Structure and folding of glucagon-like peptide-1-(7–36)-amide in aqueous trifluoroethanol studied by NMR spectroscopy

The conformational changes of free, monomeric glucagon-like peptide-1-(7–36)-amide (GLP-1) in aqueous solution with increasing concentrations of 2,2,2-trifluoroethanol (TFE) were monitored by NMR spectroscopy. It was found that GLP-1 gradually assumes a stable, single-stranded helical structure in water solution when the TFE concentration is increased from 0 to 35% (v/v). No further structural changes were observed at higher TFE concentrations. The structure of GLP-1 in 35% TFE was determined from 292 distance restraints and 44 angle restraints by distance geometry, simulating annealing and restrained energy minimization. The helical structure extends from T7 to K28, with a less well-defined region around G16 and a disordered six-residue N-terminal domain. The folding process of GLP-1 from random coil (in water) to helix (in 35% TFE) is initiated by the formation of the C-terminal segment of the helix that is extended gradually towards the N-terminus of the peptide with increasing concentration of TFE. The exchange rates of the slow exchanging amide protons indicate that the C-terminal part of the helix is more stable than the N-terminal part. Copyright © 2001 John Wiley & Sons, Ltd.     

Folding of the 25 residue Abeta(12-36) peptide in TFE/water: temperature-dependent transition from a funneled free-energy landscape to a rugged one

The free-energy landscape of the Alzheimer beta-amyloid peptide Abeta(12-36) in a 40% (v/v) 2,2,2-trifluoroethanol (TFE)/water solution was determined by using multicanonical molecular dynamics simulations. Simulations using this enhanced conformational sampling technique were initiated from a random unfolded polypeptide conformation. Our simulations reliably folded the peptide to the experimental NMR structure, which consists of two linked helices. The shape of the free energy landscape for folding was found to be strongly dependent on temperature: Above 325 K, the overall shape was funnel-like, with the bottom of the funnel coinciding exactly with the NMR structure. Below 325 K, on the other hand, the landscape became increasingly rugged, with the emergence of new conformational clusters connected by low free-energy pathways. Finally, our simulations reveal that water and TFE solvate the polypeptide in different ways: The hydrogen bond formation between TFE and Abeta was enhanced with decreasing temperature, while that between water and Abeta was depressed.     

Capillary electrophoretic study of the binding of zinc(II) ion to bacitracin A1 in water-2,2,2-trifluoroethanol

Binding of Zn(2+) to bacitracin A(1) was studied by capillary electrophoresis in water/2,2,2-trifluoroethanol (70/30 v/v) at different apparent pH values in order to estimate the association constant of metal, the acidic dissociation constants and the Stokes radii of both free and bounded peptide in apolar environment. The Stokes radii of the free peptide species were compared with those in aqueous solution, as obtained in a recent study performed by our group, indicating that apolar environment stabilizes bacitracin A(1) in a conformational structure with the lateral chain of apolar amino acids exposed on the external surface. This conformation of the macrocyclic dodecapeptide is ready to interact with Zn(2+) ion, as pointed out by the strong increase of the association constant measured in water/2,2,2-trifluoroethanol with respect to the value obtained in aqueous solution. In addition, whereas Zn(2+) ion binding in aqueous solution provides a sensible reduction of peptide Stokes radius, no sensible variations following to ion binding were observed in hydro-organic solution. The present results suggest that the apolar environment, rather than the metal ion binding, could be responsible for the conformational transition that brings bacitracin A(1) towards its biologically active structure.*     

Conformational diversity of the fibrillogenic fusion peptide B18 in different environments from molecular dynamics simulations

The development of specific agents against amyloidoses requires an understanding of the conformational behavior of fibrillogenic peptides in different environments on the microscopic level. We present extensive molecular dynamics simulations of the fibrillogenic Bindin (103-120) B18 fusion peptide for several different environments: a water-trifluorethanol (TFE) mixture, pure water, aqueous buffer containing 100 mM NaCl, and a buffer-vapor interface. The peptide was studied as an isolated molecule in solution or at an interface. In the simulations, the conformational behavior of the peptide was found to strongly depend on the environment in agreement with experimental data. Overall, large portions of the peptide were unstructured. Preformed alpha-helical conformations were least stable in pure water and most stable in the water-TFE mixture and the buffer-vapor interface. In all environments, the alpha-helical conformation was most stable in the region around residues 113-116, which are mainly hydrophilic. Extended configurations in water or buffer folded into structures containing beta-sheets in agreement with data from circular dichroism spectroscopy. In buffer, the beta-sheet content was larger than in water and alpha-beta transitions were observed at elevated temperature. Beta-sheets were formed by hydrophobic residues; turns were formed by hydrophilic residues. A few typical beta-sheets that contain different residues are suggested. A B18 molecule in a strand-loop-strand conformation placed in buffer in contact with vapor was spontaneously adsorbed to the buffer-vapor interface with its hydrophobic side pointing toward the vapor phase. The adsorption induced the formation of turns at positions 108-119 and alpha-helical conformations in the region around residues 114-117. Alpha-helices were parallel to the interface plane in agreement with data from IR reflection absorption spectroscopy.     

