Ala Ile Research Articles

Z-Ala-Ile-OH, a dipeptide building block suitable for the formation of orthorhombic microtubes.

Self-assembling dipeptides have emerged in the last two decades as promising building blocks for the development of novel biomaterials. Among the various classes of dipeptides, aromatic dipeptides and especially diphenylalanine (Phe-Phe), which forms hexagonal nanotubes, have been the most extensively studied. However, aliphatic peptides or mixed aromatic-aliphatic dipeptides seem just as promising, exhibiting various structures ranging from amyloid fibrils to microtubes. Herein we report the single-crystal structure of an aliphatic dipeptide, alanine-isoleucine (Ala-Ile), C17H24N2O5, protected with a benzyloxycarbonyl (Z) group at the N-terminus. The protected dipeptide crystallizes in the orthorhombic space group P212121 and forms hollow microtubes with orthorhombic symmetry upon evaporation on glass surfaces, as shown by field emission scanning electron microscopy (FESEM). These findings provide an increased understanding of the correlation between the single-crystal structure of the peptide building block and its self-assembly mechanism, and expand the library of available building blocks for microtechnological applications.

Dipeptide membranes for CO2 separation: A molecular simulation study

Molecular crystals of dipeptides with a high density of uniform pores have received growing interest for gas separation. Particularly, hydrophobic dipeptides can form one-dimensional straight pores with sizes ranging from 0.37 to 0.50 nm. A molecular simulation study is reported here to investigate the membrane separation of CO2/N2 and CO2/CH4 mixtures in eight dipeptides namely Ala-Val (AV), Val-Ala (VA), Ala-Ile (AI), Ile-Ala (IA), Val-Ile (VI), Ile-Val (IV), Val-Val (VV) and Leu-Ser (LS). The gas permeation and separation performance are evaluated using a molecular dynamics simulation method with a constant-pressure difference. The pore size and helicity are revealed to be the key factors governing permeation. A higher permeability can be achieved in a dipeptide membrane with a larger pore size or a lower helicity. Among the eight, six (AV, LS, AI, VA, VV and VI) surpass the Robeson upper bound for both gas mixtures. It is identified that AI and AV outperform other dipeptides for CO2/N2 separation, while AI, VA and VV are better for CO2/CH4 separation. The permselective separation of both gas mixtures is dominated by the preferential sorption of CO2 over N2 and CH4, respectively. This simulation study provides microscopic insights into CO2 separation in dipeptide membranes and suggests their potential use for gas separation.

A Strategy for Quality Control of Vespa magnifica (Smith) Venom Based on HPLC Fingerprint Analysis and Multi-Component Separation Combined with Quantitative Analysis

As a folk medicine of the Jingpo minority in Yunnan province, the venom of Vespa magnifica has been commonly used for the treatment of rheumatoid arthritis. Quality standardization of the wasp venom is a necessary step for its pharmaceutical research and development. To control the quality of the wasp venom, a method based on high-performance liquid chromatography (HPLC) was developed for chemical fingerprint analysis. In the chromatographic fingerprinting, chemometrics procedures, including similarity analysis (SA), hierarchical clustering analysis (HCA), and principal component analysis (PCA), were applied to classify 134 batches (S1–S134) of wasp venom from different origins. The HPLC fingerprint method displayed good precision (Relative standard deviation, RSD < 0.27%), stability (in 16 h, RSD < 0.34%), and repeatability (RSD < 1.00%). Simultaneously, four compounds (VMS1, VMS2, VMS3, and VMS4) in the wasp venom were purified and identified. VMS1 was 5-hydroxytryptamine, and the other compounds were three peptides that were sequenced as follows: Gly–Arg–Pro–Hyp–Gly–Phe–Ser–Pro–Phe–Arg–Ile–Asp–NH2 (VMS2), Ile–Asn–Leu–Lys–Ala–Ile–Ala–Ala–Leu–Ala–Lys–Lys–Leu–Leu–NH2 (VMS3), and Phe–Leu–Pro–Ile–Ile–Gly–Lys–Leu–Leu–Ser–Gly–Leu–Leu–NH2 (VMS4). The quantifications for these components were 110.2 mg/g, 26.9 mg/g, 216.3 mg/g, and 58.0 mg/g, respectively. The results of this work indicated that the combination of the chemical fingerprint and quantitative analysis offers a reasonable way to evaluate the quality of wasp venom.

