Conformational change of a G-quadruplex under molecular crowding conditions

Abstract

This study examined the influence of the molecular crowding condition induced by polyethylene glycol (PEG) on the G-quadruplex structure of the thrombin-binding aptamer sequence, 5′-GGGTTGGGTGTGGGTTGGG (G3), in a solution containing a sufficient concentration of mono cations (K⁺ and Na⁺). Although the G3 sequence preferably formed the antiparallel type G-quadruplex structure in a Na⁺ solution, conversion to the parallel type occurred when PEG was added. The antiparallel type was maintained at low PEG concentrations. When the PEG concentration reached 30%, the antiparallel type and parallel type coexist. At PEG concentrations above 40%, the G-quadruplex structure adopted the parallel type completely. In the presence of K⁺ ions, G3 showed a parallel conformation and remained as a parallel conformation with increasing PEG concentration. The dissociation temperature increased with increasing PEG concentration in all cases, suggesting that the G-quadruplex conformation is more stable under molecular crowding conditions.

Communicated by Ramaswamy H. Sarma     

Elucidating the interaction of Spathodea campanulata leaf extracts mediated potential bactericidal gold nanoparticles with human serum albumin: spectroscopic analysis

Nanomaterials in different form have been thoroughly used in the area of pharmaceutics and medicine for drug delivery. The large scale of nanoparticles (NPs) synthesis from plant extract is much safe, cheap and eco-friendly. Here, we demonstrated a new, one-step, ultra-fast biosynthesis of gold nanoparticles (sc-AuNPs, 19.54?nm) by using aqueous Spathodea campanulata leaf extracts as a reducing and capping agent. And also, we presented the synthesis of citrate capped gold nanoparticles (cit-AuNPs) of approximately same size (19.66?nm). These two NPs were characterized by UV-Visible, dynamic light scattering, transmission electron microscope and energy dispersive X-ray spectroscopy. Fourier transform infrared spectroscopy confirmed that the functional groups like OH, NH, OH of COOH and CO were contributed in the sc-AuNPs formation. The negative zeta potential (?20.5, ?22.8?mV) established the stability and dispersion of the sc- and cit-AuNPs. The anti-bacterial activity of the sc- and cit-AuNPs were checked against Escherichia coli (DH5-Alpha). Minimum inhibitory concentration was 2.4 and 3.0?nM, respectively for sc- and cit-AuNPs. The interaction study of the sc-AuNPs/cit-AuNPs-human serum albumin (HSA) system was done by UV-Visible absorbance, fluorescence, circular dichroism, time resolved fluorescence spectroscopy and the measurement of zeta potential. Absorbance, three dimensional fluorescence, synchronous fluorescence and circular dichroism spectroscopy showed a minor conformational change of HSA upon interaction with the sc-AuNPs compared to cit-AuNPs. The present comparative study will advance our knowledge about the binding mode, mechanism and conformational change of the protein upon interaction with green synthesized sc-AuNPs and cit-AuNPs.

Communicated by Ramaswamy H. Sarma     

Conformation of alamethicin in phospholipid vesicles: implications for insertion models

The secondary structure of alamethicin, a membrane channel-forming polypeptide, has been examined by circular dichroism spectroscopy to determine the relationship of its conformation in organic solution to its conformation in a membrane-bound state. The spectrum of alamethicin in small unilamellar dimyristoyl phosphatidylcholine vesicles is significantly different from its spectrum in 10% methanol/acetonitrile, the solvent from which it was crystallized (Fox and Richards: Nature 300:325-330, 1982), as well as its spectrum in methanol, the solvent in which NMR studies have been done (Banerjee and Chan: Biochemistry 22:3709-3713, 1983). This suggests that structural models based on studies of the molecule in organic solvents may not be entirely appropriate for the membrane-bound state. To distinguish between different models for channel formation and insertion, two different methods were used to associate the alamethicin with vesicles; in addition, the effect of oligomerization on the conformation of the membrane-bound state was investigated. These studies are consistent with a modified insertion model in which alamethicin monomers, dimers, or trimers associate with the bilayer and then spontaneously oligomerize to form a prechannel with a higher helix content. This aggregate could then "open" upon application of an appropriate gating transmembrane potential.     

沼水蛙抗菌肽brevinin-2GHa1分离纯化及结构分析

目前,已自青蛙皮肤分泌物中分离获得多种具有较强抗菌活性的多肽．本文利用电刺激法自沼水蛙背腺和耳后腺获得其皮肤分泌物,利用凝胶过滤色谱(Sephadex G-50)和反相高效液相色谱 (reverse-phase high performance liquid chromatography, RP-HPLC)分离纯化,获得一种新型抗菌肽,命名为brevinin- 2GHa1. 抑菌实验显示,该抗菌肽对革兰氏阳性菌和革兰氏阴性菌均有抑制作用,对大肠杆菌、金黄色葡萄球菌、枯草芽孢杆菌和沙门氏菌的最小抑制浓度分别为： 7.8、3.9、2.0 μg/mL和250.0 μg/mL. 该抗菌肽在水中为无规卷曲结构,在浓度为10 mmol/L SDS水溶液和不同浓度三氟乙醇水溶液中则呈α-螺旋结构,该抗菌肽结构的研究对阐明其抑菌机制具有重要作用.     