Evaluation of NMR diffusion measurements for the conformational analysis of flexible peptides

The use of diffusion coefficients measured with pulsed-field gradient NMR spectroscopy for the determination of the relative population of conformers in solutions of the human Growth Hormone peptide fragment, hGH(9–19), has been studied in aqueous and in trifluoroethanol (TFE)/ water solutions. The peptide is a good model compound for this study because it adopts a predominantly random coil conformation in aqueous solution and is helical in TFE. The results of the diffusion measurements suggest that the peptide exhibits predominantly random coil structures in aqueous solution and adopts a more helical conformation in solutions containing increasing mole fractions of TFE, consistent with the qualitative findings of the standard CD and NMR experiments to probe peptide conformation. These results indicate that diffusion coefficients measured with NMR can provide additional information about temperature- and solvent-induced changes in the extent of the helical conformer for hGH(9–19) in aqueous solution and in solutions containing various mole fraction of TFE, respectively.     

Evaluation of NMR diffusion measurements for the conformational analysis of flexible peptides

The use of diffusion coefficients measured with pulsed-field gradient NMR spectroscopy for the determination of the relative population of conformers in solutions of the human Growth Hormone peptide fragment, hGH(9-19), has been studied in aqueous and in trifluoroethanol (TFE)/ water solutions. The peptide is a good model compound for this study because it adopts a predominantly random coil conformation in aqueous solution and is helical in TFE. The results of the diffusion measurements suggest that the peptide exhibits predominantly random coil structures in aqueous solution and adopts a more helical conformation in solutions containing increasing mole fractions of TFE, consistent with the qualitative findings of the standard CD and NMR experiments to probe peptide conformation. These results indicate that diffusion coefficients measured with NMR can provide additional information about temperature- and solvent-induced changes in the extent of the helical conformer for hGH(9-19) in aqueous solution and in solutions containing various mole fraction of TFE, respectively.     

Tandem repeating modular proteins avoid aggregation in single molecule force spectroscopy experiments

We have used single molecule force spectroscopy to explore the unfolding and refolding behavior of the immunoglobulin-like I27 protein in aqueous 2,2,2-trifluoroethanol (TFE). In bulk solution experiments, a 28% v/v TFE solution has previously been observed to enhance intermolecular attractions and lead to misfolding and aggregation of tandem modular proteins of high sequence identity. In our single molecule experiments, however, we measure successful refolding of the polyprotein I27(8) in all TFE solutions up to 35% v/v. Using a single molecule micromanipulation technique, we have shown that refolding of a polyprotein with identical repeats is not hindered by the presence of this cosolvent. These experimental results provide new insight into the properties of tandem repeating proteins and raise interesting questions as to the evolutionary success of such proteins in avoiding misfolding and aggregation.     

Probing the conformational features of a phage display polypeptide sequence directed against single-walled carbon nanohorn surfaces