New serum biomarker identification and analysis by mass spectrometry in cervical precancerous lesion and acute cervicitis in South China.

Background: According to the statistics of WHO/IARC, cervical cancer (CC) has become the fourth malignant cancer of female worldwide and it is one of the main causes of death of women in developing countries.Purpose: Potential plasma and metabolic biomarkers for CC precancerous lesions and cervicitis were indicated by LC-MS techniques, and their underlying mechanisms and functions were analyzed.Methods: Plasma samples were selected from healthy people (control), low-grade squamous intraepithelial lesions (LSIL), high-grade squamous intraepithelial lesions (HSIL), CC, and post-treatment patients. All polypeptide types and sequences were detected by LC-MS/MS and the results were normalized by using Pareto-scaling. Potential metabolic biomarkers were screened by applying MetaboAnalyst 4.0 software and XCMS software, and analysis of variance and enrichment analysis were performed. Metabolic pathway analysis and functional enrichment analysis were used to further investigate the significance and pathological mechanisms of potential biomarkers.Results: Compared with healthy people, 9 differentially expressed metabolites were screened, 4 of which were up-regulated and 5 were down-regulated. LSIL group screened 7 differentially expressed metabolites, 5 of which were up-regulated and 2 were down-regulated; CC group screened 12 differentially expressed metabolites were screened, of which 9 were up-regulated and 3 were down-regulated. Eight differentially expressed metabolites were screened in the IF group, of which 5 showed up-regulation and 3 showed down-regulation. In functional enrichment analysis, differential metabolism was found to be associated with addition and coagulation cascades. Among all potential biomarkers, 2-amino-3-methyl-1-butanol, L-carnitine, Asn Asn Gln Arg, Ala Cys Ser Trp, Soladulcidine, Ala Ile Gln Arg, 2-amino-3 -Methyl-1-butanol, L-carnitine, Asn Asn Gln Arg, Ala Cys Ser Trp, Soladulcidine, Ala Ile Gln Arg can be used as predictors of precancerous lesions at different stages of CC. Among all biomarkers, 6α-fluoro-11β1,17-dihydroxypren-4-ene-3,20-dione has higher expression in the CC and HSIL groups and lower expression in the treatment group.Conclusion: By applying molecular markers to assess the progression of the disease, the accuracy and specificity of the diagnosis can be improved, which has certain prospects in clinical applications.

Dipeptide Crystals as Reverse Osmosis Membranes for Water Desalination: Atomistic Simulation

An atomistic simulation study is reported to investigate the capability of dipeptide crystals as reverse osmosis (RO) membranes for water desalination. Eight dipeptides are considered, namely, Ala-Val (AV), Val-Ala (VA), Ala-Ile (AI), Ile-Ala (IA), Val-Ile (VI), Ile-Val (IV), Val-Val (VV), and Leu-Ser (LS). It is revealed that water flux is governed by both pore size and helicity. With a relatively larger pore size, AV, AI, VV, and LS exhibit a higher water flux than VA, IA, VI, and IV. Despite similar pore size in AI and VA, a higher flux is observed in AI because of a lower helicity. On the other hand, VI, LS, IV, and IA possess higher salt rejection (>90%, and 100% for VI) than the rest (<70%). The salt rejection is determined by the electric potential difference across the membrane, induced by the staggered arrangement of −NH3+ and −COO– groups in the dipeptides. This unique arrangement of charge groups is not observed in other types of RO membranes. A higher electric potential difference allows more ...

