Protein Deamidation Research Articles

The Fundamental Neurobiological Mechanism of Oxidative Stress-Related 4E-BP2 Protein Deamidation

Memory impairment is caused by the absence of the 4E-BP2 protein in the brain. This protein undergoes deamidation spontaneously in the neurons. 4E-BP2 deamidation significantly alters protein synthesis in the neurons and affects the balance of protein production required for a healthy nervous system. Any imbalance in protein production in the nervous system causes neurodegenerative diseases. Discovering what causes 4E-BP2 deamidation will make it possible to control this balance of protein production and develop effective treatments against neurodegenerative diseases such as Alzheimer’s and Parkinson’s. The purpose of this work is to discover the neurobiological mechanism that causes the deamidation reaction in the 4E-BP2 protein by performing immunoblotting in the retinal ganglia, the optic nerve, the dorsal root ganglia, the sciatic nerve, and the whole brain, extracted via dissection from 2-month-old, Wild-type male mice. The results show that axons and their unique properties cause neuron-specific 4E-BP2 deamidation in the nervous system, confirming conclusively that axons are the critical factors behind the fundamental neurobiological mechanism of 4E-BP2 protein deamidation.

Insights into structural and proteomic alterations related to pH-induced changes and protein deamidation in hair.

The hair shaft is often exposed to shampoo and haircare products that have unknown or varying pH levels. These products contain a combination of surfactants and other active ingredients to treat the hair or the scalp. As amphoteric proteins, hair keratins have limited buffering capacity, so variations in pH can have multifaceted impacts on them. However, there is limited knowledge about how pH affects keratins and keratin-associated proteins (KAPs). Therefore, this study aims to examine the effects of varying pH levels (pH 3-pH 12) on hair structure and analyse consequent alterations in the hair proteome using mass spectrometry-based proteomics. A scanning electron microscope was used to examine changes in hair-shaft morphology due to exposure to various pH levels, while mass spectrometry was employed to analyse protein alterations. We found that exposing the hair shaft to varying pH levels led to specific effects on the cuticle, including cuticle lifting at certain pH levels, while proteomics analysis identified alterations in the hair proteome along with significant deamidation of keratins types I and II and KAPs. More pronounced effects were observed at extreme acidic conditions (pH 3) and alkaline conditions (above pH 8) on both hair morphology and hair proteins. pH levels between pH 5 and pH 7 had minimal impact on hair structure and proteins, suggesting that haircare products with pH in this range are ideal for hair-shaft health. In contrast, alkaline pH levels were found to negatively affect hair. The structure evaluation and proteomics data emphasize the critical role of pH in hair health. The extreme acidic or alkaline pH impacts the hair structure and hair proteins. The study highlights the optimal pH range for maintaining healthy hair.

Plant protein-based complex coacervation via protein deamidation

Protein-polysaccharide complex coacervates, as common electrostatic assembly, have been widely used in probiotic encapsulation, emulsifiers, and binders. However, due to their own compact structure, plant proteins usually complex with polysaccharides to form solid-like precipitates via liquid-solid phase separation (LSPS) instead of droplet-like coacervates via liquid-liquid phase separation (LLPS). In this study, we adopted an enzymatic deamidation approach to promote the transition of protein-polysaccharide complexes from precipitates to coacervates. β-conglycinin (β-CG), as a common plant protein, was modified by protein-glutaminase (PG) and complexed with chitosan oligosaccharide (COS) to obtain droplet-like coacervates. Native-PAGE and SDS-PAGE results demonstrated that depolymerization of β-CG occurred during deamidation, leading to the production of oligomers and changes in the surface charge patchiness of β-CG. Isothermal titration calorimetry (ITC) results showed that precipitates were mainly driven by exotherm, while coacervates were driven by entropy gain. This study offers a novel approach for the generation of plant protein-based coacervates.

EnvZ/OmpR Controls Protein Expression and Modifications in Cronobacter sakazakii for Virulence and Environmental Resilience.

