Folding and assembly of hemoglobin monitored by electrospray mass spectrometry using an on-line dialysis system

Engineering an Extracellular Matrix Mimic Using Hemoglobin Protein Nanofibrils

Extracellular matrix (ECM) is essential for tissue development, providing structural support and a microenvironment that is necessary for cells. As tissue engineering advances, there is a growing demand for ECM mimics. Polycaprolactone (PCL) is a commonly used synthetic polymer for ECM mimic materials. However, its biologically inactive surface limits its direct application in tissue engineering. Our study aimed to improve the biocompatibility of PCL by incorporating hemoglobin nanofibrils (HbFs) into PCL using an electrospinning technique. HbFs were formed from bovine hemoglobin (Hb) extracted from industrial byproducts and designed to offer PCL an improved cell adhesion property. The fabricated HbFs@PCL electrospun scaffold exhibits improved fibroblast adherence, proliferation, and deeper fibroblast infiltration into the scaffold compared with the pure PCL scaffold, indicating its potential to be an ECM mimic. This study represents the pioneering utilization of Hb-sourced nanofibrils in the electrospun PCL scaffolds for tissue engineering applications.

Native Mass Spectrometry and Collision-Induced Unfolding of Laser-Ablated Proteins

Infrared laser ablation sample transfer (LAST) was used to collect samples from solid surfaces for mass spectrometry under native spray conditions. Native mass spectrometry was utilized to probe the charge states and collision-induced unfolding (CIU) characteristics of bovine serum albumin (BSA), bovine hemoglobin (BHb), and jack-bean concanavalin A (ConA) via direct injection electrospray, after liquid extraction surface sampling, and after LAST. Each protein was deposited from solution on solid surfaces and laser-ablated for off-line analysis or sampled for online analysis. It was found that the protein ion gas-phase charge-state distributions were comparable for direct infusion, liquid extraction, and laser ablation experiments. Moreover, calculated average collision cross section (CCS) values from direct injection, liquid extraction, and laser ablation experiments were consistent with previously reported literature values. Additionally, an equivalent number of mobility features and conformational turnovers were identified from unfolding pathways from all three methods for all charge states of each protein analyzed in this work. The presented work suggests that laser ablation yields intact proteins (BSA, BHb, and ConA), is compatible with native mass spectrometry, and could be suitable for spatially resolved interrogation of unfolding pathways of proteins.

Glutathione-Hemin/Hematin Adduct Formation to Disintegrate Cytotoxic Oxidant Hemin/Hematin in Human K562 Cells and Red Blood Cells' Hemolysates: Impact of Glutathione on the Hemolytic Disorders and Homeostasis

Hemin, an oxidized form of heme, acts as potent oxidant to regulate glutathione (GSH) content in pro-erythroid K562 nucleated cells, via activation of the KEAP1/NRF2 defensive signaling pathway. Moreover, GSH, as an essential metabolite, is involved in the regulation of cell-redox homeostasis and proposed to scavenge cytotoxic free heme, which is released from hemoglobin of damaged red blood cells (RBCs) during different hemolytic disorders. In the present study, we aimed to uncover the molecular mechanism by which GSH inhibits hemin-induced cytotoxicity (HIC) by affecting hemin’s structural integrity in K562 cells and in RBC hemolysates. GSH, along with other thiols (cysteine, thioglycolic acid, and mercaptoethanol) altered the spectrum of hemin, while each of them co-added with hemin in cultures of K562 cells prevented HIC and growth arrest and markedly reduced the intracellular level of hemin. In addition, GSH endogenous levels served as a barrier to HIC in K562 cells, as shown by the depletion in GSH. LC-MS/MS analysis of the in vitro reaction between hemin and GSH revealed at least five different isomers of GSH–hemin adducts, as well as hydroxy derivatives as reaction products, which are characterized by unique mass spectra (MS). The latter allowed the detection of adducts in human RBC hemolysates. Based on these findings, we proposed a molecular mechanism via which GSH prevents HIC and structurally disintegrates heme. An analogous reaction was observed in RBC hemolysates via direct inter-reaction between hematin (ferric and hydroxide heme) released from hemoglobin and GSH. Overall, GSH–hematin adducts could be considered as novel entities of the human metabolome of RBCs in hemolytic disorders.

