Deep Plasma Proteome Profiling by Modulating Single Nanoparticle Protein Corona with Small Molecules

The protein corona, a dynamic biomolecular layer that forms on nanoparticle (NP) surfaces upon exposure to biological fluids is emerging as a valuable diagnostic tool for improving plasma proteome coverage analyzed by liquid chromatography-mass spectrometry (LC-MS/MS). Here, we show that spiking small molecules, including metabolites, lipids, vitamins, and nutrients, into plasma can induce diverse protein corona patterns on otherwise identical NPs, significantly enhancing the depth of plasma proteome profiling. The protein coronas on polystyrene NPs when exposed to plasma treated with an array of small molecules (n=10) allowed for detection of 1793 proteins marking an 8.25-fold increase in the number of quantified proteins compared to plasma alone (218 proteins) and a 2.63-fold increase relative to the untreated protein corona (681 proteins). Furthermore, we discovered that adding 1000 μg/ml phosphatidylcholine could singularly increase the number of unique proteins within the protein corona (897 proteins). This specific concentration of phosphatidylcholine selectively depleted the four most abundant plasma proteins, including albumin, thus reducing concentration dynamic range of plasma proteome and boosting LC-MS/MS sensitivity for detection of proteins with lower abundance. By employing an optimized data-independent acquisition (DIA) approach, the inclusion of phosphatidylcholine led to the detection of 1436 proteins in plasma. This significant achievement is made utilizing only a single NP type and one small molecule to analyze a single plasma sample, setting a new standard in proteomic depth of the plasma sample. Given the critical role of plasma proteomics in biomarker discovery and disease monitoring, we anticipate widespread adoption of this methodology for identification and clinical translation of proteomic biomarkers into FDA approved diagnostics.

Ultralight Ultrafast Enzymes

Inorganic materials depleted of heavy stable isotopes are known to deviate strongly in some physicochemical properties from their isotopically natural counterparts. Here we explored for the first time the effect of simultaneous depletion of the heavy carbon, hydrogen, oxygen and nitrogen isotopes on the bacterium E. coli and the enzymes expressed in it. Bacteria showed faster growth, with most proteins exhibiting higher thermal stability, while for recombinant enzymes expressed in depleted media, faster kinetics was discovered. At room temperature, luciferase, thioredoxin and dihydrofolate reductase and Pfu DNA polymerase showed up to a 250 % increase in activity compared to the native counterparts, with an additional ∼50 % increase at 10 °C. Diminished conformational and vibrational entropy is hypothesized to be the cause of the accelerated kinetics. Ultralight enzymes may find an application where extreme reaction rates are required.

A uniform data processing pipeline enables harmonized nanoparticle protein corona analysis across proteomics core facilities

Protein corona, a layer of biomolecules primarily comprising proteins, forms dynamically on nanoparticles in biological fluids and is crucial for predicting nanomedicine safety and efficacy. The protein composition of the corona layer is typically analyzed using liquid chromatography-mass spectrometry (LC-MS/MS). Our recent study, involving identical samples analyzed by 17 proteomics facilities, highlighted significant data variability, with only 1.8% of proteins consistently identified across these centers. Here, we implement an aggregated database search unifying parameters such as variable modifications, enzyme specificity, number of allowed missed cleavages and a stringent 1% false discovery rate at the protein and peptide levels. Such uniform search dramatically harmonizes the proteomics data, increasing the reproducibility and the percentage of consistency-identified unique proteins across distinct cores. Specifically, out of the 717 quantified proteins, 253 (35.3%) are shared among the top 5 facilities (and 16.2% among top 11 facilities). Furthermore, we note that reduction and alkylation are important steps in protein corona sample processing and as expected, omitting these steps reduces the number of total quantified peptides by around 20%. These findings underscore the need for standardized procedures in protein corona analysis, which is vital for advancing clinical applications of nanoscale biotechnologies.

