Peptide Research Articles

Advances in the Regulation of Periostin for Osteoarthritic Cartilage Repair Applications

Emerging evidence indicates periostin (POSTN) is upregulated in patients with OA, and studies have shown that it can induce the activation of inflammatory cytokines and catabolic enzymes, making it a potential therapeutic target. Link N (LN) is a peptide fragment derived from the link protein and has been demonstrated as an anabolic-like factor and anti-catabolic and anti-inflammatory factors both in vitro and in vivo. This study aims to determine if LN can regulate POSTN expression and function in OA cartilage. Articular cartilage was recovered from donors undergoing total knee replacements to isolate chondrocytes and prepare osteochondral explants. Cells and explants were treated with POSTN and LN (1 and 100 μg) and measured for changes in POSTN expression and various matrix proteins, catabolic and proinflammatory factors, and signaling. To determine the effects of POSTN expression in vivo, a rabbit OA model was used. Immunoprecipitation and in silico modeling were used to determine peptide/POSTN interactions. Western blotting, PCR, and immunohistochemistry demonstrated that LN decreased POSTN expression both in vitro and in vivo. LN was also able to directly inhibit POSTN signaling in OA chondrocytes. In silico docking suggested the direct interaction of LN with POSTN at residues responsible for its oligomerization. Immunoprecipitation experiments confirmed the direct interaction of LN with POSTN and the destabilization of its oligomerization. This study demonstrates the ability of a peptide, LN, to suppress the overexpression and function of POSTN in OA cartilage.

Truncated Albumins as Novel Surrogate Biomarkers in Diabetes Therapy: Epiphenomena and Potential Clinical Applications.

Aims/Hypothesis: Among various albumin posttranslational modifications (PTMs), N- and C-terminal truncations (HSA-DA and HSA-L) have also shown biomarker potential in disease states. We examined albumin truncation longitudinal trends and correlations during diabetes therapy toward possible future clinical applications. Methods: In a preliminary longitudinal therapy investigation, mass spectrometry was employed to track PTMs of human serum albumin (HSA), including glycation (GA), cysteinylation (CA or HNA1; reversible), di/trioxidation (OA or HNA2; irreversible), and truncation (TA). These modifications were correlated with ongoing therapy in four distinct subject groups: type 1 diabetes (T1DM), type 2 diabetes (T2DM), prediabetes-obesity (PDOB), and healthy controls (NORM), observed over a follow-up period extending up to 280 days. Results: Diabetes was associated with significant reduction ("deficiency") of measured albumin truncations (For HSA-DA: T2DM = 0.32 ± 0.3%, p = 2E-08; T1DM = 1.02 ± 0.4%, p = 3E-05; PDOB = 1.61 ± 0.2%, p = 0.004; compared to NORM = 2.08 ± 0.2%). Albumin truncation reduction was more striking in T2DM (HSA-DA: T2DM vs. T1DM: p = 0.004). Improvements in glycemic control and decrease of albumin glycation during diabetes therapy were associated with concomitant increase of albumin truncations toward the "healthy" normal ranges, and vice versa ("mirror image" trends). Accordingly, albumin truncation correlated inversely with albumin glycation (HSA-DA vs. GA: R = -0.53, p = 1E-09). Conclusions: The "epiphenomenon" of albumin truncation (reflecting the severity of mean hyperglycemia and also insulin resistance) can possibly provide novel, sensitive, and complementary biomarkers (e.g., via simpler HSA-DA peptide fragment immunoassays) to monitor efficacy of diabetes therapy and also progression from "healthy" to prediabetes and type 2 diabetes, highlighting potential diagnostic and prognostic utility in clinical diabetes care.

Mining the secreted and membrane transcriptome of Hyalomma dromedarii ticks for identification of potential protective antigens.

