Peptide Methionine Research Articles

Mechanistic Insights Into Post‐Translational α‐Keto‐β‐Amino Acid Formation by a Radical S‐Adenosyl Methionine Peptide Splicease

AbstractRadical S‐adenosyl methionine enzymes catalyze a diverse repertoire of post‐translational modifications in protein and peptide substrates. Among these, an exceptional and mechanistically obscure example is the installation of α‐keto‐β‐amino acid residues by formal excision of a tyrosine‐derived tyramine unit. The responsible spliceases are key maturases in a widespread family of natural products termed spliceotides that comprise potent protease inhibitors, with the installed β‐residues being crucial for bioactivity. Here, we established the in vitro activity of the model splicease PcpXY to interrogate the mechanism of non‐canonical protein splicing. Identification of shunt and coproducts, deuterium labeling studies, and density functional theory energy calculations of hypothesized intermediates support a mechanism involving hydrogen abstraction at tyrosine Cα as the initial site of peptide radical formation and release of 4‐hydroxybenzaldehyde as the tyrosine‐derived coproduct. The data illuminate key features of this unprecedented radical‐mediated biotransformation yielding ketoamide pharmacophores that are also present in peptidomimetic therapeutics.

Mechanistic Insights Into Post-Translational α-Keto-β-Amino Acid Formation by a Radical S-Adenosyl Methionine Peptide Splicease.

Radical S-adenosyl methionine enzymes catalyze a diverse repertoire of post-translational modifications in protein and peptide substrates. Among these, an exceptional and mechanistically obscure example is the installation of α-keto-β-amino acid residues by formal excision of a tyrosine-derived tyramine unit. The responsible spliceases are key maturases in a widespread family of natural products termed spliceotides that comprise potent protease inhibitors, with the installed β-residues being crucial for bioactivity. Here, we established the in vitro activity of the model splicease PcpXY to interrogate the mechanism of non-canonical protein splicing. Identification of shunt and coproducts, deuterium labeling studies, and density functional theory energy calculations of hypothesized intermediates support a mechanism involving hydrogen abstraction at tyrosine Cα as the initial site of peptide radical formation and release of 4-hydroxybenzaldehyde as the tyrosine-derived coproduct. The data illuminate key features of this unprecedented radical-mediated biotransformation yielding ketoamide pharmacophores that are also present in peptidomimetic therapeutics.

Host-guest binding between cucurbit[8]uril and amphiphilic peptides achieved tunable supramolecular aggregates for cancer diagnosis.

The manipulation of biocompatible supramolecular nanostructures at subcellular and cellular levels has become one of the increasingly significant topics but remains a formidable challenge in chemical and biological science. In this work, a controllable supramolecular aggregate based on host-guest competitive binding is elaborately constructed using cucurbit[8]uril, methionine-containing amphiphilic peptide, and perylene diimide, displaying in situ oxidation-driven macrocycle-confined fluorescence enhancement for cell imaging and morphological reconstruction for cancer cell death. The experimental results demonstrate that cucurbit[8]uril possesses a high binding affinity with the methionine peptide, while this value sharply decreases after the methionine residue is oxidized to sulfoxide or sulfone. Therefore, perylene diimide can be competitively included by cucurbit[8]uril in the co-assemblies, eventually resulting in a 10-fold fluorescence enhancement and the conversion of topological morphology from nano-sized particles to micron-sized sheets. Moreover, the obtained ternary assemblies can be oxidized by endogenous reactive oxygen species in cancer cells, thus not only providing enhanced fluorescence for cell imaging, but also leading to endoplasmic reticulum dysfunction and significant cell death. Therefore, the controllable and oxidation-responsive morphological transformation based on the host-guest competitive binding in biological media can be viewed as a feasible means for efficient disease theragnosis.

Selective C−H Acyloxylation of Sulfides/Disulfides Enabled by Hypervalent Iodine Reagents

AbstractHerein, we report the α−C−H acyloxylation of sulfides and disulfides enabled by hypervalent iodine(III) reagents via photoredox catalysis. The methoxylbenziodoxole derivatives serve as the hydrogen atom transfer agent, the mild oxidant, and the acyloxylation source in the reaction. External nucleophiles can also be introduced to the α−C−H of sulfides. The reaction applies to various aryl and alkyl sulfides including methionine peptide derivatives. Disulfides are applicable for the first time with excellent chemoselectivity and functional group compatibility.

