同步辐射圆二色谱及其在糖生物学及生物分子中的应用

同步辐射圆二色谱与普通圆二色谱相比,特点在于向真空紫外波段（〈200nm）拓展,以及同步辐射所提供的高强度紫外和真空紫外光源。糖的圆二色谱结构主要在200nm以下。蛋白质和核酸在200nm以下的真空紫外范围,也具有丰富的光谱结构。因此向真空紫外拓展,伴随新的电子跃迁,对应新的光谱结构,包含更丰富的结构信息,确定的结构种类就越多和越精确。同步辐射高强度的真空紫外光源,是获得高质量真空紫外圆二色谱数据的保证,为糖及糖蛋白、蛋白质和核酸研究提供了溶液中结构探测新的实验方法。综述同步辐射圆二色谱特点及其在结构生物学中的应用,以及新发展的蛋白质圆二色谱数据库（PCDDB）。介绍已对外开放的北京同步辐射实验室同步辐射圆二色谱探测,及其在蛋白质、糖和核酸研究中的应用,以及基于微流控混合芯片的亚毫秒动态探测发展。     

圆二色光谱在蛋白质结构研究中的应用

近几年来,圆二色光谱在蛋白质结构研究中的应用越来越广泛。通过对远紫外圆二色光谱的测量,可以推导出稀溶液中蛋白质的二级结构,进而分析和辨别蛋白质的三级结构类型;通过对近紫外圆二色光谱的测量和分析,可以推断蛋白质分子中芳香氨基酸残基和二硫键的微环境变化,研究介质与蛋白质结构间的关系;通过测定实验参数和环境条件变化时的圆二色光谱,可以研究蛋白质构像变化过程中的热力学和动力学特性。     

用碱水解的方法测定蛋白质的消光系数

在蛋白质结构与功能的研究中,有时蛋白质溶液的浓度是一个重要的参数.紫外吸收法是测定蛋白质溶液浓度最为常用的方法,而已知蛋白质的消光系数是用紫外吸收法准确测定蛋白质溶液浓度的前提条件.在0.1 mol/L NaOH溶液中,蛋白质发生碱性水解,因而蛋白质溶液可以看作是色氨酸和酪氨酸的二元体系.以此为依据,给出了用碱水解的方法测定蛋白质消光系数的方法.这一方法操作步骤简便易行,蛋白质消光系数的计算公式简单明了.用这一碱水解的方法分别测定了几种氨基酸组成不同的蛋白质的消光系数,与文献数据对照,得到了令人满意的结果,测定误差均小于±5％.     

蛋白质溶液可逆热变性及其与肽链构象关系的研究

用微量扫描量热技术及远紫外圆二色谱研究了蛋白质水溶液的浓度和ｐＨ对蛋白质热变性可逆性的影响及其与在热变性时肽链构象的关系。结果表明,当蛋白质溶液的浓度为０．０４％、ｐＨ为３时可实现完全可逆的热变性,然而蛋白质溶液宏观上的热变性并不意味着微观上蛋白质分子肽链的完全伸展。     

RGD-葡激酶的凝胶过滤层析法复性及其纯化

构建的溶栓和抗栓双重功能的RGD-葡激酶突变体(RGD-Sak)在大肠杆菌中高表达,目的蛋白质以包涵体形式存在。为获得有活性的蛋白质,需要对包涵体进行变复性。利用凝胶层析方法对包涵体中RGD-Sak进行复性,并与稀释复性法进行比较,发现凝胶柱复性方法具有操作周期短、简便、成本低而高效等优点。复性后蛋白质用Q-Sepharose FF离子交换进一步纯化,纯度达95%,酪蛋白凝胶板活性测定表明两种复性法得到的蛋白质比活性相当。圆二色谱测定显示两种复性法得到的蛋白质的二级结构成份和谱形一致,说明在两种复性过程中完成了RGD-Sak分子的正确折叠。     

磷酸丙糖异构酶的折叠及稳定性研究

从鸡胸肌中纯化出磷酸丙糖异构酶(triosephosphateisomerase,TIM),通过蛋白质内源荧光,圆二色性,紫外吸收二阶导数光谱等多种研究溶液构象的方法,对TIM被盐酸胍和热变性过程进行了详细的研究.结果表明,用不同测量方法得到TIM的变性过程均高度协同,没有观察到折叠中间态,应用单分子二态去折叠模型计算了TIM去折叠的热力学参数.通过圆二色光谱在222nm处的变化监测的TIM热变性过程也是高度协同的二态过程,天然态TIM的表观Tm为64.6℃.在低浓度盐酸胍存在下,TIM的热稳定性降低.讨论了二体蛋白质的可能去折叠机制,证明在使用的实验条件下磷酸丙糖异构酶去折叠过程中二级结构与三级结构的变化是同时发生的,其去折叠遵循观察不到二体解离的表观二态过程.     

