基于氨基酸位置特异性的蛋白质Loop区结构预测改进方法

蛋白质loop区的结构预测是理解蛋白质功能的重要一环,而长loop区的结构预测至今还是生物信息学中的难题.目前己经出现了多种loop结构的算法,其中LEAP是预测精度最高的算法之一,但它在长loop区初始主链构象采样上仍有较大的改进余地.本文中我们将蛋白质二级结构预测算法SPINE X与LEAP算法结合起来,构建了新的主链扭转角分布图(拉氏图),在主链初始构象采样中引入氨基酸在蛋白序列中的位置特异性信息,使得初始构象的采样更具针对性,对取自CASP10单链蛋白的loop测试集的分析表明,对长度为10,11,12个氨基酸的长loop区,改进后算法都比原始LEAP算法的预测精度有显著提升.这种引入氨基酸位置特异性从而提高预测精度的思路有望进一步推广至loop结构预测的其他算法.     

EPR和NMR自旋标记法研究部分折叠蛋白质构象

部分折叠蛋白质的特征是在溶液中有部分二级结构,但是三级结构接触比较松散或者较少,其意义可能是蛋白质折叠过程的中间态,或者有重要的生理功能. 利用EPR和NMR波谱可以表征其构象特征,从而构建其二级结构、三级结构、四级结构以及构象变化的结构模型. 利用分子生物学的点突变技术可以在蛋白质主链上插入1个或2个半胱氨酸残基,然后把顺磁自旋标记物特异地共价结合在半胱氨酸的侧链巯基上来制备自旋标记样品. 位点特异性自旋标记电子顺磁共振（SDSL-EPR）波谱是通过测定2个自旋标记间的偶极相互作用,从而推测2个硝基氧自由基间的距离. 核磁共振（NMR）波谱则是通过测定单个自旋标记中心对周围原子核驰豫效应增强（PRE）的效应,推测出顺磁中心相对于周围原子核的距离. 连续波EPR和NMR自旋标记方法可以测定2.5 nm左右的偶极相互作用距离,属于长程的距离约束,这对于确定部分折叠蛋白质的构象至关重要. 该文将就蛋白质部分折叠态研究的生物学意义,自旋标记方法以及EPR和NMR方法研究其构象特征举例描述.     

蛋白质折叠的非格子模型

用粒子群算法对蛋白质的简化模型进行研究,体系中各原子间的相互作用由一物理势表示.通过全局优化体系的势函数得到蛋白质的结构数据,与实验测得的结构数据之间的均方根偏差RMSD为6.12(A).记录了能量最小值及回转半径随程序运行步骤的变化以及RMSD值与最低能量值的分布关系,这些结果反映了蛋白质折叠的一些基本特征.     

臭氧对胎牛血清氧化损伤的表面增强拉曼光谱

对实验室细胞培养用的国产胎牛血清在臭氧作用前后进行了表面增强拉曼光谱测试,范围200～1 800 cm-1.发现臭氧作用1 h后拉曼谱线强度大大减弱,作用3 h后谱线强度进一步减弱,但减弱的程度明显减慢,说明臭氧氧化作用具有快速的特点.臭氧作用下蛋白质主链的有序构象(α-螺旋,β折叠)明显减少,对β折叠的损伤更为严重,β回折几乎消失.芳香族氨基酸和半胱氨酸侧链在臭氧作用下氧化损伤非常明显.这些特征谱线的变化,反映了臭氧的氧化作用使蛋白质变性,构象变化以及降解.     

蛋白质在弯曲空间内的折叠

蛋白质是一种由氨基酸所组成的特殊高聚物．一般的高聚物在很低的温度下，都会坍缩成一个球形，但蛋白质却不然，它们一般会折叠成一种特定的紧密形状．如果蛋白质不能折叠成该种形状的结构，它将不能完成其指定的功能，同时也会带来疾病．例如某些未曾折叠的蛋白质可以凝聚成一根面条状的长链，这种结构现在已被证明是对应着神经退化的疾病，如Alzheime症．     

表面增强拉曼光谱对于蛋白质二级结构的酰胺III谱带表征

本文利用斜角沉积法制备银纳米棒阵列基底用于蛋白质二级结构的检测,结合酰胺Ⅲ谱带光谱分析,建立了一种基于表面增强拉曼光谱(SERS)蛋白质二级结构的表征方法.用这种方法获得了两种典型蛋白质(溶菌酶和细胞色素C)的SERS信号.通过分析蛋白质骨架酰胺Ⅲ的光谱,研究了浓度对蛋白质折叠状态的影响.结果表明在一定范围内随着浓度的增加,溶菌酶的α-螺旋结构和β-折叠结构成分增加,而细胞色素C的二级结构基本保持不变.     

