Deamidation Reactions of Asparagine- and Glutamine-Containing Dipeptides Investigated by Ion Spectroscopy

Streamlined Multi-Attribute Assessment of an Array of Clinical-Stage Antibodies: Relationship Between Degradation and Stability

Clinical antibodies are an important class of drugs for the treatment of both chronic and acute diseases. Their manufacturability is subject to evaluation to ensure product quality and efficacy. One critical quality attribute is deamidation, a non-enzymatic process that is observed to occur during thermal stress, at low or high pH, or a combination thereof. Deamidation may induce antibody instability and lead to aggregation, which may pose immunogenicity concerns. The introduction of a negative charge via deamidation may impact the desired therapeutic function (i) within the complementarity-determining region, potentially causing loss of efficacy; or (ii) within the fragment crystallizable region, limiting the effector function involving antibody-dependent cellular cytotoxicity. Here we describe a transformative solution that allows for a comparative assessment of deamidation and its impact on stability and aggregation. The innovative streamlined method evaluates the intact protein in its formulation conditions. This breakthrough platform technology is comprised of a quantum cascade laser microscope, a slide cell array that allows for flexibility in the design of experiments, and dedicated software. The enhanced spectral resolution is achieved using two-dimensional correlation, co-distribution, and two-trace two-dimensional correlation spectroscopies that reveal the molecular impact of deamidation. Eight re-engineered immunoglobulin G4 scaffold clinical antibodies under control and forced degradation conditions were evaluated for deamidation and aggregation. We determined the site of deamidation, the overall extent of deamidation, and where applicable, whether the deamidation event led to self-association or aggregation of the clinical antibody and the molecular events that led to the instability. The results were confirmed using orthogonal techniques for four of the samples.

Identification of organic micro-pollutants in surface water using MS-based infrared ion spectroscopy

Comprehensive monitoring of organic micro-pollutants (OMPs) in drinking water sources relies on non-target screening (NTS) using liquid-chromatography and high-resolution mass spectrometry (LC-HRMS). Identification of OMPs is typically based on accurate mass and tandem mass spectrometry (MS/MS) data by matching against entries in compound databases and MS/MS spectral libraries. MS/MS spectra are, however, not always diagnostic for the full molecular structure and, moreover, emerging OMPs or OMP transformation products may not be present in libraries. Here we demonstrate how infrared ion spectroscopy (IRIS), an emerging MS-based method for structural elucidation, can aid in the identification of OMPs. IRIS measures the IR spectrum of an m/z-isolated ion in a mass spectrometer, providing an orthogonal diagnostic for molecular identification. Here, we demonstrate the workflow for identification of OMPs in river water and show how quantum-chemically predicted IR spectra can be used to screen potential candidates and suggest structural assignments. A crucial step herein is to define a set of candidate structures, presumably including the actual OMP, for which we present several strategies based on domain knowledge, the IR spectrum and MS/MS spectrum.

Immobilization of Agaricus bisporus Polyphenol Oxidase 4 on mesoporous silica: Towards mimicking key enzymatic processes in peat soils

HYPOTHESIS

The use of immobilized enzyme-type biocatalysts to mimic specific processes in soil can be considered one of the most promising alternatives to overcome the difficulties behind the structural elucidation of riverine humic-derived iron-complexes. Herein, we propose that the immobilization of the functional mushroom tyrosinase, Agaricus bisporus Polyphenol Oxidase 4 (AbPPO4) on mesoporous SBA-15-type silica could contribute to the study of small aquatic humic ligands such as phenols.

EXPERIMENTS

The silica support was functionalized with amino-groups in order to investigate the impact of surface charge on the tyrosinase loading efficiency as well as on the catalytic performance of adsorbed AbPPO4. The oxidation of various phenols was catalyzed by the AbPPO4-loaded bioconjugates, yielding high levels of conversion and confirming the retention of enzyme activity after immobilization. The structures of the oxidized products were elucidated by integrating chromatographic and spectroscopic techniques. We also evaluated the stability of the immobilized enzyme over a wide range of pH values, temperatures, storage-times and sequential catalytic cycles.

