含有D型氨基酸的新型毒肽——芋螺马芬在pH 5的溶液结构

Conomarphin, a novel conopeptide containing D-amino acid, was identified from the venom of Conus marmoreus and classified into M-superfamily of conotoxin. In this article, we reported the 3D structure of conomarphin at pH 5 determined using 2D 1H NMR method in aqueous solution. Twenty converged structures of this peptide were obtained based on 205 distance constraints, 8 dihedral angle constraints, and 2 hydrogen bond constraints. The root mean square deviation (RMSD) values of the backbone atoms were (0.074依0.029) nm. The refined structure of conomarphin at pH 5 contained a short 310-helix at C-terminal of the peptide. It was also characterized by a loose loop centered at Ala6. Comparison of structural and electrostatic potential between conomarphin at pH 3 and pH 5 were presented. Although the solution structure of conomarphin at pH 5 shared part of the same secondary structure element with the structure of conomarphin at pH 3, it adopted a distinctive backbone conformation with the overall molecule resembling a“flexcual arm”when viewed fromthe front. Structural differences imply that this conopeptide is rather pH sensitive and its bioactivity in vivo might be related to the acidity.     

Attractive double-layer forces and charge regulation upon interaction between electrografted amine layers and silica

Chitosan (CS) and poly(acrylic acid) (PAA) were crosslinked by an ionic gelation method to form super absorbent polymers (SAPs). CS and PAA form amide bonds between the amino and carboxyl groups. The CS-PAA copolymers were synthetically engineered by varying the feed ratios of the prepolymer units. The copolymer materials possess tunable sorption and mucoadhesive properties with a backbone structure resembling proteinaceous materials. The sorption properties of the copolymers toward methylene blue (MB) in aqueous solution were studied using UV-Vis spectrophotometry at ambient pH and 295 K. The copolymers showed markedly varied interactions with MB, from physisorption- to chemisorption-like behavior, in accordance with their composition, surface area, and pore structure characteristics. The sorption isotherms were evaluated with the Sips model to provide estimates of the sorption properties. The sorbent surface area (271 and 943 m²/g) and the sorption capacity (Q_m = 1.03 and 3.59 mmol/g) were estimated for the CS-PAA copolymer/MB systems in aqueous solution.     

Proton NMR study on two structures of 3′-O-(acetylimino)3′-de(phosphinico)-thymidylyl-(3,5′)-deoxythymidine in aqueous solution

The solution structure of one of dithymidine monophosphate (TpT) analogues, containing an (N-acetyl)imino backbone linkage (NCOCH₃) of 3′-O-(acetylimino)3′-de(phosphinico)-thymidylyl-(3,5′)-deoxythymidine (T_NT), has been determined by proton NMR. Two structures, designated as major and minor forms, in a ratio of about 3:2 coexist when the solution temperature is <25°C. Both forms adopt anti conformation with respect to the glycosidic bond, S-type deoxyribofuranose pucker, and have no base stacking. The backbone torsion angles ε′, φ_ON, φ_NC, and γ′ are trans, gauche⁺, gauche⁺, and gauche⁺ for the major form; and gauche⁻, gauche⁻, gauche⁻, and gauche⁺ for the minor form. Only major form is found at >25°C.     

The potential of N-alkoxymethyl groups as peptide backbone protectants

In this study, the potential of N-alkoxymethyl groups as protectants for the peptide backbone has been investigated. These groups were found to be compatible with the standard conditions of Fmoc/^tBu SPPS, and can be cleaved off from the peptide backbone by acids. Thus, backbone N-alkoxymethyl groups may be useful to prevent undesired side-reactions and/or interchain aggregation during peptide elongation on the solid-phase. However, the main issue for their application as protecting groups is the difficulty to incorporate them into the peptide backbone.     

