The physical chemistry of hemes and hemopeptides III. Synthesis and physicochemical properties of cytochrome c-related heme-pentapeptide soluble in organic solvents

Synthesis is described of a N_α- and C-protected pentapeptide (Cys—Gly—Gly—Cys—His) which corresponds to the segment 14–18 in the primary structure of cytochrome c. The preparation of hemipentapeptide which contains peptide covalently linked to 2.4 side chains of the tetrapyrrolic ring is described.The hemipentapeptide is soluble in organic solvents and can be reduced in heterogeneous solvent mixture. In benzene its absorption and EPR spectra show that the iron ion is a high spin state. The titration of model compound in the oxidized and reduced forms was followed by optical absorption and it indicates a one-base fixation to form hexacoordinated complexes showing the presence of histidine residue liganded to the iron ion in the hemichrome and hemochrome obtained. The stability constants are 1.3 · 10³ and 1.7 · 10³ l/mole, respectively.From these results and by analogy with the absorption spectra of biological systems or others models, the presence of histidine residue on iron ion in the model compound is discussed.     

虎纹蛙皮肤分泌物抗氧化二肽——Gln/Lys-Met的纯化及鉴定

目前已自青蛙皮肤分泌物中提取出多种属于“第三套抗氧化系统”的多肽,它们具有较强的抗氧化作用.本文从虎纹蛙皮肤分泌物中提取具有抗氧化活性的多肽物质,并检测其活性.利用电刺激虎纹蛙背部腺和耳后腺获得其皮肤分泌物,利用凝胶过滤色谱Sephadex G-50和反相高效液相色谱（reverse-phase high performance liquid chromatography, RP-HPLC）进行分离纯化.以2,2-二苯基-1-苦肼基（2,2-diphenyl-1- picrylhydrazyl, DPPH·）清除率为指标,测定多肽的抗氧化活性,经ESI- MS（electrospray ionization mass spectrometry）质谱测定该多肽的相对分子质量.结果显示,自虎纹蛙皮肤分泌物中获得一种具有抗氧化活性的二肽,其分子质量为0.277 kD,可能的氨基酸序列为Gln/Lys-Met.虎纹蛙皮肤分泌物中的该二肽是发挥抗氧化作用的重要组成部分.     

Current Concepts in Intestinal Peptide Absorption

Today there is considerable interest in oral peptide delivery. However, oral administration of peptides is limited by a low bioavailability and a high variability in plasma levels. A review is given of the literature describing the major barriers in peptide absorption, the basic mechanisms of intestinal peptide transport, the experimental models and the pharmaceutical approaches currently used in the investigation of peptide and protein absorption processes.     

A molecular dynamics study of the pentacyclo-undecane (PCU) cage polypeptides of the type Ac-3Ala-Cage-3Ala-NHMe

An extensive exploration of the conformational space of the seven-residue peptide sequences, Ac-Ala-Ala-Ala-Cage-Ala-Ala-Ala-NHMe and the model peptide Ac-Ala-Ala-Ala-Ala-Ala-Ala-Ala-NHMe, was carried out using single trajectories of molecular dynamics (MD) in the solution phase using the periodic boundary conditions. Our MD studies revealed that the majority of the motifs of the PCU cage peptide exist as type I–III β-turns along with their mirror conformations, viz. type I′–III′ β-turns. This peptide sequence adopted a U-shaped backbone, with alpha-helical characteristics. The results reported here provide further evidence that the PCU cage amino acid exhibits C_7eq, C_7aq, α_R and α_L conformations in aqueous solution.     