Cronobacter sakazakii is a notorious foodborne opportunistic pathogen, particularly affecting vulnerable populations such as premature infants, and poses significant public health challenges. This study aimed to elucidate the role of the envZ/ompR genes in environmental tolerance, pathogenicity, and protein regulation of C. sakazakii. An envZ/ompR knockout mutant was constructed and assessed for its impact on bacterial growth, virulence, environmental tolerance, and protein regulation. Results demonstrate that deletion of envZ/ompR genes leads to reduced growth rate and attenuated virulence in animal models. Additionally, the knockout strain exhibited compromised environmental tolerance, particularly in desiccation and oxidative stress conditions, along with impaired adhesion and invasion abilities in epithelial cells. Proteomic analysis revealed significant alterations in protein expression and phosphorylation patterns, highlighting potential compensatory mechanisms triggered by gene deletion. Furthermore, investigation into protein deamidation and glucose metabolism uncovered a link between envZ/ompR deletion and energy metabolism dysregulation. Interestingly, the downregulation of MalK and GrxC proteins was identified as contributing factors to altered desiccation tolerance and disrupted redox homeostasis, respectively, providing mechanistic insights into the phenotypic changes observed. Overall, this study enhances understanding of the multifaceted roles of envZ/ompR in C. sakazakii physiology and pathogenesis, shedding light on potential targets for therapeutic intervention and food safety strategies.

Effects of protein-glutaminase on the properties of glutinous rice flour, paste, and gel food: Based on the interactions between the deamidated protein and starch

In the present study, protein-glutaminase (PG) from Chryseobacterium proteolyticum was applied to improve the processing properties of glutinous rice flour (GRF). After PG modification, the degree of deamidation of glutinous rice protein (GRP) reached 13.6% at 2.0 h, with smaller particle size and decreased zeta potential. The interaction of GRP with starch in PG-modified GRF (PM-GRF) was changed, exhibiting in protein aggregates decreasing and exposure of starch on the surface of GRF. Compared with unmodified GRF (UM-GRF), the solubility and turbidity of PM-GRF were both increased. The rheological properties reflected that the viscosity of PM-GRF paste was increased, and the freeze-thaw stability was also enhanced. Moreover, the textural characteristics showed that the hardness of PM-GRF balls remarkably reduced and the springiness increased. These results indicate that deamidation by PG could be an efficient method for improving characteristics of GRP and GRF.

Computational Insights into Protein Aging: Spontaneous Deamidation of Glutamine.

Spontaneous deamidation of amino acids is a physiologically important process, particularly for protein aging and diseases. Despite its widespread occurrence, the mechanism of glutamine deamidation particularly within proteins remains poorly understood. We have used a multiscale computational approach to investigate glutamine deamidation in the tripeptide Glycine-Glutamine-Glycine (Gly-Gln-Gly) and γS-Crystallin protein. Specifically, both the 5- and 6-membered water-assisted deamidation pathways in the tripeptide have been elucidated and compared. Both are found to occur in three stages: iminol formation, cyclization, and deamination. The rate-limiting step in each mechanism is nucleophilic attack of the backbone iminol nitrogen, formed in the first stage, at the glutamine's side-chain carbonyl carbon. For the 6- and 5-membered mechanisms, this occurs with a free energy cost of 136.4 and 179.5 kJ mol-1, respectively. Thus, overall, in the Gly-Gln-Gly tripeptide, the 6-membered pathway is preferred. Furthermore, the free energies for forming cyclic intermediates and products at selected Gln residues (based on experimentally reported % deamidation) in γS-Crystallin have been obtained. It is found that the 5-membered product complex is exergonic at -25.3 kJ mol-1, while the 6-membered product complex is calculated to be endergonic at 90.7 kJ mol-1. Thus, the deamidation pathway in folded and constrained proteins may not exclusively follow the 6-membered route. Molecular dynamics (MD) simulations of γS-Crystallin indicate that deamidation is more likely to occur when two or more water molecules are in the proximity of the glutamine residue. Consequently, significant conformational changes are found to accompany Gln120 deamidation in γS-Crystallin. This in turn can influence water availability at the other Gln residues considered and hence potentially their deamidation. Collectively, these results provide comprehensive insights into spontaneous water-assisted deamidation of glutamine residues in peptides and into the role and impact of Gln deamidation in proteins.

Some Examples of Bacterial Toxins as Tools.