Massive Solubility Changes in Neuronal Proteins upon Simulated Traumatic Brain Injury Reveal the Role of Shockwaves in Irreversible Damage

We investigated the immediate molecular consequences of traumatic brain injuries (TBIs) using a novel proteomics approach. We simulated TBIs using an innovative laboratory apparatus that employed a 5.1 kg dummy head that held neuronal cells and generated a ≤4000 g-force acceleration upon impact. A Proteome Integral Solubility Alteration (PISA) assay was then employed to monitor protein solubility changes in a system-wide manner. Dynamic impacts led to both a reduction in neuron viability and massive solubility changes in the proteome. The affected proteins mapped not only to the expected pathways, such as those of cell adhesion, collagen, and laminin structures, as well as the response to stress, but also to other dense protein networks, such as immune response, complement, and coagulation cascades. The cellular effects were found to be mainly due to the shockwave rather than the g-force acceleration. Soft materials could reduce the impact's severity only until they were fully compressed. This study shows a way of developing a proteome-based meter for measuring irreversible shockwave-induced cell damage and provides a resource for identifying protein biomarkers of TBIs and potential drug targets for the development of products aimed at primary prevention and intervention.

DOPA Residues Endow Collagen with Radical Scavenging Capacity

Here we uncover collagen, the main structural protein of all connective tissues, as a redox-active material. We identify dihydroxyphenylalanine (DOPA) residues, post-translational oxidation products of tyrosine residues, to be common in collagen derived from different connective tissues. We observe that these DOPA residues endow collagen with substantial radical scavenging capacity. When reducing radicals, DOPA residues work as redox relay: they convert to the quinone and generate hydrogen peroxide. In this dual function, DOPA outcompetes its amino acid precursors and ascorbic acid. Our results establish DOPA residues as redox-active side chains of collagens, probably protecting connective tissues against radicals formed under mechanical stress and/or inflammation.

Sex-Specific Silica Nanoparticle Protein Corona Compositions Exposed to Male and Female BALB/c Mice Plasmas

As various nanoparticles (NPs) are increasingly being used in nanomedicine products for more effective and less toxic therapy and diagnosis of diseases, there is a growing need to understand their biological fate in different sexes. Herein, we report a proof-of-concept result of sex-specific protein corona compositions on the surface of silica NPs as a function of their size and porosity upon incubation with plasma proteins of female and male BALB/c mice. Our results demonstrate substantial differences between male and female protein corona profiles on the surface of silica nanoparticles. By comparing protein abundances between male and female protein coronas of mesoporous silica nanoparticles and Stöber silica nanoparticles of ∼100, 50, and 100 nm in diameter, respectively, we detected 17, 4, and 4 distinct proteins, respectively, that were found at significantly different concentrations for these constructs. These initial findings demonstrate that animal sex can influence protein corona formation on silica NPs as a function of the physicochemical properties. A more thorough consideration of the role of plasma sex would enable nanomedicine community to design and develop safer and more efficient diagnostic and therapeutic nanomedicine products for both sexes.

Multi-omics analysis of magnetically levitated plasma biomolecules

We recently discovered that superparamagnetic iron oxide nanoparticles (SPIONs) can levitate plasma biomolecules in the magnetic levitation (MagLev) system and cause formation of ellipsoidal biomolecular bands. To better understand the composition of the levitated biomolecules in various bands, we comprehensively characterized them by multi-omics analyses. To probe whether the biomolecular composition of the levitated ellipsoidal bands correlates with the health of plasma donors, we used plasma from individuals who had various types of multiple sclerosis (MS), as a model disease with significant clinical importance. Our findings reveal that, while the composition of proteins does not show much variability, there are significant differences in the lipidome and metabolome profiles of each magnetically levitated ellipsoidal band. By comparing the lipidome and metabolome compositions of various plasma samples, we found that the levitated biomolecular ellipsoidal bands do contain information on the health status of the plasma donors. More specifically, we demonstrate that there are particular lipids and metabolites in various layers of each specific plasma pattern that significantly contribute to the discrimination of different MS subtypes, i.e., relapsing-remitting MS (RRMS), secondary-progressive MS (SPMS), and primary-progressive MS (PPMS). These findings will pave the way for utilization of MagLev of biomolecules in biomarker discovery for identification of diseases and discrimination of their subtypes.

