家蝇幼虫抗菌肽MDL-1的构象分析

用红外光谱、圆二色谱和荧光光谱研究家蝇幼虫抗菌肽MDL-1的结构特征及其在不同条件下的构象变化. 红外光谱检测结果显示抗菌肽MDL-1结构中含有螺旋、无规卷曲、折叠构象的吸收特征; 圆二色谱显示抗菌肽MDL-1结构相对比较稳定, 抗菌肽在不同浓度溶液中的构象发生改变; 荧光光谱法研究发现家蝇幼虫抗菌肽MDL-1在280 nm波长的激发光下, 荧光光谱为Tyr残基和Trp残基共同提供, 而且Trp残基不是位于抗菌肽分子的表面, 而是位于分子的内部, 该研究结果为进一步探讨抗菌肽的抗菌机理奠定了基础.     

Novel open-chain and cyclic conformationally constrained (R)- and (S)-α,α-disubstituted tyrosine analogues

A series of novel open-chain and cyclic conformationally constrained (R)- and (S)-α,α-disubstituted tyrosine analogues 1a–e were synthesized in good yields and high optical purities (Schemes 1 and 2). The absolute configurations of these tyrosine analogues were unambiguously determined based on the X-ray structures of the precursor diastereoisomeric peptides of type 4 and 5 . Four of these structures are described (Figs. 1–4), showing β-turn type-I geometries for dipeptides 4a, 5b , and 4c and an extended conformation for peptide 5c (Table 3). The conversion of the free amino acids 1a–c into suitably protected building blocks 11a–d and 15d,e for peptide synthesis is discussed (Schemes 3 and 4).     

Synthesis of 3,4-di-O-acylated glucose-derived furanoid sugar amino acids (Gaa): conformational analysis of a Leu-enkephalin analog containing di-O-myristoylated Gaa

3,4-Di-O-acylated derivatives 1-3 of a glucose-derived furanoid sugar amino acid (Gaa) were synthesized as novel peptide building blocks to study their effects on peptide conformation. Structural analysis of the di-O-myristoylated Gaa 3-containing Leu-enkephalin analog 4 by various NMR techniques and constrained molecular dynamics (MD) simulation studies established a well-defined β-turn structure in DMSO-d₆ with an intramolecular hydrogen bond between PheNH → TyrCO.     

Self-assembly of short peptide amphiphiles: the cooperative effect of hydrophobic interaction and hydrogen bonding

The interplay between hydrogen bonding, hydrophobic interaction and the molecular geometry of amino acid side-chains is crucial to the development of nanostructures of short peptide amphiphiles. An important step towards developing their practical use is to understand how different amino acid side-chains tune hydrophobic interaction and hydrogen bonding and how this process leads to the control of the size and shape of the nanostructures. In this study, we have designed and synthesized three sets of short amphiphilic peptides (I(3)K, LI(2)K and L(3)K; L(3)K, L(4)K and L(5)K; I(3)K, I(4)K and I(5)K) and investigated how I and L affected their self-assembly in aqueous solution. The results have demonstrated a strong tendency of I groups to promote the growth of β-sheet hydrogen bonding and the subsequent formation of nanofibrillar shapes. All I(m)K (m = 3-5) peptides assembled into nanofibers with consistent β-sheet conformation, whereas the nanofiber diameters decreased as m increased due to geometrical constraint in peptide chain packing. In contrast, L groups had a weak tendency to promote β-sheet structuring and their hydrophobicity became dominant and resulted in globular micelles in L(3)K assembly. However, increase in the number of hydrophobic sequences to L(5)K induced β-sheet conformation due to the cooperative hydrophobic effect and the consequent formation of long nanofibers. The assembly of L(4)K was, therefore, intermediate between L(3)K and L(5)K, similar to the case of LI(2)K within the set of L(3)K, LI(2)K and I(3)K, with a steady transition from the dominance of hydrophobic interaction to hydrogen bonding. Thus, changes in hydrophobic length and swapping of L and I can alter the size and shape of the self-assembled nanostructures from these simple peptide amphiphiles.     