体积排阻液相色谱法质粒的含量测定

首次以体积排阻液相色谱法进行质粒提取液浓度的测定研究,通过纯质粒溶液在260 nm处的紫外吸峰面积与质粒浓度之间数据的线性最小二乘拟合,得到了反映质粒浓度和紫外吸收峰峰面积之间关系的标准曲线:Y=2×10~(-5) X,通过验证实验,确定了质粒提取液中不同组分,如核糖核酸,蛋白质等在色谱图中的出峰位置.结合标准曲线测定了自制的质粒提取液的质粒浓度为0.32 mg/mL.该方法方便,快捷,准确.     

牛胰多肽（BPP）二级结构的红外光谱和圆二色谱分析

牛胰多肽（ｂｏｖｉｎｅｐａｎｃｒｅａｔｉｃｐｏｌｙｐｅｐｔｉｄｅ,ＢＰＰ）是胰脏分泌的一种含有３６个氨基酸的多肽［１］,ＢＰＰ能预防和治疗由胆酸盐诱发的大鼠急性胰腺炎,具有细胞保护作用。本文用傅里叶变换红外光谱（ＦＴ－ＩＲ）和圆二色谱（ＣＤ）,对ＢＰＰ在水溶液中的二级结构进行了研究。两种方法的分析结果互相补充,进一步确定了ＢＰＰ在溶液状态的二级结构。本研究为进一步探讨ＢＰＰ抑制膜融合的机理打下了基础。     

大肠杆菌冷休克蛋白CspC的分离纯化及部分性质测定

经Sepharose Q Fast Flow阴离子交换层析和Superdex 30凝胶过滤层析,从大肠杆菌(Escherichia coli)细胞内分离纯化了一种小分子蛋白质,SDS-聚丙烯酰胺凝胶电泳(SDS-PAGE)纯度鉴定为单一条带,经质谱分析、N端测序、同源序列比较,确定该蛋白质为大肠杆菌冷休克蛋白CspC.在此基础上,用圆二色光谱测定了其二级结构含量,初步探索了其热稳定性及与单链DNA结合后的构象变化.     

牛胰多肽（BPP）二级结构的红外光谱和圆二色谱分析

牛胰多肽（ｂｏｖｉｎｅ ｐａｎｃｒｅａｔｉｃ ｐｏｌｙｐｅｐｔｉｄｅ，ＢＰＰ）是胰脏分泌的一种含有３６个氨基酸的多肽「１」，ＢＰＰ能预防和治疗由胆酸盐诱发的大鼠急性胰腺炎，具有细胞保护作用。本文用傅里叶变换红外光谱（ＦＴ－ＩＲ）和圆二色谱（ＣＤ），对ＢＰＰ在水溶液中的二级结构进行了研究，两种方法的分析结果互相补充，进一步确定了ＢＰＰ在溶液状态的二级结构，本研究为进一步探讨ＢＰＰ抑制膜融合的机理打下     

Development of vacuum-ultraviolet circular dichroism measurement system using a polarizing undulator

We have developed an improved circular dichroism (CD) and linear dichroism (LD) simultaneous measurement system for the vacuum ultraviolet (VUV) region by polarization modulation techniques using a four-period Onuki-type crossed undulator as a polarized light source. The system has been constructed at the VUV beamline BL-5 in the electron storage ring TERAS, at AIST. Our improvements, in particular the adoption of an optical chopper as the detection method of incident light, have resulted in a flat baseline and a consequent simplification of the Mueller matrix calculation for our optical system. Based on the Mueller matrix calculation, we have successfully measured real VUV-CD and LD spectra of leucine films for wavelengths down to 160 nm with absolute optical constants. The obtained spectra show good consistency with spectra measured by conventional methods.     

Circular dichroism user facility at the National Synchrotron Light Source: estimation of protein secondary structure.