Determination of the major solution conformation of tyrocidine A,using molecular mechanics energy minimization and NMR-derived distance and torsion angle constraints

Molecular mechanics energy calculations coupled with nuclear magnetic resonance-determined distance and torsion angle constraints have been used to determine the three-dimensional structure of tyrocidine A, a cyclic decapeptide which exists largely as a single conformation in solution. Two open-chain polyalanine models were used to represent separate halves of the peptide backbone and a combinatorial method of searching conformation space used to generate candidate structures consistent with experimental distance constraints. These structures were energy-minimized using the AMBER molecular mechanics forcefield and the resulting conformations classified by factor analysis of their Cartesian coordinates. Representative low-energy conformers of the two halves of the backbone were fused together and two candidate conformations of the completed backbone refined by further minimization using both distance and torsional constraints. Side chains were then added as their experimentally preferred rotamers and the whole molecule minimized without constraints to give the final model structure. This shows type II' and III ß turns at residues 4–5 and 9–10, respectively, coupled by twisted antiparallel strands which show hydrogen bonds between all four pairs of opposing peptide groups. The backbone conformation of residues 2–6 closely resembles that found in the crystal structure of gramicidin S.     

Cloning and Expression of a Novel Xylanase Gene (Auxyn11D) from Aspergillus usamii E001 in Pichia pastoris

A full-length complementary DNA (cDNA) of Auxyn11D, a gene that encodes a novel endo-??-1,4-d-xylanase of Aspergillus usamii E001 (abbreviated to AuXyn11D), was obtained using 3??- and 5??-rapid amplification of cDNA ends (RACE) methods. The cDNA sequence is 855?bp in length, containing 5??- and 3??-untranslated regions and a 696-bp open reading frame (ORF) that encodes a 32-aa signal peptide and a 199-aa mature peptide (namely AuXyn11D). Multiple homology alignment of amino acid sequences verified that AuXyn11D belongs to glycoside hydrolase family 11. Moreover, a mature peptide-encoding cDNA fragment of Auxyn11D was cloned and expressed in Pichia pastoris GS115. One P. pastoris transformant expressing the highest recombinant AuXyn11D (reAuXyn11D) activity of 15.0?U/mL, labeled as P. pastoris GSAuXyn4-16, was chosen by shake flask test. SDS?CPAGE assay demonstrated that the reAuXyn11D, a glycosylated protein with an apparent molecular mass of 32.0?kDa, was secreted into the medium. The purified reAuXyn11D displayed the highest activity at pH 4.5 and 55?°C. It was stable at a pH range of 3.5?C6.5 and at a temperature of 50?°C or below. Its activity was not significantly affected by most of metal ions tested and EDTA, but increased by Ca²⁺ and inhibited by Mn²⁺. The K _m and V _max of the reAuXyn11D towards birchwood xylan were 6.32?mg/mL and 391.6?U/mg, respectively.     

The Radical Ion Chemistry of S-Nitrosylated Peptides

The radical ion chemistry of a suite of S-nitrosopeptides has been investigated. Doubly and triply-protonated ions of peptides NYCGLPGEYWLGNDK, NYCGLPGEYWLGNDR, NYCGLPGERWLGNDR, NACGAPGEKWAGNDK, NYCGLPGEKYLGNDK, NYGLPGCEKWYGNDK and NYGLPGEKWYGCNDK were subjected to electron capture dissociation (ECD), and collision-induced dissociation (CID). The peptide sequences were selected such that the effect of the site of S-nitrosylation, the nature and position of the basic amino acid residues, and the nature of the other amino acid side chains, could be interrogated. The ECD mass spectra were dominated by a peak corresponding to loss of ^?NO from the charge-reduced precursor, which can be explained by a modified Utah-Washington mechanism. Some backbone fragmentation in which the nitrosyl modification was preserved was also observed in the ECD of some peptides. Molecular dynamics simulations of peptide ion structure suggest that the ECD behavior was dependent on the surface accessibility of the protonated residue. CID of the S-nitrosylated peptides resulted in homolysis of the S?CN bond to form a long-lived radical with loss of ^?NO. The radical peptide ions were isolated and subjected to ECD and CID. ECD of the radical peptide ions provided an interesting comparison to ECD of the unmodified peptides. The dominant process was electron capture without further dissociation (ECnoD). CID of the radical peptide ions resulted in cysteine, leucine, and asparagine side chain losses, and radical-induced backbone fragmentation at tryptophan, tyrosine, and asparagine residues, in addition to charge-directed backbone fragmentation.     