Controlled self-assembly of amphiphilic oligopeptides into shape-specific nanoarchitectures

Here, we report a novel, programmable, molecular self-assembling system to fabricate shape-specific, three-dimensional nanoarchitectures. Three types of simple 16-mer peptides consisting of hydrophobic Leu and hydrophilic Lys, LKL16, KLK16, and LK16, were prepared as building blocks for nanofabrications. A detailed analysis of the conformation and self-assembling mechanism was performed by using circular dichroism (CD), FTIR spectroscopy, and atomic force microscopy (AFM). A wide variety of self-assembled nanoarchitectures, such as beta-sheet-plates, beta-sheet-fibers, alpha-helix-particles, and alpha-helix-plates, could be fabricated by tuning the peptide sequence, reaction time, and solution pH. The ability to control the self-assembled nanostructures should provide a simple and/or essential insight into the mechanism of peptide aggregation, including amyloid formation, and it should be useful for the design of novel bio-related nanomaterials.     

Synthesis of peptide alkylthioesters using the intramolecular N,S-acyl shift properties of bis(2-sulfanylethyl)amido peptides

The design of novel methods giving access to peptide alkylthioesters, the key building blocks for protein synthesis using Native Chemical Ligation, is an important area of research. Bis(2-sulfanylethyl)amido peptides (SEA peptides) 1 equilibrate in aqueous solution with S-2-(2-mercaptoethylamino)ethyl thioester peptides 2 through an N,S-acyl shift mechanism. HPLC was used to study the rate of equilibration for different C-terminal amino acids and the position of equilibrium as a function of pH. We show also that thioester form 2 can participate efficiently in a thiol-thioester exchange reaction with 5% aqueous 3-mercaptopropionic acid. The highest reaction rate was obtained at pH 4. These experimental conditions are significantly less acidic than those reported in the past for related systems. The method was validated with the synthesis of a 24-mer peptide thioester. Consequently, SEA peptides 1 constitute a powerful platform for access to native chemical ligation methodologies.     

Template-directed self-assembly of a designed amphiphilic hexapeptide on mica surface

Self-assembly of small molecules into highly ordered nanostructures offers many important potential applications in science research and industry. Precise self-assembling with the assistance of inorganic substrate is considered as an ideal strategy. In this experiment, the highly ordered mica surface was used to template the assembling of a novel designed amphiphilic hexapeptide to form orderly parallel fibers. The nanostructure and the self-assembly mechanism were investigated by atomic force microscopy (AFM), transmission electron microscopy, Fourier transform infrared spectroscopy, and circular dichroism techniques. By the experimental results, a dramatic conformation transition from random coil and/or α-helix into β-sheet was found after the peptide assembled on the mica surface under certain conditions, which was considered as a key factor for the ordered nanostructure. Finally, according to the AFM images and the simulated length of peptide molecules, a trilaminar β-sheet structure model was proposed to explain the hierarchical self-assembly mechanism.     

Coordination of copper(II) ions by the fragments of neuropeptide gamma containing D1, H9, H12 residues and products of copper-catalyzed oxidation