Mitochondrial N-formyl methionine peptides contribute to exaggerated neutrophil activation in patients with COVID-19

ABSTRACT Neutrophil dysregulation is well established in COVID-19. However, factors contributing to neutrophil activation in COVID-19 are not clear. We assessed if N-formyl methionine (fMet) contributes to neutrophil activation in COVID-19. Elevated levels of calprotectin, neutrophil extracellular traps (NETs) and fMet were observed in COVID-19 patients (n = 68), particularly in critically ill patients, as compared to HC (n = 19, p < 0.0001). Of note, the levels of NETs were higher in ICU patients with COVID-19 than in ICU patients without COVID-19 (p < 0.05), suggesting a prominent contribution of NETs in COVID-19. Additionally, plasma from COVID-19 patients with mild and moderate/severe symptoms induced in vitro neutrophil activation through fMet/FPR1 (formyl peptide receptor-1) dependent mechanisms (p < 0.0001). fMet levels correlated with calprotectin levels validating fMet-mediated neutrophil activation in COVID-19 patients (r = 0.60, p = 0.0007). Our data indicate that fMet is an important factor contributing to neutrophil activation in COVID-19 disease and may represent a potential target for therapeutic intervention.

Mitochondrial N-formyl methionine peptides associate with disease activity as well as contribute to neutrophil activation in patients with rheumatoid arthritis

ObjectivesLiterature suggests that neutrophils of patients with rheumatoid arthritis (RA) are primed to respond to N-formyl methionine group (formylated peptides). Animal models indicate that formylated peptides contribute to joint damage via neutrophil recruitment and inflammation in joints. Non-steroidal anti-inflammatory drugs are also known to inhibit formyl peptide-induced neutrophil activation. The predominant source of formylated peptides in sterile inflammatory conditions like RA is mitochondria, organelles with prokaryotic molecular signatures. However, there is no direct evidence of mitochondrial formyl peptides (mtNFPs) in the circulation of patients with RA and their potential role in neutrophil-mediated inflammation in RA, including their clinical significance. MethodsLevels of mtNFPs (total fMet, MT-ND6) were analyzed using ELISA in plasma and serum obtained from patients in 3 cross-sectional RA cohorts (n = 275), a longitudinal inception cohort (n = 192) followed for a median of 8 years, and age/gender-matched healthy controls (total n = 134). Neutrophil activation assays were done in the absence or presence of formyl peptide receptor 1 (FPR1) inhibitor cyclosporine H. ResultsElevated levels of total fMet were observed in the circulation of patients with RA as compared to healthy controls (p < 0.0001) associating with disease activity and could distinguish patients with the active disease from patients with inactive disease or patients in remission. Baseline levels of total fMet correlated with current and future joint involvement, respectively and predicted the development of rheumatoid nodules (OR = 1.2, p = 0.04). Further, total fMet levels improved the prognostic ability of ACPA in predicting erosive disease (OR of 7.9, p = 0.001). Total fMet levels correlated with markers of inflammation and neutrophil activation. Circulating mtNFPs induced neutrophil activation in vitro through FPR1-dependent mechanisms. ConclusionsCirculating mtNFPs could be novel biomarkers of disease monitoring and prognosis for RA and in investigating neutrophil-mediated inflammation in RA. We propose, FPR1 as a novel therapeutic target for RA.

Preventive Effects of Tryptophan-Methionine Dipeptide on Neural Inflammation and Alzheimer's Pathology.