High-performance liquid chromatographic separation of kyotorphin, a basic Tyr---Arg dipetide, in rat brain tissue and quantification using fluorimetric detection

Two HPLC procedures based on sample derivatization at the N-terminal Tyr moiety with agents yielding fluorescent derivatives were applied to the selective and sensitive detection as well as quantification of the basic kyotorphin, Tyr---Arg dipeptide, in rat brain tissue. The first one is a post-column fluorescence derivatization method, whereby the peptides extracted from the brain tissue are separated on an octadecylsilyl-silica gel column, followed by on-line fluorescence derivatization for detection. The other one is a pre-column derivatization method, where the extracted peptides are first reacted with fluorogenic agents at the N-terminal Tyr moiety to their corresponding fluorescent derivatives, subsequently separated on an octadecyl-poly(vinyl alcohol) copolymer gel column, and signal responses are measured fluorimetrically. Both methods permitted the quantification of the synthetic kyotorphin added to the rat brain tissues. The concentration range of kyotorphin-like biogenic peptide was 60–100 pmol/g in the cortex, striatum and hypothalamus tissues.     

A comprehensive library of blocked dipeptides reveals intrinsic backbone conformational propensities of unfolded proteins

Despite prolonged scientific efforts to elucidate the intrinsic peptide backbone preferences of amino-acids based on understanding of intermolecular forces, many open questions remain, particularly concerning neighboring peptide interaction effects on the backbone conformational distribution of short peptides and unfolded proteins. Here, we show that spectroscopic studies of a complete library of 400 dipeptides reveal that, irrespective of side-chain properties, the backbone conformation distribution is narrow and they adopt polyproline II and β-strand, indicating the importance of backbone peptide solvation and electronic effects. By directly comparing the dipeptide circular dichroism and NMR results with those of unfolded proteins, the comprehensive dipeptides form a complete set of structural motifs of unfolded proteins. We thus anticipate that the present dipeptide library with spectroscopic data can serve as a useful database for understanding the nature of unfolded protein structures and for further refinements of molecular mechanical parameters.     

Crystal structure of the dipeptide binding protein from Escherichia coli involved in active transport and chemotaxis.

The Escherichia coli periplasmic dipeptide binding protein functions in both peptide transport and taxis toward peptides. The structure of the dipeptide binding protein in complex with Gly-Leu (glycyl-L-leucine) has been determined at 3.2 A resolution. The binding site for dipeptides is designed to recognize the ligand's backbone while providing space to accommodate a variety of side chains. Some repositioning of protein side chains lining the binding site must occur when the dipeptide's second residue is larger than leucine. The protein's fold is very similar to that of the Salmonella typhimurium oligopeptide binding protein, and a comparison of the structures reveals the structural basis for the dipeptide binding protein's preference for shorter peptides.     

Application of Dmb-Dipeptides in the Fmoc SPPS of Difficult and Aspartimide-Prone Sequences

Mutter’s pseudoproline dipeptides and Sheppard’s Hmb derivatives are powerful tools for enhancing synthetic efficiency in Fmoc SPPS. They work by exploiting the natural propensity of N-alkyl amino acids to disrupt the formation of the secondary structures during peptide assembly. Their use results in better and more predictable acylation and deprotection kinetics, enhanced reaction rates, and improved yields of crude products. However, these approaches have certain limitations: pseudoproline dipeptides can only be used for sequences containing serine or threonine, and the coupling of the amino acid following the Hmb residue can be extremely difficult. To alleviate some of these shortcomings, we have prepared a range of Fmoc-Aaa-(Dmb)Gly-OH dipeptides and tested their efficacy in the synthesis of a number of challenging hydrophobic peptides. We also compared the efficiency of N-Dmb against N-Hmb backbone protection in preventing aspartimide formation in the Fmoc SPPS of peptides containing the Asp-Gly sequence.     

Structural characterization of a cyclic dipeptidomimetic: the effect of ring size on a 1,2,5-trisubstituted-3-oxo-1,4-diazepine system

A series of dipeptidomimetics derived from C(alpha)(i)-to-N(i-1) side chain-to-backbone amide cyclization of adjacent amino acids are structurally characterized. The resulting ring systems are either 1,2,5-trisubstituted-3-oxo-1,4-diazepine (DAP) structurally related to benzodiazepines, commonly used in drug candidates and therapeutic agents, or higher homologs of it. Here, we examine the structural consequences of enlarging the ring size from seven members to eight-, nine-, and ten-membered rings. The structural features determined by high-resolution NMR methods, relying largely on homo- and heteronuclear coupling constants, indicate that variation of the ring leads to alternative conformations and topological orientations of the attached chemical moieties or functional groups. Controlling the topological display of the ring substituents required for biological action, using a molecular scaffold made up entirely of functional groups found in peptides, should facilitate the rational, stepwise transformation of peptide lead candidate into a nonpeptidic drug candidate.     