A potentiometric, spectroscopic (UV-Vis, CD and EPR) and mass spectrometric (ESI-MS) study of Cu(II) binding to the (1-2,7-21)NPG, Asp(1)-Ala-Ile(7)-Ser-His(9)-Lys-Arg-His(12)-Lys-Thr-Asp-Ser-Phe-Val-Gly-Leu-Met(21)-NH(2), and Ac-(1-2,7-21)NPG, Ac-Asp(1)-Ala-Ile(7)-Ser-His(9)-Lys-Arg-His(12)-Lys-Thr-Asp-Ser-Phe-Val-Gly-Leu-Met(21)-NH(2), fragments of neuropeptide gamma were carried out. The results clearly indicate the stabilization of the 1 N {NH(2), β-COO(-)}, 2 N {NH(2), β-COO(-), N(Im)} and 3 N {NH(2), β-COO(-), 2N(Im)} complexes by the coordination of the β-carboxylate group of the D(1) residue. For the (1-2,7-21)NPG the CuH(2)L complex with 3 N {NH(2), β-COO(-), 2N(Im)}, the binding mode dominates in a wide pH range of 4-8.5. With the sequential increase of pH, deprotonated amide nitrogens are involved in copper coordination. For the Ac-(1-2,7-21)NPG peptide the imidazole nitrogen atoms are the primary metal binding sites forming macrochelates in the pH range 4 to 7. The CuHL complex with 4 N {N(Im), N(-), N(-), N(Im)} coordination mode is formed in pH range 6-9. Deprotonation and co-ordination of the third amide nitrogen were detected at pH ～8.6. Metal-catalyzed oxidation (MCO) of proteins is mainly a site-specific process in which one or a few amino acids at metal-binding sites on the protein are preferentially oxidized. To elucidate the products of the copper(II)-catalyzed oxidation of the (1-2,7-21)NPG and Ac-(1-2,7-21)NPG, the liquid chromatography-mass spectrometry (LC-MS) method and Cu(II)/hydrogen peroxide as a model oxidizing system were employed. In the presence of hydrogen peroxide with 1?:?4 peptide-H(2)O(2) molar ratio for the Ac-(1-2,7-21)NPG peptide the oxidation of the methionine residue to methionine sulfoxide and for (1-2,7-21)NPG to sulfone was observed. For the Cu(II)-peptide-hydrogen peroxide in 1?:?1?:?4 molar ratio systems, oxidation of the histidine residues to 2-oxohistidines was detected. Under experimental conditions the (1-2,7-21)NPG and Ac-(1-2,7-21)NPG undergo fragmentations by cleavage of the S(8)-H(9), H(9)-K(10), R(11)-H(12) and H(12)-K(13) peptide bonds supporting the participation of the H(9) and H(12) residues in the coordination of copper(II) ions. For the (1-2,7-21)NPG peptide chain the involvement of the D(1) residue in the coordination of metal ions is supported by the alkoxyl radical modification of this amino acid residue.     

Synthesis and conformational properties of model dipeptides containing novel axially chiral α,β-didehydroamino acids at the (i+1) position of a β-turn conformation

A series of model dipeptides containing some novel axially chiral α,β-didehydroamino acids at the (i+1) position has been synthesised by reaction of the corresponding 4-(4-alkylcyclohexylidene)-2-phenyl-1,3-oxazol-5(4H)-one with (S)-phenylalanine cyclohexylamide. The conformations of two dipeptides in the crystal state have been studied by X-ray diffraction crystallographic analysis. The backbone torsion angles suggest that both peptides adopt similar type-II′ β-turn conformations. NMR spectroscopy has revealed that relatively rigid β-turn structures also persist in solution and that the absolute configurations of the axially chiral α,β-didehydroamino acids do not significantly influence the conformation of the peptide chain. Both heterochiral and homochiral dipeptides are found to accommodate the same βII′-turn conformation. Axially chiral α,β-didehydroamino acids (R_a)- and (S_a)-4-methyl-, 4-phenyl- and (4-tert-butylcyclohexylidene)glycine can be considered as elongated structural analogues of alanine, phenylglycine and tert-leucine of R and S configuration since, in these chiral α,β-didehydroamino acids, the methyl, phenyl and tert-butyl groups are located about 4.3 Å away from the peptide backbone in which they are incorporated.     