Measurements of heterogeneity in proteomics analysis of the nanoparticle protein corona across core facilities

Robust characterization of the protein corona-the layer of proteins that spontaneously forms on the surface of nanoparticles immersed in biological fluids-is vital for prediction of the safety, biodistribution, and diagnostic/therapeutic efficacy of nanomedicines. Protein corona identity and abundance characterization is entirely dependent on liquid chromatography coupled to mass spectroscopy (LC-MS/MS), though the variability of this technique for the purpose of protein corona characterization remains poorly understood. Here we investigate the variability of LC-MS/MS workflows in analysis of identical aliquots of protein coronas by sending them to different proteomics core-facilities and analyzing the retrieved datasets. While the shared data between the cores correlate well, there is considerable heterogeneity in the data retrieved from different cores. Specifically, out of 4022 identified unique proteins, only 73 (1.8%) are shared across the core facilities providing semiquantitative analysis. These findings suggest that protein corona datasets cannot be easily compared across independent studies and more broadly compromise the interpretation of protein corona research, with implications in biomarker discovery as well as the safety and efficacy of our nanoscale biotechnologies.

Proteomics-Compatible Fourier Transform Isotopic Ratio Mass Spectrometry of Polypeptides

Measuring the relative abundances of heavy stable isotopes of the elements C, H, N, and O in proteins is of interest in environmental science, archeology, zoology, medicine, and other fields. The isotopic abundance measurements of the fine structure of immonium ions with ultrahigh resolution mass spectrometry obtained in gas-phase fragmentation of polypeptides have previously uncovered anomalous deuterium enrichment in (hydroxy)proline of bone collagen in marine mammals. Here, we provide a detailed description and validation of this approach and demonstrate per mil-range precision of isotopic ratio measurements in aliphatic residues from proteins and cell lysates. The analysis consists of proteomics-type experiment demanding sub-microgram amounts of a protein sample and providing concomitantly protein sequence data allowing one to verify sample purity and establish its identity. A novel software tool protein amino acid-resolved isotopic ratio mass spectrometry (PAIR-MS) is presented for extracting isotopic ratio data from the raw data files acquired on an Orbitrap mass spectrometer.

Redox regulation of PTPN22 affects the severity of T-cell-dependent autoimmune inflammation

Chronic autoimmune diseases are associated with mutations in PTPN22, a modifier of T cell receptor (TCR) signaling. As with all protein tyrosine phosphatases, the activity of PTPN22 is redox regulated, but if or how such regulation can modulate inflammatory pathways in vivo is not known. To determine this, we created a mouse with a cysteine-to-serine mutation at position 129 in PTPN22 (C129S), a residue proposed to alter the redox regulatory properties of PTPN22 by forming a disulfide with the catalytic C227 residue. The C129S mutant mouse showed a stronger T-cell-dependent inflammatory response and development of T-cell-dependent autoimmune arthritis due to enhanced TCR signaling and activation of T cells, an effect neutralized by a mutation in Ncf1, a component of the NOX2 complex. Activity assays with purified proteins suggest that the functional results can be explained by an increased sensitivity to oxidation of the C129S mutated PTPN22 protein. We also observed that the disulfide of native PTPN22 can be directly reduced by the thioredoxin system, while the C129S mutant lacking this disulfide was less amenable to reductive reactivation. In conclusion, we show that PTPN22 functionally interacts with Ncf1 and is regulated by oxidation via the noncatalytic C129 residue and oxidation-prone PTPN22 leads to increased severity in the development of T-cell-dependent autoimmunity.