FINDINGS

This is the first report where the latent AbPPO4 is confined within silica mesopores. The improved catalytic performance of the adsorbed AbPPO4 shows the potential use of these silica-based mesoporous biocatalysts for the preparation of a column-type bioreactor for in situ identification of soil samples.

Computing the Differences between Asn-X and Gln-X Deamidation and Their Impact on Pharmaceutical and Physiological Proteins: A Theoretical Investigation Using Model Dipeptides

Protein deamidation is a degradation mechanism that significantly impacts both pharmaceutical and physiological proteins. Deamidation impacts two amino acids, Asn and Gln, where the net neutral residues are converted into their acidic forms. While there are multiple similarities between the reaction mechanisms of the two residues, the impact of Gln deamidation has been noted to be most significant on physiological proteins while Asn deamidation has been linked to both pharmaceutical and physiological proteins. For this purpose, we sought to analyze the thermochemical and kinetic properties of the different reactions of Gln deamidation relative to Asn deamidation. In this study, we mapped the deamidation of Gln-X dipeptides into Glu-X dipeptides using density functional theory (DFT). Full network mapping facilitated the prediction of reaction selectivity between the two primary pathways, as well as between the two products of Gln-X deamidation as a function of solvent dielectric. To achieve this analysis, we studied a total of 77 dipeptide reactions per solvent dielectric (308 total reactions). Modeled at a neutral pH and using quantum chemical and statistical thermodynamic methods, we computed the following values: enthalpy of reaction (ΔH_RXN), entropy (ΔS_RXN), Gibbs free energy of reaction (ΔG_RXN), activation energy (E_A), and the Arrhenius preexponential factor (log(A)) for each dipeptide. Additionally, using chemical reaction principles, we generated a database of computed rate coefficients for all possible N-terminus Gln-X deamidation reactions at a neutral pH, predicted the most likely deamidation reaction mechanism for each dipeptide reaction, analyzed our results against our prior study on Asn-X deamidation, and matched our results against qualitative trends previously noted by experimental literature.

Disulfide bonds in the SAPA domain of the pulmonary surfactant protein B precursor

The disulfide bonds formed in the SAPA domain of a recombinant version of the NH₂-terminal propeptide (SP-B_N) from the precursor of human pulmonary surfactant protein B (SP-B) were identified through sequential digestion of SP-B_N with GluC/trypsin or thermolysin/GluC, followed by mass spectrometry (MS) analysis. MS spectra allowed identification of disulfide bonds between Cys³²-Cys⁴⁹ and Cys⁴⁰-Cys⁵⁵, and we propose a disulfide connectivity pattern of 1-3 and 2-4 within the SAPA domain, with the Cys residues numbered according to their position from the N-terminus of the propeptide sequence. The peaks with m/z ∼ 2136 and ∼ 1780 in the MS spectrum of the GluC/trypsin digest were assigned to peptides ²⁴AWTTSSLACAQGPE³⁷ and ⁴⁵QALQCR⁵⁰ linked by Cys³²-Cys⁴⁹ and ³⁸FWCQSLE⁴⁴ and ⁵¹ALGHCLQE⁵⁸ linked by Cys⁴⁰-Cys⁵⁵ respectively. Tandem mass spectrometry (MS/MS) analysis verified the position of the bonds. The results of the series ions, immonium ions and internal fragment ions were all compatible with the proposed 1-3/2-4 position of the disulfide bonds in the SAPA domain. This X-pattern differs from the kringle-type found in the SAPB domain of the SAPLIP proteins, where the first Cys in the sequence links to the last, the second to the penultimate and the third to the fourth one. Regarding the SAPB domain of the SP-B_N propeptide, the MS analysis of both digests identified the bond Cys¹⁰⁰-Cys¹¹², numbered 7-8, which is coincident with the bond position in the kringle motif. SIGNIFICANCE: The SAPLIP (saposin-like proteins) family encompasses several proteins with homology to saposins (sphingolipids activator proteins). These are proteins with mainly alpha-helical folds, compact packing including well conserved disulfide bonds and ability to interact with phospholipids and membranes. There are two types of saposin-like domains termed as Saposin A (SAPA) and Saposin B (SAPB) domains. While disulfide connectivity has been well established in several SAPB domains, the position of disulfide bonds in SAPA domains is still unknown. The present study approaches a detailed proteomic study to determine disulfide connectivity in the SAPA domain of the precursor of human pulmonary surfactant-associated protein SP-B. This task has been a challenge requiring the combination of different sequential proteolytic treatments followed by MS analysis including MALDI-TOF and tandem mass MS/MS spectrometry. The determination for first time of the position of disulfide bonds in SAPA domains is an important step to understand the structural determinants defining its biological functions.

