are urgently needed during the pandemic, and more broadly, can inform coronavirus virology and host biology.

Structural analysis of glutathionyl hemoglobin using native mass spectrometry.

Glutathionylation is an example of reversible post-translation modification of proteins where free and accessible cysteine residues of proteins undergo thiol-disulfide exchange with oxidized glutathione (GSSG). In general, glutathionylation occurs under the condition of elevated oxidative stress in vivo. In human hemoglobin, Cys93 residue of ß globin chain was found to undergo this oxidative modification. Glutathionyl hemoglobin (GSHb) was reported to act as a biomarker of oxidative stress under several clinical conditions such as chronic renal failure, iron deficiency anemia, hyperlipidemia, diabetes mellitus, Friedreich's ataxia, atherosclerosis. Previously we showed that the functional abnormality associated with six-fold tighter oxygen binding of GSHb supposedly attributed to the conformational transition of the deoxy state of GSHb towards oxy hemoglobin like conformation. In the present study, we investigated the structural integrity and overall architecture of the quaternary structure of GSHb using native mass spectrometry and ion mobility mass spectrometry platforms. The dissociation equilibrium constants of both tetramer/dimer (Kd1) and dimer/monomer equilibrium (Kd2) was observed to increase by 1.91 folds and 3.64 folds respectively. However, the collision cross-section area of the tetrameric hemoglobin molecule remained unchanged upon glutathionylation. The molecular dynamics simulation data of normal human hemoglobin and GSHb was employed to support our experimental findings.

Glycation profile of minor abundant erythrocyte proteome across varying glycemic index in diabetes mellitus.

PURPOSE: Long-term glycemic index in patients with diabetes mellitus (DM) is measured by glycated hemoglobin (HbA1c) besides blood glucose. In DM, the primary amino groups of proteins get glycated via non-enzymatic post-translational modification. This study aims at identifying and characterizing site-specific glycation of erythrocyte proteome across varying glycemic index in patients with DM. EXPERIMENTS: We isolated the glycated erythrocyte proteome devoid of hemoglobin from control and diabetic samples using boronate affinity chromatography. Proteomic analysis was performed using nanoLC/ESI-MS proteomics platform. The site-specific modification on different proteins was deciphered using a customized database. RESULTS: We report 37 glycated proteins identified and characterized from samples with HbA1c of 6%, 8%, 12%, and 16%. Our results show that both extent and site-specific modification of proteins increased with increasing HbA1c. The observed residue-specific modifications of catalase, peroxiredoxin, carbonic anhydrase, lactate dehydrogenase B and delta-aminolevulinic acid dehydratase were correlated with the literature report on their functional disorder in DM. CONCLUSIONS: and clinical relevance: 37 glycated erythrocyte proteins apart from hemoglobin were characterized from DM patient samples with varying HbA1c values. We correlated the site-specific glycation and associated functional disorder of five representative proteins. However, the clinical correlation with the observed modifications needs further investigation.

Characterization of residue-specific glutathionylation of CSF proteins in multiple sclerosis - A MS-based approach.

Reduction of a disulfide linkage between cysteine residues in proteins, a standard step in the preanalytical preparation of samples in conventional proteomics approach, presents a challenge to characterize S-glutathionylation of proteins. S-glutathionylation of proteins has been reported in medical conditions associated with high oxidative stress. In the present study, we attempted to characterize glutathionylation of CSF proteins in patients with multiple sclerosis which is associated with high oxidative stress. Using the nano-LC/ESI-MS platform, we adopted a modified proteomics approach and a targeted database search to investigate glutathionylation at the residue level of CSF proteins. Compared to patients with Intracranial hypertension, the following CSF proteins: Extracellular Superoxide dismutase (ECSOD) at Cys195, α1-antitrypsin (A1AT) at Cys232, Phospholipid transfer protein (PLTP) at Cys318, Alpha-2-HS-glycoprotein at Cys340, Ectonucleotide pyrophosphate (ENPP-2) at Cys773, Gelsolin at Cys304, Interleukin-18 (IL-18) at Cys38 and Ig heavy chain V III region POM at Cys22 were found to be glutathionylated in patients with multiple sclerosis during a relapse. ECSOD, A1AT, and PLTP were observed to be glutathionylated at the functionally important cysteine residues. In conclusion, in the present study using a modified proteomics approach we have identified and characterized glutathionylation of CSF proteins in patients with multiple sclerosis.