Refolding of Hemoglobin Under Macromolecular Confinement: Impersonating In Vivo Volume Exclusion

Biomacromolecules evolve and function inside the cell under crowded conditions. The effect of macromolecular crowding and confinement on nature and interactions of biomacromolecules cannot be ruled out. This study demonstrates the effect of volume exclusion due to macromolecular crowding on refolding rate of Gn-HCl induced unfolded hemoglobin. The in vivo like crowding milieu was created using dextran 70. Unfolding of Hb was followed by the absorbance at 280 nm and intrinsic fluorescence intensity along with a bathochromic shift that shows the destabilization of Hb in the presence of the denaturing agent. This was supported by a decrease in soret absorbance, increased hydrodynamic radii and loss in secondary structure, evidenced from dynamic light scattering and circular dichroism experiments respectively. Refolding process of Hb was followed by an increase in soret absorbance, decrease in intrinsic fluorescence intensity with a hypsochromic shift, decreased hydrodynamic radii and gain in secondary structural content. The results revealed that the effect of confinement and volume exclusion is insignificant on the process of Hb refolding.

Single molecule force spectroscopy reveals that a two-coordinate ferric site is critical for the folding of holo-rubredoxin

Metalloproteins play important roles in a wide range of biological processes. The folding process of metalloproteins is complex due to the synergistic effects of the folding of their polypeptide chains and the incorporation of metal cofactors. The folding mechanism of the simplest iron-sulfur protein rubredoxin, which contains one ferric ion coordinated by four cysteinyl sulfurs, is revealed using optical tweezers for the first time. The folding of the rubredoxin polypeptide chain is rapid and robust, while the reconstitution of the iron-sulfur center is greatly dependent upon the coordination state of the ferric ion on the unfolded polypeptide chain. If the ferric ion is coordinated by two neighboring cysteines, rubredoxin can readily fold with the iron-sulfur center fully reconstituted. However, if the ferric ion is only mono-coordinated, rubredoxin can fold but the iron-sulfur center is not reconstituted. Our results suggested that the folding of holo-rubredoxin follows a novel binding-folding-reconstitution mechanism, which is distinct from the folding mechanisms proposed for the folding of metalloproteins. Our study highlights the critical importance of the two-coordinate ferric site in the folding of holo-rubredoxin, which may have some important implications to our understanding of the folding mechanism of more complex metalloproteins in vivo.

Stability of glyoxal- and methylglyoxal-modified hemoglobin on dried blood spot cards as analyzed by nanoflow liquid chromatography tandem mass spectrometry

Blood sampling by the dried blood spot (DBS) technique has become commonly applied in newborn screening. It is often used for analysis of small molecules, such as metabolites. Recently, DBS sampling has been applied for quantification of post-translational protein modifications. Glyoxal and methylglyoxal are two simple oxoaldehydes released from glycated proteins in the Maillard reaction. They are widely distributed in the environment (e.g. cigarette smoke) and found in foods and beverages. Glyoxal and methylglyoxal are shown to react with biomolecules including DNA and proteins. In this laboratory, we previously identified the sites of modification by these two oxoaldehydes in human hemoglobin and found that the extents of modification at certain sites of lysine and arginine residues are significantly higher in type 2 diabetes mellitus patients than in nondiabetic individuals. In this study, we examine the stability of these modifications of hemoglobin stored on DBS cards at room temperature or 4 °C in the ambient air. After hemoglobin was extracted from the DBS cards, it was digested by trypsin and analyzed by nanoflow liquid chromatography coupled with nanospray ionization tandem mass spectrometry. The results show that the extents of all these PTMs are stable within 14 and 21 days when stored on DBS at room temperature and at 4 °C, respectively. Extraction of globin from DBS cards is mostly advantageous for hemolytic blood samples. This assay is sensitive as only a quarter of a DBS card containing ca. 12 μL of blood is required. Thus, it is practically useful to measure the extents of glyoxal- and methylglyoxal-induced hemoglobin modifications from DBS cards.

Correlation between Glyoxal-Induced DNA Cross-Links and Hemoglobin Modifications in Human Blood Measured by Mass Spectrometry