Members belonging to the tick genus Hyalomma function as a multi-host reservoir for several pathogens and important parasites infesting large animals, such as camels, goats, cattle and sheep. In Egypt, there is a high risk of pathogen transmission as camels and cattle are imported from Sudan and Ethiopia and shipped to slaughterhouses and animal markets located in populated areas. Hyalomma dromedarii ticks are semi-desert vectors and, similar to other members of the genus Hyalomma, characterized by long-term feeding. During this process, different physiological, biochemical and immunological interactions occur within both the feeding ticks and their hosts. These biological changes affect the different tick developmental phases. The aim of this study was to explore the transcriptome of mixed messenger RNAs (mRNAs) collected from H. dromedarii eggs, larvae, nymphs and fed and unfed adults, using the Gateway cDNA library prepared in pCMV sport6.1 vector METHODS: The clones were sequenced and searched for potential secreted, membrane-associated or transmembrane (SMaT) sequences. The identified SMaT sequences were compared to the National Center for Biotechnology Information (NCBI) non-redundant protein sequence database using Blastx. Annotation and functional classification were achieved by comparison to sequences in the UniProtKB/Swiss-Prot and VectorBase databases and to the publicly available annotated proteomes of six hard tick species (H. asiaticum, Rhipicephalus sanguineus sensu lato, Dermacentor silvarum, Rhipicephalus microplus, Ixodes scapularis and Haemaphysalis longicornis) in addition to the published H. dromedarii sialotranscriptome. For the common sequences, we predicted the physicochemical properties, secondary structures and antigenicity of the fragments similar to matched sequences in the UniProtKB/Swiss-Prot database using three different methods. The quality-trimmed sequences from the cDNA library revealed 319 SMaT transcripts among 1248 sequenced clones. Annotation of the SMaT sequences using the UniProtKB/Swiss-Prot database revealed only 232 non-redundant sequences with at least one match. According to the UniProtKB/Swiss-Prot and Vectorbase databases, the SMaT sequences were either secreted (extracellular) (29 sequences) or cellular (transmembrane and membrane-associated) (203 sequences). These were classified into 10 functional classes: biogenesis (49 sequences), defense (9 sequences), development (36 sequences), signal transduction (28 sequences), transport (15 sequences), protein modification (33 sequences), homeostasis (6 sequences), metabolism (45 sequences) and miscellaneous/uncharacterized (11 sequences). A total of 60 sequences were shared between H. dromedarii SMaT, the sialotransciptome and six other hard tick species. The peptide fragments of these sequences that aligned to proteins from the UniProtKB/Swiss-Prot database were predicted to be promising epitopes and mapped to 10 functional classes at different ratios. Our immuno-informatics analysis identified 60 sequences common among hard tick species and encoded by H. dromedarii salivary glands. These annotated SMaT sequences of H. dromedarii will pave the way for the identification and discovery of novel potential protective antigens that are either secreted, membrane-associated or transmembrane.

Short Fragmented Peptides from Pardachirus Marmoratus Exhibit Stronger Anticancer Activities in In Silico Residue Replacement and Analyses.

Cancer is a worldwide issue. It has been observed that conventional therapies face many problems, such as side effects and drug resistance. Recent research reportedly used marine-derived products to treat various diseases and explored their potential in treating cancers. This study aims to discover short-length anticancer peptides derived from pardaxin 6 through an in silico approach. Fragmented peptides ranging from 5 to 15 amino acids were derived from the pardaxin 6 parental peptide. These peptides were further replaced with one residue and, along with the original fragmented peptides, were predicted for their SVM scores and physicochemical properties. The top 5 derivative peptides were further examined for their toxicity, hemolytic probability, peptide structures, docking models, and energy scores using various web servers. The trend of in silico analysis outputs across 5 to 15 amino acid fragments was further analyzed. Results showed that when the amino acids were increased, SVM scores of the original fragmented peptides were also increased. Designed peptides had increased SVM scores, which was aligned with previous studies where the single residue replacement transformed the non-anticancer peptide into an anticancer agent. Moreover, in vitro studies validated that the designed peptides retained or enhanced anticancer effects against different cancer cell lines. Interestingly, a decreasing trend was observed in those fragmented derivative peptides. Single residue replacement in fragmented pardaxin 6 was found to produce stronger anticancer agents through in silico predictions. Through bioinformatics tools, fragmented peptides improved the efficiency of marine-derived drugs with higher efficacy and lower hemolytic effects in treating cancers.