Mass Spectrometry, Structural Analysis, and Anti-Inflammatory Properties of Photo-Cross-Linked Human Albumin Hydrogels

Albumin-based hydrogels offer unique benefits such as biodegradability and high binding affinity to various biomolecules, which make them suitable candidates for biomedical applications. Here, we report a non-immunogenic photocurable human serum-based (HSA) hydrogel synthesized by methacryloylation of human serum albumin by methacrylic anhydride (MAA). We used matrix-assisted laser desorption ionization-time-of-flight mass spectrometry, liquid chromatography-tandem mass spectrometry, as well as size exclusion chromatography to evaluate the extent of modification, hydrolytic and enzymatic degradation of methacrylated albumin macromer and its cross-linked hydrogels. The impacts of methacryloylation and cross-linking on alteration of inflammatory response and toxicity were evaluated in vitro using brain-derived HMC3 macrophages and Ex-Ovo chick chorioallantoic membrane assay. Results revealed that the lysines in HSA were the primary targets reacting with MAA, though modification of cysteine, threonine, serine, and tyrosine, with MAA was also confirmed. Both methacrylated HSA and its derived hydrogels were nontoxic and did not induce inflammatory pathways, while significantly reducing macrophage adhesion to the hydrogels; one of the key steps in the process of foreign body reaction to biomaterials. Cytokine and growth factor analysis showed that albumin-based hydrogels demonstrated anti-inflammatory response modulating cellular events in HMC3 macrophages. Ex-Ovo results also confirmed the biocompatibility of HSA macromer and hydrogels along with slight angiogenesis-modulating effects. Photocurable albumin hydrogels may be used as a non-immunogenic platform for various biomedical applications including passivation coatings.

Abnormal (Hydroxy)proline Deuterium Content Redefines Hydrogen Chemical Mass

Analyzing the δ²H values in individual amino acids of proteins extracted from vertebrates, we unexpectedly found in some samples, notably bone collagen from seals, more than twice as much deuterium in proline and hydroxyproline residues than in seawater. This corresponds to at least 4 times higher δ²H than in any previously reported biogenic sample. We ruled out diet as a plausible mechanism for such anomalous enrichment. This finding puts into question the old adage that “you are what you eat”.

System-wide identification and prioritization of enzyme substrates by thermal analysis

Despite the immense importance of enzyme-substrate reactions, there is a lack of general and unbiased tools for identifying and prioritizing substrate proteins that are modified by the enzyme on the structural level. Here we describe a high-throughput unbiased proteomics method called System-wide Identification and prioritization of Enzyme Substrates by Thermal Analysis (SIESTA). The approach assumes that the enzymatic post-translational modification of substrate proteins is likely to change their thermal stability. In our proof-of-concept studies, SIESTA successfully identifies several known and novel substrate candidates for selenoprotein thioredoxin reductase 1, protein kinase B (AKT1) and poly-(ADP-ribose) polymerase-10 systems. Wider application of SIESTA can enhance our understanding of the role of enzymes in homeostasis and disease, opening opportunities to investigate the effect of post-translational modifications on signal transduction and facilitate drug discovery.

Can the biomolecular corona induce an allergic reaction?-A proof-of-concept study

