Functional arginine-containing amino acid sequences in peptides and proteins

L-Arginine is a source of nitrogen oxide and plays a great role in a number of other biochemical processes. Functions and prospects for practical application of five groups of arginine-containing amino acid sequences and synthetic polyarginine sequences are considered. The physiological characteristics of well-known arginine-containing peptides, such as RGD containing, kyotorphin, and tuftsin, are described in detail.     

Role of peptide structure in lipid-peptide interactions: high-sensitivity differential scanning calorimetry and electron spin resonance studies of the structural properties of dimyristoylphosphatidylcholine membranes interacting with pentagastrin-related pentapeptides

The effects of amino acid substitutions in the pentapeptide pentagastrin on the nature of its interactions with dimyristoylphosphatidylcholine (DMPC) are assessed by differential scanning calorimetry and electron spin resonance. In two peptide analogues, the Asp at position 4 in pentagastrin (N-t-Boc-beta-Ala-Trp-Met-Asp-Phe-NH2) is replaced by Gly or Phe. These uncharged, more hydrophobic peptides have little effect on the transition temperature of DMPC, but they broaden the transition and lower the transition enthalpy as do integral membrane proteins. These peptides also mimic the behavior of integral membrane proteins in decreasing the order of a 5-doxylstearic acid spin probe below the transition temperature and in exhibiting a second immobilized lipid component using a 16-doxylstearic acid spin probe in DMPC. Three charged peptides were studied: pentagastrin, an analogue with positions 4 and 5 reversed (i.e., ending in Phe-Asp-NH2), and one with Asp replaced by Arg at position 4. All three of these charged peptides altered the phase transition behavior of DMPC to give two components, one above and one below the transition temperature of the pure lipid. With increasing peptide concentration, the higher melting transition became more prominent. The arginine-containing peptide produced the largest shifts in melting temperature followed by pentagastrin and then the "reversed" peptide. The arginine-containing peptide also increased the enthalpy of the transition. These peptides also increased the ordering of DMPC below the phase transition as measured with both 5- and 16-doxylstearic acid. The ordering effect was most pronounced with the arginine-containing peptide using the 5-doxylstearic acid probe. The results demonstrate that even the zwitterionic DMPC can interact more strongly with positively charged peptides than with negatively charged ones. In addition, peptide sequence as well as composition is important in determining the nature of peptide-lipid interactions. The markedly different effects of these pentagastrin peptides on the phase transition and motional properties of DMPC occur despite the similar depth of burial of these peptides with DMPC.     

Trypsin peptide patterns of tryptophan synthase beta2 protein among four species of the Enterobacteriaceae.

The tryptophan synthase beta 2 protein (EC 4.2.1.20) of Escherichia coli, Enterobacter aerogenes, Serratia marcescens, and Erwinia carotovora was purified and compared. Two-dimensional total peptide patterns for each of the four beta2 proteins obtained after digestion with trypsin showed that approximately three quarters of the total peptides are common to all four peptides. Examination of only arginine-containing peptides showed that approximately half of these peptides are common. From a comparative standpoint, the data provide evidence that the primary structure of beta 2 proteins is relatively similar, indicating that the trpB cistron is evolutionarily conserved in the enteric bacteria group.     

Selective determination of arginine-containing and tyrosine-containing peptides using capillary electrophoresis and laser-induced fluorescence detection.

The use of two different amino acid-selective fluorogenic reagents for the derivatization of peptides is investigated. One such scheme utilizes a selective reaction of benzoin with the guanidine moiety to derivatize arginine residues occurring in a peptide. The second scheme involves the formylation of tyrosine, followed by reaction with 4-methoxy-1,2-phenylenediamine. The use of capillary electrophoresis and laser-induced fluorescence detection allows enhanced efficiencies and sensitivities to be obtained for the separations of either arginine- or tyrosine-containing peptides. A helium-cadmium laser (325 nm) is ideally suited for the laser-based detection system due to a close match of the excitation maxima of derivatized peptides from both reactions. A detection limit of 270 amol is achieved for model arginine-containing peptides, while the detection limit for model tyrosine-containing peptides is measured at 390 amol. Both derivatization reactions are found to be useful for high-sensitivity peptide mapping applications in which only the peptides containing the derivatized amino acids are detected.     