Pathogenic bacteria produce diverse protein toxins to disturb the host's defenses. This includes the opening of epithelial barriers to establish bacterial growth in deeper tissues of the host and to modulate immune cell functions. To achieve this, many toxins share the ability to enter mammalian cells, where they catalyze the modification of cellular proteins. The enzymatic activity is diverse and ranges from ribosyl- or glycosyl-transferase activity, the deamidation of proteins, and adenylate-cyclase activity to proteolytic cleavage. Protein toxins are highly active enzymes often with tight specificity for an intracellular protein or a protein family coupled with the intrinsic capability of entering mammalian cells. A broad understanding of their molecular mechanisms established bacterial toxins as powerful tools for cell biology. Both the enzymatic part and the pore-forming/protein transport capacity are currently used as tools engineered to study signaling pathways or to transport cargo like labeled compounds, nucleic acids, peptides, or proteins directly into the cytosol. Using several representative examples, this review is intended to provide a short overview of the state of the art in the use of bacterial toxins or parts thereof as tools.

Development of celiac-safe foods: prevention of transglutaminase 2 (TG2) deamidation of gluten in healthy non-celiac volunteers.

clinicaltrials.gov, identifier (NCT06005376).

Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins.

Post-translational modifications (PTMs) of proteins play a vital role in their function and stability. These modifications influence protein folding, signaling, protein-protein interactions, enzyme activity, binding affinity, aggregation, degradation, and much more. To date, over 400 types of PTMs have been described, representing chemical diversity well beyond the genetically encoded amino acids. Such modifications pose a challenge to the successful design of proteins, but also represent a major opportunity to diversify the protein engineering toolbox. To this end, we first trained artificial neural networks (ANNs) to predict eighteen of the most abundant PTMs, including protein glycosylation, phosphorylation, methylation, and deamidation. In a second step, these models were implemented inside the computational protein modeling suite Rosetta, which allows flexible combination with existing protocols to model the modified sites and understand their impact on protein stability as well as function. Lastly, we developed a new design protocol that either maximizes or minimizes the predicted probability of a particular site being modified. We find that this combination of ANN prediction and structure-based design can enable the modification of existing, as well as the introduction of novel, PTMs. The potential applications of our work include, but are not limited to, glycan masking of epitopes, strengthening protein-protein interactions through phosphorylation, as well as protecting proteins from deamidation liabilities. These applications are especially important for the design of new protein therapeutics where PTMs can drastically change the therapeutic properties of a protein. Our work adds novel tools to Rosetta's protein engineering toolbox that allow for the rational design of PTMs.

Does protein deamidation enhance rice protein concentrate’s ability to produce and stabilize high internal phase emulsions?

Rice is one of the most consumed grains in the world. Rice protein has great nutritional value as a hypoallergenic protein and due to its high lysine content, a limiting amino acid in several other plant protein sources. However, rice protein has low solubility, hampering its use in many applications in the food industry. In this context, alkaline deamidation (0.5 h, 343 K, and pH 11) was applied to modify the protein structure of rice protein concentrate (RPC). After deamidation, two protein powders were produced: (i) one containing the whole protein fraction recovered after RPC deamidation (DT) and (ii) another containing only the soluble fraction recovered after RPC deamidation (DS). Protein dispersions were characterized by SDS-PAGE, zeta potential, solubility, surface hydrophobicity, and capacity to hold water and oil. RPC could not structure canola oil into a high internal phase emulsion (HIPE) due to its low solubility. DT and DS dispersions displayed solubility much higher than RPC and enabled the structuration of HIPEs with 75 % (w/w) canola oil and 25 % of DT or DS dispersions (2, 4, and 6 % w/w). HIPEs were characterized regarding particle size, microstructure, Turbiscan and oil loss stabilities, and rheological behavior for 60 days. Turbiscan analysis and oil loss measurements showed high stability, and the thixotropy tests showed high recovery in all HIPEs. Higher protein concentrations and DS dispersions produced HIPEs with smaller particle sizes. However, rheological measurements indicate that HIPEs produced with DT dispersions had better results, maintaining their structure over the 60 days. Furthermore, DT is cheaper to produce; therefore, DT 4 and 6 % w/w were the most promising for producing HIPEs. The HIPEs produced in this study displayed great potential as fat replacers.