The ultraviolet circular dichroism of a protein can be used to estimate the net fraction of its amino acids in different classes of secondary structure. Recent advances in the accuracy of such calculations have resulted from improved computational techniques, as well as extension of the spectral region analyzed to wavelengths less than 180 nm, a wavelength range beyond the limit of most laboratory-based circular dichroism spectrometers. We describe a spectrometer that uses UV radiation from the National Synchrotron Light Source at the Brookhaven National Laboratory to record circular dichroism spectra of proteins (and other biologically important molecules) in aqueous solution over the optimum wavelength range required for calculation of secondary structures. This instrument is available for use by scientists from academic, commercial and research institutions.     

Origin of the anomalous circular dichroism spectra of many apomyoglobin mutants

Several authors have reported that many sperm whale apomyoglobin mutants show anomalous circular dichroism spectra. These mutants have a low molar ellipticity compared to the wild-type protein but in several cases have the same stability of unfolding. A model in which native apomyoglobin is not folded in the same manner as that in other proteins and in which mutants show progressive reductions in their degree of folding has been suggested to explain this phenomenon. However, nuclear magnetic resonance of the native apomyoglobin conformation has shown that this state is folded and compact, raising the possibility that the anomalous circular dichroism spectra could have another explanation. We studied several mutants with anomalous circular dichroism spectra and found that these proteins were all contaminated with nucleic acid that contributed to the ultraviolet absorption and caused uncertainty in the determination of protein concentration. The resulting overestimation of the concentration of apomyoglobin explains the phenomenon of anomalous circular dichroism spectra. We describe a procedure to remove the contaminant nucleic acid which yields accurate protein concentration measurements and provides the normal circular dichroism spectra. Our findings support a well-structured native conformation for apomyoglobin and may also be of the interest to scientists working with the purification of recombinant proteins.     

Circular dichroism analyses of membrane proteins: an examination of differential light scattering and absorption flattening effects in large membrane vesicles and membrane sheets

The circular dichroism spectra of membrane suspensions are distorted by differential light scattering and absorption flattening effects, which arise as a consequence of the large size of the membrane particles relative to the wavelength of light and the high concentration of proteins in the membranes. In this paper, the consequences of these phenomena on the protein spectra of large membrane particles are discussed, and methods for eliminating them are examined. The distortions due to differential light scattering are relatively small in membrane systems, and can be compensated for by use of a large detector acceptance angle geometry. Several methods for correcting for differential flattening, which introduces a substantial distortion, have been evaluated, and a new method, the flattening quotient approach, which produces by far the best results, is described. Since the secondary structures calculated from circular dichroism spectra are highly dependent on accurate spectral shape and magnitude, this method for correcting the spectra may find general application in circular dichroism studies of membrane proteins.     

Estimation of the number of alpha-helical and beta-strand segments in proteins using circular dichroism spectroscopy

A simple approach to estimate the number of alpha-helical and beta-strand segments from protein circular dichroism spectra is described. The alpha-helix and beta-sheet conformations in globular protein structures, assigned by DSSP and STRIDE algorithms, were divided into regular and distorted fractions by considering a certain number of terminal residues in a given alpha-helix or beta-strand segment to be distorted. The resulting secondary structure fractions for 29 reference proteins were used in the analyses of circular dichroism spectra by the SELCON method. From the performance indices of the analyses, we determined that, on an average, four residues per alpha-helix and two residues per beta-strand may be considered distorted in proteins. The number of alpha-helical and beta-strand segments and their average length in a given protein were estimated from the fraction of distorted alpha-helix and beta-strand conformations determined from the analysis of circular dichroism spectra. The statistical test for the reference protein set shows the high reliability of such a classification of protein secondary structure. The method was used to analyze the circular dichroism spectra of four additional proteins and the predicted structural characteristics agree with the crystal structure data.     

Secondary-structure analysis of proteins by vacuum-ultraviolet circular dichroism spectroscopy

The vacuum ultraviolet circular dichroism (VUVCD) spectra of 15 globular proteins (myoglobin, hemoglobin, human serum albumin, cytochrome c, peroxidase, alpha-lactalbumin, lysozyme, ovalbumin, ribonuclease A, beta-lactoglobulin, pepsin, trypsinogen, alpha-chymotrypsinogen, soybean trypsin inhibitor, and concanavalin A) were measured in aqueous solutions at 25 degrees C in the wavelength region from 260 to 160 nm under a high vacuum, using a synchrotron-radiation VUVCD spectrophotometer. The VUVCD spectra below 190 nm revealed some characteristic bands corresponding to different secondary structures. The contents of alpha-helices, beta-strands, turns, and unordered structures were estimated using the SELCON3 program with VUVCD spectra data on the 15 proteins. Prediction of the secondary-structure contents was greatly improved by extending the circular dichroism spectra to 165 nm. The numbers of alpha-helix and beta-strand segments calculated from the distorted alpha-helix and beta-strand contents did not differ greatly from those obtained from X-ray crystal structures. These results demonstrate that synchrotron-radiation VUVCD spectroscopy is a powerful tool for analyzing the secondary structures of proteins.     