Role of Disulfide Bonds in Activity and Stability of Tigerinin-1R.

Tigerinin-1R (Arg–Val–Cys–Ser–Ala–Ile–Pro–Leu–Pro–Ile–Cys–His–NH2), a cationic 12-mer peptide containing a disulfide bond extracted from frog skin secretions, lacks antibacterial activity, but has the ability to stimulate insulin release both in vitro and in vivo. To study the structure–function relationships of tigerinin-1R, we designed and synthesized five analogs, including tigerinin-cyclic, tigerinin-1R-L4, tigerinin-linear, [C3K]tigerinin-1R, and [C11K]tigerinin-1R. Tigerinin-1R promoted insulin secretion in a concentration-dependent manner in INS-1 cells without obvious cytotoxicity. At a concentration of 10−5 M, [C11K]tigerinin-1R exhibited the highest stimulation ability, suggesting that the positive charge at the C-terminus may contribute to the in vitro insulin-releasing activity of tigerinin-1R. Tigerinin-1R peptides stimulated insulin release in INS-1 cells through a universal mechanism that involves mobilization of intracellular calcium without disrupting the cell membrane. In vivo experiments showed that both tigerinin-1R and [C11K]tigerinin-1R improved glucose tolerance in overnight-fasted mice. Due to its structural stability, tigerinin-1R showed superior hypoglycemic activity to [C11K]tigerinin-1R, which suggested a critical role of the disulfide bonds. In addition, we also identified a protective effect of tigerinin-1R peptides in apoptosis induced by oxidative stress. These results further confirm the potential for the development of tigerinin-1R as an anti-diabetic therapeutic agent in clinical practice.

Characterization and structure identification of an antimicrobial peptide, hominicin, produced by Staphylococcus hominis MBBL 2–9

Hominicin, antimicrobial peptide displaying potent activity against Staphylococcus aureus ATCC 25923, methicillin-resistant S. aureus (MRSA) ATCC 11435 and vancomycin-intermediate S. aureus (VISA) CCARM 3501, was purified by chloroform extraction, ion-exchange column chromatography and reverse-phase HPLC from culture supernatant of Staphylococcushominis MBBL 2–9. Hominicin exhibited heat stability up to 121°C for 15min and activity under both acidic and basic conditions (from pH 2.0 to 10.0). Hominicin was cleaved into two fragments after treatment with proteinase K, resulting in the loss of its antibacterial activity, while it was resistant to trypsin, α-chymotrypsin, pepsin and lipase. The molecular mass of hominicin determined by mass spectrometry was 2038.4Da. LC–mass spectrometry and NMR spectroscopy analyses of the two fragments revealed the sequence of hominicin as DmIle–Dhb–Pro–Ala–Dhb–Pro–Phe–Dhb–Pro–Ala–Ile–Thr–Glu–Ile–Dhb–Ala–Ala–Val–Ile–Ala–Dmp, which had no similarity with other antimicrobial peptides previously reported. The present study is the first report of this novel antimicrobial peptide, which has uncommon amino acid residues like the ones in Class I group and shows potent activity against clinically relevant S. aureus, MRSA and VISA.

A New Approach to Characterizing Sorption in Materials with Flexible Micropores

Microporous dipeptides, also known as organic zeolites or biozeolites, as examples of small-pore peptide nanotubes provide a convenient set of materials for developing a systematic approach based on 129Xe NMR spectroscopy for the derivation of thermodynamic and molecular scale information on temperature dependent pore filling. The sorption of xenon in the isolated 1D chiral nanochannels of eight microporous dipeptides Ala-Val (AV), Val-Ala (VA), Leu-Ser (LS), Ala-Ile (AI), Val-Val (VV), Ile-Ala (IA), Ile-Val (IV), Val-Ile (VI) (all LL isomers) was monitored in situ with continuous-flow 129Xe NMR spectroscopy over a temperature range of 173−343 K. The materials all showed strongly anisotropic signals, with isotropic chemical shift changing from 95 to 281 ppm depending on the dipeptide used and/or temperature. The isosteric heats of sorption (qst) and entropy factors were determined from two independent models. The sorption process was complicated by reversible phase transformations of some dipeptides and irreversible changes due to aging of samples, both of which may be of considerable importance in applications of soft materials. The interpretation of the line shapes and chemical shift anisotropy as a function of temperature provided information on the structure of the xenon-cavity complex and made it possible taking into account the helicity and flexibility of the nanochannels and the dynamics of xenon. The approach illustrates a powerful way of analyzing pore space in soft microporous materials, yielding a quantitative thermodynamic description of sorption and the characteristics of the pore space and sorption events that occur on molecular-scale level during pore filling.