Antithrombin activity of methyl esters of arginine-containing peptides

The capacity of methyl esters of arginine-containing substrates to inhibit the proteolytic activity of thrombin is studied. A relationship between the structure of peptides and their capacity to inhibit the thrombin-fibrinogen reaction is investigated. Parameters Ks, k2 and k3, which characterize individual stages of the protein process are calculated from experimentally obtained kcat, Km and I50 values. It is shown that the antithrombin activity of peptides becomes maximal only in the case when residues of hydrophobic amino acids would be simultaneously present both at the positions of P2 and P3 of oligopeptides.     

Inhibition of the proteolytic activity of thrombin by methyl esters of arginine-containing oligopeptides

The kinetics of thrombin-catalyzed hydrolysis of the esters of arginine-containing di- and tripeptides at pH 8.5 and the inhibition of fibrinogen-thrombin reaction by these compounds are studied. The experimentally obtained values of Km, kcat, I50 and the suggestion about the competitive character of the antithrombin action of the peptides allowed the individual kinetic parameters to be calculated. The data obtained indicate that the efficiency of the thrombin-catalyzed hydrolysis of the peptides or a degree of the retardation of the proteolytic activity of thrombin by the esters under investigation depend on the hydrophobicity of the amino acid residues located at subsides P2 and P3 of the peptides. An increase of the hydrophobicity has induced a decrease in the rate constants k2 and k3 and an increase in the inhibition power of the oligopeptides.     

Synthetic beta-turn peptides as substrates for a tyrosine protein kinase

An attempt has been made at defining the secondary structural requirement for phosphorylation of substrates of a protein tyrosine kinase from the leukemia virus-transformed LSTRA cell line. An examination of the sites of phosphorylation of substrates of protein tyrosine kinases indicated a relatively high probability of the beta-turn as the secondary structural feature at these sites. We have, therefore, synthesized three tyrosine peptides: Ala-Pro-Tyr-Gly-NHCH3, Leu-Pro-Tyr-Ala-NHCH3, and Pro-Gly-Ala-Tyr-NH2, of which the first two peptides, but not the third, would be expected to contain the tyrosine residue in a beta-turn. Circular dichroism and infrared spectral data on the peptides confirmed this expectation. Phosphorylation data on the peptides by the tyrosine kinase showed that the two beta-turn peptides were phosphorylated with Vmax and Km values comparable to those of the 13-residue-long arginine-containing synthetic peptide substrate having a sequence homologous to the autophosphorylation site of the LSTRA kinase. The peptides used here contain the shortest sequence length among the reported synthetic peptide substrates for protein tyrosine kinases. Their preference for the beta-turn indicated that this conformation may serve as the recognition site for tyrosine phosphorylation.     

Biosensor analysis of anti-citrullinated protein/peptide antibody affinity

Anti-citrullinated protein/peptide antibodies (ACPAs) are detected in rheumatoid arthritis (RA) sera and because of their strict association with the disease are considered marker antibodies, probably endowed with pathogenic potential. Antibody affinity is one of the parameters affecting pathogenicity. Three diagnostic citrullinated peptides—viral citrullinated peptide 1 (VCP1) and VCP2 derived from Epstein–Barr virus (EBV)-encoded proteins and histone citrullinated peptide 1 (HCP1) derived from histone H4—were synthesized as tetrameric multiple antigen peptides and immobilized on sensor chips CM5 type in a Biacore T100 instrument. Specific binding of purified antibodies from RA patients to the three peptides was analyzed by surface plasmon resonance using two arginine-containing sequences as controls. Employing a 1:1 binding model for affinity constant calculation, ACPAs interacted with VCP1 and VCP2 with lower apparent affinity (10⁻⁶ M > K_D > 10⁻⁷ M) and interacted with HCP1 with higher apparent affinity (K_D = 10⁻⁸ M). The results indicate that the binding to citrullinated peptides is characterized by wide differences in affinity, with slower association and faster dissociation rates in the case of antibodies to viral citrullinated peptides as compared with antibodies specific for the histone peptide. This biosensor analysis shows the high cross-reactivity of purified ACPAs that bind other citrullinated peptides besides the one used for purification.     