Cell penetrating peptide (CPP) gold(iii) - complex - bioconjugates: from chemical design to interaction with cancer cells for nanomedicine applications

This study promotes an innovative synthesis of a nanotheragnostic scaffold capable of targeting and destroying pancreatic cancer cells (PDAC) using the Biotinylated NFL-TBS.40-63 peptide (BIOT-NFL), known to enter various glioblastoma cancer cells (GBM) where it specifically destroys their microtubule network. This recently proposed methodology (P7391FR00-50481 LIV) applied to other peptides VIM (Vimentin) and TAT (Twin-Arginine Translocation) (CPP peptides) has many advantages, such as targeted selective internalization and high stability under experimental conditions, modulated by steric and chemical configurations of peptides. The successful interaction of peptides on gold surfaces has been confirmed by UV-visible, dynamic light scattering (DLS), Zeta potential (ZP) and Raman spectroscopy analyses. The cellular internalization in pancreatic ductal adenocarcinoma (PDAC; MIA PACA-2) and GBM (F98) cells was monitored by transmission electron microscopy (TEM) and showed a better cellular internalization in the presence of peptides with gold nanoparticles. In this work, we also evaluated the power of these hybrid peptide-nanoparticles as photothermal agents after cancer cell internalization. These findings envisage novel perspectives for the development of high peptide-nanotheragnostics.

Influence of a Hydroxyl Group on the Deamidation and Dehydration Reactions of Protonated Asparagine-Serine Investigated by Combined Spectroscopic, Guided Ion Beam, and Theoretical Approaches

Deamidation of asparaginyl (Asn) peptides is a spontaneous post-translational modification that plays a significant role in degenerative diseases and other biological processes under physiological conditions. In the gas phase, deamidation of protonated peptides is a major fragmentation channel upon activation by collision-induced dissociation. Here, we present a full description of the deamidation process from protonated asparagine-serine, [AsnSer+H]⁺, via infrared (IR) action spectroscopy and threshold collision-induced dissociation (TCID) experiments in combination with theoretical calculations. The IR results demonstrate that deamidation proceeds via bifurcating reaction pathways leading to furanone- and succinimide-type product ion structures, with a population analysis indicating the latter product dominates. Theory demonstrates that nucleophilic attack of the peptidyl amide oxygen onto the Asn side chain leads to furanone formation, whereas nucleophilic attack by the peptidyl amide nitrogen onto the Asn side-chain carbonyl carbon leads to the formation of the succinimide product structure. TCID experiments find that furanone formation has a threshold energy of 145 ± 12 kJ/mol and succinimide formation occurs with a threshold energy of 131 ± 12 kJ/mol, consistent with theoretical energies and with the spectroscopic results indicating that succinimide dominates. The results provide information regarding the inductive and steric effects of the Ser side chain on the deamidation process. The other major channel observed in the TCID experiments of [AsnSer+H]⁺ is dehydration, where a threshold energy of 104 ± 10 kJ/mol is determined. A complete IR and theoretical analysis of this pathway is also provided. As for deamidation, a bifurcating pathway is found with both dominant oxazoline and minor diketopiperazine products identified. Here, the Ser side chain is directly involved in both pathways.