Glyoxal is an oxoaldehyde generated from the degradation of glucose-protein conjugates and from lipid peroxidation in foods and in vivo, and it is also present in the environment (e.g., cigarette smoke). The major endogenous source of glyoxal is glucose autoxidation, and the glyoxal concentrations in plasma are higher in diabetic patients than in nondiabetics. Glyoxal reacts with biomolecules forming covalently modified DNA and protein adducts. We previously developed sensitive and specific assays based on nanoflow liquid chromatography-nanospray ionization tandem mass spectrometry (nanoLC-NSI/MS/MS) for quantification of DNA cross-linked adducts (dG-gx-dC and dG-gx-dA) and for hemoglobin adducts derived from glyoxal. In this study, we isolated and analyzed both leukocyte DNA and hemoglobin from the blood of diabetic patients and compared the adduct levels with those from nondiabetic subjects using the modified assays. The results indicated that the extents of glyoxal-induced hemoglobin modifications on α-Lys-11, α-Arg-92, β-Lys-17, and β-Lys-66 were statistically higher in diabetic patients than nondiabetics and they correlated with HbA1c significantly. Moreover, the levels of dG-gx-dC in leukocyte DNA correlated positively with the extents of globin modification at α-Lys-11 and β-Lys-17, while levels of dG-gx-dA correlated with those at α-Lys-11 and α-Arg-92 in nonsmoking subjects. Comparing the levels and the correlation coefficients of these hemoglobin and DNA adducts including or excluding smokers, it appears that smoking is not a major contributor to glyoxal-induced adduction of hemoglobin and leukocyte DNA. To the best of our knowledge, this is one of the few reports of positive correlation between DNA and protein adducts of the same compound (glyoxal) in the blood from the same subjects. Because of the high abundance of hemoglobin in blood, the results indicate that quantification of glyoxal-modified peptides in hemoglobin might serve as a dosimetry for glyoxal and a practical surrogate biomarker for assessing glyoxal-induced DNA damage and its prevention.

Age-Associated Methylation in Human Hemoglobin and Its Stability on Dried Blood Spots As Analyzed by Nanoflow Liquid Chromatography Tandem Mass Spectrometry

Methylation of biomolecules is involved in many important biological processes. The contributing methylating agents arise from endogenous and exogenous sources (such as cigarette smoking). Human hemoglobin is easily accessible from blood and has been used as a molecular dosimeter for monitoring chemical exposure. We recently developed a method for characterization and quantification of the extents of methylation and ethylation in hemoglobin by nanoflow liquid chromatography tandem mass spectrometry under the selected reaction monitoring mode. Using this method, the relative extents of methylated and ethylated peptides in hemoglobin were quantified in nonsmoking subjects at various ages in this study. Among the nine methylation sites, we found that the extents of methylation were significantly higher in elderly subjects at the N-terminal and His-20 of α-globin, and at the N-terminal and Glu-26 of β-globin. Moreover, the extents of methylation at these sites were significantly correlated with the age of the subjects. On the other hand, no statistically significant difference was found in the ethylated peptides. We also examined the stability of methylated and ethylated hemoglobin when stored on dried blood spot cards. The extents of these modifications on hemoglobin are stable for at least 4 weeks stored at room temperature. Our results suggest that age should be considered as a factor when measuring hemoglobin methylation and that dried blood spot is a valuable biomonitoring technique for hemoglobin modifications in epidemiological studies.

Contrasting effects of pH on the modulation of the structural integrity of hemoglobin induced by sodium deoxycholate

Bile salt-mediated conformational modification of hemoglobin (Hb) was examined at three different pHs i.e., 3.2, 7.4 and 9.0. The added bile salt, sodium deoxycholate (NaDC), decreases the α-helicity in Hb (α-helix: 71.3% → 61.7% in the presence of 9.6 mM NaDC, and 83.2% → 66.2% in the presence of 14 mM NaDC, at pH 7.4 and 9.0, respectively), while a reverse pattern of modification in the Circular Dichroism (CD) spectra of Hb is found at pH 3.2. The acid-induced denatured Hb (pH 3.2) regains its structural integrity by changing conformation from a random coil to an α-helix rich secondary structure upon addition of NaDC (α-helix: 10.4% → 53.4%, β-sheet: 31.0% → 18.5% and random coil: 58.6% → 28.1%, in the presence of 0.65 mM NaDC). Also, a step-wise binding interaction pattern of Hb with NaDC was revealed at pH 7.4 and 9.0 upon variation of steady-state fluorescence intensity and average lifetime of Hb. From the fluorescence lifetime decay pattern, the decrement of energy transfer from Trp to a heme group was found upon the addition of NaDC at pH 7.4 and 9.0. However, at pH 3.2, the modification of the time-resolved fluorescence decay behavior of Hb within NaDC is typically reversed, where the energy transfer from Trp to heme is restored to some extent. Thermodynamic analysis suggests that the Hb-NaDC binding interaction is characterized by a dominant entropic contribution interpreted on the basis of release of ordered water molecules to the bulk aqueous phase.