Ferumoxytol nanoparticles are being used clinically for the treatment of anemia and molecular imaging in patients. It is well documented that while most patients tolerate ferumoxytol well, a small percentage of patients (i.e., 0.01%) develop severe allergic reactions. The purpose of our proof-of-concept study was to determine whether patients with or without hypersensitivity reactions have specific protein corona profiles around ferumoxytol nanoparticles. In a retrospective, institutional review board approved pilot study, we enrolled 13 pediatric patients (5 girls, 8 boys, mean age 16.9 ± 8.2 years) who received a ferumoxytol-enhanced magnetic resonance imaging and who did (group 1, n = 5) or did not (group 2, n = 8) develop an allergic reaction. Blood samples of these patients were incubated with ferumoxytol, and the formation of a hard protein corona around ferumoxytol nanoparticles was measured by dynamic light scattering, zeta potential, and liquid chromatography-mass spectrometry. We also performed in vitro immune response analyses to randomly selected coronas from each group. Our results provide preliminary evidence that ex vivo analysis of the biomolecular corona may provide useful and predictive information on the possibility of severe allergic reactions to ferumoxytol nanoparticles. In the future, patients with predisposition of an allergic reaction to ferumoxytol may be diagnosed based on the proteomic patterns of the corona around ferumoxytol in their blood sample.

Investigation of interaction parameters in mixed micelle using pulsed field gradient NMR spectroscopy

Pulsed field gradient NMR spectroscopy was used to determine the partitioning of surfactant between monomeric and micellar forms in a mixed CTAB (hexadecyltetramethylammonium bromide) and Triton X-100 [p-(1,1,3-tetramethylbutyl)polyoxyethylene] system. In addition, potentiometric and surface tension measurements were used to determine the free concentration of ionic surfactant and the critical micelle concentration (CMC) of mixtures of n-alkyltrimethylammonium bromide (C(n)TAB, n=12, 14, 16, 18) and Triton X-100. Regular solution theory cannot describe the behavior of the activity coefficient and the excess Gibbs free energy of mixtures of ionic and nonionic surfactants. To overcome these shortcomings, we developed a new model that combines Van Laar expressions and the theory of nonrandom mixing in mixed micelles. The Van Laar expressions contain an additional parameter, rho, which reflects differences in the size of the components of the mixture. Nonrandom mixing theory was introduced to describe nonrandom mixing in mixed micelles. This effect was modeled by a packing parameter, P*. The proposed model provided a good description of the behavior of binary surfactant mixtures. The results indicated that head group size and packing constraints are important contributors to nonideal surfactant behavior. In addition, the results showed that as the chain length of the C(n)TAB molecule in C(n)TAB/Triton X-100 mixtures was increased, the head group size parameter remained constant, but the interaction and packing parameters increased. Increase of the temperature caused an increase in the interaction parameter beta and a decrease in the packing parameter (P*).

Thermodynamic studies of mixed ionic/nonionic surfactant systems

Mixtures of alkyltrimethylammonium bromide (CnTAB, n=12, 14, 16, 18) and Triton X-100 were studied at a range of mole fractions of ionic surfactant per nonionic surfactant. For each mixture, the cmc obtained from surface tension measurements differed from that obtained using potentiometry. The behavior of these mixed-surfactant systems showed three different regions with increasing total surfactant concentration. From the surface tension and potentiometry data, we obtained the free monomer concentration of ionic surfactant (mi), the micellar mole fraction of surfactant (xi), and the degree of dissociation (alpha) of ionic surfactant. We also obtained the free monomer concentration of Triton X-100 (m2) using PFG-NMR technique. A new equation was introduced to evaluate the activity coefficient in the micellar phase. The excess free energy (GE) and the synergetic parameters of mixtures were determined at various mole fractions of CnTAB/Triton X-100. Finally, the complexity of the synergism parameters was investigated.

New Approach for Determination of Macroscopic Binding Constants of Ligands to Macromolecules

A new method has been developed for determining macroscopic binding constants of a few surfactants to some macromolecules. Then, the binding of ionic surfactants (cetyltrimethyl ammonium bromide, tetradecyltrimethyl ammonium bromide, and sodium tetradecyl sulfate) [STS]) to macromolecules (bovine serum albumin, human serum albumin, and polyvinyl pyrollidone was investigated. The binding constants and binding isotherms were calculated using this new method. Experimental data were obtained through a potentiometry technique. Finally, the results obtained were compared with the results obtained based on the Wyman binding potential concept. Copyright 1999 Academic Press.