Structural changes induced in tussah silk (Antheraea pernyi) fibroin films by immersion in methanol

The crystalline transition induced by immersion in a methanol/water mixture of tussah silk fibroin (from Antheraea pernyi) film obtained by casting from a 1% solution was studied by x-ray diffraction, differential scanning calorimetry, and infrared spectroscopy. The molecular conformation of the fibroin, consisting mostly of the α-helix and random-coil forms, was transformed into a random-coil and β-rich conformation containing only a small amount of α-helix after immersion for no more than 5 min. The intersheet packing of the β-crystal of the original tussah silk fibroin film was imperfect in the early stage of immersion. However, crystallization proceeded further when the immersion time exceeded 10 min. As a result the sheets in the β-form crystal became closely packed because of the decrease in the content of the random-coil form. The exothermic peak, which appeared at 226°C in the original fibroin and was attributed to the random-coil → β-structure transition, disappeared completely after immersion for 5 min.     

pH值和钙离子对尖吻蝮蛇抗血小板凝集素二级结构的影响

尖吻蝮蛇毒中抗血小板凝集素是凝血因子IX/凝血因子X结合蛋白，它具有抗凝血和抑制血小板凝集双重活性。用红外光谱、拉曼光谱和CD谱研究了抗血小板凝集素的二级结构以及pH值和钙离子对其二级结构的影响。用CD谱测得，在水溶液中，抗血小板凝集素的主要骨架构象为β-折叠(26.3%)和α-螺旋(19.6%)结构。拉曼光谱显示，在粉末状态，其α-螺旋含量显著降低。CD谱还表明，抗血小板凝集素在pH值3.0～11.0范围内保持稳定的天然结构，钙离子诱导的抗血小板凝集素结构变化是可逆的，钙离子在稳定抗血小板凝集素的天然结构中起重要作用。     

Conformational preference in thiophene-2-carbaldehyde

The 100 MHz ¹H NMR spectra of thiophene-2-carbaldehyde have been obtained in different solvents and analysed. It was found that the SO-cis conformation is more stable in all solvents, and that the proportion of the SO-trans population increases with decreasing polarity of the solvent. CNDO/2 calculations predict that the SO-cis is more stable than the SO-trans conformation. The aldehyde coupling to the ring was calculated by the CNDO/2 method and compared with the experimental value.     

Aib-rich peptides containing lactam-bridged side chains as models of the 3(10)-helix.

Aib-rich side chain lactam-bridged oligomers with n =1, 2, 3, were designed and synthesized as putative models of the 3(10)-helix. These peptides were conformationally characterized in aqueous solution containing SDS micelles by CD, NMR, and computer simulations. The lactam bridge between the side chains of L-Glu and L-Lys in (i) and (i+3) positions was introduced in order to enhance the conformational preference toward the right-handed 3(10)-helix. The NMR results clearly indicate that there is an increase of 3(10)-helix formation upon chain elongation. In the dimer and trimer (n = 2 and n = 3, respectively, in the structure reported above) the observed NOE connectivities are compatible with the 3(10)-helical arrangement, confirmed by the temperature coefficients of the amide proton resonances which suggest the presence of a hydrogen-bonded structure. The phi and psi dihedral angles of the structures obtained by molecular dynamics calculations are also compatible with the 3(10)-helix. Identification of the hydrogen-bond pattern indicate that C=O(i)- - -HN(i+3) hydrogen bonds, typical of the 3(10)-helical conformation, are highly probable in all low-energy structures. The CD spectra of these Aib-rich lactam-bridged oligopeptides, obtained in the same solvent system used for NMR experiments, provide important insight into the spectroscopic characteristics of the 3(10)-helix.     

Electronic and molecular structures of HCNn polymers: (HCN)3n

The CNDO/2 method using the tight-binding approximation for polymers was applied to several forms of (HCN)_3n polymers. From these calculations, we conclude that the polymer exists in the helical form rather than the planar trans zigzag, TTT, form. It was found that, from comparison of the TTT form with the polyglycine II type (Gly-II) form, the intrasegment energy of the TTT form is lower than for the Gly-II type form while the intersegment energy of the Gly-II form is lower than for the TTT form. It was also revealed that, in the typical α-helix type structures, hydrogen bonding between the central and the fourth nearest neighbour segments may play an important stabilizing role.     