Spontaneous protein–protein crosslinking at glutamine and glutamic acid residues in long-lived proteins

Long-lived proteins (LLPs) are susceptible to the accumulation of both enzymatic and spontaneous post-translational modifications (PTMs). A prominent PTM observed in LLPs is covalent protein–protein crosslinking. In this study, we examined aged human lenses and found several proteins to be crosslinked at Glu and Gln residues. This new covalent bond involves the amino group of Lys or an α-amino group. A number of these crosslinks were found in intermediate filament proteins. Such crosslinks could be reproduced experimentally by incubation of Glu- or Gln-containing peptides and their formation was consistent with an amino group attacking a glutarimide intermediate. These findings show that both Gln and Glu residues can act as sites for spontaneous covalent crosslinking in LLPs and they provide a mechanistic explanation for an otherwise puzzling observation, that a major fraction of Aβ in the human brain is crosslinked via Glu 22 and the N-terminal amino group.

Bottom-up sample preparation for the LC-MS/MS quantification of anti-cancer monoclonal antibodies in bio matrices

Therapeutic monoclonal antibodies (mAbs) are rapidly taking over the treatment of many malignancies, and an astonishing number of mAbs is in development. This causes a high demand for quantification of mAbs in biomatrices both for measuring therapeutic mAb concentrations and to support pharmacokinetics and pharmacodynamics studies. Conventionally, ligand-binding assays are used for these purposes, but LC-MS is gaining popularity. Although intact (top-down) and subunit (middle-down) mAb quantification is reported, signature peptide (bottom-up) quantification is currently most advantageous. This review provides an overview of the reported bottom-up mAb quantification methods in biomatrices as well as general recommendations regarding signature peptide and internal standard selection, reagent use and optimization of digestion in bottom-up quantification methods.

Mechanism of protein cleavage at asparagine leading to protein-protein cross-links

Long-lived proteins (LLPs) are present in numerous tissues within the human body. With age, they deteriorate, often leading to the formation of irreversible modifications such as peptide bond cleavage and covalent cross-linking. Currently understanding of the mechanism of formation of these cross-links is limited. As part of an ongoing study, proteomics was used to characterise sites of novel covalent cross-linking in the human lens. In this process, Lys residues were found cross-linked to C-terminal aspartates that had been present in the original protein as Asn residues. Cross-links were identified in major lens proteins such as αA-crystallin, αB-crystallin and aquaporin 0. Quantification of the level of an AQP0/AQP0 cross-linked peptide showed increased cross-linking with age and in cataract lenses. Using model peptides, a mechanism of cross-link formation was elucidated that involves spontaneous peptide bond cleavage on the C-terminal side of Asn residues resulting in the formation of a C-terminal succinimide. This succinimide does not form cross-links, but can hydrolyse to a mixture of C-terminal Asn and C-terminal Asp amide peptides. The C-terminal Asp amide is unstable at neutral pH and decomposes to a succinic anhydride. If the side chain of Lys attacks the anhydride, a covalent cross-link will be formed. This multi-step mechanism represents a link between two spontaneous events: peptide bond cleavage at Asn and covalent cross-linking. Since Asn deamidation and cleavage are abundant age-related modifications in LLPs, this finding suggests that such susceptible Asn residues should also be considered as potential sites for spontaneous covalent cross-linking.

Role of Chemical Dynamics Simulations in Mass Spectrometry Studies of Collision-Induced Dissociation and Collisions of Biological Ions with Organic Surfaces

In this article, a perspective is given of chemical dynamics simulations of collisions of biological ions with surfaces and of collision-induced dissociation (CID) of ions. The simulations provide an atomic-level understanding of the collisions and, overall, are in quite good agreement with experiment. An integral component of ion/surface collisions is energy transfer to the internal degrees of freedom of both the ion and the surface. The simulations reveal how this energy transfer depends on the collision energy, incident angle, biological ion, and surface. With energy transfer to the ion's vibration fragmentation may occur, i.e. surface-induced dissociation (SID), and the simulations discovered a new fragmentation mechanism, called shattering, for which the ion fragments as it collides with the surface. The simulations also provide insight into the atomistic dynamics of soft-landing and reactive-landing of ions on surfaces. The CID simulations compared activation by multiple "soft" collisions, resulting in random excitation, versus high energy single collisions and nonrandom excitation. These two activation methods may result in different fragment ions. Simulations provide fragmentation products in agreement with experiments and, hence, can provide additional information regarding the reaction mechanisms taking place in experiment. Such studies paved the way on using simulations as an independent and predictive tool in increasing fundamental understanding of CID and related processes.