Single-walled carbon nanohorns (SWNHs) are interesting carbon nanostructures that have applications to science and technology. Using M13 phage display technology, polypeptides directed again SWNHs surfaces have been created for a number of nanotechnology and pharmaceutical purposes, yet the molecular mechanism of polypeptide sequence interaction and binding to SWNHs surfaces is not known. Recently, we identified a linear 12-AA M13 phage pIII sequence, NH-12-5-2 (DYFSSPYYEQLF), that binds with high affinity to SWNHs surfaces. To probe the structure of this pIII tail polypeptide further, we investigated the conformation of a model peptide representing the 12 AA NH-12-5-2 sequence. At neutral pH, the NH-12-5-2 model polypeptide is conformationally labile and exhibits two-state conformational exchange involving the D1-S5 N-terminal segment. Simultaneous with this conformational exchange process is the observation that the P6 residue exhibits imido ring conformational variation. In the presence of the structure-stabilizing solvent, TFE, or at pH 2.5, both the exchange process and Pro ring motion phenomena disappear, indicating that the structure of this peptide sequence can be stabilized by extrinsic factors. Interestingly, we observe NMR parameters (ROEs, (3)J coupling constants) for NH-12-5-2 in 90% v/v TFE that are consistent with the presence of a partial helical structure, similar to what was observed at low pH in our earlier CD experiments. We conclude that the NH-12-5-2 model polypeptide sequence possesses an inherent conformational instability that involves the D1-S5 sequence segment and the P6 residue but that this instability can be offset by extrinsic factors (e.g., charge neutralization, imido ring interconversion, and hydrophobic-hydrophobic interactions). These nonbonding interactions may play a role in the recognition and binding of this phage sequence region to SWNHs surfaces.     

Toward the supramolecular structure of collagen: a molecular dynamics approach

The structure, stability, and conformational dynamics of an assembly of two pentameric bundles made of collagen-like triple helical segments are explored using 1.2 ns molecular dynamics simulations in three environments: 8.0% (v/v) formaldehyde/water solution, 1.4% (v/v) gallic acid/water solution, and pure water. Stable supramolecular arrangements, where the two collagen units are very close to each other at interacting distances, are identified via docking and energy minimization procedures. Analysis of the interaction with formaldehyde and gallic acid suggests that they perturb the protein in a similar way depending on hydrogen-bonding capability, hydrophobic association properties, and the size and concentration of the compound.     

特殊缔合体系TFE水溶液分子动力学模拟

三氟乙醇(TFE)水溶液是一类特殊的缔合体系. 采用分子动力学模拟方法结合核磁共振化学位移研究了TFE水溶液体系全浓度范围的氢键网络, 并对动力学模拟结果和核磁共振化学位移进行了比较. 从径向分布函数(RDF)发现, TFE水溶液中存在着强氢键, 而体系中的C—H…O弱相互作用较为明显, 也不能忽略. 氢键网络分析发现TFE 水溶液体系的氢键大致分为以下三个区域: 在水富集区域, 水分子倾向于自身缔合形成稳定的簇结构, 随着TFE 浓度的增加, 水的有序结构受到破坏, 水分子和TFE分子发生交叉缔合作用形成氢键; 在TFE富集区域, 水分子较少, TFE分子自身通过氢键形成多缔体结构. 此外, 分子动力学统计的平均氢键数的变化和文献报导的核磁共振化学位移变化趋势相同, 实验和理论的结果吻合较好.     

Self-association of an amphipathic helix peptide inhibitor of HIV-1 integrase assessed by electro spray ionization mass spectrometry in trifluoroethanol/water mixtures

Establishing the auto-associative properties of a molecule in solution can be important for determination of its structure and function. EAA26 (VESMNEELKKIIAQVRAQAEHLKTAY) has been designed to inhibit HIV-1 integrase via formation of a stable coiled-coil structure with a nearly homologous segment in the enzyme. The latter catalyzes the permanent incorporation of a DNA copy of the retrovirus genome into host cell DNA, and is thus essential to the life of the retrovirus. This makes integrase an obvious drug target in the therapy of AIDS. The present work has demonstrated, using electrospray ionization mass spectrometry (ESI-MS), that EAA26 is monomeric in pure water, and tetrameric and dimeric at respectively low and medium concentrations of 2,2,2-trifluoroethanol (TFE), and again monomeric at higher TFE concentrations. Thus, the apolar solvent TFE may contribute to either stabilization or disruption of the intermolecular hydrophobic contacts depending on its concentration in aqueous solution. Previous NMR and ultracentifugation results are thus confirmed, indicating the reliability of ESI-MS for defining the self-association state of biologically relevant peptides in both water and organic-water solutions.     