Preventive approaches for age-related memory decline and dementia have become a high priority in the aging society because of the lack of therapeutic approaches. Recent epidemiological studies have reported that fermented dairy products can help prevent dementia. Previously, we identified tryptophan–tyrosine (WY) and tryptophan–methionine (WM) peptides as the suppressants of activation of the primary microglia and showed that WY peptide consumption suppresses inflammation in the brains of Alzheimer’s disease model mice. However, the effects of the WM peptide on inflammation in the brain and Alzheimer’s pathology have not been investigated. Here, we evaluated the effect of WM peptide consumption on Alzheimer’s disease model (5×FAD) mice. In 5×FAD mice, intake of WM peptide suppressed the production of inflammatory cytokines, activation of microglia, and infiltration of activated microglia around β amyloid (Aβ) depositions. WM peptide intake reduced Aβ deposition in the cortex and hippocampus and then improved the object recognition memory. Taken together with previous reports, the current findings indicate that ingestion of tryptophan-related peptides or food material rich in tryptophan-related peptides, thereby regulating microglial activity, represents a potential preventive approach for cognitive decline and dementia related to inflammation.

Identification of Residues Critical for FPR2 Activation by the Cryptic Peptide Mitocryptide-2 Originating from the Mitochondrial DNA-Encoded Cytochrome b.

Similar to bacteria, synthesis of mitochondrial DNA-encoded proteins requires an N-formylated methionine to initiate translation. Thus, the N-formylated methionine peptides originating from mitochondria should be recognized as danger signals. To date, only one such peptide, denoted as mitocryptide-2 (MCT-2), originating from the N-terminal of the mitochondrial cytochrome b, has been isolated from mammalian tissues. Human neutrophils express FPR1 and FPR2 that detect formyl peptides, and the precise structural determinants for receptor recognition remain to be elucidated. MCT-2 is known to activate neutrophils through FPR2 but not FPR1. The aim of this study was to elucidate the structural determinants of importance for receptor preference and human neutrophil activation in MCT-2 by generating a series of MCT-2 variants. We show that there is an absolute requirement for the N-formyl group and the side chain of Met1 at position 1 of MCT-2 but also the C terminus is of importance for MCT-2 activity. We also uncovered individual side chains that positively contribute to MCT-2 activity as well as those suppressed in the response. The MCT-2 peptide and its two polymorphic variants ([Thr7]MCT-2 and [Ser8]MCT-2) all activated neutrophils, but MCT-2 containing Ile7 and Asn8 was the most potent. We also show that some peptide variants displayed a biased FPR2-signaling property related to NADPH oxidase activation and β-arrestin recruitment, respectively. In conclusion, we disclose several critical elements in MCT-2 that are required for neutrophil activation and disclose structural insights into how FPR2 recognition of this mitochondrial DNA-derived peptide may increase our understanding of the role of FPR2 in aseptic inflammation.

An Orthogonal D2 O-Based Induction System that Provides Insights into d-Amino Acid Pattern Formation by Radical S-Adenosylmethionine Peptide Epimerases.

Radical S-adenosyl methionine peptide epimerases (RSPEs) are an enzyme family that accomplishes regiospecific and irreversible introduction of multiple d-configured residues into ribosomally encoded peptides. Collectively, RSPEs can generate diverse epimerization patterns in a wide range of substrates. Previously, the lack of rapid methods to localize epimerized residues has impeded efforts to investigate the function and applicative potential of RSPEs. An efficient mass spectrometry-based assay is introduced that permits characterization of products generated in E. coli. Applying this to a range of non-natural peptide-epimerase combinations, it is shown that the d-amino acid pattern is largely but not exclusively dictated by the core peptide sequence, while the epimerization order is dependent on the enzyme-leader pair. RSPEs were found to be highly promiscuous, which allowed for modular introduction of peptide segments with defined patterns.

An Orthogonal D2O‐Based Induction System that Provides Insights into d‐Amino Acid Pattern Formation by Radical S‐Adenosylmethionine Peptide Epimerases

AbstractRadical S‐adenosyl methionine peptide epimerases (RSPEs) are an enzyme family that accomplishes regiospecific and irreversible introduction of multiple d‐configured residues into ribosomally encoded peptides. Collectively, RSPEs can generate diverse epimerization patterns in a wide range of substrates. Previously, the lack of rapid methods to localize epimerized residues has impeded efforts to investigate the function and applicative potential of RSPEs. An efficient mass spectrometry‐based assay is introduced that permits characterization of products generated in E. coli. Applying this to a range of non‐natural peptide‐epimerase combinations, it is shown that the d‐amino acid pattern is largely but not exclusively dictated by the core peptide sequence, while the epimerization order is dependent on the enzyme‐leader pair. RSPEs were found to be highly promiscuous, which allowed for modular introduction of peptide segments with defined patterns.