Cloning, expression, purification, and characterization of a designer protein with repetitive sequences

An artificial protein containing alternating hydrophilic–hydrophobic blocks of amino acids was designed in order to mimic the structure of synthetic multiblock copolymers. The hydrophobic block consisted of the six amino acids Ala Ile Leu Leu Ile Ile (AILLII) and the hydrophilic block of the eight amino acids Thr Ser Glu Asp Asp Asn Asn Gln (TSEDDNNQ). The coding DNA sequence of the cluster was inserted into an commercial pET 30a(+) vector using a two step strategy. The expression of the artificial protein in Escherichia coli was optimized using a temperature shift strategy. Only at cultivation temperature of 24 °C after induction expression was observed, whereas at 30 and 37 °C no target protein could be detected. Cells obtained from a 15 L bioreactor cultivation of E. coli were disintegrated by mechanical methods. Interestingly, glass bead milling and high pressure homogenization resulted in a different solubility of the target protein. The further purification was carried out by affinity chromatography using the soluble homogenized protein. Extreme conditions (6 M urea, 0.5 M NaCl) were applied in order to prevent aggregation to insoluble particles. The designer protein showed an extremely high tendency to form dimers or trimers caused by intermolecular interactions which were even not broken under the conditions of SDS–polyacrylamide gel electrophoresis, rendering the behavior during purification different from proteins usually found in nature. The protein preparation was not completely pure according to SDS–PAGE stained by Coomassie blue or silver. In MALDI-TOF-MS, nano-ESI qTOF-MS of the entire protein preparation and nano-ESI-MS after digestion by trypsin and chymotrypsin impurities were not detectable.

Micropores in Crystalline Dipeptides as Seen from the Crystal Structure, He Pycnometry, and129Xe NMR Spectroscopy

Eight crystalline dipeptides were studied: AV (Ala-Val), VA (Val-Ala), AI (Ala-Ile), VV (Val-Val), IA (Ile-Ala), IV (Ile-Val), VI (Val-Ile), and LS (Leu-Ser) (all LL isomers). The first seven form an isostructural series (space group P6(1)), whereas LS has a different structure (P6(5)). All structures display H-bonded tubular assemblies of the dipeptide molecules resulting in open ultramicropores in the form of isolated one-dimensional (1D) channels. The total porosity of the materials ranges from 4 to 12% (micropore volume from 0.04 to 0.12 cm(3)/g). Calculations based on the crystal structures, He pycnometry, and solid-state (129)Xe NMR methods were used to obtain a comprehensive description of the geometry and properties of the micropores. The following order was established for the channel diameter: AV > VA > AI > VV > IA > IV > VI, with >5 A for AV and <4 A for VI; LS is close to AI. The observed sorption behavior cannot be described adequately based on the crystal structure and can only be understood if one takes into account the dynamics of the host matrix. The pores are chiral, with the center of the channel describing a right-handed helix (left-handed for LS). The following order was established for the channel helicity: VA > IA > IV > AV approximately AI approximately VV > VI > LS, with a helix diameter of approximately 2 A for VA, IA, and IV and approximately 1 A or less for the remaining dipeptides. A comparison of the dipeptides studied with other supramolecular materials is given and the potential for applications is discussed.