Identification and differentiation of somapacitan, a long-acting growth hormone derivative, and recombinant human growth hormone in equine plasma by LC-HRMS for doping control purpose

Somapacitan, a long-acting growth hormone derivative, and recombinant human growth hormone (rhGH) are protein-based drugs generally used to treat growth disorders and GH deficiency in humans. Due to their potential to enhance the horse performance, the use of these drugs is prohibited at-all-times by the International Federation of Horseracing Authorities for horseracing and the Fédération Equestre Internationale for equestrian sports. In this study, we developed a test method for the identification and differentiation of somapacitan and rhGH in equine plasma by using liquid chromatography high-resolution mass spectrometry (LC–HRMS). The method involved C4 solid-phase extraction after ammonium sulfate precipitation, followed by chloroform/methanol precipitation, trypsin digestion, and analysis by LC-HRMS. The discriminative identification of somapacitan and rhGH was successfully achieved through the detection of their respective unique T10 peptide fragments. Noteworthy, the T10 peptide fragment of somapacitan was detected with its side chain structure remaining intact. The limit of identification (confirmation) (LOI) was determined to be 5 ng/mL for somapacitan and 2 ng/mL for rhGH in equine plasma, while the limit of detection (LOD) was 5 ng/mL for somapacitan and 1 ng/mL for rhGH. Furthermore, using the peptide fragments T1, T8, and T9 (which are shared between somapacitan and rhGH), the presence of somapacitan in equine plasma could be confirmed with higher sensitivity, achieving down to LOIs of 2 ng/mL and LODs of 1 ng/mL. The method was validated with respect to specificity, identification capability, robustness, precision, and reproducibility, paving the way for the analysis of post-administration samples from our already planned administration trials and future potential positive cases.

Discovery of a novel nanomolar angiotensin-I converting enzyme inhibitory peptide with unusual binding mechanisms derived from Chlorella pyrenoidosa

Chlorella pyrenoidosa (C. pyrenoidosa) has been cultivated in large quantities, and was proven to be antihypertensive when consumed orally. However, the antihypertensive peptides derived from C. pyrenoidosa remains scarce. In this study, trypsin was chosen to prepare the hydrolysate of C. pyrenoidosa, which was then fractionated by column chromatography. And ninety-nine peptides were identified by LC-MS/MS, after which 10 peptides were chosen by docking-based virtual screening and demonstrated the ability to inhibit ACE. Among them, LVAKA (LV-5) had the lowest IC50 (26.66 μM). LV-5, LKKAP, and PGLRP were identified as non-competitive ACE inhibitory peptides that exhibited significant stability in the face of extreme pH and high temperatures. Insilico and in-vitro simulated gastrointestinal digestion revealed that these three peptides could release ACE inhibitory peptide fragments after digestion. The sequence optimization of LV-5 led to the identification of LRAKA (LR-5), which was recognized as a novel nanomolar ACE peptide with an IC50 of 350 nM in-vitro and a potent antihypertensive effect in-vivo. Moreover, molecular dynamic simulation indicated that LR-5 interacted with an unconventional binding site in ACE. These findings underscore the potential of Chlorella as a source of antihypertensive peptides and suggest a promising future for the use of Chlorella-derived peptides in the management of hypertension.

The Hunt Lab Guide to De Novo Peptide Sequence Analysis by Tandem Mass Spectrometry

Donald Hunt has made seminal contributions to the fields of proteomics, immunology, epigenetics, and glycobiology. The foundation of every important work to come out of the Hunt Laboratory is de novo peptide sequencing. For decades, he taught hundreds of students, postdocs, engineers, and scientists to directly interpret mass spectral data. To honor his legacy and ensure that the art of de novo sequencing is not lost, we have adapted his teaching materials into “The Hunt Lab Guide to De Novo Peptide Sequence Analysis by Tandem Mass Spectrometry”. In addition to the de novo sequencing tutorials, we present two freely available software tools that facilitate manual interpretation of mass spectra and validation of search results. The first, “Hunt Lab Peptide Fragment Calculator”, calculates precursor and fragment mass-to-charge ratios for any peptide. The second program, “Predator Protein Fragment Calculator”, was inspired in part by the fragment calculator developed in the Hunt Lab. Its capabilities are enhanced to facilitate interpretation of mass spectral data derived from intact proteins. We hope that the combination of these educational tools will continue to benefit students and researchers by empowering them to interpret data on their own.