Analysis of Chlorination, Nitration, and Nitrosylation of Tyrosine and Oxidation of Methionine and Cysteine in Hemoglobin from Type 2 Diabetes Mellitus Patients by Nanoflow Liquid Chromatography Tandem Mass Spectrometry

The post-translational modification (PTM) of proteins by endogenous reactive chlorine, nitrogen, and oxygen species is implicated in certain pathological conditions, including diabetes mellitus. Evidence showed that the extents of modifications on a number of proteins are elevated in diabetic patients. Measuring modification on hemoglobin has been used to monitor the extent of exposure. This study develops an assay for simultaneous quantification of the extent of chlorination, nitration, and oxidation in human hemoglobin and to examine whether the level of any of these modifications is higher in poorly controlled type 2 diabetic mellitus patients. This mass spectrometry-based assay used the bottom-up proteomic strategy. Due to the low amount of endogenous modification, we first characterized the sites of chlorination at tyrosine in hypochlorous acid-treated hemoglobin by an accurate mass spectrometer. The extents of chlorination, nitration, and oxidation of a total of 12 sites and types of modifications in hemoglobin were measured by nanoflow liquid chromatography-nanospray ionization tandem mass spectrometry under the selected reaction monitoring mode. Relative quantification of these PTMs in hemoglobin extracted from blood samples shows that the extents of chlorination at α-Tyr-24, nitration at α-Tyr-42, and oxidation at the three methionine residues are significantly higher in diabetic patients (n = 19) than in nondiabetic individuals (n = 18). After excluding the factor of smoking, chlorination at α-Tyr-24, nitration at α-Tyr-42, and oxidation at the three methionine residues are significantly higher in the nonsmoking diabetic patients (n = 12) than in normal nonsmoking subjects (n = 11). Multiple regression analysis performed on the combined effect of age, body-mass index (BMI), and HbA1c showed that the diabetes factor HbA1c contributes significantly to the extent of chlorination at α-Tyr-24 in nonsmokers. In addition, age contributes to oxidation at α-Met-32 significantly in all subjects and in nonsmokers. These results suggest the potential of using chlorination at α-Tyr-24-containing peptide to evaluate protein damage in nonsmoking type 2 diabetes mellitus.

Electron-capture dissociation and ion mobility mass spectrometry for characterization of the hemoglobin protein assembly

Native spray has the potential to probe biophysical properties of protein assemblies. Here we report an investigation using both ECD top-down sequencing with an FTICR mass spectrometer and ion mobility (IM) measurements on a Q-TOF to investigate the collisionally induced unfolding of a native-like heterogeneous tetrameric assembly, human hemoglobin (hHb), in the gas phase. To our knowledge, this is the first report combining ECD and ion-mobility data on the same target protein assembly to delineate the effects of collisional activation on both assembly size and the extent and location of fragmentation. Although the collision-induced unfolding of the hemoglobin assembly is clearly seen by both IMMS and ECD, the latter delineates the regions that increasingly unfold as the collision energy is increased. The results are consistent with previous outcomes for homogeneous protein assemblies and reinforce our interpretation that activation opens the structure of the protein assembly from the flexible regions to make available ECD fragmentation, without dissociating the component proteins.

Study of the interaction between DNP and DIDS with human hemoglobin as binary and ternary systems: spectroscopic and molecular modeling investigation

The combination of several drugs is necessary, especially during long-term therapy. A competitive binding of the drugs can cause a decrease in the amount of drugs actually bound to the protein and increase the biologically active fraction of the drug. Here, the interaction between 4,4'-Diisothiocyano-2,2'-stilbenedisulfonic acid (DIDS) and 2,4-Dinitrophenol (DNP) with Hemoglobin (Hb) was investigated by different spectroscopic and molecular modeling techniques. Fluorescence analysis was used to estimate the effect of the DIDS and DNP on Hb as well as to define the binding properties of binary and ternary complexes. The distance r between donor and acceptor was obtained by the FRET and found to be 2.25 and 2.13 nm for DIDS and DNP in binary and 2.08 and 2.07 nm for (Hb-DNP) DIDS and (Hb-DIDS) DNP complexes in ternary systems, respectively. Time-resolved fluorescence spectroscopy confirmed static quenching for Hb in the presence of DIDS and DNP in both systems. Furthermore, an increase in ellipticity values of Hb upon interaction with DIDS and DNP showed secondary structural changes of protein that determine to disrupt of hydrogen bonds and electrostatic interactions. Our results showed that the Hb destabilize in the presence of DIDS and DNP. Molecular modeling of the possible binding sites of DIDS and DNP in binary and ternary systems in Hb confirmed the experimental results.