Analysis of the Quaternary Structure of Hemoglobin Beckman Variant and Molecular Interpretation of Its Functional Abnormality: A Mass-Spectrometry-Based Approach.

Electrostatic attraction between α and ß globin chains holds the subunits together in a tetrameric human hemoglobin molecule (α2 ß2 ). Compared to normal globin chains, the affinity of a mutant chain to its partner globin might be different in genetic variants of hemoglobin. This leads to an unequal abundance of normal and variant hemoglobin in heterozygous samples, even though the rates of synthesis of both the normal and variant chains are the same. The aforementioned affinities across various globin chains might be assessed by quantification of the different forms of the tetramers present in a variant hemoglobin sample. In the present study, by exploiting mass differences between globin chains, differently populated hemoglobin tetramers present in hemoglobin (Hb) Beckman, a ß variant (ßA135D), were structurally characterized. The relative populations of dissymmetric tetramers (α2 ß2 , α2 ßßV , and α2 ßV2 ) indicated that both ß and ßV have different affinities towards the α globin chain. Conformational dynamics analyzed from hydrogen/deuterium exchange kinetics of the three peptide fragments of Hb Beckman in its oxy state displayed molecular insight into its functional abnormality. However, in comparison to normal hemoglobin (α2 ß2 ), the point mutation did not show any change in the collision cross-sections of the functionally active conformers of the variant hemoglobin molecules (α2 ßßV and α2 ßV2 ).

Effect of altered solution conditions on tau conformational dynamics: Plausible implication on order propensity and aggregation.

Intrinsically disordered protein tau plays a central role in maintaining neuronal network by stabilizing microtubules in axon. Tau reportedly possesses random coil architecture, which is largely inert to alteration in solution conditions. However, the presence of transient compact conformers and residual structure has been evident from previous reports. Also, during Alzheimer's disease, misfolded tau detaches from microtubule and forms ordered filaments, which is the hallmark of the disease. Despite its fundamental role in neuronal physiology and in pathological cascade of several fatal neurodegenerative diseases, tau conformational dynamics remains poorly understood. In the present study, we have explored the effect of ionic strength, temperature and solvent polarity on tau40 conformational preferences using ion mobility mass spectrometry. Investigation of collision cross section revealed that while low ionic strength, elevated temperature and reduced solvent polarity mostly induced partial collapse in tau40 conformers, higher ionic strength led to an expansion of the molecule. Limited proteolysis identified segments of tau40 projection domain and proline-rich region having high order propensity and a C-terminal region having vulnerability for further expansion at altered solution conditions. The high susceptibility for disorder-to-order transition in the above region of the protein might have crucial implication on its role as microtubule spacers, and in cellular signaling cascade. The conformational adaptation of tau40 did not enhance the heparin-induced aggregation proclivity of the protein. Nevertheless, the observed correlation of electrostatic interaction with fibrillation propensity of tau40 might indicate plausible link between hyperphosphorylation at diseased state with tau conformation and self-assembly.

Assessment of Cysteine Reactivity of Human Hemoglobin at Its Residue Level: A Mass Spectrometry-Based Approach.