Role of doubly excited states in calculations of optical activity

It is shown that doubly excited states play an important role in calculations of the optical activity of molecules with well-conjugated electron systems, such as the DNA bases. In some significant cases it is necessary to include a large number of excited states in the configuration interaction (CI ) to obtain a reliable, converging result. A new version of the CNDO/OPTIC method, which includes doubly excited states in the CI , is proposed. As an application, the electric transition moments in different pyrimidines are considered. The calculated results agree with experimental data and results obtained from ab initio calculations and INDO calculations using doubly excited states in the CI .     

Headgroup effects of template monolayers on the adsorption behavior and conformation of glucose oxidase adsorbed at air/liquid interfaces

Stearic acid (SA) and octadecylamine (ODA) monolayers at the air/liquid interface were used as template layers to adsorb glucose oxidase (GOx) from aqueous solution. The effect of the template monolayers on the adsorption behavior of GOx was studied in terms of the variation of surface pressure, the evolution of surface morphology observed by BAM and AFM, and the conformation of adsorbed GOx. The results show that the presence of a template monolayer can enhance the adsorption rate of GOx; furthermore, ODA has a higher ability, compared to SA, to adsorb GOx, which is attributed to the electrostatic attractive interaction between ODA and GOx. For adsorption performed on a bare surface or on an SA monolayer, the surface pressure approaches an equilibrium value (ca. 8 mN/m) after 2 to 3 h of adsorption and remains nearly constant in the following adsorption process. For the adsorption on an ODA monolayer, the surface pressure will increase further 1 to 2 h after approaching the first equilibrium pressure, which is termed the second adsorption stage. The measurement of circular dichroism (CD) spectroscopy indicates that the Langmuir-Blodgett films of adsorbed GOx transferred at the first equilibrium state (π = 8 mN/m) have mainly a β-sheet conformation, which is independent of the type of template monolayers. However, the ODA/GOx LB film transferred at the second adsorption stage has mainly an α-helix conformation. It is concluded that the specific interaction between ODA and GOx not only leads to a higher adsorption rate and adsorbed amount of GOx but also induces a conformation change in adsorbed GOx from β-sheet to α-helix. The present results indicate that is possible to control the conformation of adsorbed protein by selecting the appropriate template monolayer.     

生物活性胶原蛋白及明胶形态的表征研究

采用弱酸处理法,从新鲜牛皮中提取了胶原蛋白,通过与明胶对比,采用CD、AFM、FTIR和荧光方法对其结构形态进行了表征研究。结果表明,所提取胶原蛋白保持了固有的生物活性,具有典型的α-螺旋结构。首次建立了稳态荧光的表征方法,不仅与其他方法具有重要互补性,而且具有准确、灵敏、快捷的特点,是表征、研究胶原蛋白及其变性/复性行为的有效手段。     

Solvent polarity controls the helical conformation of short peptides rich in Calpha-tetrasubstituted amino acids

The two peptides, rich in C(alpha)-tetrasubstituted amino acids, Ac-[Aib-L-(alphaMe)Val-Aib](2)-L-His-NH(2) (1) and Ac-[Aib-L-(alphaMe)Val-Aib](2)-O-tBu (2 a) are prevalently helical. They present the unique property of changing their conformation from the alpha- to the 3(10)-helix as a function of the polarity of the solvent: alpha in more polar solvents, 3(10) in less polar ones. Conclusive evidence of this reversible change of conformation is reported on the basis of the circular dichroism (CD) spectra and a detailed two-dimensional NMR analysis in two solvents (trifluoroethanol and methanol) refined with molecular dynamics calculations. The X-ray diffractometric analysis of the crystals of both peptides reveals that they assume a prevalent 3(10)-helix conformation in the solid state. This conformation is practically superimposable on that obtained from the NMR analysis of 1 in methanol. The NMR results further validate the reported CD signature of the 3(10)-helix and the use of the CD technique for its assessment.     