A rare occurrence of a β‐turn in an amyloid βA4 peptide

The fragment β(25–35) of the amyloid β‐peptide, like its parent βA4, has shown neurotrophic and late neurotoxic activities in cultured cells. The 3D structure of this important peptide was examined by ¹H and ¹³C 2D‐NMR and MD simulations in DMSO‐d₆ and water. The NMR parameters of chemical shift, ³J(N,Hα) coupling constants, temperature coefficients of NH chemical shifts and the pattern of intra and inter‐residue NOEs were used to deduce the structures. In DMSO‐d₆, the peptide was found to take up a type I β‐turn around the C‐terminal residues Ile⁸–Gly⁹–Leu¹⁰–Met¹¹, whereas in water at pH 5.5, it adopts a random coil conformation. This is only the second report of a β‐turn in the β‐amyloid class of peptides. The solution structures generated using restrained molecular dynamics were refined by MARDIGRAS to an R factor of 0.33 in the case of DMSO‐d₆ and to 0.56 for water. Copyright © 2002 John Wiley & Sons, Ltd.     

H/P NMR pH indicator series to eliminate the glass electrode in NMR spectroscopic pKa determinations

NMR titration is an efficient method to determine pK_a values of multiprotic acids in aqueous solution. While modern 1D/2D NMR techniques yield chemical shifts with increasing precision, the glass electrode-based pH measurement becomes the limiting factor to affect the precision of the resulting dissociation constants. The pH in the NMR tube can also be deduced from the actual chemical shift of an appropriate monoprotic indicator molecule. In the present work, the in situ NMR pH measurement has been extended for the entire pH range 0-12 using indicators with overlapping ranges of dissociation. In the first, calibrating ¹H/³¹P NMR titration, limiting chemical shifts and pK were determined for each indicator. An analysis of error propagation showed that the accuracy and precision of glass electrodes can be achieved at 1.8 < pH < 12 and even exceeded at pH extremes by NMR indicators, respectively. The assembled set of indicators was applied for in situ pH monitoring in the following “electrodeless” ¹H/³¹P NMR titration of a newly synthesized aminophosphinophosphonic acid. Multivariate nonlinear parameter estimation was used to calculate the pK values that were confirmed by potentiometric titrations.     

Voltammetric detection of ovalbumin using a peptide labeled with an electroactive compound

For this study, a new method was developed to electrochemically detect ovalbumin via its binding with the peptide-1(RNRCKGTDVQAW) in lysozymes. The peptide that exists at the C-terminal of a lysozyme was combined with ovalbumin. When an electroactive compound was introduced to the N-terminal side of the peptide through ethylene gycolbis(sulfosuccinimidyl succinate), the labeled peptide-1 served as a probe for the detection of ovalbumin. The electrode responses of labeled peptide-1 were measured after the labeled peptide-1 and ovalbumin were incubated in a 0.1 M phosphate buffer (pH 5.6). As a result, the electrode response decreased as the concentration of ovalbumin increased. The detection limit of ovalbumin was 2.3 × 10⁻¹¹ M as estimated at 3-fold the standard deviation (3σ) (n = 5). Because the steric structure of the peptide and some of the amino acid residues were related to the binding, we prepared a peptide-2, to which the N- and C-terminals of peptide-1 were alternated. The decrease in the response for the labeled peptide-2 was less than that for the labeled peptide-1. In addition, the peak current of a peptide-3, for which the D of peptide-1 was replaced with S, was hardly changed with or without ovalbumin. Therefore, it was clear that the binding was influenced by the steric factors and by the sequence of the peptide. However, a peptide-1 with bis(sulfosuccinimidyl) suberate was designed to investigate the hydrophobic influences on the probe. The change in the peak current was smaller than that of peptide-1 with ethylene gycolbis(sulfosuccinimidyl succinate), which was due to the hydrophobic properties of the alkyl chain between the peptide and the ovalbumin. The proposed method could be applied to the determination of ovalbumin in egg whites. Consequently, the concept becomes an electrochemical sensing method for proteins based on the protein–peptide interaction.     