Bone collagen from subtropical Australia is preserved for more than 50,000 years

Ancient protein studies have demonstrated their utility for looking at a wide range of evolutionary and historical questions. The majority of palaeoproteomics studies to date have been restricted to high latitudes with relatively temperate environments. A better understanding of protein preservation at lower latitudes is critical for disentangling the mechanisms involved in the deep-time survival of ancient proteins, and for broadening the geographical applicability of palaeoproteomics. In this study, we aim to assess the level of collagen preservation in the Australian fossil record. Collagen preservation was systematically examined using a combination of thermal age estimates, Fourier Transform Infrared Spectroscopy, Zooarchaeology by Mass Spectrometry, and protein deamidation calculations. We reveal unexpected subtropical survival of collagen in bones more than 50 thousand years old, showing that protein preservation can exceed chemical predictions of collagen survival in bone. These findings challenge preconceptions concerning the suitability of palaeoproteomics in subtropical Pleistocene environments. We explore potential causes of this unexpected result to identify the underlying mechanisms leading to this exceptional preservation. This study serves as a starting point for the analysis of ancient proteins in other (sub)tropical contexts, and at deeper timescales.

Immunotherapy targeting isoDGR‐protein damage extends lifespan in a mouse model of protein deamidation

Aging results from the accumulation of molecular damage that impairs normal biochemical processes. We previously reported that age‐linked damage to amino acid sequence NGR (Asn‐Gly‐Arg) results in “gain‐of‐function” conformational switching to isoDGR (isoAsp‐Gly‐Arg). This integrin‐binding motif activates leukocytes and promotes chronic inflammation, which are characteristic features of age‐linked cardiovascular disorders. We now report that anti‐isoDGR immunotherapy mitigates lifespan reduction of Pcmt1−/− mouse. We observed extensive accumulation of isoDGR and inflammatory cytokine expression in multiple tissues from Pcmt1−/− and naturally aged WT animals, which could also be induced via injection of isoDGR‐modified plasma proteins or synthetic peptides into young WT animals. However, weekly injection of anti‐isoDGR mAb (1 mg/kg) was sufficient to significantly reduce isoDGR‐protein levels in body tissues, decreased pro‐inflammatory cytokine concentrations in blood plasma, improved cognition/coordination metrics, and extended the average lifespan of Pcmt1−/− mice. Mechanistically, isoDGR‐mAb mediated immune clearance of damaged isoDGR‐proteins via antibody‐dependent cellular phagocytosis (ADCP). These results indicate that immunotherapy targeting age‐linked protein damage may represent an effective intervention strategy in a range of human degenerative disorders.

Significant Differences in Capsid Properties and Potency Between Adeno-Associated Virus Vectors Produced in Sf9 and HEK293 Cells.

For successful vector-based gene therapy manufacturing, the selected adeno-associated virus (AAV) vector production system must produce vector at sufficient scale. However, concerns have arisen regarding the quality of vector produced using different systems. In this study, we compared AAV serotypes 1, 8, and 9 produced by two different systems (Sf9/baculovirus and HEK293/transfection) and purified by two separate processes. We evaluated capsid properties, including protein composition, post-translational modification, particle content profiles, and in vitro and in vivo vector potency. Vectors produced in the Sf9/baculovirus system displayed reduced incorporation of viral protein 1 and 2 into the capsid, increased capsid protein deamidation, increased empty and partially packaged particles in vector preparations, and an overall reduced potency. The differences observed were largely independent of the harvest method and purification process. These findings illustrate the need for careful consideration when choosing an AAV vector production system for clinical production.

Impact of DnaK on protein expression and deamidation modification in Cronobacter sakazakii: insights from proteomic analysis.

This study explores the influence of DnaK on intracellular proteins in Cronobacter sakazakii, a Gram-negative bacterium known for causing infections, particularly in neonates. Proteomic and post-translational modification analyses were performed, revealing a potential link between DnaK and protein deamidation.

DnaK-Mediated Protein Deamidation: a Potential Mechanism for Virulence and Stress Adaptation in Cronobacter sakazakii.