Application of merged spectroscopic data combined with chemometric analysis for resolution of hemoglobin intermediates during chemical unfolding

Using tetradecyltrimethylammonium bromide (TTAB) as a surfactant denaturant, and augmentation of different spectroscopic data, helped to detect the intermediates of hemoglobin (Hb) during unfolding process. UV-vis, fluorescence, and circular dichroism spectroscopy were used simultaneously to monitor different aspects of hemoglobin species from the tertiary or secondary structure points of view. Application of the multivariate curve resolution-alternating least square (MCR-ALS), using the initial estimates of spectral profiles and appropriate constraints on different parts of augmented spectroscopic data, showed good efficiency for characterization of intermediates during Hb unfolding. These results indicated the existence of five protein species, including three intermediate-like compounds in this process. The unfolding pathway in the presence of TTAB included conversion of oxyhemoglobin into deoxyhemoglobin, and then ferrylhemoglobin, ferrihemoglobin or aquamethemoglobin, which finally transformed into hemichrome. This is the first application of chemometric analysis on the merged spectroscopic data related to chemical denaturation of a protein. These types of analysis in multisubunit proteins not only increase the domain of information, but also can reduce the ambiguities of the obtained results.

Native top-down mass spectrometry for the structural characterization of human hemoglobin

Native mass spectrometry (MS) has become an invaluable tool for the characterization of proteins and noncovalent protein complexes under near physiological solution conditions. Here we report the structural characterization of human hemoglobin (Hb), a 64 kDa oxygen-transporting protein complex, by high resolution native top-down MS using electrospray ionization and a 15-Tesla Fourier transform ion cyclotron resonance mass spectrometer. Native MS preserves the noncovalent interactions between the globin subunits, and electron capture dissociation (ECD) produces fragments directly from the intact Hb complex without dissociating the subunits. Using activated ion ECD, we observe the gradual unfolding process of the Hb complex in the gas phase. Without protein ion activation, the native Hb shows very limited ECD fragmentation from the N-termini, suggesting a tightly packed structure of the native complex and therefore a low fragmentation efficiency. Precursor ion activation allows a steady increase in N-terminal fragment ions, while the C-terminal fragments remain limited (38 c ions and four z ions on the α chain; 36 c ions and two z ions on the β chain). This ECD fragmentation pattern suggests that upon activation, the Hb complex starts to unfold from the N-termini of both subunits, whereas the C-terminal regions and therefore the potential regions involved in the subunit binding interactions remain intact. ECD-MS of the Hb dimer shows similar fragmentation patterns as the Hb tetramer, providing further evidence for the hypothesized unfolding process of the Hb complex in the gas phase. Native top-down ECD-MS allows efficient probing of the Hb complex structure and the subunit binding interactions in the gas phase. It may provide a fast and effective means to probe the structure of novel protein complexes that are intractable to traditional structural characterization tools.

Approaches to Interchain Cysteine-Linked ADC Characterization by Mass Spectrometry

Therapeutic antibody-drug conjugates (ADCs) harness the cell-killing potential of cytotoxic agents and the tumor targeting specificity of monoclonal antibodies to selectively kill tumor cells. Recent years have witnessed the development of several promising modalities that follow the same basic principles of ADC based therapies but which employ unique cytotoxic agents and conjugation strategies in order to realize therapeutic benefit. The complexity and heterogeneity of ADCs present a challenge to some of the conventional analytical methods that industry has relied upon for biologics characterization. This current review will highlight some of the more recent methodological approaches in mass spectrometry that have bridged the gap that is created when conventional analytical techniques provide an incomplete picture of ADC product quality. Specifically, we will discuss mass spectrometric approaches that preserve and/or capture information about the native structure of ADCs and provide unique insights into the higher order structure (HOS) of these therapeutic molecules.

Investigation on the conformation change of hemoglobin immobilized on MPA-modified electrode by electrochemical method

The conformation change of bovine hemoglobin (Hb) during the unfolding process induced by urea and acid was investigated by an electrochemical method. Hb unfolding induced by urea of different concentrations was realized by bonding Hb onto a 3-mercaptopropionic acid (MPA) modified gold electrode. The difference in unfolding percentage showed that the Hb unfolding induced by urea was a two-step, three-state transition process, while the unfolding induced by acid was a two-state transition process. The results obtained by the electrochemical method coincided closely with those obtained by UV-vis spectroscopy and fluorescence spectroscopy. Some thermodynamic parameters during the conformational change were also calculated to study the intermediate state during the Hb unfolding process. The present work may lead to an easy and effective way to study metalloproteins unfolding, and holds great promise for the design of novel sensitive biosensors.