High-performance liquid chromatographic separation of kyotorphin, a basic TyrArg dipetide, in rat brain tissue and quantification using fluorimetric detection

Two HPLC procedures based on sample derivatization at the N-terminal Tyr moiety with agents yielding fluorescent derivatives were applied to the selective and sensitive detection as well as quantification of the basic kyotorphin, TyrArg dipeptide, in rat brain tissue. The first one is a post-column fluorescence derivatization method, whereby the peptides extracted from the brain tissue are separated on an octadecylsilyl-silica gel column, followed by on-line fluorescence derivatization for detection. The other one is a pre-column derivatization method, where the extracted peptides are first reacted with fluorogenic agents at the N-terminal Tyr moiety to their corresponding fluorescent derivatives, subsequently separated on an octadecyl-poly(vinyl alcohol) copolymer gel column, and signal responses are measured fluorimetrically. Both methods permitted the quantification of the synthetic kyotorphin added to the rat brain tissues. The concentration range of kyotorphin-like biogenic peptide was 60–100 pmol/g in the cortex, striatum and hypothalamus tissues.     

Stable production of cyanophycinase in Nicotiana benthamiana and its functionality to hydrolyse cyanophycin in the murine intestine

Food supplementation with the conditionally essential amino acid arginine (Arg) has been shown to have nutritional benefits. Degradation of cyanophycin (CGP), a peptide polymer used for nitrogen storage by cyanobacteria, requires cyanophycinase (CGPase) and results in the release of β‐aspartic acid (Asp)‐Arg dipeptides. The simultaneous production of CGP and CGPase in plants could be a convenient source of Arg dipeptides. Different variants of the cphB coding region from Thermosynechococcus elongatus BP‐1 were transiently expressed in Nicotiana benthamiana plants. Translation and enzyme stability were optimized to produce high amounts of active CGPase. Protein stability was increased by the translational fusion of CGPase to the green fluorescent protein (GFP) or to the transit peptide of the small subunit of RuBisCO for peptide production in the chloroplasts. Studies in mice showed that plant‐expressed CGP fed in combination with plant‐made CGPase was hydrolysed in the intestine, and high levels of ß‐Asp‐Arg dipeptides were found in plasma, demonstrating dipeptide absorption. However, the lack of an increase in Asp and Arg or its metabolite ornithine in plasma suggests that Arg from CGP was not bioavailable in this mouse group. Intestinal degradation of CGP by CGPase led to low intestinal CGP content 4 h after consumption, but after ingestion of CGP alone, high CGP concentrations remained in the large intestine; this indicated that intact CGP was transported from the small to the large intestine and that CGP was resistant to colonic microbes.     

Aromatic dipeptide Trp–Ala can be transported by Arabidopsis peptide transporters AtPTR1 and AtPTR5

Dipeptides with an aromatic residue at the N–terminal position induced lower inward currents or blocked leak currents in Xenopus oocytes expressing the proton-coupled peptide transporter AtPTR1 or AtPTR5 of Arabidopsis thaliana compared with dipeptides with an aromatic residue at the C–terminal position. Here, AtPTR1 and AtPTR5 were expressed in a yeast mutant of peptide transporter (ptr2) with tryptophan auxotrophy. Growth assays showed that Trp–Ala could be transported by both AtPTR1 and AtPTR5 as efficiently as Ala–Trp. Our data suggested that the previous finding in Xenopus oocytes might be an artifact of heterologous expression, and that AtPTR1 and AtPTR5 expressed in yeast could transport dipeptides with an aromatic residue at the N–terminal position.     