Unveiling molecular mechanism underlying inhibition of human islet amyloid polypeptide fibrillation by benzene carboxylic acid-peptide conjugate

Type 2 diabetes (T2D) is linked to the apoptosis of insulin-producing β-cells due to the aberrant fibrillation of the human islet amyloid polypeptide (hIAPP or amylin) to cytotoxic aggregates. Profit et al. generated conjugates (C1–C7) by appending benzene carboxylic acids of varying charges to the N-terminal of hIAPP22-29 fragment peptide NFGAILSS to modulate hIAPP fibrillation and cytotoxicity. C5 (4 µM) derived by conjugating low-cost, commercially available benzene-1,2,4,5-tetracarboxylic acid known as pyromellitic acid to NFGAILSS completely abolishes the hIAPP (40 µM) self-assembly as noted in the thioflavin T (ThT) fluorescence assay. The circular dichroism (CD) spectra highlighted that C5 stabilized hIAPP in a distinctive conformation and blocked its conformational switching to amyloidogenic β-sheet structure. C5 possessing a charge-dense pyromellitic acid moiety appended on the N-terminal region of self-recognition hIAPP fragment sequence NFGAILSS created significant interest as it effectively inhibited hIAPP fibrillation and possessed lower molecular mass, smaller size, and charge as compared to hIAPP aggregation inhibitor EEEENFGAILSS (P10). However, it remains unclear how C5 traps hIAPP into a unique conformation that abolishes its self-aggregation propensity. Thus, molecular dynamics (MD) simulations have been employed to illuminate the conformational transitions and structural changes in hIAPP on the inclusion of C5. C5 displayed high-affinity binding interactions to hIAPP (ΔGbinding = −37.11 ± 3.72 kcal/mol) with major contributions from the van der Waals and electrostatic interactions. Furthermore, residue-specific binding free energy analysis depicted high-affinity binding interactions of C5 with Phe15, His18, Asp21, and Tyr37 of hIAPP that play a crucial role in hIAPP fibrillation. The negatively charged carboxylate groups of pyromellitic acid moiety of C5 displayed interactions with the key residues of hIAPP as noted in the conformational clustering analysis. Notably higher sampling of helix from 24.00 ± 0.84 % in hIAPP to 34.20 ± 1.92 % in hIAPP–C5 is consistent with the CD studies, which depicted that C5 trapped hIAPP monomer in a conformation that blocked its self-association. MD simulations illuminated the molecular mechanism and atomistic details of the C5 interactions with hIAPP, which are responsible for its inhibitory activity against hIAPP fibrillation and alleviating hIAPP aggregates-induced cytotoxicity.

Free Immunoglobulin Light Chains in Patients With Myocarditis: a New Biomarker of Inflammation and Heart Failure

To study the concentration of immunoglobulin free light chains (FLCs) in patients with myocarditis in comparison with non-inflammatory heart diseases, their relationship with inflammatory markers and the severity of chronic heart failure (CHF). This study included 77 patients (31 women, mean age 54.1±13.3 years): 41 patients with myocarditis verified by myocardial biopsy (n=18) or using a noninvasive diagnostic algorithm, 31 patients with noninflammatory CHF (comparison group), and 5 patients with monoclonal gammopathy identified during the study (4 of them were diagnosed with AL amyloidosis with heart damage). In the myocarditis group, CHF was diagnosed in 29 patients, mean stage IIA, functional class (FC) 2-3, with a mean left ventricular ejection fraction 43%. In the comparison group, patients had predominantly IIA stage, FC 2-3 CHF without systolic dysfunction. The blood concentration of kappa and lambda FLC types was measured with Cloneus S-FLC-K TIA Kit and Cloneus S-FLC-L TIA Kit. Concentrations were considered normal at FLC-kappa 4.84-14.20 mg/l, FLC-lambda 7.03-22.50 mg/l, and the FLC-kappa/lambda ratio 0.426-1.050. Increased FLC concentrations were found in 58% of patients with myocarditis and in 77% of patients in the comparison group. The FLC-lambda concentration was significantly higher in the comparison group; there were no significant differences between the groups in FLC-kappa and their ratio. The closest significant correlations in both groups and the entire cohort were noted between FLCs of either type and CHF, as well as the requirement for loop diuretics (correlation coefficients, 0.60-0.90), independent on the severity of systolic dysfunction. Myocarditis patients also showed correlations of FLCs with the titer of antibodies to cardiomyocyte nuclear antigens, levels of C-reactive protein, leukocytes, neutrophils, erythrocyte sedimentation rate, and the concentration of N-terminal fragment of brain natriuretic peptide. In a subgroup of 10 myocarditis patients who were treated with immunosuppressants, FLCs of both types were significantly lower than in the comparison group; only with the persistence of severe CHF was an increase in FLCs noted. An increased FLC concentration can be considered as an important pathogenesis component that reflects both the specific mechanisms of myocarditis and the severity of CHF. In the absence of a statistically significant increase in general inflammatory markers in the blood of myocarditis patients, the measurement of FLCs can be used as an additional diagnostic marker and predictor of the decompensated variant of the course of myocarditis. However, the diagnostic and prognostic significance of FLC concentration in patients without CHF requires a further study.