Cronobacter sakazakii is a Gram-negative bacterium that causes infections in individuals of all ages, with neonates being the most vulnerable group. The objective of this study was to explore the function of the dnaK gene in C. sakazakii and to elucidate the impact of alterations in the protein composition regulated by dnaK on virulence and stress adaptation. Our research demonstrates the critical role of the dnaK gene in various key virulence factors, including adhesion, invasion, and acid resistance in C. sakazakii. Through the use of proteomic analysis, we discovered that deletion of the dnaK gene in C. sakazakii leads to an upregulation of protein abundance and increased levels of deamidated posttranscriptional modifications, suggesting that DnaK may play a role in maintaining proper protein activity by reducing protein deamidation in bacteria. These findings indicate that DnaK-mediated protein deamidation may be a novel mechanism for virulence and stress adaptation in C. sakazakii. These findings suggest that targeting DnaK could be a promising strategy for developing drugs to treat C. sakazakii infections. IMPORTANCE Cronobacter sakazakii can cause disease in individuals of all ages, with infections in premature infants being particularly deadly and resulting in bacterial meningitis and sepsis with a high mortality rate. Our study demonstrates that dnaK in Cronobacter sakazakii plays a critical role in virulence, adhesion, invasion, and acid resistance. Using proteomic analysis to compare protein changes in response to dnaK knockout, we found that dnaK knockout significantly upregulates the abundance of some proteins but also results in the deamidation of many proteins. Our research has identified a connection between molecular chaperones and protein deamidation, which suggests a potential future drug development strategy of targeting DnaK as a drug target.

Age-Related Changes in Post-Translational Modifications of Proteins from Whole Male and Female Skeletal Elements.

One of the key questions in forensic cases relates to some form of age inference, whether this is how old a crime scene is, when in time a particular crime was committed, or how old the victim was at the time of the crime. These age-related estimations are currently achieved through morphological methods with varying degrees of accuracy. As a result, biomolecular approaches are considered of great interest, with the relative abundances of several protein markers already recognized for their potential forensic significance; however, one of the greatest advantages of proteomic investigations over genomics ones is the wide range of post-translational modifications (PTMs) that make for a complex but highly dynamic resource of information. Here, we explore the abundance of several PTMs including the glycosylation, deamidation, and oxidation of several key proteins (collagen, fetuin A, biglycan, serum albumin, fibronectin and osteopontin) as being of potential value to the development of an age estimation tool worthy of further evaluation in forensic contexts. We find that glycosylations lowered into adulthood but deamidation and oxidation increased in the same age range.

Direct deamidation analysis of intact adeno-associated virus serotype 9 capsid proteins using reversed-phase liquid chromatography

Recombinant adeno-associated viral (AAV) vectors have taken center stage as gene delivery vehicles for gene therapy. Asparagine deamidation of AAV capsid proteins has been reported to reduce vector stability and potency of AAV gene therapy products. Deamidation of asparagine residue is a common post-translational modification of proteins that is detected and quantified by liquid chromatography-tandem mass spectrometry (LC-MS)-based peptide mapping. However, artificial deamidation can be spontaneously induced during sample preparation for peptide mapping prior to LC-MS analysis. We have developed an optimized sample preparation method to reduce and minimize deamidation artifacts induced during sample preparation for peptide mapping, which typically takes several hours to complete. To shorten turnaround time of deamidation results and to avoid artificial deamidation, we developed orthogonal RPLC-MS and RPLC-fluorescence detection methods for direct deamidation analysis at the intact AAV9 capsid protein level to routinely support downstream purification, formulation development, and stability testing. Similar trends of increasing deamidation of AAV9 capsid proteins in stability samples were observed at the intact protein level and peptide level, indicating that the developed direct deamidation analysis of intact AAV9 capsid proteins is comparable to the peptide mapping-based deamidation analysis and both methods are suitable for deamidation monitoring of AAV9 capsid proteins.

Conformational Control of Fast Asparagine Deamidation in a Norovirus Capsid Protein.