High-throughput capillary electrophoresis-mass spectrometry: from analysis of amino acids to analysis of protein complexes

Recent advances in capillary electrophoresis-mass spectrometry (CE-MS) interfacing using porous tip is leading to commercialization of CE-MS with a sheathless interface for the first time. The new sheathless interface in conjunction with CE capillary coatings using self-coating background electrolytes (BGE) has significantly simplified CE-MS analysis of complex mixtures. CE-MS, with its high separation efficiency, compound identification capability, and ability to rapidly separate compounds with a wide range of mass and charge while consuming only nanoliters of samples, has become a valuable analytical technique for the analysis of complex biological mixtures. These advances have allowed a single capillary to analyze a range of compounds including amino acids, their D/L enantiomers, protein digests, intact proteins, and protein complexes. With these capabilities, CE-MS is poised to become the multipurpose tool of separation scientists. More recently, an eight-capillary CE in conjunction with an 8-inlet mass spectrometry has allowed 8 CE-MS analyses to be performed concurrently, significantly increasing throughput.

Reactive nitrogen oxide species-induced post-translational modifications in human hemoglobin and the association with cigarette smoking

Nitric oxide (NO) is essential for normal physiology, but excessive production of NO during inflammatory processes can damage the neighboring tissues. Reactive nitrogen oxide species (RNOx), including peroxynitrite (ONOO(-)), are powerful nitrating agents. Biological protein nitration is involved in several disease states, including inflammatory diseases, and it is evident by detection of 3-nitrotyrosine (3NT) in inflamed tissues. In this study, we identified peroxynitrite-induced post-translational modifications (PTMs) in human hemoglobin by accurate mass measurement as well as by the MS(2) and MS(3) spectra. Nitration on Tyr-24, Tyr-42 (α-globin), and Tyr-130 (β-globin) as well as nitrosation on Tyr-24 (α-globin) were identified. Also characterized were oxidation of all three methionine residues, α-Met-32, α-Met-76, and β-Met-55 to the sulfoxide, as well as cysteine oxidation determined as sulfinic acid on α-Cys-104 and sulfonic acid on α-Cys-104, β-Cys-93, and β-Cys-112. These modifications are detected in hemoglobin freshly isolated from human blood and the extents of modifications were semiquantified relative to the reference peptides by nanoflow liquid chromatography-nanospray ionization tandem mass spectrometry (nanoLC-NSI/MS/MS) under the selected reaction monitoring (SRM) mode. The results showed a statistically significant positive correlation between cigarette smoking and the extents of tyrosine nitration at α-Tyr-24 and at α-Tyr-42. To our knowledge, this is the first report on identification and quantification of multiple PTMs in hemoglobin from human blood and association of a specific 3NT-containing peptide with cigarette smoking. This highly sensitive and specific assay only requires hemoglobin isolated from one drop (∼10 μL) of blood. Thus, measurement of these PTMs in hemoglobin might be feasible for assessing nitrative stress in vivo.

Mass spectrometry-based carboxyl footprinting of proteins: method evaluation

Protein structure determines function in biology, and a variety of approaches have been employed to obtain structural information about proteins. Mass spectrometry-based protein footprinting is one fast-growing approach. One labeling-based footprinting approach is the use of a water-soluble carbodiimide, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) and glycine ethyl ester (GEE) to modify solvent-accessible carboxyl groups on glutamate (E) and aspartate (D). This paper describes method development of carboxyl-group modification in protein footprinting. The modification protocol was evaluated by using the protein calmodulin as a model. Because carboxyl-group modification is a slow reaction relative to protein folding and unfolding, there is an issue that modifications at certain sites may induce protein unfolding and lead to additional modification at sites that are not solvent-accessible in the wild-type protein. We investigated this possibility by using hydrogen deuterium amide exchange (H/DX). The study demonstrated that application of carboxyl group modification in probing conformational changes in calmodulin induced by Ca(2+) binding provides useful information that is not compromised by modification-induced protein unfolding.