OSTEO18, a novel urinary proteomic signature, associated with osteoporosis in heart transplant recipients

Abstract Background Immunosuppressive treatment in heart transplant (HTx) recipient causes osteoporosis. The urinary proteomic profile (UPP) includes peptide fragments derived from the bone extracellular matrix. Purpose Study aims were to develop and validate a multidimensional UPP biomarker for osteoporosis in HTx patients from single sequenced urinary peptides identifying the parent proteins. Methods A single-center HTx cohort was analyzed. Urine samples were measured by capillary electrophoresis coupled with mass spectrometry. Cases with osteoporosis and matching controls were randomly selected from all available 389 patients. In derivation case-control dataset, 1576 sequenced peptides detectable in ≥30% of patients. Applying statistical analysis on these, an 18-peptide multidimensional osteoporosis UPP biomarker (OSTEO18) was generated by support vector modeling. The 2 replication datasets included 118 and 94 patients. For further validation, the whole cohort was analyzed. Statistical methods included logistic regression and receiver operating characteristic curve (ROC) analysis. Results In derivation dataset, the AUC, sensitivity and specificity of OSTEO18 were 0.83 (95% CI: 0.76-0.90), 74.3% and 87.1%, respectively. In replication datasets, results were confirmatory. In the whole cohort (154 osteoporotic patients [39.6%]), the ORs for osteoporosis increased (p < 0.0001) across OSTEO18 quartiles from 0.39 (95% CI: 0.25-0.61) to 3.14 (2.08-4.75). With full adjustment for known osteoporosis risk factors, OSTEO18 improved AUC from 0.708 to 0.786 (p = 0.0003) for OSTEO18 categorized (optimized threshold: 0.095) and to 0.784 (p = 0.0004) for OSTEO18 as continuously distributed classifier. Conclusion OSTEO18 is a clinically meaningful novel biomarker indicative of osteoporosis in HTx recipients and is being certified as in-vitro diagnostic.

From [2Mn2S] Diamond Cores to Butterfly Rhombs: Transformations That Highlight Alternating Peptide Binding Sites.

Thiocarboxamide chelates are known to assemble [2Mn2S] diamond core complexes via μ-S bridges that connect two MnI(CO)3 fragments. These can exist as syn- and anti-isomers and interconvert via 16-electron, monomeric intermediates. Herein, we demonstrate that reduction of such Mn2 derivatives leads to a loss of one thiocarboxamide ligand and a switch of ligand binding mode from an O- to N-donor of the amide group, yielding a dianionic butterfly rhomb with a short Mn0-Mn0 distance, 2.52 Å. Structural and chemical analyses suggest that reduction of the Mn(I) centers is dependent on the protonation state of the amide-H, as total deprotonation followed by reduction does not result in the reduction of the Mn2 core. Partial deprotonation followed by reduction suggests a pathway that involves monomeric Mn(CO)3(S-O) and Mn(CO)3(S-N) intermediates. Ligand modifications to tertiary amides that remove the possibility of amide-H reduction led to complexes that preserve the [2Mn2S] diamond core during chemical reduction. Further comparison with the tethered system, linking the Mn(CO)3(S-O) sites together, suggests that dimer dissociation is necessary for the overall reductive transformation. These results highlight organomanganese carbonyl chemistry to establish illustrations of peptide fragment binding modes in the uptake of low-valent metal carbonyls related to binuclear active sites of biocatalysts.

Photochemical and Collision-Induced Cross-Linking in Stereochemically Distinct Scaffolds of Peptides and Nitrile Imines in Gas-Phase Ions.