天蚕素A-爪蟾素2杂合肽P18对MDA-MB-435s乳腺癌细胞的作用研究

目的 研究天蚕素A-爪蟾素2杂合肽P18对体外培养的人类乳腺癌细胞株MDA-MB-435s的活性作用.方法 采用MTT法检测P18对体外培养的MDA-MB-435s细胞增殖的影响;使用Live/Dead Viability/Cytotoxicity试剂盒对细胞进行染色,并在荧光显微镜下观察细胞的存活状态;通过DiBAC_4(3)染色,以荧光分光光度计检测给肽时细胞膜的膜电位变化;在透射电子显微镜下观察P18作用24 h后细胞超微结构的变化.结果 MTT试验表明P18对MDA-MB-435s细胞的增殖具有浓度依赖性的抑制作用;荧光显微镜下可观察到P18可以使MDA-MB-435s细胞膜破损,细胞死亡;P18作用时,荧光分光光度计检测到MDA-MB-435s的细胞膜发生了去极化现象;透射电子显微镜下可见大量细胞崩解坏死.结论 杂合肽P18能够引起MDA-MB-435s细胞膜的通透性改变而导致细胞坏死.     

圆二色谱激子手性法进展及其在天然产物绝对构型确定中的应用

本文综述了圆二色谱激子手性法进展及其在天然产物绝对构型确定中的应用.     

Vacuum ultraviolet circular dichroism of poly(galacturonic acid), sodium polygalacturonate and calcium polygalacturonate

Vacuum ultraviolet circular dichroism spectra are reported for poly(galacturonic acid) solution and film, sodium polygalacturonate solution and film, and calcium polygalacturonate gel. In addition to the positive c.d. band near 208 nm previously observed, we find a pair of higher energy bands at 170 180 nm (negative) and 145 nm (positive). The low energy band, assigned to an $\text{n-π}{}^1$ carboxyl transition, is blue-shifted upon gelation or film formation.     

Differentiation between transmembrane helices and peripheral helices by the deconvolution of circular dichroism spectra of membrane proteins.

The interpretation of the circular dichroism (CD) spectra of proteins to date requires additional secondary structural information of the proteins to be analyzed, such as X-ray or NMR data. Therefore, these methods are inappropriate for a CD database whose secondary structures are unknown, as in the case of the membrane proteins. The convex constraint analysis algorithm (Perczel, A., Hollósi, M., Tusnády, G., & Fasman, G. D., 1991, Protein Eng. 4, 669-679), on the other hand, operates only on a collection of spectral data to extract the common spectral components with their spectral weights. The linear combinations of these derived "pure" CD curves can reconstruct the original data set with great accuracy. For a membrane protein data set, the five-component spectra so obtained from the deconvolution consisted of two different types of alpha helices (the alpha helix in the soluble domain and the alpha T helix, for the transmembrane alpha helix), a beta-pleated sheet, a class C-like spectrum related to beta turns, and a spectrum correlated with the unordered conformation. The deconvoluted CD spectrum for the alpha T helix was characterized by a positive red-shifted band in the range 195-200 nm (+95,000 deg cm2 dmol-1), with the intensity of the negative band at 208 nm being slightly less negative than that of the 222-nm band (-50,000 and -60,000 deg cm2 dmol-1, respectively) in comparison with the regular alpha helix, with a positive band at 190 nm and two negative bands at 208 and 222 nm with magnitudes of +70,000, -30,000, and -30,000 deg cm2 dmol-1, respectively.     

Designed protein mimics of the Ebola virus glycoprotein GP2 α-helical bundle: stability and pH effects