Vapor treatment of electrospray droplets: evidence for the folding of initially denatured proteins on the sub-millisecond time-scale

The exposure of electrospray droplets generated from either highly acidic or highly basic solutions to basic or acidic vapors, respectively, admitted into the counter-current drying gas, has been shown to lead to significant changes in the observed charge state distributions of proteins. In both cases, distributions of charge states changed from relatively high charge states, indicative of largely denatured proteins, to lower charge state distributions that are more consistent with native protein conformations. Ubiquitin, cytochrome c, myoglobin, and carbonic anhydrase were used as model systems. In some cases, bimodal distributions were observed that are not noted under any solution pH conditions. The extent to which changes in charge state distributions occur depends upon the initial solution pH and the pK(a) or pK(b) of the acidic or basic reagent, respectively. The evolution of charged droplets in the sampling region of the mass spectrometer inlet aperture, where the vapor exposure takes place, occurs within roughly 1 ms. The observed changes in the spectra, therefore, are a function of the magnitude of the pH change as well as the rates at which the proteins can respond to this change. The exposure of electrospray droplets in this fashion may provide means for accessing transient folding states for further characterization by mass spectrometry.

Alkali metal cation-induced destabilization of gas-phase protein-ligand complexes: consequences and prevention

Electrospray ionization, now a well established technique for studying noncovalent protein-ligand interactions, is prone to production of alkali metal adducts. Here it is shown that this adduction significantly destabilizes the interactions between two model proteins and their ligands and that destabilization correlates with cation size. For both the [FKBP·FK506] and [lysozyme·NAG(n)] systems, dissociation of the metalated complex occurs at markedly lower collision energies than their purely protonated equivalents. Dependency upon size of the metal(+) demonstrates the importance of electrostatic charge density during the dissociation process. Differences in the gas phase basicities (GBapp) of the multiply charged protein ions and proton and sodium affinities of the ligands explain the observed charge partitioning during dissociation of the complexes. Ion mobility-mass spectrometry measurements demonstrate that metal cation adduction does not induce a significant increase in unfolding of the polypeptides, indicating that this is not the principal mechanism responsible for destabilization. Destabilizing effects can be largely reduced by exposing the electrospray to solvent (e.g., acetonitrile) vapor, a method that acts to reduce the amount of adduct formation as well as decrease the charge states of the resulting ions. This approach leads to more accurate determination of apparent K(D)s in the presence of trace alkali metals.

Obtaining antimicrobial peptides by controlled peptic hydrolysis of bovine hemoglobin

Under standard conditions, the peptides and specially the active peptides were obtained from either the denatured hemoglobin that all structures are completely modified or either the native hemoglobin where all structures are intact. In these conditions, antibacterial peptides were isolated from a very complex peptidic hydrolysate which contains more than one hundred peptides having various sizes and characteristics, involving a complex purification process. The new hydrolysis conditions were obtained by using 40% methanol, 30% ethanol, 20% propanol or 10% butanol. These conditions, where only the secondary structure of hemoglobin retains intact, were followed in order to enrich the hydrolyzed hemoglobin by active peptides or obtain new antibacterial peptides. In these controlled peptic hydrolysis of hemoglobin, a selective and restrictive hydrolysate contained only 29 peptides was obtained. 26 peptides have an antibacterial activity against Micrococcus luteus, Listeria innocua, and Escherichia coli with MIC from 187.1 to 1 μM. Among these peptides, 13 new antibacterial peptides are obtained only in these new hydrolysis conditions.

Protein-protein binding affinities in solution determined by electrospray mass spectrometry

Electrospray ionization (ESI) allows the transfer of multi-protein complexes into the gas phase, thereby providing a simple approach for monitoring the stoichiometry of these noncovalent assemblies by mass spectrometry (MS). It remains unclear, however, whether the measured ion abundance ratios of free and bound species are suitable for determining solution-phase binding affinities (K(d) values). Many types of mass spectrometers employ rf-only quadrupoles as ion guides. This work demonstrates that the settings used for these devices are a key factor for ensuring uniform transmission behavior, which is a prerequisite for meaningful affinity measurements. Using bovine β-lactoglobulin and hemoglobin as model systems, it is demonstrated that under carefully adjusted conditions the "direct" ESI-MS approach is capable of providing K(d) values that are in good agreement with previously published solution-phase data. Of the several ion sources tested, a regular ESI emitter operated with pressure-driven flow at 1 μL min(-1) provided the most favorable results. Potential problems in these experiments include conformationally-induced differences in ionization efficiencies, inadvertent collision-induced dissociation, and ESI-induced clustering artifacts. A number of simple tests can be conducted to assess whether or not these factors are prevalent under the conditions used. In addition, the fidelity of the method can be scrutinized by performing measurements over a wide concentration range. Overall, this work supports the viability of the direct ESI-MS approach for determining binding affinities of protein-protein complexes in solution.