Systematic comparison of statistical analyses of electronic and vibrational circular dichroism for secondary structure prediction of selected proteins

The electronic (ultraviolet) circular dichroism (UVCD) and vibrational circular dichroism (VCD) of 20 proteins are systematically compared as to their relationship to the secondary structures of these proteins. The UVCD spectra are statistically treated by use of the same factor analysis methods used previously for VCD. The UVCD spectra can be reproduced as linear combinations of five subspectra. The first subspectrum reflected the expected alpha-helical UVCD shape, particularly at longer wavelengths, while the higher order ones had less obvious similarity to standard bandshapes. Cluster analysis on the UVCD factor analysis coefficients reflected the clustering on the basis of the fractional secondary structure parameters (from X-ray) but was less clear than VCD. Qualitative complementarity of protein VCD and UVCD spectra was demonstrated by combined cluster analysis of their respective factor analysis coefficients. Quantitative relationships between spectral coefficients and fractional secondary structure were determined by multiple regression analyses using only statistically important coefficients. These resulted in an ability to reproduce four of the structural parameters with errors for individual proteins comparable to the VCD result. In UVCD, the standard deviations of the regression fit for beta-sheet were worse and for the undefined part of the structure were better than in VCD. Parallel analyses using the partial least-squares method showed UVCD in that case to have more error than VCD in reproducing the training set structural parameters. Comparison of the regression and partial least-squares methods illustrated limitations of total back-transformation of the UVCD spectra into structural parameters.     

Contribution of side-chain chromophores to the optical activity of proteins: Model compound studies. IV. The indole chromophore of yohimbinic acid.

The optical properties of the indole chromophore of the indole alkaloid yohimbinic acid have been investigated as a function of molecular conformation. Theoretical rotatory strengths have been calculated and compared with experimental circular dichroism spectra. Optical data that may be suitable for calculating the chiroptical properties of the near ultraviolet electronic transitions of the indole chromophores, which occur in tryptophan residues of proteins, have been developed. The far ultraviolet transitions of yohimbinic acid have also been investigated.     

Compact optical cell system for vacuum ultraviolet absorption and circular dichroism spectroscopy and its application to aqueous solution sample

We have designed a compact optical cell for studying the absorption and circular dichroism (CD) of a solution sample in the vacuum ultraviolet (VUV) region using a temperature control unit. The cell size was 34 mm in diameter and 14 mm in length. Such compactness was obtained by coating the VUV scintillator onto the outside of the back window. Because this scintillator converts the transmitted VUV light to visible light, the outside of this cell is operated under atmospheric pressure. The temperature of the sample solution was maintained in the range of 5 degrees C to 80 degrees C using a temperature control unit with a Peltier thermoelectric element. Changes in the sample temperature were observed by monitoring the absorption intensity of water. Through the study of VUV-CD spectra of ammonium camphor-10-sulfonate aqueous solutions and the transmitted spectrum of an empty cell, it was concluded that this cell unit has sufficient performance for use in VUV spectroscopy.     

Circular dichroism of collagen, gelatin, and poly(proline) II in the vacuum ultraviolet.

Circular dichroism spectra for acid-soluble calfskin collagen, gelatin, and poly(proline) II in solution have been extended into the vacuum ultraviolet region. The extended spectrum of gelatin reveals that the circular dichroism of this unordered polymer is more closely related to the spectrum of charged polypeptides than might be evident from near ultraviolet work. A short-wavelength band is found at about 172 nm, which corresponds in position, magnitude, and sign to a band recorded earlier for poly(L -glutamic acid) at pH 8.0. This band is observed in a helical structure for the first time in the vacuum ultraviolet circular dichroism and absorption spectra of poly(proline) II. Both circular dichroism and absorption spectra point to the assignement of this band as the nσ*. Neither the nσ* nor the expected positive lobe of the ππ* helix band is observed in the extended circular dichroism spectrum of collagen. We postulate that these two bands cancel here in analogy to the case of α-helical poly(L -glutamic acid).