Conformationally Controlled sp3-Hydrocarbon-Based α-Helix Mimetics

With over 60 % of protein–protein interfaces featuring an α-helix, the use of α-helix mimetics as inhibitors of these interactions is a prevalent therapeutic strategy. However, methods to control the conformation of mimetics, thus enabling maximum efficacy, can be restrictive. Alternatively, conformation can be controlled through the introduction of destabilizing syn-pentane interactions. This tactic, which is often adopted by Nature, is not a common feature of lead optimization owing to the significant synthetic effort required. Through assembly-line synthesis with NMR and computational analysis, we have shown that alternating syn–anti configured contiguously substituted hydrocarbons, by avoiding syn-pentane interactions, adopt well-defined conformations that present functional groups in an arrangement that mimics the α-helix. The design of a p53 mimetic that binds to Mdm2 with moderate to good affinity, demonstrates the therapeutic promise of these scaffolds.     

Structure and molecular conformation of tussah silk fibroin films: Effect of heat treatment

Structural changes of tussah (Antheraea pernyi) silk fibroin films induced by heat treatment were studied as a function of the treatment temperature in the range 200–250°C. The DSC curve of tussah films with α-helix molecular conformation displayed characteristic endo and exo peaks at 216 and 226°C, respectively. These peaks first weakened and then completely disappeared after heating at 230°C. Accordingly, the TMA thermal shrinkage at 206°C disappeared when the films were heated at 230°C. The onset of weight loss was monitored at 210°C by means of TG measurements. X-ray diffraction profiles gradually changed from α-helix to β-sheet crystalline structure as the treatment temperature increased from 200 to 250°C. On raising the heating temperature above 200°C, the intensity of IR and Raman bands characteristic of β-sheet conformation increased in the whole ranges of amide and skeletal modes. The sample treated at 200°C showed a spectral pattern intermediate between α-helix and β-sheet molecular conformation. The IR marker band for random coil structure, still detectable at 200°C, disappeared at higher treatment temperatures. Spectral changes attributable to the onset of thermal degradation appeared at 230°C. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 35: 841–847, 1997     

Direct quantum chemical calculation of rotatory strengths of methylpyrrolidones : Model compounds containing a peptide group

CNDO/S method is used to compute the rotatory strengths of L-5-methylpyrrolid-2-one and S-3-methylpyrrolid-2-one, cyclic compounds containing a peptide group. The observed circular dichroism (CD) bands in the regions of 185 and 220 nm corresponded to π → π^* and n → π^* transitions, respectively. The computed rotatory strengths indicate that nonplanarity of pyrrolidone ring makes a substantial contribution to the CD of compounds under consideration. The comparison of computed and experimental rotatory strengths suggests that both compounds have a nonplanar ring conformation.     

A quantum-mechanical study of the chain-length dependent stability of the extended and 310-helix conformations in dehydroalanine oligopeptides

Summary A quantum-chemical study of the chain-length dependent stability of the extended, 2₇-ribbon and 3₁₀-helix conformations in dehydroalanine (Ala) oligopeptides has been performed by using both semiempirical AM1 and ab initio 4–31G methodologies. The validity of both methods in the study of the conformational properties of Ala oligopeptides was tested first on the dipeptide. The results of this test showed that 4–31G and AM1 calculations are in good agreement with 6–31G^* calculations and experimental data. In order to monitor the conformational conversions, Ala oligopeptides comprising two to six residues were constructed. Molecular geometries were fully optimized using AM1, and the final conformations were verified to be minima by analysis of the corresponding second-derivative matrices. Conformational studies revealed that the 3₁₀-helix is stabilized with respect to the 2₇-ribbon when the number of residues is three or four, at the AM1 and ab initio 4–31G level respectively, while the extended form is the most stable in all the calculations performed. On the other hand, if a linear behaviour is assumed for longer chains, our calculations show a trend that would predict a conversion from extended form to 3₁₀-helix in oligopeptides with around six (ab initio 4–31G) or eight (AM1) Ala residues. In order to explain these conformational changes, the cooperative effects for the different conformers were investigated. Large cooperative energy effects were found for the 3₁₀-helix conformation.     