Structure of N-terminal cyanogen bromide fragment of human plasma albumin.

The complete amino acid sequence of 87 residues of cyanogen bromide fragment CB1 (Asp), the N-terminal fragment of human plasma albumine molecule, has been established. The sequence was determined from the characterization of all tryptic peptides and of chymotryptic arginine-containing peptides in the fragment digested. Overlaps were obtained by tryptic and chymotryptic cleavage of the maleylated S-sulfo derivative of fragment CB1(Asp). Residue 34 is the only cysteine residue in the albumin molecule and it was determined in the form of S-carboxymethyl-cysteine. Edman and dansyl-Edman degradation were used for the sequential analysis.     

Thylakoid DeltapH-dependent precursor proteins bind to a cpTatC-Hcf106 complex before Tha4-dependent transport

The thylakoid DeltapH-dependent pathway transports folded proteins with twin arginine-containing signal peptides. Identified components of the machinery include cpTatC, Hcf106, and Tha4. The reaction occurs in two steps: precursor binding to the machinery, and transport across the membrane. Here, we show that a cpTatC-Hcf106 complex serves as receptor for specific binding of twin arginine-containing precursors. Antibodies to either Hcf106 or cpTatC, but not Tha4, inhibited precursor binding. Blue native gel electrophoresis and coimmunoprecipitation of digitonin-solubilized thylakoids showed that Hcf106 and cpTatC are members of an approximately 700-kD complex that lacks Tha4. Thylakoid-bound precursor proteins were also associated with an approximately 700-kD complex and were coimmunoprecipitated with antibodies to cpTatC or Hcf106. Chemical cross-linking revealed that precursors make direct contact with cpTatC and Hcf106 and confirmed that Tha4 is not associated with precursor, cpTatC, or Hcf106 in the membrane. Precursor binding to the cpTatC-Hcf106 complex required both the twin arginine and the hydrophobic core of the signal peptide. Precursors remained bound to the complex when Tha4 was sequestered by antibody, even in the presence of DeltapH. These results indicate that precursor binding to the cpTatC-Hcf106 complex constitutes the recognition event for this pathway and that subsequent participation by Tha4 leads to translocation.     

Fluorescence histochemistry of peptide hormone-producing cells: Observations on the phenanthrenequinone method for the demonstration of arginine residues

Summary Phenanthrenequinone is a sensitive and specific fluorescence histochemical reagent for monosubstituted guanidines. It is probable that it selectively demonstrates the guanidino group of arginine residues of proteins and peptides. Phenanthrenequinone induces moderate to intense fluorescence in gastric chief cells, parenchymal cells of the pancreas, and certain peptide hormone-producing cell types such as the GH cells of the adenohypophysis and the glucagon cells of the pancreatic islets. Similar fluorescence spectra were obtained from an arginine-containing peptide in a histochemical model and from the GH cells of the adenohypophysis following exposure to phenanthrenequinone. We conclude that the cells demonstrated with this reagent store peptides or proteins rich in arginine.     

Validation of a multiplex chip-based assay for the detection of autoantibodies against citrullinated peptides

Introduction

Autoantibodies directed against citrullinated proteins/peptides (ACPAs) are highly specific and predictive for the development of rheumatoid arthritis (RA). Different subgroups of RA patients, which have different prognoses and may require different treatments, are characterized by different autoantibody profiles. The objective of this study was to develop a microarray for the detection of multiple RA-associated autoantibodies, initially focusing on responses against citrullinated epitopes on candidate autoantigens in RA.