In general, the reactivity of cysteine residues of proteins is measured by 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) kinetics using spectrophotometry. Proteins with several cysteine residues may exhibit varying DTNB kinetics but residue level information can only be obtained with the prior knowledge of their three-dimensional structure. However, this method is limited in its application to the proteins containing chromophores having overlapping absorption profile with 2-nitro-5-thiobenzoic acid, such as hemoglobin (Hb). Additionally, this method is incapable of assigning cysteine reactivity at the residue levels of proteins with unknown crystal structures. However, a mass spectrometry (MS)-based platform might provide a solution to these problems. In the present study, alkylation kinetics of cysteine residues of adult human Hb (Hb A; α2ß2) and sickle cell Hb (Hb S; HBB: c.20A>T) were investigated using matrix-assisted laser desorption/ionization (MALDI) MS. Differential site-specific reactivities of cysteine residues of Hb were investigated using alkylation kinetics with iodoacetamide (IAM). The observed reactivities corroborated well with the differential surface accessibilities of cysteine residues in the crystal structures of human Hb. The proposed method might be used to investigate cysteine reactivities of all the genetic and post-translational variants of Hb discovered to date. In addition, this method can be extended to explore cysteine reactivities of proteins, irrespective of the presence of chromophores and availability of crystal structures.

Protein Structure-Function Correlation in Living Human Red Blood Cells Probed by Isotope Exchange-based Mass Spectrometry.

To gain insight into the underlying mechanisms of various biological events, it is important to study the structure-function correlation of proteins within cells. Structural probes used in spectroscopic tools to investigate protein conformation are similar across all proteins. Therefore, structural studies are restricted to purified proteins in vitro and these findings are extrapolated in cells to correlate their functions in vivo. However, due to cellular complexity, in vivo and in vitro environments are radically different. Here, we show a novel way to monitor the structural transition of human hemoglobin upon oxygen binding in living red blood cells (RBCs), using hydrogen/deuterium exchange-based mass spectrometry (H/DX-MS). Exploiting permeability of D2O across cell membrane, the isotope exchange of polypeptide backbone amide hydrogens of hemoglobin was carried out inside RBCs and monitored using matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). To explore the conformational transition associated with oxygenation of hemoglobin in vivo, the isotope exchange kinetics was simplified using the method of initial rates. RBC might be considered as an in vivo system of pure hemoglobin. Thus, as a proof-of-concept, the observed results were correlated with structural transition of hemoglobin associated with its function established in vitro. This is the first report on structural changes of a protein upon ligand binding in its endogenous environment. The proposed method might be applicable to proteins in their native state, irrespective of location, concentration, and size. The present in-cell approach opens a new avenue to unravel a plethora of biological processes like ligand binding, folding, and post-translational modification of proteins in living cells.

Mass spectrometry based characterization of Hb Beckman variant in a falsely elevated HbA(1c) sample.

Glycated hemoglobin (HbA1c) is a 'gold standard' biomarker for assessing the glycemic index of an individual. HbA1c is formed due to nonenzymatic glycosylation at N-terminal valine residue of the ß-globin chain. Cation exchange based high performance liquid chromatography (CE-HPLC) is mostly used to quantify HbA1c in blood sample. A few genetic variants of hemoglobin and post-translationally modified variants of hemoglobin interfere with CE-HPLC-based quantification, resulting in its false positive estimation. Using mass spectrometry, we analyzed a blood sample with abnormally high HbA1c (52.1%) in the CE-HPLC method. The observed HbA1c did not corroborate the blood glucose level of the patient. A mass spectrometry based bottom up proteomics approach, intact globin chain mass analysis, and chemical modification of the proteolytic peptides identified the presence of Hb Beckman, a genetic variant of hemoglobin, in the experimental sample. A similar surface area to charge ratio between HbA1c and Hb Beckman might have resulted in the coelution of the variant with HbA1c in CE-HPLC. Therefore, in the screening of diabetes mellitus through the estimation of HbA1c, it is important to look for genetic variants of hemoglobin in samples that show abnormally high glycemic index, and HbA1c must be estimated using an alternative method.

Current proteomics methods applicable to dissecting the DNA damage response.