Sodium, ammonium, calcium, and magnesium forms of zeolite Y for the adsorption of glucose and fructose from aqueous solutions

The kinetics of adsorption by sodium, ammonium, calcium and magnesium forms of zeolite Y from aqueous solutions containing 25% w/v of either one or an equimolar mixture of glucose (G) and fructose (F) have been studied batch-wise at 50 degrees C. The adsorption of aqueous pure G was fast, while that of aqueous pure F depended on the cationic form, approaching that of G on the Mg-Y, and slowing down in the sequence of Mg2+ > NH4+ > Ca2+ > Na+ of the cations. The adsorption behavior from solutions containing both G and F indicated significant hindering effects of F on G on Na-Y. Na-Y and Mg-Y did not exhibit rate-based selectivity, while Ca-Y an NH4-Y adsorbed G faster than F. Addition of CaCl2 to the mixture of Ca-Y and aqueous solution of G and F improved the separation, by hindering the adsorption of F. Addition of NH4Cl to the mixture of the sugar solution and NH4-Y, on the other hand, had a negative effect on the separation. NH4-Y was found to be desorbing about 30% of the adsorbed sugars and this value was found to be around 50% for Ca-Y. Re-adsorption experiments resulted in similar or somewhat higher percentages of amounts adsorbed compared to adsorption on fresh samples. Both NH4-Y and Ca-Y were found to be re-adsorbing around 50% of the sugars they adsorbed on fresh samples.     

NMR conformational analysis of antide, a potent antagonist of the gonadotropin releasing hormone

Antide is a decapeptide [(N-Ac-D-Nal(1)-D-Cpa(2)-D-Pal(3)-Ser(4)-Lys(Nic)(5)-D-Lys(Nic)(6)-Leu(7)-Ilys(8)-Pro(9)-D-Ala(10)-NH(2)] that acts in vivo as an antagonist of GnRH (gonadotropin-releasing hormone). The conformational behavior of antide has been studied in water, TFE, DMF, and DMSO solutions by means of 2D-NMR spectroscopy and molecular dynamics calculations. Antide adopts in aqueous solution a delta-shaped backbone conformation, which is characterized by an irregular turn around residues D-Pal(3)-Ser(4) and by the close spatial proximity of the side chains belonging to D-Nal(1) and Ilys(8) (as many as 17 NOE peaks were detected between these side chains). The side-chain protons of Ilys(8) (especially the H(gamma) ones) present remarkably upfield shifted resonances, because of ring current effects induced by the naphthyl moiety. The upfield shifted resonances of the Ilys(8) H(gamma) hydrogen atoms are strictly characteristic of the water delta-shaped conformation and can be considered as structure markers. The observation of ring current shifted Ilys(8) H(gamma) resonances under different conditions (temperature, pH, solvent) indicates a remarkable stability of the water delta-shaped conformation. Such a conformation is at least partially disrupted in solvent mixtures containing high percentages of organic solvents. TFE can induce a well-defined conformation, which is characterized by an S-shaped backbone conformation. In DMF and DMSO solution, the molecule is basically endowed with a random coil conformation and high fluxionality. Antide fulfills the conformational requirements that are known to play a crucial role in receptor recognition, namely (i) the presence of a turn in the backbone and (ii) the all-trans nature of peptide bonds. In addition, the structural rigidity of antide likely adds a further contribution to the receptor binding affinity.     

Preparation and Properties of Alginate/Water‐Soluble Chitin Blend Fibers

Water‐soluble chitin (half‐deacetylated chitin) was prepared from chitosan by N‐acetylation with acetic anhydride. Alginate/water‐soluble chitin blend fibers were prepared by spinning their mixture solution through a viscose‐type spinneret into a coagulating bath containing aqueous CaCl₂ and ethanol. The structure and properties of the blend fibers were studied with the aids of infrared spectra (IR), X‐ray diffraction (XRD) and scanning electron microscopy (SEM). structure analysis indicated good miscibility existed between alginate and water‐soluble chitin, due to the strong interaction from the intermolecular hydrogen bonds and electrostatic interactions. Best values for the dry tensile strength and breaking elongation were obtained when the water‐soluble chitin content was 30 wt%. The wet tensile strength and breaking elongation decreased with the increase of water‐soluble chitin content. The introduction of water‐soluble chitin in the blend fiber can improve the water‐retention properties of the blend fiber compared to pure alginate fiber. The fibers treated with aqueous solution of silver nitrate have good antibacterial activity to Staphylococcus aureus.     