Intramolecular cross-linking between peptides and nitrile-imine intermediates was studied in stereochemically distinct conjugates in which the reacting components were mounted on cis-1,2-cyclohexane and trans-1,4-cyclohexane scaffolds that we call 1,2-s-peptides and 1,4-s-peptides, respectively. The nitrile-imine intermediates were generated by N2 loss from 2,5-diaryltetrazole tags upon UV-photodissociation at 213 and 250 nm or by collision-induced dissociation, and further interrogated by CID and UVPD-MS3. Peptide fragment ion series originating from linear structures and macrocyclic cross-links were distinguished and used to quantify the cross-linking yields. The yields in MS2 varied between 27% for AAAG conjugates to 78% for GAAAK conjugates, depending on the peptide sequence. The CID-MS3 yields were in a 57-97% range, depending on the peptide sequence. Structures of 1,2-s-peptide and 1,4-s-peptide ions as well as several of their nitrile-imine intermediates and cross-links were investigated by high-resolution cyclic ion mobility in combination with Born-Oppenheimer molecular dynamics and density functional theory calculations. Matches between the experimental and calculated collision cross sections and ion relative Gibbs energies were used to assign peptide structures. Peptide conjugates C-terminated with Gly and Lys residues underwent cross-linking by the carboxyl group, as established by MS3 sequencing and corroborated by carboxyl blocking experiments that lowered the cross-linking yields. Peptide conjugates C-terminated with Arg also cross-linked via the side-chain guanidine group. A notable feature of the 1,4-s-peptide ions was the participation of low-energy twist-boat cyclohexane conformers that was enforced by strong hydrogen bonds between the peptide and nitrile imine.

Efficiency Enhancement in Peptide Hydrogelators: The Crucial Role of Side Chain Hydrogen Bonding Over Aromatic π-π Interactions.

Short peptide assemblies that form supramolecular hydrogels are stabilized by both intermolecular noncovalent interactions among amino acid side chains and hydrogen bonding between peptide backbone amides. Previous research has emphasized the inclusion of aromatic amino acids in short peptide sequences, positing that aromatic π-π interactions contribute significantly to inducing efficient hydrogelation i.e., at low minimum gelation concentrations (MGCs). However, herein, we demonstrate that additional hydrogen bonding interactions from amino acid side chains play a more pivotal role in the efficiency of peptide hydrogelation compared to aromatic π-π interactions. We investigated two sets of Fluorenylmethoxycarbonyl (Fmoc)-functionalized α-synuclein and human islet amyloid peptide fragments [Fmoc-NVGGAVVT (Syn-N) and Fmoc-NFGAIL (IAP-N)], substituting asparagine (N) with phenylalanine (Syn-F/IAP-F), alanine (Syn-A/IAP-A), and glutamine (Syn-Q/IAP-Q). This allowed us to explore the effects of aromatic (π-system), aliphatic (hydrophobic), and hydrogen bonding effects with varying chain lengths on hydrogel formation. Our results reveal that Syn-N and Syn-Q exhibit MGC of 0.03 and 0.05 wt %, respectively, classifying them as super hydrogelators (MGC < 0.1 wt %). These values are 4.0-6.6-fold lower than Syn-F and Syn-A, with Syn-N demonstrating greater efficiency than Syn-Q. Similarly, IAP-N exhibited a substantial decrease in MGC by 8.75, 3.75, and 2.5 folds compared to IAP-A, IAP-F, and IAP-Q, respectively. Experimental evidence and molecular dynamic simulation suggest that -CO-NH2 of asparagine side chains effectively engaged in hydrogen bonding, thereby immobilizing water molecules at low gelator concentrations. Although glutamine shares similar -CO-NH2 functionality, its hydrogelation efficiency is less pronounced compared to asparagine, likely due to its longer alkyl chain, which may hinder the formation of a hydrogen bonding network in the self-assembled structure compared to asparagine-containing peptides. These findings offer valuable insights for designing efficient peptide hydrogelators or lowering MGCs by substituting amino acids with asparagine/glutamine in peptide sequences. Additionally, modifying peptide properties through asparagine/glutamine substitution could optimize hydrogel properties for specific applications.

A Clickase-Mediated Immunoassay Based on Nanopore and Bionic Signal Labels for Ultrasensitive, Portable, and On-Site Detection of Ricin.