Synthesis,conformation and cytotoxicity of new,branched polymeric polypeptides containing hydrophobic amino acid or arginine moiety

In this paper we report on the synthesis and solution conformation of a new set of structurally related polycationic branched chain polypeptides (poly[Lys(X _i -dl-Ala _m )]) with hydrophobic (Ile, Nle, Val) or cationic (Arg) amino acids at the N-terminal end of the side chains as well as their cytotoxic effect on murine bone marrow derived macrophages. Solution conformation of the polypeptides was studied with circular dichroism spectroscopy under different conditions (pH, ionic strength). The results of these comparative studies indicate that a) polypeptides could adopt an ordered (mainly helical) conformation at physiological pH and salt concentration (pH 7.4, 0.2 M NaCl); b) the nature of side chain terminal amino acid (X) could determine under which conditions the ordered structure was formed. Thus, the solution conformation of branched polypeptides could be modulated by the selection of amino acid X under physiological conditions. All polypeptides with hydrophobic amino acid at the terminal position were essentially non-toxic on macrophages, whereas the polypeptide with terminal Arg proved to be markedly cytotoxic.

     

Coordination ability of insect kinin analogs

Spectroscopic data, including electronic absorption, CD and EPR results, as well as theoretical calculations have shown that the insertion of 4-aminopyroglutamate, a novel cis-peptide bond mimic, in the insect kinin peptide leads to an effective ligand towards Cu(II) ions at basic pH ranges. The 4-aminopyroglutamate motif induces a specific peptide conformation which favors the formation of one or two five-membered chelating rings stabilizing a bent structure, with the coordination of 3N-type or 4N-type in the metallopeptide molecule involving in metal bonding C-terminal of modified peptide. It is worth noting that the copper(II) bonding does not undergo hydrolysis even at a very high pH range.     

Investigation of the carrier function of polypeptides. Synthesis,conformation and cytotoxicity of oxazolone conjugates of poly(Lys) and poly[Lys-(DL-ALAm)]

A new group of synthetic macromolecular conjugates was synthesised in which poly(Lys) or a branched polypeptide poly[Lys-(DL-Ala_m)] (m≅3) were used as carrier and 4-(ethoxymethylene)-2–phenyl–5 (4H)-oxazolone as hapten. These conjugates were characterized by amino acid analysis, identification of terminal residues of the side chain, sedimentation analysis. The conformation of conjugates and of carrier polypeptides were analyzed by circular dichroism spectroscopy in water solutions at various pH and ionic strengths. These data indicated a marked dependence of the conformation of the conjugate on the structure of carrier and on the number of the side chain terminal haptens (phOx). In vitro cytotoxicity of these polymers was also investigated using two different assays, by measuring the viability of isolated rat liver cells and the effect on growth of HeLa cells. Toxicity of polypeptides could be diminished by conjugates containing a higher amount of oxazolone. These conjugates with defined conformation and toxicological properties are considered suitable to analyse the carrier function of branched polypeptides, particularly the interaction with the immunological network.     

柔性环己烷六酸和刚性草酸配体桥连的稀土配位聚合物的水热合成与结构研究

草酸铽与水合环己烷六酸(H6LⅠ.H2O)(顺式椅式构型LⅠ:a,e,a,e,a,e)在水热条件下反应生成一种新颖的三维稀土配位聚合物[Tb4(LⅡ)(ox)3(H2O)8](LⅡ为反式椅式构型:e,e,e,e,e,e;ox为草酸根),通过元素分析和红外光谱对这个配位聚合物进行了表征。X射线单晶衍射分析表明该配合物属于三斜晶系,P1空间群,晶胞参数为:a=0.60203(4)nm,b=1.08278(8)nm,c=1.29446(9)nm,α=67.908 0(10)°,β=82.109 0(10)°,γ=83.887 0(10)°,V=0.773 07(9)nm3,Z=2。在这个配合物的形成中,顺式构型的H6LⅠ配体发生构型转变形成LⅡ配体,LⅡ配体采取μ8-桥连模式将Tb离子连接成一个具有孔洞的二维(Tb-LⅡ)配位层。由μ2-和μ4-桥连模式构成的一维(Tb-ox)链将二维(Tb-LⅡ)层连接成一个具有孔道的三维配位框架,ox配体和水分子通过配位作用和氢键作用填充在孔道中。     