Toward direct determination of conformations of protein building units from multidimensional NMR experiments I. A theoretical case study of For‐Gly‐NH2 and For‐L‐Ala‐NH2

NMR chemical shielding anisotropy tensors have been computed, employing several basis sets and the GIAO‐RHF and GIAO‐MP2 formalisms of electronic structure theory, for all the atoms of the five and nine typical backbone conformers of For‐Gly‐NH₂ and For‐L ‐Ala‐NH₂, respectively. Multidimensional chemical shift plots, as a function of the respective backbone fold, have been generated for both peptide models. On the 2D ¹H^NH‐¹⁵N^NH and ¹⁵N^NH‐¹³C^α plots the most notable feature is that at all levels of theory studied the backbone conformers cluster in different regions. Computed chemical shifts, as well as their averages, have been compared to relevant experimental values taken from the BioMagnetic Resonance Bank (BMRB). At the highest levels of theory, for all nuclei but the amide protons, deviations between statistically averaged theoretical and experimental shifts are as low as 1–3%. These results indicate that chemical shift information from selected multiple‐pulse NMR experiments (e.g., 2D‐HSQC and 3D‐HNCA) could directly be employed to extract folding information for polypeptides and proteins. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 882–900, 2000     

Detecting solution pH changes using poly (N-isopropylacrylamide)-co-acrylic acid microgel-based etalon modified quartz crystal microbalances

Poly (N-isopropylacrylamide)-co-acrylic acid (pNIPAm-co-AAc) microgel-based etalons have been shown to have visible color and unique spectral properties, which both depend on solution temperature and pH. In this investigation, pNIPAm-co-AAc microgel-based etalons were fabricated on the Au electrode of a quartz crystal microbalance (QCM), and the resonant frequency of the QCM monitored as a function of temperature, at pH 3.0. Furthermore, the resonant frequency at either pH 3.0 or 7.0 was monitored while keeping the solution temperature constant at various temperatures. In all cases, when the solution temperature was below the collapse transition for the microgels (∼32 °C), the resonant frequency at pH 3.0 was lower than at pH 7.0, which we attribute to the film transitioning from a deswollen to swollen state, respectively. It was observed that the magnitude of the resonant frequency change increased as the solution temperature approached the collapse temperature for the microgels. The overall sensitivity to pH was determined to be 1.3 × 10⁻⁸ M [H⁺] Hz⁻¹ and a theoretical detection limit of 390 nM was obtained. This sensitivity will be exploited further for future biosensing applications.     

Gas-phase reactivity and molecular modeling studies on triply protonated dodecapeptides that contain four basic residues

Gas-phase deprotonation and hydrogen/deuterium (H/D) exchange reactions for ions from three model dodecapeptides were studied by Fourier transform ion cyclotron resonance mass spectrometry. Molecular dynamics calculations were employed to provide information on conformations and Coulomb energies. The peptides, (KGG)₄, (K₂G₄)₂, and K₄G₈, each contain four high basicity lysine residues and eight low basicity glycine residues; however, in the present work only three lysine residues were protonated. Proton transfer reactions with a series of reference amines revealed apparent gas-phase acidities in a narrow range of 207. 3–209. 6 kcal/mol, with deprotonation efficiencies following the order [K₄G₈+3H]³⁺ > [(KGG)₄+3H]³⁺ > [(K₂G₄)₂+3H]³⁺. The three ions also react similarly with d ₄-methanol: each exchanged a maximum of 23–25 of their 25 labile hydrogens, with the first 15–17 exchanges occurring at rate constants of (1. 6–2. 6) × 10^?11 cm³ molecule^?1 s^?1. The experimental results agree with molecular modeling findings of similar conformations and Coulomb energies for the three peptide ions. The [M+3H]³⁺ data are compared to data obtained previously in our laboratory for the “fully” protonated [M+4H]⁴⁺ (Zhang, X.; Ewing, N. P.; Cassady, C. J. Int. J. Mass Spectrom. Ion Phys., in press). For (KGG)₄ and (K₂G₄)₂, there is a marked difference in H/D exchange reactivity between 3+ ions and 4+ ions. The 4+ ions, which have diffuse conformations, slowly exchange only 14 hydrogens, whereas their more compact 3+ counterparts exchange 23–25 hydrogens at a 5-times greater rate. In contrast, the 3+ and 4+ ions of K₄G₈ have similar compact conformations and exchange reactivity. The results indicate that a multiply hydrogen-bonded intermediate between the deuterating reagent and the peptide ion is necessary for facile H/D exchange. The slower, incomplete H/D exchange of [(KGG)₄+4H]⁴⁺ and [(K₂G₄)₂+4H]⁴⁺ is attributed to the inability of their protonated lysine n-butylamino groups (which extend away from the peptide backbone) to form this intermediate.     