Methods

The microarray is based on Phadia''s ImmunoCAP ISAC system, with which reactivity to more than 100 antigens can be analyzed simultaneously, by using minute serum volumes (< 10 μl). Twelve citrullinated peptides, and the corresponding native arginine-containing control peptides, were immobilized in an arrayed fashion onto a chemically modified glass slide, allowing a three-dimensional layer with high binding capacity. The assay was optimized concerning serum dilution and glass surface, whereas each individual antigen was optimized concerning coupling chemistry, antigen concentration, and selection of spotting buffer. The performance of each peptide in the ImmunoCAP ISAC system was compared with the performance in enzyme-linked immunosorbent assays (ELISAs). Serum from 927 RA patients and 461 healthy controls from a matched case-control study were applied onto reaction sites on glass slides, followed by fluorescent-labeled anti-human immunoglobulin G (IgG) antibody. Fluorescence intensities were detected with a laser scanner, and the results analyzed by using image-analysis software.

Results

Strong correlations between the ImmunoCAP ISAC system and ELISA results were found for individual citrullinated peptides (Spearman ρ typically between 0.75 and 0.90). Reactivity of RA sera with the peptides was seen mainly in the anticyclic citrullinated peptide 2 (CCP2)-positive subset, but some additional reactivity with single citrullinated peptides was seen in the anti-CCP2-negative subset. Adjusting for reactivity against arginine-containing control peptides did not uniformly change the diagnostic performance for antibodies against the individual citrullinated peptides.

Conclusions

The multiplexed array, for detection of autoantibodies against multiple citrullinated epitopes on candidate RA autoantigens, will be of benefit in studies of RA pathogenesis, diagnosis, and potentially as a guide to individualized treatment.     

Solid-state IR-LD spectroscopic and theoretical analysis of arginine-containing peptides

Structural prediction and IR-characteristic bands assignment of arginine-containing tri- and tetrapeptides glycyl-glycyl-arginine (GGArg) and glycyl-glycyl-arginyl-alanine (GGArgAla) have been carried out, using linear-dichroic infrared (IR-LD) spectroscopy of oriented solid-samples in a nematic liquid crystal suspension. Spectroscopic data have been supported with ab initio analysis (Hartree-Fock level of theory and 6-31++G** basis set). Predicted geometry parameters have been compared with known crystallographic ones of similar peptides, indicating a good correlation.     

Increased sensitivity of tryptic peptide detection by MALDI-TOF mass spectrometry is achieved by conversion of lysine to homoarginine

Mass spectrometric techniques for identification of proteins by "mass fingerprinting" (matching the masses of tryptic peptides from a protein digest to the theoretical peptides in a database) such as matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) are rapidly growing in popularity as the demand for high throughput analysis of the proteome increases. This is due, in part, to the ability to automate the technique and the rapid rate with which mass spectra may be acquired. An important factor in the accuracy of the technique is the number of tryptic peptides that are identified in the various searching algorithms that exist. The greater sequence coverage of the parent protein that is obtained, the higher the level of confidence in the identification that is determined. One impediment to high levels of sequence coverage is the bias of MALDI-TOF mass spectrometry to arginine-containing peptides. Increasing the sensitivity to lysine-containing peptides should increase the sequence coverage obtained. In order to achieve this result we have developed conditions to modify the epsilon-amine group of lysine in tryptic peptides with O-methylisourea. The conditions utilized result in the conversion of lysine to homoarginine with no modification of the amine terminus of the peptides. The sensitivity of MALDI-TOF mass spectrometry detection of peptides was increased dramatically following modification. The modification chemistry may be applied to tryptic peptide mixtures prior to desalting and spotting onto MALDI-TOF plates. This technique will be particularly useful for identifying proteins with a high lysine/arginine ratio.     

Mapping precursor-binding site on TatC subunit of twin arginine-specific protein translocase by site-specific photo cross-linking

A number of secreted precursor proteins of bacteria, archaea, and plant chloroplasts stand out by a conserved twin arginine-containing sequence motif in their signal peptides. Many of these precursor proteins are secreted in a completely folded conformation by specific twin arginine translocation (Tat) machineries. Tat machineries are high molecular mass complexes consisting of two types of membrane proteins, a hexahelical TatC protein, and usually one or two single-spanning membrane proteins, called TatA and TatB. TatC has previously been shown to be involved in the recognition of twin arginine signal peptides. We have performed an extensive site-specific cross-linking analysis of the Escherichia coli TatC protein under resting and translocating conditions. This strategy allowed us to map the recognition site for twin arginine signal peptides to the cytosolic N-terminal region and first cytosolic loop of TatC. In addition, discrete contact sites between TatC, TatB, and TatA were revealed. We discuss a tentative model of how a twin arginine signal sequence might be accommodated in the Tat translocase.     