Optical activity of lactones and lactams-III : Circular dichroism spectra of 5-oxazolidinones

The synthesis and the chiroptical properties of several 5-oxazolidinones derived from α-amino acids are reported. The existence of an equilibrium between the two enantiomeric envelope conformations of 5-membered ring has been inferred from CD and NMR spectra. In a few cases the small contribution of the planar ring conformation to the equilibrium is proposed. The nature of the lowest energy transition and the usefulness of the Weigang lactone sector rule for Cotton effect sign predictions are discussed on the basis of CNDO/2-CI calculations.     

Insight into the effects of graphene oxide sheets on the conformation and activity of glucose oxidase: towards developing a nanomaterial-based protein conformation assay

Protein conformation associates with particular properties of proteins and relates to protein-mediated diseases. Detailed elucidation of secondary and tertiary formation, stability, and the structural and dynamic properties of proteins has been one of the main topics studied in chemistry and biology. In this work, the conformation changes in glucose oxidase (GOx) induced by the graphene oxide (GO) sheets were studied in detail by various spectroscopic techniques including ultraviolet-visible (UV-vis) absorption, fluorescence, and circular dichroism (CD) spectroscopy. The results indicated that GOx underwent substantial conformation changes after assembling on the surface of GO. The interaction of GOx with GO could induce the exposure of the FAD (flavin adenine dinucleotide) moiety to solvent and transfer tryptophan (Trp) residues to a more hydrophobic environment. The calculation from CD spectra showed that GO could induce the conversion of α-helix to β-sheet structures, even unfolding of the protein. These alterations in the conformation of GOx resulted in a significant decrease in the catalytic activity of the enzyme in glucose oxidation. The possible reasons for these conformation changes in GOx are also discussed. This work not only provides insight into the interaction between atomically flat graphitic structures and various biological systems but also creates a framework for analyzing the biosafety of nanomaterials in terms of the biological behavior of biomacromolecules. The results obtained here can direct the further applications of the nanomaterials.     

Chromatographic Resolution,Circular Dichroism Spectra,Absolute Configurations,and Crystal Structures of Bridged Biphenyls,Containing Sulfide,Sulfoxide, and Sulfone Groups in the Bridge

Four chiral 1,1′‐biphenyls with one or two sulfur‐containing bridges in 2,2′‐ or 2,2′‐ and 6,6′‐positions, viz. 1,11‐dimethyl‐5,7‐dihydrodibenzo[c,e]thiepin ( 1 ), its S‐oxide ( 2 ) and S,S‐dioxide ( 3 ), and the doubly bridged 10,12‐dihydro‐4H,6H‐[2]benzothiepino[6,5,4‐def][2]benzothiepin ( 4 ) have been studied by chromatography, CD spectroscopy, X‐ray crystallography, and empirical force‐field and CNDO/S calculations. The structures obtained by force‐field calculations showed good agreement with the crystal structures determined for 2 and 3 . Compounds 2 , 3 , and 4 , but not 1 , could be resolved into enantiomers by chromatography on swollen microcrystalline triacetylcellulose. The barrier for biphenyl inversion in 2 was found to be higher than 167 kJ⋅mol⁻¹ by an attempted thermal racemization. The CD spectra of the enantiomers of 2 – 4 were recorded and resolved into individual bands, and the corresponding rotational strengths were calculated. The transitions showed considerable similarity to those of a 1,1′‐biphenyl with hydrocarbon bridge (cf. 5 ), albeit with bathochromic shifts, which permitted the assignment of the absolute configurations of the enantiomers of 2 – 4 . The assignments were supported by comparison of the experimental CD spectra with spectra calculated by the CNDO/S method. All first‐eluted enantiomers were found to have the (S)‐configuration.     