AHSP (α-haemoglobin-stabilizing protein) stabilizes apo-α-haemoglobin in a partially folded state

To produce functional Hb (haemoglobin), nascent α-globin (αo) and β-globin (βo) chains must each bind a single haem molecule (to form αh and βh) and interact together to form heterodimers. The precise sequence of binding events is unknown, and it has been suggested that additional factors might enhance the efficiency of Hb folding. AHSP (α-haemoglobin-stabilizing protein) has been shown previously to bind αh and regulate redox activity of the haem iron. In the present study, we used a combination of classical and dynamic light scattering and NMR spectroscopy to demonstrate that AHSP forms a heterodimeric complex with αo that inhibits αo aggregation and promotes αo folding in the absence of haem. These findings indicate that AHSP may function as an αo-specific chaperone, and suggest an important role for αo in guiding Hb assembly by stabilizing βo and inhibiting off-pathway self-association of βh.

Observation of symmetric denaturation of hemoglobin subunits by electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry (ESI-MS) has been used to characterize the denaturation of porcine hemoglobin (Hb) induced by solvent changes. This work provides evidence for the symmetric nature of Hb denaturation and demonstrates that heme losses from α- and β-monomers occur in parallel, in response to the addition of acid and organic co-solvents in solution. When subject to one of the following solution conditions (pH 3.2-4.0 or 15-30% acetonitrile-water or 30-45% methanol-water solution), α- and β-globins undergo symmetric dissociation to release the heme groups, which is detected by ESI-MS. Circular dichroism (CD) and fluorescence spectroscopy (FS) data show that the acid-induced and organic solvent-induced heme release, as observed in the mass spectra, can probably be ascribed to different aspects of the conformational changes taking place in the protein. The acidity of the solvent has a significant effect on the secondary structure, whereas organic content level in solution (15-30% acetonitrile or 30-45% methanol) tends to destroy the tertiary structure of Hb globins, both leading to release of the heme from each subunit.

Probing hemoglobin structure by means of traveling-wave ion mobility mass spectrometry

Hemoglobin (Hb) is a tetrameric noncovalent complex consisting of two alpha- and two beta-globin chains each associated with a heme group. Its exact assembly pathway is a matter of debate. Disorders of hemoglobin are the most common inherited disorders and subsequently the molecule has been extensively studied. This work attempts to further elucidate the structural properties of the hemoglobin tetramer and its components. Gas-phase conformations of hemoglobin tetramers and their constituents were investigated by means of traveling-wave ion mobility mass spectrometry. Sickle (HbS) and normal (HbA) hemoglobin molecules were analyzed to determine whether conformational differences in their quaternary structure could be observed. Rotationally averaged collision cross sections were estimated for tetramer, dimer, apo-, and holo-monomers with reference to a protein standard with known cross sections. Estimates of cross section obtained for the tetramers were compared to values calculated from X-ray crystallographic structures. HbS was consistently estimated to have a larger cross section than that of HbA, comparable with values obtained from X-ray crystallographic structures. Nontetrameric species observed included apo- and holo- forms of alpha- and beta-monomers and heterodimers; alpha- and beta-monomers in both apo- and holo- forms were found to have similar cross sections, suggesting they maintain a similar fold in the gas phase in both the presence and the absence of heme. Heme-deficient dimer, observed in the spectrum when analyzing commercially prepared Hb, was not observed when analyzing fresh blood. This implies that holo-alpha-apo-beta is not an essential intermediate within the Hb assembly pathway, as previously proposed.

Gas-phase H/D exchange and collision cross sections of hemoglobin monomers, dimers, and tetramers

The conformations of gas-phase ions of hemoglobin, and its dimer and monomer subunits have been studied with H/D exchange and cross section measurements. During the H/D exchange measurements, tetramers undergo slow dissociation to dimers, and dimers to monomers, but this did not prevent drawing conclusions about the relative exchange levels of monomers, dimers, and tetramers. Assembly of the monomers into tetramers, hexamers, and octamers causes the monomers to exchange a greater fraction of their hydrogens. Dimer ions, however, exchange a lower fraction of their hydrogens than monomers or tetramers. Solvation of tetramers affects the exchange kinetics. Solvation molecules do not appear to exchange, and solvation lowers the overall exchange level of the tetramers. Cross section measurements show that monomer ions in low charge states, and tetramer ions have compact structures, comparable in size to the native conformations in solution. Dimers have remarkably compact structures, considerably smaller than the native conformation in solution and smaller than might be expected from the monomer or tetramer cross sections. This is consistent with the relatively low level of exchange of the dimers.