Monolayer formation of short helical turn forming peptide derivatives at the air–water and air–solid interfaces

Two tetrapeptide derivatives [peptide A (Boc–Ala–Ile–Ile–Gly–OMe) and peptide B (Boc–Ala–Ile–Leu–Ser–OMe)], that take helical turn conformation in solution, were shown to form monolayer at the air/water interface. Circular dichroism (CD) measurements indicate that peptide A has more helical turn propensity than peptide B in sodium dodecyl sulphate (SDS) micelles. Langmuir–Blodgget film study of peptides A and B suggest that both the peptides form stable monolayer at the air/water interface. Spectroscopic investigations reveal that peptide A forms helical turn assemblage on transferring the film into hydrophilic quartz and hydrophobic ZnSe surfaces. Whereas, peptide B adopts β-sheet structure on hydrophilic surface and a mixture of β-sheet and helical turn conformation on hydrophobic surface.

Novel Uperin Peptides From the Dorsal Glands of the Australian Floodplain Toadlet Uperoleia inundata

The dorsal glandular extract of the floodplain toadlet Uperoleia inundata contains more than 50 peptides: we report the amino acid sequences and bioactivity data of 13 of these. The peptides have been sequenced by using a combination of mass spectrometry and automated Edman sequencing. Ten of the peptides have been synthesized in order to confirm their structures, and to enable bioassays to be carried out. Ten peptides are host- defence agents, including ( i ) a powerful new neuropeptide of the tachykinin family which we name uperin 1.1 [ pGlu Ala Asp Pro Asn Ala Phe Tyr Gly Leu Met (NH2)], and (ii) nine antibiotic peptides including five uperins 2 [e.g. uperin 2.1, Gly Ile Val Asp Phe Ala Lys Lys Val Val Gly Gly Ile Arg Asn Ala Leu Gly Ile (OH)], three uperins 3 [e.g. uperin 3.1, Gly Val Leu Asp Ala Phe Arg Lys Ile Ala Thr Val Val Lys Asn Val Val (NH2)] and uperin 4.1 [ Gly Val Gly Ser Phe Ile His Lys Val Val Ser Ala Ile Lys Asn Val Ala (NH2)]. The function of the three other characterized peptides in the amphibian integument is not known, viz. ( i ) uperin 5.1 [ Phe Gln Phe Val Asn Pro Ser Asp Ile Val Phe Gly Ser (OH)] and (ii) the two uperins 6 [e.g. uperin 6.1, Gly Leu Ala Gly Ala Ile Ser Ser Ala Leu Asp Lys Leu Lys Gln Ser Gln Leu Ile Lys Asn Tyr Ala Lys Lys Leu Gly Tyr Pro Arg (OH)].

Tandem mass spectrometry of peptides. III—differentiation between leucine and isoleucine based on neutral losses

AbstractThe neutral species generated during the collisionally activated dissociation (CAD) of the protonated dipeptides Ala–Leu, Ala–Ile, Leu–Ala and Ile–Ala are post‐ionized by collision and detected in neutral fragment‐reionization (+NfR+) mass spectra. These spectra are dominated by fragment ions diagnostic for the C‐terminal amino acid, as confirmed by comparison with reference collision‐induced dissociative ionization (CIDI) mass spectra of authentic Ala, Leu and Ile. CIDI of Leu and Ile yields distinct and structurally indicative products. These are also observed upon +NfR+ of [Ala–Leu]H+ and [Ala–Ile]H+, respectively, thus allowing one to deduce the correct sequence. In contrast, [Leu–Ala]H+ and [Ile–Ala]H+, which possess identical C‐termini, form no differentiating neutral losses upon CAD.