Structure and molecular conformation of tussah silk fibroin films: Effect of methanol

Structural changes of tussah (Antheraea pernyi) silk fibroin films treated with different water-methanol solutions at 20°C were studied as a function of methanol concentration and immersion time. X-ray diffraction measurements showed that the α-helix structure, typical of untreated tussah films, did not change for short immersion times (2 min), regardless of methanol concentration. However, crystallization to β-sheet structure was observed following immersion of tussah films for 30 min in methanol solutions ranging from 20 to 60% (v/v). IR spectra of tussah films untreated and methanol treated for 2 min exhibited strong absorption bands at 1265, 892, and 622 cm^?1, typical of the α-helix conformation. The intensity of the bands assigned to the β-sheet conformation (1245, 965, and 698 cm^?1) increased for the sample treated with 40% methanol for 30 min. Raman spectra of tussah films with α-helix molecular conformation exhibited strong bands at 1657 (amide I), 1263 (amide III), 1106, 908, 530, and 376 cm^?1. Following α → β conformational transition, amide I and III bands shifted to 1668, and to 1241, 1230 cm^?1, respectively. The band at 1106 cm^?1 disappeared and new bands appeared at 1095 and 1073 cm^?1, whereas the intensity of the bands at 530 and 376 cm^?1 decreased significantly. ©1995 John Wiley & Sons, Inc.     

Conformation and electrochemical reduction of myoglobin in PEO oligomers

Horse-heart myoglobin (Mb) was modified with poly(ethylene oxide) (PEO) to solubilize it in PEO oligomers. PEO-modified Mb (PEO–Mb) showed a quasi-reversible electrochemical redox reaction in PEO₂₀₀ (molar mass of 200 g). PEO–Mbs, modified with lower molecular weight of PEO chains, were soluble in PEO oligomers with wider range of molecular weight. A conformation of PEO–Mb was studied with circular dichroism spectroscopy in phosphate buffer solution (PBS) or PEO oligomers. The α-helix content of PEO–Mb, determined by the molar ellipticity at 222 nm, decreased from 71% to about 58% after PEO modification. However, the degree of PEO modification did not affect the α-helix content of PEO–Mbs. On the other hand, the α-helix content of PEO–Mbs was reduced by lowering the molecular weight of the modified PEO chains. Since the α-helix content of PEO–Mb in PBS and that in the PEO oligomers were almost identical, the conformation of PEO–Mb in PBS was considered to be maintained even in PEO oligomers. Although the reduction rate constant of PEO–Mb in PEO oligomers depended on the total molecular weight of the PEO–Mbs, their relation did not obey the Stokes–Einstein equation. The reduction of the PEO–Mb was probably affected by the interfacial electron transfer process at the electrode surface rather than by diffusion in the PEO oligomer.     

用概率统计法估算天花粉蛋白的二级结构

本文应用Levitt提出的蛋白质中氨基酸对二级结构的特定偏爱的统计方法估算天花粉蛋白的二级结构。计算结果表明,在天花粉蛋白中α-螺旋为32％,β-折叠为28％,反转为20％,其他类型为20％。这一计算结果与X射线衍射研究、圆二色性谱研究的结果相近。     

Structural Investigation of Hybrid Peptide Foldamers Composed of α-Dipeptide Equivalent β-Oxy-δ5-amino Acids

Due to their equivalent lengths, δ-amino acids can serve as surrogates of α-dipeptides. However, δ-amino acids with proteinogenic side chains have not been well studied because of synthetic difficulties and because of their insolubility in organic solvents. Recently we reported the spontaneous supramolecular gelation of δ-peptides composed of β(O)-δ⁵-amino acids. Here, we report the incorporation of β(O)-δ⁵-amino acids as guests into the host α-helix, α,γ-hybrid peptide 12-helix and their single-crystal conformations. In addition, we studied the solution conformations of hybrid peptides composed of 1:1 alternating α and β(O)-δ⁵-amino acids. In contrast to the control α-helix structures, the crystal structure of peptides with β(O)-δ⁵-amino acids exhibit α-helical conformations consisting of both 13- and 10-membered H-bonds. The α,δ-hybrid peptide adopted mixed 13/11-helix conformation in solution with alternating H-bond directionality. Crystal-structure analysis revealed that the α,γ⁴-hybrid peptide accommodated the guest β(O)-δ⁵-amino acid without significant deviation to the overall helix folding. The results reported here emphasize that β(O)-δ⁵-amino acids with proteinogenic side chains can be accommodated into regular α-helix or 12-helix as guests without much deviation of the overall helix folding of the peptides.