Effects of Rice Bran, Flax Seed, and Sunflower Seed on Growth Performance, Carcass Characteristics, Fatty Acid Composition, Free Amino Acid and Peptide Contents, and Sensory Evaluations of Native Korean Cattle (Hanwoo).

This study was conducted to evaluate the effect of dietary supplementation with rice bran, flax seed, or sunflower seed to finishing native Korean cattle (Hanwoo) on growth performances, carcass characteristics, fatty acid composition, free amino acid and peptide contents, and sensory evaluations of Longissimus muscle (LM). A total of 39 Hanwoo steers (average age of 22.2 mo and average body weight (BW) of 552.2 kg) were randomly divided into Control, rice bran (RB), flax seed (FS), or Sunflower seed (SS) groups. The steers were group fed for 273 d until they reached an average age of 31.2 mo. Final BW was 768.2, 785.8, 786.2, and 789.0 kg, and average daily gain was 0.79, 0.85, 0.82, and 0.84 kg for the Control, RS, FS, and SS groups, respectively (p>0.05). Fat thickness of the FS group (19.8 mm) was greater (p<0.05) than that of the other groups. Final yield grade converted into numerical values was 2.0 for the RB group, 1.7 for the Control and SS groups, and 1.4 for the FS group. Marbling degrees for the Control, SS, RB, and FS groups were 5.3, 5.1, 4.7, and 4.6, respectively. Percentages of palmitic acid (C16:0), stearic acid (C18:0), and arachidic acid (C20:0) in the LM were not different among the groups. Palmitoleic (C16:1) acid was higher (p<0.05) in the SS group. The concentration of oleic acid was highest (p<0.05) in the Control group (47.73%). The level of linolenic acid (C18:3) was 2.3 times higher (p<0.05) in the FS group compared to the other groups. Methionine concentration was (p<0.05) higher in FS (1.7 mg/100 g) and SS (1.2 mg/100 g) steers than in the Control or RB groups. Glutamic acid and α-aminoadipic acid (α-AAA) contents were (p<0.05) higher in the FS group compared to the other groups. LM from the FS group had numerically higher (p>0.05) scores for flavor, umami, and overall palatability in sensory evaluations. In conclusion, supplementation of flax seed to diets of finishing Hanwoo steers improved sensory evaluations which might have been caused by increases in flavor related amino acids such as methionine, glutamic acid and α-AAA and peptides, anserine and carnosine, and their complex reactions.

Electron transfer reactions of methionine peptides with photochemically generated ruthenium(III)–polypyridyl complexes

Abstract The dynamics of the oxidation of five methionine carrying peptides with six Ru(III)–polypyridyl complexes in aqueous acetonitrile medium have been followed by spectrophotometric technique. The electron transfer (ET) reaction of [Ru(NN) 3 ] 3+ complex (NN = polypyridyl ligand) with peptide containing methionine is sensitive to the change in the structure of ligand of Ru(III) complex and N-terminal component of the peptide Met-Gly Met-Ala Met-Ser Met-Val and Met-Leu. The reaction follows the overall second-order kinetics, first order each in the oxidant and the substrate. Based on the substituent and solvent effects, an outer-sphere electron transfer from the sulfur center of the peptide to Ru(III) has been proposed as the rate controlling step of the reaction. The ET nature of the reaction is confirmed from the recorded transient absorption spectrum of peptide containing methionine sulfur radical cation by laser flash photolysis technique. Marcus theory is successfully applied to the ET reaction.