The DNA damage response (DDR) entails reorganization of proteins and protein complexes involved in DNA repair. The coordinated regulation of these proteomic changes maintains genome stability. Traditionally, regulators and mediators of DDR have been investigated individually. However, recent advances in mass spectrometry (MS)-based proteomics enable us to globally quantify changes in protein abundance, post-translational modifications (PTMs), protein localization, and protein-protein interactions (PPIs) in cells. Furthermore, structural proteomics approaches, such as crosslinking MS (XL-MS), hydrogen/deuterium exchange MS (H/DX-MS), Native MS (nMS), provide large structural information of proteins and protein complexes, complementary to the data collected from conventional methods, and promote integrated structural modeling. In this review, we will overview the current cutting-edge functional and structural proteomics techniques that are being actively utilized and developed to help interrogate proteomic changes that regulate the DDR.

Glutathionylation induced structural changes in oxy human hemoglobin analyzed by backbone amide hydrogen/deuterium exchange and MALDI-mass spectrometry.

Glutathionyl hemoglobin, a post-translationally modified form of hemoglobin, has been reported to serve as a marker of oxidative stress in several clinical conditions. This modification causes perturbations in the hemoglobin functionality by increasing oxygen affinity and reducing cooperativity. Moreover, glutathionylation of sickle hemoglobin was reported to lead to a significant reduction in the propensity of sickling of erythrocytes. The root cause of the above functional abnormality is not known in detail, as the crystal structure of the molecule is yet to be discovered. In this study, we investigated the effects of glutathionylation on quaternary structure of hemoglobin using hydrogen/deuterium exchange (H/DX) based mass spectrometry. H/DX kinetics of nine peptides from α and ß globin chains of hemoglobin were analyzed to understand the conformational change in deoxy to oxy transition of normal hemoglobin and structural perturbations associated with glutathionylation of oxy hemoglobin. Significant structural changes brought about by the glutathionylation of oxy hemoglobin were observed in the following regions of globin chains: ß86-102, ß1-14, α34-46, ß32-41, ß130-146, ß115-129, ß73-81. Isotope exchange kinetics monitored through mass spectrometry is a useful technique to understand structural perturbation on post-translational modification of proteins in solution phase.

Structural perturbation of human hemoglobin on glutathionylation probed by hydrogen-deuterium exchange and MALDI mass spectrometry.

Glutathionyl hemoglobin, an example of post-translationally modified hemoglobin, has been studied as a marker of oxidative stress in various diseased conditions. Compared to normal hemoglobin, glutathionyl hemoglobin has been found to have increased oxygen affinity and reduced cooperativity. However, detailed information concerning the structural perturbation of hemoglobin associated with glutathionylation is lacking. In the present study, we report structural changes associated with glutathionylation of deoxyhemoglobin by hydrogen/deuterium (H/D) exchange coupled to matrix assisted laser desorption ionization (MALDI) mass spectrometry. We analyzed isotope exchange kinetics of backbone amide hydrogen of eleven peptic peptides in the deoxy state of both hemoglobin and glutathionyl hemoglobin molecules. Analysis of the deuterium incorporation kinetics for both molecules showed structural changes associated with the following peptides: α34-46, α1-29, ß32-41, ß86-102, ß115-129, and ß130-146. H/D exchange experiments suggest that glutathionylation of hemoglobin results in a change in conformation located at the above-mentioned regions of the hemoglobin molecule. MALDI mass spectrometry based H/D exchange experiment might be a simple way of monitoring structural changes associated with post-translational modification of protein.

Structural analysis of glycated human hemoglobin using native mass spectrometry.