Self-diffusion coefficients and structure of the trivalent transplutonium ion curium and gadolinium in aqueous solution

Self-diffusion coefficients D of the trivalent aquo ion Cm³⁺ have been determined in aqueous Nd(ClO₄)₃?HClO₄ solutions (pH 2.5) at 25°C, by the open-end capillary method (O. E. C. M.). The variation of D versus the square root of the concentration of inactive solution is an exponential form in the studied range of concentration. The limiting value D₀ at zero ionic strength is 6.0·10^?6 cm²·s^?1. The curve \(D = f(\sqrt c )\) relating to Cm³⁺ can be compared to those of²⁴¹Am³⁺ and¹⁵³Gd³⁺ obtained under similar conditions. We find a similar ionic structure of Cm³⁺ with Am³⁺ and Gd³⁺. They have the same hydration as a tripositive of 5f and 4f ions in the absence of hydrolysis, complexing, or pairing at pH 2.5. The present study contributes to show the analogy of the solvation structure of trivalent actinide ions in aqueous solution at pH 2.5 with that of the trivalent lanthanide ions as a help for predicting the thermodynamic properties.     

A New Coumarin-Acridone Compound as a Fluorescence Probe for Fe3+ and Its Application in Living Cells and Zebrafish

A new coumarin-acridone fluorescent probe S was designed and synthesized, and the structure was confirmed with ¹H/¹³C NMR spectrometry, single-crystal X-ray diffraction, and high-resolution mass spectrometry. This probe has high sensitivity and selectivity for Fe³⁺ over other testing metal ions at 420 or 436 nm in acetonitrile–MOPS (3-Morpholinopropanesulfonic Acid) buffer solution (20.0 μM, pH = 6.9, 8:2 (v/v)). Under physiological conditions, the probe displayed satisfying time stability with a detection limit of 1.77 µM. In addition, probe S was successfully used to detect intracellular iron changes through a fluorescence-off mode, and the imaging results of cells and zebrafish confirmed their low cytotoxicity and satisfactory cell membrane permeability, as well as their potential biological applications.     

CE-MS Identification of Amino Acid Sequence Inversion as a New Degradation Pathway of an Aspartyl Model Tripeptide

CE-MS was employed to identify two unknown degradation products of the model tripeptide Phe-α-Asp-Gly heated at 80 °C in aqueous solution at pH 7.4. Both compounds displayed essentially identical mass spectra indicating the presence of peptide diastereomers. The [M + H]⁺-ion at m/z 338 suggested a tripeptide composed of the amino acids Phe, Gly and Asp. The fragmentation pattern indicated that Phe was not located at the N-terminus. Subsequently, the linear peptide α-Asp-Phe-Gly and the branched peptide Asp(Gly)-Phe were synthesized and analyzed by CE-MS. The mass spectrum of synthetic α-Asp-Phe-Gly was identical to that of the unknown compounds confirming the structure of the degradation products. Asp(Gly)-Phe displayed a complex fragmentation pattern. In conclusion, amino acid sequence inversion represents another degradation pathway of Phe-α-Asp-Gly at pH 7.4 besides known reactions including isomerization, enantiomerization, cyclization to diketopiperazine derivatives and backbone hydrolysis. The mechanism of the rearrangement of the amino acid sequence is proposed to proceed via an aza-bridged intermediate.