Collisional dynamics simulations revealing fragmentation properties of Zn(ii)-bound poly-peptide

Collisional simulations show how peptide fragmentation is modified by the presence of Zn(ii).

Apparent degradation forms of rhG-CSF under forced conditions: Insights for better quality-control of bioproducts

Stability and quality control of therapeutic protein formulations is a substantial part of drug development process. The objective of this study is to obtain information about stability of a recombinant human granulocyte colony stimulating factor (rhG-CSF) against various stress factors. This will play a crucial role in the finished product formulation development. In this study, rhG-CSF was exposed to various chemical and physical stress conditions at different levels in order to identify degradation pathways and the nature of impurities generated. Experiments were performed by a combination of orthogonal analytical techniques (reversed phase chromatography (RP-HPLC), size exclusion chromatography (SEC-HPLC), polyacrylamide gel electrophoresis (SDS-PAGE) and isoelectric focusing (IEF)) to set and characterize the different degraded samples. The SEC-HPLC results suggest that the major degradation factors generating aggregated forms of the protein are basically thermal stress, freeze-thaw cycles and vortexing. Meanwhile, deamidated rhG-CSF was induced by basic pH as shown by IEF electrophoregram. As well, oxidized forms were generated increasingly with the time of exposure to hydrogen peroxide as outlined by RP-HPLC analysis. Based on these results, it was possible to define the storage and handling conditions of rhG-CSF finished product during its shelf life.

Investigation of the position of the radical in z3-ions resulting from electron transfer dissociation using infrared ion spectroscopy

The molecular structures of six open-shell z₃-ions resulting from electron transfer dissociation mass spectrometry (ETD MS) were investigated using infrared ion spectroscopy in combination with density functional theory and molecular mechanics/molecular dynamics calculations.

w-Type ions formed by electron transfer dissociation of Cys-containing peptides investigated by infrared ion spectroscopy

In mass spectrometry-based peptide sequencing, electron transfer dissociation (ETD) and electron capture dissociation (ECD) have become well-established fragmentation methods complementary to collision-induced dissociation. The dominant fragmentation pathways during ETD and ECD primarily involve the formation of c- and z^• -type ions by cleavage of the peptide backbone at the N─C_α bond, although neutral losses from amino acid side chains have also been observed. Residue-specific neutral side chain losses provide useful information when conducting database searching and de novo sequencing. Here, we use a combination of infrared ion spectroscopy and quantum-chemical calculations to assign the structures of two ETD-generated w-type fragment ions. These ions are spontaneously formed from ETD-generated z^• -type fragments by neutral loss of 33 Da in peptides containing a cysteine residue. Analysis of the infrared ion spectra confirms that these z^• -ions expel a thiol radical (SH^• ) and that a vinyl C═C group is formed at the cleavage site. z^• -type fragments containing a Cys residue but not at the cleavage site do not spontaneously expel a thiol radical, but only upon additional collisional activation after ETD.

Protonated Asparaginyl-Alanine Decomposition: a TCID, SORI-CID, and Computational Analysis

Deamidation of asparagine residues, one of the fastest known post-translational modifications in proteins, plays a significant role in various biological functions and degenerative, aging diseases. Here, we present a full description of deamidation (as well as other key dissociation processes) from protonated asparaginyl-alanine, H⁺(AsnAla), by studying its kinetic energy-dependent threshold collision-induced dissociation (TCID) with Xe using a guided ion beam tandem mass spectrometer. Relative thresholds compare favorably with those acquired by sustained off-resonance irradiation-CID of H⁺(AsnAla) with Ar in a Fourier transform ion cyclotron resonance mass spectrometer. Absolute threshold energies from the TCID studies are compared to relative single point energies of major reaction species calculated at the B3LYP, B3LYP-GD3BJ, B3P86, MP2(full), and M06-2X levels of theory. Relative energies of key TSs and products allow for the characterization of the important rate-limiting steps involved in H⁺(AsnAla) decomposition. The influence of water solvation on key TSs is also explored computationally, where bridging the gap between gas-phase and solvated studies is an important aspect of the biological relevance of this analysis. The comprehensive results presented (in addition to complementary studies discussed herein) allow for an insightful comparison to previous deamidation studies such that effects of the C-terminal residue side chain can be elucidated. Graphical abstract ᅟ.