Carnosine and Homocarnosine,the Forgotten,Enigmatic Peptides of the Brain

Carnosine (beta-alanyl-histidine) and homocarnosine (gamma-aminobutyryl-histidine) are major constituents of excitable tissues, brain and skeletal muscles, but their physiological functions are yet unknown. Using primary cell culture systems, synthesis and uptake of carnosine exclusively by glial cells could be demonstrated. Uptake of carnosine was found to be mediated by a high affinity, energy-dependent dipeptide transport system, subsequently identified as the peptide transporter PepT2. With the synthesis of beta-Ala-Lys-Nepsilon-AMCA as a fluorescent reporter molecule, accumulation of this dipeptide derivative could be monitored under viable conditions not only in astroglia cells but also in folliculostellate cells of the anterior pituitary and in gonadal resident macrophages. This reporter dipeptide provided a most valuable tool to identify an intrapituitary communication system by tracing folliculostellate cells in acute slice preparation. Moreover, this substance could also be used to prepare pituitary cell cultures enriched with or depleted of folliculostellate cells that are needed for further studies.     

The metabolic fate of 14C-labeled immunoadjuvant peptidoglycan monomer: II. In vitro studies

Peptidoglycan monomer (GlcNAc-MurNac-L-Ala-D-isoglutamine-meso-diaminopimelic acid-D-Ala-D-Ala), labeled with ¹⁴C both in the disaccharide and pentapeptide portions, was incubated with slices of mouse liver, kidney or spleen as well as with mouse and human blood cells, plasma and serum. Peptidoglycan monomer was isolated unchanged after incubations with mouse organs and blood cells. However, upon incubation with mouse or human blood, 10–50% of the peptidoglycan monomer underwent hydrolysis to the corresponding disaccharide and pentapeptide. After incubations with plasma and serum more than 90% of the [^14C]peptidoglycan monomer was metabolized: about 50% of the administered radioactive dose was recovered in the disaccharide unit and about 35% in the pentapeptide part. These results suggest that in blood, plasma and serum of mouse and man, an $\text{N-}\text{acetylmuramoyl-}\text{L}\text{-alanine}$ amidase (mucopeptide amidohydrolase, EC 3.5.1.28) exists which splits the amide bond between the lactyl carboxyl group of the muramyl residue and the amino group of the peptide moiety in the peptidoglycan molecule.     

Use of a gel-forming dipeptide derivative as a carrier for antigen presentation

A dipeptide of the formula Fmoc-Leu-Asp and some other related dipeptides were synthesized in solution by standard methods. When such peptides are dissolved in water at concentrations below 1% at 100 °C and cooled below 60 °C they form turbid solutions and eventaully visocelastic gels at lower temperatures. Such gels are thermoreversible and can also be disrupted by mechanical agitation. At a concentration of 2 mg/ml the peptide Fmoc-Leu-Asp forms an aqueous gel at 60 °C with a shear modulus of 80 Pa measured at a frequency of 1 rad/s. Peptide solutions undergo an abrupt increase in light scattering between 1 and 1.5 mg/ml at both 23 and 60 °C. By analogy with previous observations of other systems, this increse appears to be due to the formation of filamentous micelles and the aggregation of filamaents into a three-dimensional network. When low molecular weight adamantanamine derivatives, which are inherently non-antigenci antiviral drugs, were incorporated into the Fmoc-Leu-Asp gel and injected into rabbits, high titre specific antibodies were efficiently produced without the need for additional adjuvant. Both the physical properties of the gel and its effect on the antigenicity of low molecular weight compounds suggest a number of practical applications.     

Effects of Acetonitrile-Water Mixtures on α-Chymotrypsin Catalyzed Dipeptide Synthesis

-Chymotrpysin (EC 3.4 21.1) was immobilized by deposition on celite and subsequent cross-linking with glutaraldehyde. The effects of different mixtures of aqueous buffer and acetonitrile on the immobilized preparation were evaluated using a dipeptide synthesis as model reaction. The initial reaction rate at 6-95% of water increased with increasing water content. The maximum yield of peptide had two maxima; the first one at 6% of water (92%) and the second one at 80% of water (39%). The presence of two maxima was due to severe enzyme inactivation at intermediate water contents (50-60%). The immobilisation procedure slowed the inactivation of -chymotrypsin. Cross-linked enzyme was inactivated to a lesser extent than both free enzyme and enzyme that had been deposited on celite. The increased resistance to inactivation was, however, not sufficient to make peptide synthesis attractive at intermediate water contents (50-60%). In order to obtain good peptide yields, low water contents (below 10%) should be used.     