Solvation phenomena of a tetrapeptide in water/trifluoroethanol and water/ethanol mixtures: a diffusion NMR,intermolecular NOE,and molecular dynamics study

Solvation of a tetrapeptide, NAc-Ser-Phe-Val-Gly-OMe (1), in water and in water/alcohol mixtures with 2,2,2-trifluoroethanol (TFE)/water or ethanol (ETH)/water has been studied by diffusion NMR and intermolecular NOE measurements. The experimental results were compared with those obtained from detailed Molecular Dynamics (MD) calculations. Independently, all three methods revealed preferential solvation on the surface of the peptide by TFE in the water/TFE mixtures, but not by ETH in the water/ETH mixtures. The MD calculations show that the TFE concentration coating the peptide is higher than that in the bulk, while for ethanol, the concentration is nearly equal to that in the bulk. Calculated site-specific preferential solvation data between TFE, ETH, and water with the different peptide groups have been compared with the NMR data and shown to be in general agreement with the experimental facts.     

The pH-dependence of preferential solvation as studied by intermolecular homo- and heteronuclear NOE measurements of adenosine in water–trifluoroethanol mixtures

A study of the state of solvation of the adenine ring in adenosine and adenosine 5-monophosphate disodium salt in water and in a (7.5:2.5) water–TFE mixture has been carried out by measurement of homo- and heteronuclear intermolecular NOE enhancements between water or TFE and the aromatic protons of these compounds. The results give evidence of site specificity in solute–solvent interaction for both solvent systems and preferential solvation of the solute by TFE in the water–TFE mixture. Significant pH dependence of these interactions has been discovered.     

Conformational studies of basic poly (α-amino acid)s in reversed micelles

The conformation of various basic poly (-amino acid)s was investigated by CD measurements in aqueous solutions containing bis (2-ethylhexyl)sodium sulfosuccinate (AOT) as well as in the AOT reversed micelles. The addition of AOT into an aqueous solution of poly(L-lysine) induces the conformational transition from coil to ordered structure, followed by aggregation. On the other hand, poly(L-lysine) assumes-structure in the reversed micelles at low w_ovalue (w_o=[H₂O]/[AOT]). Similarly to poly(L-lysine), poly(L-ornithine) takes an ordered structure in the aqueous solution containing AOT and-structure in the reversed micelles. In this case, however, these ordered structures are not so stable, compared with that of poly(L-lysine). Poly(L-arginine) undergoes the conformational transition from coil to helix by addition of AOT into the aqueous solution. Further addition of AOT allows transformation into-structure. Copoly(L-lysyl-L-leucine) with 63% leucine residue was shown to take a stable helical conformation even in pure water. In the reversed micelles, however, this ordered structure is significantly changed probably because the hydrophobic interaction among the leucyl residues is lowered in the reversed micelles.     

The effect of cyclodextrin mixtures on aqueous solubility of beclomethasone dipropionate

The aim of present study was to evaluate the effect of natural, synthetic cyclodextrins (CDs) and CD mixtures on aqueous solubility of beclomethasone dipropionate (BDP). The phase solubility studies were done in the presence of 6 CDs. Furthermore, aqueous solubility of BDP was tested in the presence of CD mixtures. The solubility of BDP in water was increased by 30, 77, 155 and 30 folds in the solution containing 20%?w/v α-CD, hydroxylpropyl β-CD (HP-β-CD), hydroxypropyl γ-CD (HP-γ-CD) and sulphobutylether β-CD (SBE-β-CD), respectively. CD mixtures had remarkable effect on the aqueous solubility of BDP so that solubility in water increased between 200 and 1,500 times in the presence of different CD mixtures. Further addition of sodium acetate to the solubilisation medium reduced the aqueous solubility. In conclusion, CD complexation was able to improve the aqueous solubility of BDP. The synergistic effect of cyclodextrin mixture was observed.     

Mixture design optimization of extraction and mobile phase media for fingerprint analysis of Bauhinia variegata L

Two statistical mixture designs were used to optimize the proportions of solvents used in both the extraction medium and the reversed liquid chromatographic mobile phase to improve the quality of chromatographic fingerprints of Bauhinia variegata L extracts. For modeling, the number of peaks was used as a measure of fingerprint information. Three mobile phases, each with a chromatographic strength of two, gave good results. A methanol/water (77:23 v/v) mixture resulted in 17 peaks in the chromatographic fingerprint whereas acetonitrile/water (64.5:35.5 v/v) and methanol/acetonitrile/water (35:35:30 v/v/v) mixtures resulted in 18 and 20 peaks, respectively. The corresponding optimum solvent compositions to extract chemical substances for these three mobile phases were ethanol/acetone (25:75 v/v/v) and dichloromethane/acetone (70:30 v/v) mixtures, and pure dichloromethane, respectively. The mixture designs are useful for understanding the influence of different solvents on the strengths of the extraction medium and the mobile phase.