Spectroscopic Characterization of an Extensive Set of c-Type Peptide Fragment Ions Formed by Electron Transfer Dissociation Suggests Exclusive Formation of Amide Isomers

Electron attachment dissociation (electron capture dissociation (ECD) and electron transfer dissociation (ETD)) applied to gaseous multiply protonated peptides leads predominantly to backbone N-C_α bond cleavages and the formation of c- and z-type fragment ions. The mechanisms involved in the formation of these ions have been the subject of much discussion. Here, we determine the molecular structures of an extensive set of c-type ions produced by ETD using infrared ion spectroscopy. Nine c₃- and c₄-ions are investigated to establish their C-terminal structure as either enol-imine or amide isomers by comparison of the experimental infrared spectra with quantum-chemically predicted spectra for both structural variants. The spectra suggest that all c-ions investigated possess an amide structure; the absence of the NH bending mode at approximately 1000-1200 cm^-1 serves as an important diagnostic feature.

Deamidation of Protonated Asparagine-Valine Investigated by a Combined Spectroscopic, Guided Ion Beam, and Theoretical Study

Peptide deamidation of asparaginyl residues is a spontaneous post-translational modification that is believed to play a role in aging and several diseases. It is also a well-known small-molecule loss channel in the MS/MS spectra of protonated peptides. Here we investigate the deamidation reaction, as well as other decomposition pathways, of the protonated dipeptide asparagine-valine ([AsnVal + H]+) upon low-energy activation in a mass spectrometer. Using a combination of infrared ion spectroscopy, guided ion beam tandem mass spectrometry, and theoretical calculations, we have been able to identify product ion structures and determine the energetics and mechanisms for decomposition. Deamidation proceeds via ammonia loss from the asparagine side chain, initiated by a nucleophilic attack of the peptide bond oxygen on the γ-carbon of the Asn side chain. This leads to the formation of a furanone ring containing product ion characterized by a threshold energy of 129 ± 5 kJ/mol (15 kJ/mol higher in energy than dehydration of [AsnVal + H]+, the lowest energy dissociation channel available to the system). Competing formation of a succinimide ring containing product, as has been observed for protonated asparagine-glycine ([AsnGly + H]+) and asparagine-alanine ([AsnAla + H]+), was not observed here. Quantum-chemical modeling of the reaction pathways confirms these subtle differences in dissociation behavior. Measured reaction thresholds are in agreement with predicted theoretical reaction energies computed at several levels of theory.

Chemical dynamics simulations of CID of peptide ions: comparisons between TIK(H+)2 and TLK(H+)2 fragmentation dynamics, and with thermal simulations

Gas phase unimolecular fragmentation of the two model doubly protonated tripeptides threonine-isoleucine-lysine (TIK) and threonine-leucine-lysine (TLK) is studied using chemical dynamics simulations. Attention is focused on different aspects of collision induced dissociation (CID): fragmentation pathways, energy transfer, theoretical mass spectra, fragmentation mechanisms, and the possibility of distinguishing isoleucine (I) and leucine (L). Furthermore, discussion is given regarding the differences between single collision CID activation, which results from a localized impact between the ions and a colliding molecule N₂, and previous thermal activation simulation results; Z. Homayoon, S. Pratihar, E. Dratz, R. Snider, R. Spezia, G. L. Barnes, V. Macaluso, A. Martin-Somer and W. L. Hase, J. Phys. Chem. A, 2016, 120, 8211-8227. Upon thermal activation unimolecular fragmentation is statistical and in accord with RRKM unimolecular rate theory. Simulations show that in collisional activation some non-statistical fragmentation occurs, including shattering, which is not present when the ions dissociate statistically. Products formed by non-statistical shattering mechanisms may be related to characteristic mass spectrometry peaks which distinguish the two isomers I and L.