Accelerated spontaneous deamidation of asparagine 373 and subsequent conversion into an isoaspartate has been shown to attenuate the binding of histo blood group antigens (HBGAs) to the protruding domain (P-domain) of the capsid protein of a prevalent norovirus strain (GII.4). Here, we link an unusual backbone conformation of asparagine 373 to its fast site-specific deamidation. NMR spectroscopy and ion exchange chromatography have been used to monitor the deamidation reaction of P-domains of two closely related GII.4 norovirus strains, specific point mutants, and control peptides. MD simulations over several microseconds have been instrumental to rationalize the experimental findings. While conventional descriptors such as available surface area, root-mean-square fluctuations, or nucleophilic attack distance fail as explanations, the population of a rare syn-backbone conformation distinguishes asparagine 373 from all other asparagine residues. We suggest that stabilization of this unusual conformation enhances the nucleophilicity of the backbone nitrogen of aspartate 374, in turn accelerating the deamidation of asparagine 373. This finding should be relevant to the development of reliable prediction algorithms for sites of rapid asparagine deamidation in proteins.

Metal-induced oxidative stress and human plasma protein oxidation after SARS-CoV-2 infection

Pathogenesis of COVID-19 by SARS-CoV-2 resulted in a global pandemic and public health emergency in 2020. Viral infection can induce oxidative stress through reactive oxygen species (ROS). Inflammation and environmental stress are major sources of oxidative stress after infection. Micronutrients such as iron, copper, zinc, and manganese play various roles in human tissues and their imbalance in blood can impact immune responses against pathogens including SARS CoV-2. We hypothesized that alteration of free metal ions during infection and metal-catalyzed oxidation plays a critical role towards pathogenesis after infection. We analyzed convalescent and hospitalized COVID-19 patient plasma using orthogonal analytical techniques to determine redox active metal concentrations, overall protein oxidation, oxidative modifications, and protein levels via proteomics to understand the consequences of metal-induced oxidative stress in COVID-19 plasma proteins. Metal analysis using ICP-MS showed significantly greater concentrations of copper in COVID-19 plasma compared to healthy controls. We demonstrate significantly greater total protein carbonylation, other oxidative modifications, and deamidation of plasma proteins in COVID-19 plasma compared to healthy controls. Proteomics analysis showed that levels of redox active proteins including hemoglobulin were elevated in COVID-19 plasma. Molecular modeling concurred with potential interactions between iron binding proteins and SARS CoV-2 surface proteins. Overall, increased levels of redox active metals and protein oxidation indicate that oxidative stress-induced protein oxidation in COVID-19 may be a consequence of the interactions of SARS-CoV-2 proteins with host cell metal binding proteins resulting in altered cellular homeostasis.

Preparation, structure evaluation, and improvement in foaming characteristics of fibrotic pea protein isolate by cold plasma synergistic organic acid treatment

Developing hypoallergenic pea protein isolate (PPI)-based foam stabilizers with high foam stability is of great significance to the nutrition and stability of foamed food in the future food industry. Here, a novel non-thermal fibrosis protein modification technology based on cold plasma synergistic tartaric acid (CPA) treatment was used to induce PPI deamidation and thus improve protein solubility, foamability, and foam stability. The results showed that CPA treatment (100 W, 10 min) caused deamidation of approximately 20.02% PPI. The morphology of the CAP-treated PPI aggregate started undergoing fibrosis, with the fiber strip having a length of 7.00–11.00 μm and a width of 0.60–1.00 μm. With CAP treatment, conductivity (111.60 S/m to 129.87 S/m), light transmittance (47.90%–86.90%), foamability (10.00%–112.22%), and foam stability (25.00%–76.82%) significantly increased. Moreover, the thermal denaturation temperature of PPI decreased from 85.29 °C to 82.00 °C. CPA treatment destroyed protein subunits or disulfide bonds and changed the composition and primary structure of PPI. Fourier transform infrared spectroscopy and ultraviolet analysis showed that the α-helix and β-folding contents of the protein's secondary structure were reduced, leading to the unfolding of the rigid structure of PPI, the exposure of hydrophobic groups, and the enhancement of the protein polarityin solution. This research has certain guiding significance and practical value for expanding PPI in the foam food industry and protein membrane field. • Cold plasma synergistic tartaric acid (CPA), a non-thermal deamidation fibrosis technology, was used to prepare fibrotic pea protein isolate (PPI). • CPA technology significantly improved the efficiency of protein deamidation. • CPA technology improved protein solubility, foamability and stability. • This study has significance and practical value for the application expansion of PPI.