     

Selected-control hydrothermal synthesis and formation mechanism of 1D ammonium vanadate

Selective-controlled structure and shape of ammonium vanadate nanocrystals were successfully synthesized by a simple hydrothermal method without the presence of catalysts or templates. It was found that tuning the pH of the growth solution was a crucial step for the control of the phase-compositional, structure and morphology transformation. The final products were NH₄V₄O₁₀ nanobelts, (NH₄)₂V₆O₁₆·1.5H₂O nanowires, and (NH₄)₆V₁₀O₂₈·6H₂O nanobundles, respectively, when the pH of the growth solution varied from 2.5 to 1.5, then to 0.5. The hydrogen bonding interaction and the surface free energies were responsible for the formation of the ammonium vanadates with the different structure and morphology. The conductivity measurements showed the one-dimensional (1D) ammonium vanadates were semiconductors at room temperature. The conductivity of 1D ammonium vanadates varied from 1.95×10⁻⁴ to 2.45×10⁻³ S cm⁻¹ due to the different structures.     

A rapid spectrophotometric method for the determination of transparent exopolymer particles (TEP) in freshwater

A simple and rapid spectrophotometric method is proposed for the determination of transparent exopolymer particles (TEP) in freshwater samples. In this method, TEP reacts with excess of alcian blue solution yielding a low solubility dye-TEP complex. After centrifugation, the concentration of the remaining dye in the supernatant was determined at 602 nm and its concentration was related to the concentration of TEP in freshwater. The effect of alcian blue concentration from 1.5×10⁻³ to 9.0×10⁻³% (m/v), solution pH from 2.5 to 6.9 and stirring time from 20 to 120 s on the analytical curve was investigated. Under the optimum conditions established, such as alcian blue concentration of 3.0×10⁻³% (m/v); pH of 4.0 (0.2 mol l⁻¹ acetate buffer solution) and stirring time of 1 min, the analytical curve was linear from 0.50 to 10 μg ml⁻¹ (A=0.34−0.037[GX]; r²=0.9999; where A is the absorbance and [GX] the gum xanthan concentration in μg ml⁻¹) with a detection limit of 0.10 μg ml⁻¹. The recovery of TEP (as gum xanthan) for two samples ranged from 95.3 to 108 and the relative standard deviations (R.S.D.s) were lower than 0.8% for gum xanthan solutions at concentrations of 1.0 and 1.5 μg ml⁻¹ (n=8). The results obtained for TEP in freshwater samples using the proposed spectrophotometric method and those obtained using a literature method are in agreement at the 95% confidence level and within an acceptable range of error.     

Production of theasinensins A and D, epigallocatechin gallate dimers of black tea, by oxidation-reduction dismutation of dehydrotheasinensin A

Theasinensins A and D are B,B′-linked dimers of (−)-epigallocatechin 3-O-gallate connected through R and S biphenyl bonds, respectively, and are major constituents of black tea. Enzymatic oxidation of epigallocatechin 3-O-gallate produced dehydrotheasinensin A, and the structure was shown to be equivalent to an o-quinone of theasinensin A. When the aqueous solution of dehydrotheasinensin A was heated, theasinensin D was produced along with galloyl oolongtheanin. On the other hand, dehydrotheasinensin A was converted to theasinensins A and D along with oxidation products in phosphate buffer at pH 6.8 at room temperature. The results strongly suggested that theasinensins in black tea were produced by oxidation-reduction dismutation of dehydrotheasinensin.     

X‐Ray Crystal Structure of a Second‐Generation Peptide Dendrimer in Complex with Pseudomonas aeruginosa Lectin LecB

Dendrimers are regularly branched molecular trees which are notoriously difficult to crystallize. Herein we report the crystal structure of a C‐fucosylated second generation peptide dendrimer as complex with lectin LecB in which the only dendrimer‐lectin contact is the LecB bound glycoside (PDB 6S5S). In contrast to a previously reported crystal structure of a first‐generation peptide dendrimer as LecB complex in which the dendrimer formed trimers connected by intermolecular β‐sheets (PDB 5D2A), the present structure features a globular monomeric state held together by intramolecular backbone hydrogen bonds and assembled into a non‐covalent dimer stabilized by hydrophobic contacts between leucine side‐chains and proline‐phenylalanine CH‐π stacking interactions. Molecular dynamics and circular dichroism studies suggest that this crystal structure resembles the structure of the peptide dendrimer in solution. Structures of a partially resolved dendrimer (PDB 6S5R) and of C‐fucosylated disulfide bridged peptide dimers connecting different LecB tetramers are also reported (PDB 6S7G, PDB 6S5P).