Ebola virus (EboV) belongs to the Filoviridae family of viruses that causes severe and fatal hemhorragic fever. Infection by EboV involves fusion between the virus and host cell membranes mediated by the envelope glycoprotein GP2 of the virus. Similar to the envelope glycoproteins of other viruses, the central feature of the GP2 ectodomain postfusion structure is a six-helix bundle formed by the protein's N- and C-heptad repeat regions (NHR and CHR, respectively). Folding of this six-helix bundle provides the energetic driving force for membrane fusion; in other viruses, designed agents that disrupt formation of the six-helix bundle act as potent fusion inhibitors. To interrogate determinants of EboV GP2-mediated membrane fusion, we designed model proteins that consist of the NHR and CHR segments linked by short protein linkers. Circular dichroism and gel filtration studies indicate that these proteins adopt stable α-helical folds consistent with design. Thermal denaturation indicated that the GP2 six-helix bundle is highly stable at pH 5.3 (melting temperature, T(m) , of 86.8 ± 2.0°C and van't Hoff enthalpy, ΔH(vH) , of -28.2 ± 1.0 kcal/mol) and comparable in stability to other viral membrane fusion six-helix bundles. We found that the stability of our designed α-helical bundle proteins was dependent on buffering conditions with increasing stability at lower pH. Small pH differences (5.3-6.1) had dramatic effects (ΔT(m) = 37°C) suggesting a mechanism for conformational control that is dependent on environmental pH. These results suggest a role for low pH in stabilizing six-helix bundle formation during the process of GP2-mediated viral membrane fusion.     

Conformation and activity ofPhaseolus coccineus var. rubronanus lectin

The conformation of native and denaturedPhaseolus coccineus var. rubronanus lectin was studied by circular dichroism (CD) and correlated to the hemagglutinating activity. The far-UV CD spectrum at 25°C showed a broad, negative band around 223 nm and a positive one at 196 nm. CD data analysis of the lectin indicated a -sheet-rich protein. At high temperatures, the spectrum was blue-shifted with increasing magnitude; these changes correlated well with the loss of the activity. The conformation of lectin betweenpH 2 and 10 remained essentially unchanged. AtpH 13 the CD spectrum resembled that of unordered form with a negative band near 200 nm and the activity was completely lost. The denatured lectin in 6 M guanidine hydrochloride would be renatured upon diluting the denaturant to 0.75 M; the changes in CD spectrum again correlated well with the loss of the activity. The effect of sodium dodecyl sulfate on the lectin was drastic; it sharply increased thea-helix at the expense of the -sheet and reduced the activity; the changes reached a plateau above 20 mM surfactant.     

Chiroptical properties of lecithin reverse micelles and organogels

The ultraviolet absorbance and circular dichroism (CD) spectra of lecithin reverse micelles and gels were investigated in order to establish whether the formation of these noncovalent macromolecular aggregates, which was induced by the addition of water to solutions of lecithin in organic solvents, was accompanied by specific spectroscopic changes. Systems containing the synthetic short-chain lecithins, 1,2-hexanoyl-, 1,2-diheptanoyl-, 1,2-dioctanoyl-, and 1,2-dinonaoyl-sn-glycero-3-phosphatidylcholines were used as models for the long-chain lecithins, soybean phosphatidylcholine and palmitoyl-oleoyl-phosphatidylcholine. All the molecules studied had asymmetric centres, formed reverse micelles under appropriate conditions, and, while both the long-chain lecithins also formed gels, none of the short-chain molecules did. As well as having CD spectra that were simpler to interpret, spectroscopic observations on solutions of the short-chain lecithins could be carried out over a large water content range. The ester chromophore of these compounds was shown to be highly sensitive to variation in both the solvent environment and the temperature, and components of both direct solvent effects and conformational change upon the addition of water were detected in the spectra. The spectra of the longer chain lecithins were complicated by the presence of double bonds although, here again, it was found that significant changes occurred as the water content increased, as monitored by the ester chromophore. However, no specific effect that could be ascribed to gelation alone was detected. The overall picture that emerged was that the ester chromophore of anhydrous micelles gave rise to a specific negative band in the CD spectrum (λ_max ≈ 210 nm) whereas a positive CD signal (λ_max ≈ 233 nm) was associated with the same chromophore in filled (i.e., hydrated) micelles. The two signals correspond to two different conformational states of the lecithin molecule, the hydrated state being not only more conformationally restricted but also providing a less polar environment for the ester groups, while the addition of water to the system shifts the conformational equilibrium. These observations have been interpreted as showing that only a limited range of lecithin conformation is compatible with the formation of the micellar structure and that it is this constraint, together with those introduced by the overall geometry of the aggregated state, that gives rise to the changes observed in the CD spectrum.     

Bacteriorhodopsin vesicles. An outline of the requirements for light-dependent H+ pumping

A systematic study was performed to determine under which conditions bacteriorhodopsin can be applied as an energy generator in reconstituted systems. It is concluded that reconstitution of an active light-driven proton pump is possible over a wide range of conditions.High extents (per bacteriorhodopsin molecule) of proton uptake by reconstituted vesicles are found at a high lipid to protein ratio, after long sonication and at high pH. No active proton pump is obtained if reconstitution is attempted at high pH with neutral phospholipids or at low ionic strength with negatively charged lipids. Attention was also paid to the requirement of a crystalline array for active pumping; most likely, monomeric bacteriorhodopsin molecules can effectively pump protons.