Cloning,Expression, and Biochemical Characterization of a Novel Acidic GH16 β-Agarase,AgaJ11, from <Emphasis Type="Italic">Gayadomonas joobiniege</Emphasis> G7

A novel β-agarase AgaJ11 belonging to the glycoside hydrolase (GH) 16 family was identified from an agar-degrading bacterium Gayadomonas joobiniege G7. AgaJ11 was composed of 317 amino acids (35 kDa), including a 26-amino acid signal peptide, and had the highest similarity (44 % identity) to a putative β-agarase from an agarolytic marine bacterium Agarivorans albus MKT 106. The agarase activity of purified AgaJ11 was confirmed by zymogram analysis. The optimum pH and temperature for AgaJ11 activity were determined to be 4.5 and 40 °C, respectively. Notably, AgaJ11 is an acidic β-agarase that was active only at a narrow pH range from 4 to 5, and less than 30 % of its enzymatic activity was retained at other pH conditions. The K _m and V _max of AgaJ11 for agarose were 21.42 mg/ml and 25 U/mg, respectively. AgaJ11 did not require metal ions for its activity, but severe inhibition by several metal ions was observed. Thin layer chromatography and agarose-liquefying analyses revealed that AgaJ11 is an endo-type β-agarase that hydrolyzes agarose into neoagarohexaose, neoagarotetraose, and neoagarobiose. Therefore, this study shows that AgaJ11 from G. joobiniege G7 is a novel GH16 β-agarase with an acidic enzymatic feature that may be useful for industrial applications.     

A 1,3-phenyl-linked hydantoin oligomer scaffold as a β-strand mimetic

A synthetic scaffold that mimics a peptide β-strand has been designed and synthesised based on a 1,3-phenyl-linked hydantoin oligomer. The conformational preferences of this oligomer were investigated using molecular modelling and solution NMR experiments and suggest a planar conformation that accurately mimics the i, i + 2 and i + 4 residues of a peptide β-strand.     

Etudes configurationnelles et conformationnelles de quelques chlorures de désoxy-6 β-L-héxopyrannosyle chlorosulfonyles et de leurs glycosides de méthyle

A total analysis of the NMR spectra of 6-deoxy-L -hexopyranoses in the α-configuration and of the corresponding β-anomers was carried out. The parameters obtained are characteristic of a 1C (L ) chair conformation, having the anomeric substituent in an axial orientation for the methyl α-fuco-, α-rhamno- and α-chinovopyranosides and for the α-fuco- and α-rhamnopyranosyl chlorides. The structure is also of a 1C (L ) chair type for the methyl β-fuco- and β-chinovopyranosides; the geometry is the same for the β-fuco- and β-rhamnopyranosyl chlorides despite the anomeric effect of a chlorine atom. However, the NMR parameters of the β-chinovopyranosyl chloride are not explicable on the basis of a chair conformation with an equatorial chlorine or a boat structure.     

Versatile Post-synthetic Modifications of Helical β-Peptide Foldamers Derived from a Thioether-Containing Cyclic β-Amino Acid

We introduce a novel cyclic β-amino acid, trans-(3S,4R)-4-aminotetrahydrothiophene-3-carboxylic acid (ATTC), as a versatile building block for designing peptide foldamers with controlled secondary structures. We synthesized and characterized a series of β-peptide hexamers containing ATTC using various techniques, including X-ray crystallography, circular dichroism, and NMR spectroscopy. Our findings reveal that ATTC-containing foldamers can adopt 12-helical conformations similar to their isosteres and offer the possibility of fine-tuning their properties via post-synthetic modifications. In particular, chemoselective conjugation strategies demonstrate that ATTC provides unique post-synthetic modification opportunities, which expand their potential applications across diverse research areas. Collectively, our study highlights the versatility and utility of ATTC as an alternative to previously reported cyclic β-amino acid building blocks in both structural and functional aspects, paving the way for future research in the realm of peptide foldamers and beyond.     