It is of particular importance to develop an effective method that possesses several merits simultaneously of rapid, ultrasensitive, portable, and on-site detection potential for food safety detection. Herein, we propose a clickase-mediated immunoassay based on nanopore and bionic signal labels for the detection of ricin. The introduction of Cu/Cys clickase and nanopore simultaneously effectively addressed the inherent limitations of natural enzymes and colorimetric signal output, respectively. Using this method, bionic signal labels can be easily formed through DNA and Gram-positive bacterial cell wall terminal peptide fragments (labeled by alkynyl and azide, respectively) and vancomycin. Translocation of the D-P@vancomycin through the nanopore generated highly specific oscillation current traces. This method showed a great on-site detection potential and superior analytical performance owing to the combination of the specificity of antibodies, high CuAAC click reaction catalytic efficiency of clickase, ultrasensitivity of the nanopore, and high signal resolution of D-P@vancomycin. Moreover, the practical applicability of the established method was also verified, achieving a limit of detection (LOD) down to 200.9 ag/mL with a wide linear relationship under the optimized conditions. In conclusion, this method is promising for rapid, portable, ultrasensitive, and on-site food safety detection.

Nucleoprotein Phase-Separation Affinities Revealed via Atomistic Simulations of Short Peptide and RNA Fragments.

Liquid-liquid phase separation of proteins and nucleic acids into condensate phases is a versatile mechanism for ensuring the compartmentalization of cellular biochemistry. RNA molecules play critical roles in these condensates, particularly in transcriptional regulation and stress responses, exhibiting a wide range of thermodynamic and dynamic behaviors. However, deciphering the molecular grammar that governs the stability and dynamics of protein-RNA condensates remains challenging due to the multicomponent and heterogeneous nature of condensates. In this study, we employ atomistic simulations of 20 distinct mixtures containing minimal RNA and peptide fragments which allows us to dissect the phase-separating affinities of all 20 amino acids in the presence of RNA. Our findings elucidate chemically specific interactions, hydration profiles, and ionic effects that synergistically promote or suppress protein-RNA phase separation. We map a ternary phase diagram of interactions, identifying four distinct groups of residues that promote, maintain, suppress, and disrupt protein-RNA clusters.

Development and applications of enzymatic peptide and protein ligation.

Chemical synthesis of complex peptides and proteins continues to play increasingly important roles in industry and academia, where strategies for covalent ligation of two or more peptide fragments to produce longer peptides and proteins in convergent manners have become critical. In recent decades, efficient and site-selective ligation strategies mediated by exploiting the biocatalytic capacity of nature's diverse toolkit (i.e., enzymes) have been widely recognized as a powerful extension of existing chemical strategies. In this review, we present a chronological overview of the development of proteases, transpeptidases, transglutaminases, and ubiquitin ligases. We survey the different properties between the ligation reactions of various enzymes, including the selectivity and efficiency of the reaction, the ligation "scar" left in the product, the type of amide bond formed (natural or isopeptide), the synthetic availability of the reactants, and whether the enzymes are orthogonal to another. This review also describes how the inherent specificity of these enzymes can be exploited for peptide and protein ligation.

Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics.

Data-independent acquisition (DIA)-based mass spectrometry is becoming an increasingly popular mass spectrometry acquisition strategy for carrying out quantitative proteomics experiments. Most of the popular DIA search engines make use of in silico generated spectral libraries. However, the generation of high-quality spectral libraries for DIA data analysis remains a challenge, particularly because most such libraries are generated directly from data-dependent acquisition (DDA) data or are from in silico prediction using models trained on DDA data. In this study, we developed Carafe, a tool that generates high-quality experiment-specific in silico spectral libraries by training deep learning models directly on DIA data. We demonstrate the performance of Carafe on a wide range of DIA datasets, where we observe improved fragment ion intensity prediction and peptide detection relative to existing pretrained DDA models.

Novel Insights into Ethanol-Soluble Oyster Peptide-Zinc-Chelating Agents: Structural Characterization, Chelation Mechanism, and Potential Protection on MEHP-Induced Leydig Cells.