Determination of the lipophilicity of some peptides: Effect of surface pH of silica

The lipophilicities of 22 peptides were determined by reversed-phase thin-layer chromatography using methanol as organic modifier in the concentration range 0–90 vol.-% on silica supports with surface pH values of 2.0, 4.5, 6.0, 7.5 and 9.0. Only one of the 22 peptides (TrpAlaIle) followed the general rule, i.e., its R M value decreased linearly with increasing proportion of organic modifier over the whole concentration range. Most peptides exhibited typical silanophilic retention behaviour, the R M value decreasing with increasing organic phase concentration in the lower concentration range and then increasing with further increase in the proportion of organic modifier. In some instances the lipophilicity increased linearly with increasing proportion of methanol. The silanophilic effect depended not only on the structure of the peptide, but also on the surface pH of the silica support. The retention behaviour of peptides can be well described by a polynomial function, the linear and quadratic forms of methanol concentration and surface pH being the independent variables. Principal component analysis showed that the presence of a ring structure in the peptides has the greatest impact on their retention behaviour, the overall polarity (basic, neutral or acidic) being of secondary importance. The number of amino acids in the peptide has a negligible effect on the chromatographic behaviour.

The conserved carboxy-terminal cysteine of nuclear lamins is essential for lamin association with the nuclear envelope.

We have analyzed the interaction of soluble nuclear lamins with the nuclear envelope by microinjection of normal and mutated lamins into the cytoplasm of Xenopus laevis oocytes. Our results demonstrate that the conserved cysteine of the carboxy-terminal tetrapeptide Cys Ala/Ser Ile Met of lamins is essential for their association with the nuclear envelope. Removal of this sequence or replacement of the cysteine by serine resulted in Xenopus lamin L1 remaining in a soluble, non-envelope-associated state within the nucleus. Similar mutations of Xenopus lamin A resulted in only partial reduction of nuclear envelope association, indicating that lamin A contains additional signals that can partially compensate for the lack of the cysteine. Mammalian lamin C lacks this tetrapeptide and is not associated with the nuclear envelope in our experimental system. Cloning of the tetrapeptide Cys Ala Ile Met to the carboxy terminus of human lamin C resulted in lamin being found in a nuclear envelope-associated form in oocytes. Mutations at the amino terminus and in the alpha-helical region of lamin L1 revealed that the carboxy terminus mediates the association of lamins with the nuclear envelope; however, this alone is insufficient for maintenance of a stable association with the nuclear envelope.

The covalent structure of pig kidney fructose 1,6-bisphosphatase: sequence of the 60-residue NH 2-terminal peptide produced by digestion with subtilisin

Digestion of the native pig kidney fructose 1,6-bisphosphatase tetramer with subtilisin cleaves each of the 35,000-molecular-weight subunits to yield two major fragments: the S-subunit ( M r ca. 29,000), and the S-peptide ( M r 6,500). The following amino acid sequence has been determined for the S peptide: AcThrAspGlnAlaAlaPheAspThrAsnIle Val ThrLeuThrArgPheValMetGluGlnGlyArgLysAla ArgGlyThrGlyGlu MetThrGlnLeuLeuAsnSerLeuCysThrAlaValLys AlaIleSerThrAla z.sbnd;ValArgLysAlaGlyIleAlaHisLeuTyrGlyIleAla. Comparison of this sequence with that of the NH 2-terminal 60 residues of the enzyme from rabbit liver (El-Dorry et al., 1977, Arch. Biochem. Biophys. 182, 763) reveals strong homology with 52 identical positions and absolute identity in sequence from residues 26 to 60.Although subtilisin cleavage of fructose 1,6-bisphosphatase results in diminished sensitivity of the enzyme to AMP inhibition, we have found no AMP inhibition-related amino acid residues in the sequenced S-peptide. The loss of AMP sensitivity that occurs upon pyridoxal-P modification of the enzyme does not result in the modification of lysyl residues in the S-peptide. Neither photoaffinity labeling of fructose 1,6-bisphosphatase with 8-azido-AMP nor modification of the cysteinyl residue proximal to the AMP allosteric site resulted in the modification of residues located in the NH 2-terminal 60-amino acid peptide.