Probing the role of the C-H...O hydrogen bond stabilized polypeptide chain reversal at the C-terminus of designed peptide helices. Structural characterization of three decapeptides

The structural characterization in crystals of three designed decapeptides containing a double d-segment at the C-terminus is described. The crystal structures of the peptides Boc-Leu-Aib-Val-Xxx-Leu-Aib-Val-(D)Ala-(D)Leu-Aib-OMe, (Xxx = Gly 2, (D)Ala 3, Aib 4) have been determined and compared with those reported earlier for peptide 1 (Xxx = Ala) and the all l analogue Boc-Leu-Aib-Val-Ala-Leu-Aib-Val-Ala-Leu-Aib-OMe, which yielded a perfect right-handed alpha-helical structure. Peptides 1 and 2 reveal a right-handed helical segment spanning residues 1 to 7, ending in a Schellman motif with (D)Ala(8) functioning as the terminating residue. Polypeptide chain reversal occurs at residue 9, a novel feature that appears to be the consequence of a C-H.O hydrogen bond between residue 4 C(alpha)H and residue 9 CO groups. The structures of peptides 3 and 4, which lack the pro R hydrogen at the C(alpha) atom of residue 4, are dramatically different. Peptide 3 adopts a right-handed helical conformation over the 1 to 7 segment. Residues 8 and 9 adopt alpha(L) conformations forming a C-terminus type I' beta-turn, corresponding to an incipient left-handed twist of the polypeptide chain. In peptide 4, helix termination occurs at Aib(6), with residues 6 to 9 forming a left-handed helix, resulting in a structure that accommodates direct fusion of two helical segments of opposite twist. Peptides 3 and 4 provide examples of chiral residues occurring in the less favored sense of helical twist; (D)Ala(4) in peptide 3 adopts an alpha(R) conformation, while (L)Val(7) in 4 adopts an alpha(L) conformation. The structural comparison of the decapeptides reported here provides evidence for the role of specific C-H.O hydrogen bonds in stabilizing chain reversals at helix termini, which may be relevant in aligning contiguous helical and strand segments in polypeptide structures.     

α-烯基-β-环糊精毛细管电色谱整体柱的制备与评价

将烯丙基缩水甘油醚(AGE)和β-环糊精在碱性条件下作用得到带有α烯基的环糊精衍生物——4(3-烯丙氧-2-羟基)丙氧基-β-环糊精(PCD),利用这种衍生物和甲基丙烯酸甘油酯(GMA)为功能单体,在毛细管中通过原位聚合反应,一步法制备得到了新型β-环糊精聚合物毛细管电色谱手性整体柱.在毛细管电色谱(CEC)模式下,应...     

Peptides constrained by an aliphatic linkage between two C(alpha) sites: design, synthesis, and unexpected conformational properties of an i,(i + 4)-linked peptide.

A novel route for the synthesis of cyclic peptides constrained by an aliphatic bridge between two C(alpha)sites, using a triply orthogonal protecting group strategy, is described. The synthesis of the orthogonally protected bis-amino acid 1, via an enantioselective route utilizing the Sch?llkopf and Evans methodologies, is first described. This is then incorporated into a short, alanine-rich peptide 13, using a novel triply orthogonal protecting group strategy to couple first one, then the other, amino acid moiety in such a way that an aliphatic bridge is formed between the i and i + 4 positions. Unexpectedly, the resulting constrained peptide does not adopt a helical conformation: instead, it is shown by CD at low temperature to adopt a left-handed type II beta-turn conformation in aqueous media and a right-handed type I beta-turn conformation in TFE.