A simple method for protein N-terminal confirmation by stable isotope labeling and matrix-assisted laser desorption/ionization mass spectrometry

The protein N-terminal sequence is essential for protein identification and confirmation of the removal of N-terminal methionine or signal peptides. Without special labeling, it is difficult to distinguish the protein N-terminus from lots of peptides derived by enzymatic digestion by mass spectrometry (MS). Here, a robust method based on specific d0/d3-acetylation of the protein N-terminal amino group and selective monitoring of the doublet acetylated peptide was introduced. After the protein was guanidinated, it was acetylated by a 1:1 mixture of acetic anhydride-d0 and acetic anhydride-d6, the derivatized protein was trypsin-digested, and monitored by matrix-assisted laser desorption/ionization (MALDI) MS. Only the amino group of the protein N-terminal peptide would be tagged by one unique d0/d3-acetyl group, which appeared as a pair of characteristic isotopic peaks with a mass difference of 3 Da in the profile of peptide mass fingerprinting (PMF), whilst other internal peptides did not have such a characteristic isotopic pattern. In the next step, the recognized N-terminal peptide could be selected as a precursor ion for tandem mass spectrometric (MS/MS) analysis. Four proteins were successfully tested by this method and all N-terminal peptides were specially assigned. The results indicate the potential usage of this method in protein N-terminal identification.

Characterization and Solution Structure of Mouse Myristoylated Methionine Sulfoxide Reductase A

Methionine sulfoxide reductase A is an essential enzyme in the antioxidant system which scavenges reactive oxygen species through cyclic oxidation and reduction of methionine and methionine sulfoxide. The cytosolic form of the enzyme is myristoylated, but it is not known to translocate to membranes, and the function of myristoylation is not established. We compared the biochemical and biophysical properties of myristoylated and nonmyristoylated mouse methionine sulfoxide reductase A. These were almost identical for both forms of the enzyme, except that the myristoylated form reduced methionine sulfoxide in protein much faster than the nonmyristoylated form. We determined the solution structure of the myristoylated protein and found that the myristoyl group lies in a relatively surface exposed "myristoyl nest." We propose that this structure functions to enhance protein-protein interaction.

A Change in the 310- to α-Helical Transition Point in the Heptapeptides Containing Sulfur and Selenium

Crystal structures of three heptapeptides Boc-Ala-Leu-Aib-XXX-Ala-Leu-Aib-OMe (where XXX = methionine in peptide A, selenomethionine in peptide B, and S- benzyl cysteine in peptide C) reveal mixed 310-/α-helical conformations with R factors of 6.94, 5.79, and 5.98, respectively. All the structures were solved in the P212121 space group. 310- to α-helical transitions are observed in all of these peptides. The helices begin as a 310-helical segment at the N-terminus and then transit for peptides A and C at residue Aib(3) carbonyl (O(3)), while for peptide B the transition occurs at residue Leu(2) carbonyl oxygen (O(2)). There are water molecules associated in the crystal of each of these peptides and they form different types of hydrogen bonding patterns in each crystal. The observations suggest that 310- to α-helical transition is sequence dependent in these short heptapeptide sequences.

Structural and Topological Studies of Methionine Radical Cations in Dipeptides: Electron Sharing in Two-Center Three-Electron Bonds

One electron oxidation of methionine in peptides is highly dependent on the local structure. The sulfur-centered radical cation can complex with oxygen, nitrogen, or other sulfur atoms from a neighboring residue or from the peptidic bond, forming an intramolecular S therefore X two-center three-electron bond (X = S, N, O). This stabilization was investigated computationally in the radical cations of three peptides, methionine glycine (Met Gly) and its reverse sequence Gly Met, and Met Met. Geometry optimizations were done at the BH&HLYP/6-31G(d) level of theory and the effect of solvation was taken into account using a continuum model (CPCM). Up to seven stable conformations were considered for each peptide, with formation of 5-10 member cycles involving nitrogen from the peptidic bond or from the amine, oxygen from the peptidic bond or from the carboxylate group, or sulfur from the other residue for Met Met. The absorption wavelengths corresponding to the sigma --> sigma* transition calculated for each complex at the TD-BH&HLYP/6-311+G(d,p)//BH&HLYP/6-31G(d) level of theory vary from the near-UV for the S therefore O bonds to the green visible for the S therefore S bonds. For X = N, they increase with the SN distance as expected for a 2c-3e bond, whereas for X = O they slightly decrease. Characterization of these 2c-3e bonds as a function of the sequence, using the ELF and the AIM topological analyses, shows the different natures of the S therefore X bonds, which is purely 2c-3e for X = S, mainly 2c-3e with a part of electrostatic interaction for X = N and mainly electrostatic for X = O.