A quenched fluorescent dipeptide for assaying dispase- and thermolysin-like proteases

Metalloproteases such as dispase and thermolysin play a crucial role in the life cycle of bacteria. Commonly, they prefer hydrophobic amino acids at P1' of substrate proteins, thereby cleaving the peptide bond at the alpha amino group. Activity of such proteases has been measured by the use of tailor-made oligopeptides provided with fluorescence resonance energy transfer dyes. We can now show that the short dipeptide Dabcyl-Ser-Phe-EDANS is an appropriate substrate of dispase and thermolysin. It was cleaved by both enzymes at the single peptide bond accompanied by a steep increase in fluorescence. Substantial quenching effects of the formed products were observed only when more than 80microM substrate was hydrolyzed. High affinity of the proteases for the dipeptide resulted in low K(m) values of 91+/-9 and 104+/-18microM, which are comparable to those measured for longer peptides. Dabcyl-Ser-Phe-EDANS was also used to determine the pH and optimal temperature of dispase, which were found at pH 7.0 and 50 degrees C. Buffer substances such as acetate, citrate, and tris(hydroxymethyl)aminomethane had no significant effect on enzyme activity. Measurements up to 100 degrees C revealed that hydrolysis of the quenched fluorescent dipeptide took place only in the presence of active dispase.     

Salt-Enhanced Aminolysis of Acyl-α-Chymotrypsins by Dipeptides

Increase in KC1 concentration from 0.1 m to 3 m enhances the chymotrypsin-catalyzed acyl-transfer to a series of dipeptides, H₂N—CH(R₁)C(O)NHCH(R₂)C(O)O, by factors between 15 and 44. The observed positive salt effect seems to be a screening of the unfavorable electrostatic interaction between the dipeptide carboxyl group and a negatively charged area in the S' subsite on the enzyme surface. The effect is of practical use in preparative peptide synthesis—in 3 m KCl solutions the analytical yields of tripeptides of up to 99 per cent have been obtained.     

A theoretical study of pentacyclo-undecane cage peptides of the type [Ac-X-Y-NHMe].

The conformational preferences of peptides of the type, Ac-X-Y-NHMe, where X and Y = Ala, cage and Pro, were studied by means of computational techniques within the framework of a molecular mechanics approach. For each of the eight peptide analogues, extensive conformational searches were carried out using molecular dynamics (MD) and simulated annealing (SA) protocols in an iterative fashion. Both results are in good agreement and complement each other. The conformational search indicates that the cage residue restricts the conformational freedom of the dipeptide considerably in comparison with the other model residues used. This study revealed that proline exhibits a greater tendency in promoting reverse-turn characteristics in comparison to the cage peptides, which show promising beta-turn characteristics. It was also found that 300-500 K is not sufficient to overcome rotational barriers for cage peptides. In all cases, the low-energy conformers have a tendency to form bent structures.     

Analysis of the conformational profile of trishomocubane amino acid dipeptide

4-Amino-(D3)-trishomocubane-4-carboxylic acid is a constrained alpha-amino acid residue that exhibits promising conformational characteristics, i.e., helical and beta-turns. As part of the development of conformational guidelines for the design of peptides and protein surrogates, the conformational energy calculations on trishomocubane using molecular mechanics and ab initio methods are presented. The C(alpha) carbon of trishomocubane forms part of the cyclic structure, and consequently a peptidic environment was simulated with an acetyl group on its N-terminus and a methylamide group on its C-terminus. Ramachandran maps computed at the molecular mechanics level using the standard AMBER (parm94) force field libraries compared reasonably well with the corresponding maps computed at the Hartree Fock level, using the 6-31G* basis set. Trishomocubane peptide (Ac-Tris-NHMe) is characterized by four low energy conformers corresponding to the C7ax, C7eq, 3(10), and alpha(L) helical structures.