The molecular weight of, and evidence for two types of subunits in, the molybdenum-iron protein of Azotobacter vinelandii nitrogenase.

The weight-average molecular weight of the Mo-Fe protein isolated from Azotobacter vinelandii has been determined by sedimentation-equilibrium techniques. In buffer, the value is 245000+/-5000; in 8M-urea, the value is 61000+/-1000. The protein was separated into two components by chromatography on CM-cellulose in 7M-urea, pH 4.5. These components have similar molecular weights but were shown to differ in charge, amino acid content and arginine-containing peptides. It is proposed that the tetramer has the subunit composition (nalpha2nbeta2).     

Application of arylsulphonyl side-chain protected arginines in solid-phase peptide synthesis based on 9-fluorenylmethoxycarbonyl amino protecting strategy.

One of the main problems still hampering solid-phase peptide synthesis using orthogonal protection strategies based on the 9-fluorenylmethoxycarbonyl amino protecting group is the difficult removal of currently used arginine arylsulphonyl guanidino protecting groups. Poor acid liability of 4-methoxy-2,3,6-trimethylbenzenesulphonyl-protected arginine has led to the popularity of the newer 2,2,5,7,8- pentamethylchroman-6-sulphonyl guanidino protecting group. This group was initially believed to have liability to trifluoroacetic acid, the reagent commonly used to simultaneously deprotect peptides and detach them from the synthesis resin, comparable to tert.-butyl and trityl type protecting groups used for the protection of other peptide side-chain functionalities. In a comparison of three established cleavage/deprotection mixtures we have shown that this is not always the case, particularly in multiple arginine peptides. We have found that only hard-acid deprotection with trimethylsilyl bromide reliably removed both arylsulphonyl guanidino protecting groups from a variety of arginine-containing peptides.     

Identification of novel short peptide inhibitors of soluble 37/48 kDa oligomers of amyloid β42

Since the soluble oligomers of 42-residue amyloid β (Aβ42) might be neurotoxins at an early stage of Alzheimer's disease (AD), inhibition of soluble Aβ42 oligomerization should be effective in the treatment of AD. We have found by phage display that a 7-residue peptide, SRPGLRR, exhibited inhibitory activity against soluble 37/48 kDa oligomers of Aβ42. In the present study, we newly prepared 3- and 4-residue random peptides libraries and performed pannings of them against soluble Aβ42 to search for important factors in the inhibition of Aβ42 oligomerization. After the fifth round, arginine-containing peptides were enriched in both libraries. SDS-PAGE and size-exclusion chromatography indicated that the inhibitory activities of 4-residue peptides against the soluble 37/48 kDa oligomers of Aβ42 were higher than those of the 3-residue peptides, and RFRK exhibited strong inhibitory activity as well as SRPGLRR. These short peptides should be useful for the suppression of soluble Aβ42 oligomer formation.     

Identification of Novel Short Peptide Inhibitors of Soluble 37/48 kDa Oligomers of Amyloid β42

Since the soluble oligomers of 42-residue amyloid β (Aβ42) might be neurotoxins at an early stage of Alzheimer’s disease (AD), inhibition of soluble Aβ42 oligomerization should be effective in the treatment of AD. We have found by phage display that a 7-residue peptide, SRPGLRR, exhibited inhibitory activity against soluble 37/48 kDa oligomers of Aβ42. In the present study, we newly prepared 3- and 4-residue random peptides libraries and performed pannings of them against soluble Aβ42 to search for important factors in the inhibition of Aβ42 oligomerization. After the fifth round, arginine-containing peptides were enriched in both libraries. SDS–PAGE and size-exclusion chromatography indicated that the inhibitory activities of 4-residue peptides against the soluble 37/48 kDa oligomers of Aβ42 were higher than those of the 3-residue peptides, and RFRK exhibited strong inhibitory activity as well as SRPGLRR. These short peptides should be useful for the suppression of soluble Aβ42 oligomer formation.