Glycated hemoglobin (GHb) is the indicator of the long-term glycemic index of an individual. GHb is formed by the irreversible modification of N-terminal α-amino group of ß globin chain with glucose via Amadori rearrangement. Cation exchange chromatography exploits the difference in surface charges between GHb and native hemoglobin (HbA0 ) for their separation and quantification. However, glucose condensation is specific to primary amino groups. Therefore, structural characterization of GHb synthesized in vivo is essential as multiple glycation may interfere with GHb assessment. The stoichiometric composition of different glycated hemoglobin from a 19% GHb sample was deduced using native mass spectrometry. We observed a comparable population of α and ß glycated tetramers for mono-glycated HbA0 . Surprisingly, doubly and triply glycated HbA0 also showed mono-glycated α and ß globins. Thus, we propose that glycation of hemoglobin (HbA) occurs symmetrically across α and ß globins with preference to unmodified globin first. Correlation between conventional and mass spectrometry-based quantification of GHb showed a reliable estimation of the glycemic index of individuals carrying HbA0 . Mutant HbAs have different retention time than HbA0 due to the differences in their surface charge. Thus, their glycated analog may elute at different retention time compared to GHb. Consequently, our method would be ideal for assessing the glycemic index of an individual carrying mutant HbA.

Conformational heterogeneity of tau: Implication on intrinsic disorder, acid stability and fibrillation in Alzheimer's disease.

The self-assembly of intrinsically disordered protein tau into paired helical filament forms one of the hallmarks of Alzheimer's disease. However, the facets of innately disordered structure of tau and its conversion to a ß-sheet-rich fibril during several tauopathies are poorly understood. Here, we provide a direct insight into the ensemble of highly heterogeneous conformational families of tau at physiological pH, by nano-electrospray mass spectrometry coupled with ion mobility. The average collision cross section of the most unfolded conformer was higher by >2 fold than that of the most folded one. Acidic pH largely induced unfolding in tau, obliterating the compact conformers completely. The highly unfolded conformers were the key species bestowing the unusual solubility to tau at low pH, with limited contribution from intramolecular long-range interfaces giving rise to ordered conformers. Contrarily, alkaline pH shifted tau towards folded conformations due to charge neutralization, keeping the overall random coil architecture intact. Intriguingly, the heparin-induced in vitro aggregation propensity of the protein attenuated at both acidic and alkaline pH, illustrating the significance of altered conformations in pathological functions of tau. Our observations at low pH indicate that a reorganization of the intricate network of momentary long-range contacts in tau might have implication in its aggregation pathology. Disease-modifying therapies for Alzheimer's disease targeting either to disrupt the essential fibril-forming interaction at third microtubule-binding repeat of tau or to perturb specific binding interaction of tau with endogenous polyanionic species might be of high benefit.

Interaction of p-benzoquinone with hemoglobin in smoker's blood causes alteration of structure and loss of oxygen binding capacity.

Cigarette smoke (CS) is an important source of morbidity and early mortality worldwide. Besides causing various life-threatening diseases, CS is also known to cause hypoxia. Chronic hypoxia would induce early aging and premature death. Continuation of smoking during pregnancy is a known risk for the unborn child. Although carbon monoxide (CO) is considered to be a cause of hypoxia, the effect of other component(s) of CS on hypoxia is not known. Here we show by immunoblots and mass spectra analyses that in smoker's blood p-benzoquinone (p-BQ) derived from CS forms covalent adducts with cysteine 93 residues in both the ß chains of hemoglobin (Hb) producing Hb-p-BQ adducts. UV-vis spectra and CD spectra analyses show that upon complexation with p-BQ the structure of Hb is altered. Compared to nonsmoker's Hb, the content of α-helix decreased significantly in smoker's Hb (p = 0.0224). p-BQ also induces aggregation of smoker's Hb as demonstrated by SDS-PAGE, dynamic light scattering and atomic force microscopy. Alteration of Hb structure in smoker's blood is accompanied by reduced oxygen binding capacity. Our results provide the first proof that p-BQ is a cause of hypoxia in smokers. We also show that although both p-BQ and CO are responsible for causing hypoxia in smokers, exposure to CO further affects the function over and above that produced by Hb-p-BQ adduct.