Numerous studies have reported that mono-(2-ethylhexyl) phthalate (MEHP) (bioactive metabolite of Di(2-ethylhexyl) phthalate) has inhibitory effects on Leydig cells. This study aims to prepare an oyster peptide-zinc complex (PEP-Zn) to alleviate MEHP-induced damage in Leydig cells. Zinc-binding peptides were obtained through the following processes: zinc-immobilized affinity chromatography (IMAC-Zn2+), liquid chromatography-mass spectrometry technology (LC-MS/MS) analysis, molecular docking, molecular dynamic simulation, and structural characterization. Then, the Zn-binding peptide (PEP) named Glu-His-Ala-Pro-Asn-His-Asp-Asn-Pro-Gly-Asp-Leu (EHAPNHDNPGDL) was identified. EHAPNHDNPGDL showed the highest zinc-chelating ability of 49.74 ± 1.44%, which was higher than that of the ethanol-soluble oyster peptides (27.50 ± 0.41%). In the EHAPNHDNPGDL-Zn complex, Asn-5, Asp-7, Asn-8, His-2, and Asp-11 played an important role in binding to the zinc ion. Additionally, EHAPNHDNPGDL-Zn was found to increase the cell viability, significantly increase the relative activity of antioxidant enzymes and testosterone content, and decrease malondialdehyde (MDA) content in MEHP-induced TM3 cells. The results also indicated that EHAPNHDNPGDL-Zn could alleviate MEHP-induced apoptosis by reducing the protein level of p53, p21, and Bax, and increasing the protein level of Bcl-2. These results indicate that the zinc-chelating peptides derived from oyster peptides could be used as a potential dietary zinc supplement.

Enhancing De Novo Protein Sequencing through the C-Terminal Labeling Strategy: Resolving Isobaric Ambiguities by Electron-Transfer/Higher Energy Collision Dissociation (EThcD).

De novo protein sequencing via a bottom-up approach requires various proteases to produce overlapping peptides. However, peptides generated by proteases other than trypsin, LysC, and ArgC often yield C-terminal fragments with suboptimal ionization in positive mode mass spectrometry (MS). This study introduces a novel peptide labeling strategy that involves modifying peptides at the C-terminal and at the carboxyl groups of Aspartic and Glutamic acid with arginine methyl ester (R-met) to improve peptide fragmentation and resolve isobaric ambiguities encountered during sequencing. An amidation reaction is used with coupling reagents to conjugate R-met to the peptide's C-terminal end, introducing a functional group that enhances the detectability of C-terminal peptide fragment ions by mass spectrometry. Subsequently, selecting a charge state of +2 or higher can facilitate optimal fragmentation of the derivatized peptides using electron-transfer/higher energy collision dissociation (EThcD), thereby generating essential w-ions to resolve common isobaric ambiguities. Demonstrating this strategy across diverse protein types, including albumin and antibodies and using different proteases for digestion, highlights the unique characteristics of combining the proposed amidation reaction with the specific proteases tested.

The chromatin remodeler SMARCA5 binds to d-block metal supports: Characterization of affinities by IMAC chromatography and QM analysis.

The ISWI family protein SMARCA5 contains the ATP-binding pocket that coordinates the catalytic Mg2+ ion and water molecules for ATP hydrolysis. In this study, we demonstrate that SMARCA5 can also possess an alternative metal-binding ability. First, we isolated SMARCA5 on the cobalt column (IMAC) to near homogeneity. Examination of the interactions of SMARCA5 with metal-chelating supports showed that, apart from Co2+, it binds to Cu2+, Zn2+ and Ni2+. The efficiency of the binding to the last-listed metal was influenced by the chelating ligand, resulting in a strong preference for Ni-NTA over the Ni-CM-Asp equivalent. To gain insight in the preferential affinity for the Ni-NTA ligand, QM calculations were performed on model systems and metal-ligand complexes with a limited protein fragment of SMARCA5 containing the double-histidine (dHis) motif. The calculations correlated the observed affinity with the relative stability of the d-block metals to tetradentate ligand coordination over tridentate, as well as their overall octahedral coordination capacity. Likewise, binding free energies derived from model imidazole complexes mirrored the observed Ni-NTA/Ni-CM-Asp preferential affinity. Finally, similar calculations on complexes with a SMARCA5 peptide fragment derived from the AlphaFold structural prediction, captured almost accurately the expected relative stability of the TM complexes, and produced a large energetic separation (~10 kcal∙mol-1) between Ni-NTA and Ni-CM-Asp in favour of the former.