Conformational influences of N2-methylation in chemotactic peptides.

Physical and structural data on two of a series of related N-formyl methionine peptides are reported. The effects of peptide bond N-methylation on chemotactic response and on conformational properties observed in solution, in the solid state and by conformational energy calculations are described.

Stabilization and Reactions of Sulfur Radical Cations: Relevance to One-Electron Oxidation of Methionine in Peptides and Proteins

Methionine is a key amino acid that has numerous roles in essential vital processes. Moreover, methionine oxidation is biologically important during conditions of oxidative stress and represents an important step in the development of some severe pathologies. Considerable work has been performed to understand the mechanisms of one-electron oxidation of the Met-residue as a function of its proteic environment. The most important recent results obtained by means of time-resolved techniques (laser flash photolysis and pulse radiolysis) on model peptides containing single or multiple Met-residues and in selected naturally occurring peptides (Met-enkephalin and ?-amyloid peptide) and proteins (thioredoxin and calmodulin) have been reviewed.

One-electron oxidation of methionine peptides — Stability of the three-electron S—N(amide) bond

The possibility of sulfur–nitrogen (S—N) three-electron bond formation in a one-electron oxidized methionine peptide model was investigated computationally following the detection of such species in pulse radiolysis experiments (C. Schöneich, D. Pogocki, G.L. Hug, and K. Bobrowski. J. Am. Chem. Soc. 125, 13700 (2003)). Geometry optimiza tions were carried out at the B3LYP/6-31G(d) level of theory. Relative free energies in aqueous solution at pH 7 were predicted for all intermediates with enthalpy evaluations at the CCSD(T)/6-31+G(d′) level and free energies of solvation predicted using a continuum model (CPCM). Both the initial oxidation product and the intermediate formed at higher pH were identified as cyclic S—N bonded species in which the intramolecular three-electron interaction is between the S atom and the π orbital of the amide group. TD-B3LYP calculations of the UV spectra support the assignments. A mechanism for the conversion to the most stable α-C-centered radical is proposed. The mechanism involves a novel deprotonation–reprotonation via an intermediate backbone-delocalized radical anion.Key words: methionine oxidation, three-electron bonding, S—N bonding, B3LYP.

Interactions of molybdocene dichloride with histidine- and methionine-containing peptides

The reaction behavior of the antitumor active metallocene dihalide Cp 2MoCl 2 (Cp = η 5-cyclopentadienyl) towards AcHis, AcHis(1-Me), AcHis(3-Me), His-Gly, AcHis-Gly-His, AcMet, Gly-Met-Gly and cyclo-Met-Met has been studied in solution at 2.5 ⩽ pD ⩽ 7.4 by using 1H NMR spectroscopy. The histidine-containing substrates were found to bind the Cp 2Mo 2+ unit through the terminal carboxylate group or through the N1 nitrogen of the imidazole ring, depending on the pD value. At physiological pH, coordination takes place exclusively at the imidazole ring with the percentage of Cp 2Mo 2+-His adducts in 1:1 mixtures being about 70%. By contrast, the thioether group in the side chain of methionine has a very low affinity for the Cp 2Mo 2+ group. Monodentate S-coordination could not be detected. For AcMet, binding through the carboxylate group was observed as the only coordination mode, while in the case of Gly-Met-Gly Mo–S interaction occurs in combination with carboxylate coordination leading to a S,O-macrochelate in low yield. Coordination to methionine peptides only takes place at pD ⩽ 6, while at physiological pH interactions with the weak donor sites are not observed due to predominating dimerization of [Cp 2Mo(H 2O)(OH)] + to [Cp 2Mo(μ-OH) 2MoCp 2] 2+. At c(Cl −) = 100 mM competitive Cl − coordination reduces the amount of carboxylate and S,O-coordination significantly, while imidazole coordination is not affected.