聚丙烯腈PAN分子链的第一性原理研究

利用RHF方法,选择基组STO3G,对聚丙烯腈PAN分子链CH3(CHCNCH2)9CH2CN的10个单体进行理论研究.在结构优化方面,PAN分子链稳定结构为反式构象.主链C-C平均键长155.6pm,支链C-C平均键长149.7pm,C-N平均键长115.5pm.在电荷分布方面,主链C原子电荷分布呈现出一定的周期性,与C-N键相连的主链C原子电荷量小于相邻的主链C原子的电荷量,两者的电负性有一定的差异.存在这种差异的原因在于支链N原子的存在,支链N原子具有更强的电负性.最后对PAN结构链的振动模式进行分析得出,在对PAN进行预氧化及碳化处理时,先发生的是脱氢反应,随着温度的升高,产生环化,从而使环化与脱氢同时存在.     

表面增强拉曼光谱对于蛋白质二级结构的酰胺Ⅲ谱带表征（英文）

本文利用斜角沉积法制备银纳米棒阵列基底用于蛋白质二级结构的检测,结合酰胺Ⅲ谱带光谱分析,建立了一种基于表面增强拉曼光谱(SERS)蛋白质二级结构的表征方法.用这种方法获得了两种典型蛋白质(溶菌酶和细胞色素C)的SERS信号.通过分析蛋白质骨架酰胺Ⅲ的光谱,研究了浓度对蛋白质折叠状态的影响.结果表明在一定范围内随着浓度的增加,溶菌酶的α-螺旋结构和β-折叠结构成分增加,而细胞色素C的二级结构基本保持不变.     

朗之万方程及其在蛋白质折叠动力学中的应用

研究了朗之万方程的动力学性质,并用它模拟了蛋白质分子的折叠过程.首先在相空间中对朗之万方程做连续映射,发现做布朗运动的粒子在位置坐标上存在明显的概率分布,这表明蛋白质折叠过程中分子空间构型是非遍历的.此外,本文还通过数值模拟得到了去折叠态蛋白质的紧密度指标,并验证了它与实验结果以及其他理论方法的一致性.本文还提出了一种利用重整化方法研究熔球体状态蛋白质的理论模型,并提供了考虑疏水基影响的蛋白质折叠过程的模拟思路. 关键词： 朗之万方程 蛋白质折叠非遍历性 紧密度指标 重整化     

重组人B淋巴细胞刺激因子的激光拉曼光谱

人B淋巴细胞刺激因子(BAFF)是一种由285个氨基酸组成的Ⅱ型跨膜蛋白质,我们测试了重组的人B淋巴细胞刺激因子(r-BAFF)固体粉末和水溶液的拉曼光谱,通过分析酰胺Ⅰ和酰胺Ⅲ的拉曼特征谱带,判断出重组的人B淋巴细胞刺激因子(r-BAFF)固体粉末状态下构象全为β-折叠结构和β-回转结构,而在水溶液中的二级结构主要仍为β-折叠结构和β-回转结构,另外可能有少量的α-螺旋结构。同时对其侧链构象及环境也做了初步分析。     

Hybrid Wavelength and Code Division Multiple Access in Optical Networks

A review of schemes for multiple access in fiber optic networks shows that a hybrid of wavelength and code division multiple access (WCDMA) combines the best features of both. In particular, the hybrid scheme retains the large information carrying capacity of wavelength division multiple access (WDMA) and flexibility of code division multiple access (CDMA). In this paper WDMA, optical CDMA (OCDMA), and WCDMA networks are discussed. In OCDMA networks, concept of incoherent and coherent coding including inverse decoding and matched filter is introduced. The delay performance of both WDMA and WCDMA networks, under the simple suboptimum access protocols based on cyclic search, is computed. It has been shown quantitatively that tuning delay significantly affects the delay performance of both WDMA and WCDMA networks. Futhermore, delay performance of WCDMA networks is always better than the WDMA networks for the same tuning delay, load, and number of users.     

Guided-Wave Two-Dimensional Acousto-Optic Scanner Using Proton-Exchanged Lithium Niobate Waveguide

Two-dimensional scanning of a 0.6328 mum guided-light beam has been realized using noncolinear acousto-optic (AO) coplanar Bragg diffraction together with colinear AO guided-mode to substrate radiation-mode conversion in a Z-cut Xpropagation LiNbO3 proton-exchanged (PE) waveguide. The two surface acoustic (SAW) waves utilized are at the center frequencies of 500 and 200 MHz, propagating in the Y and X axes, respectively. Two-dimensional scanning of approximately 720 resolvable light beam spots, namely, 18 40 (horizontal vertical) scanning, has been demonstrated using a light beam of 1.0 mm aperture. The total number of resolvable beam spots can be greatly increased from 720 by simply utilizing SAW transducers of larger bandwidth and a light beam of greater aperture. It should also be possible to significantly increase the diffraction efficiency from 3 % by optimizing the parameters of the PE waveguide and the SAWs.     

Femtosecond Transform-Limited Pulse Generation by Compensating for the Linear Chirp of SPM Spectra in Dispersion Shifted Fibers

A simple technique of pulse compression, based on the linear chirp compensation of self-phase modulation (SPM) spectra in dispersion shifted fibers, is demonstrated. The optimization procedure is carried out, for a short span of a single-mode fiber, using a parabolic law, which describes the behavior of the squared output pulse width versus the pump peak power in the case of Gaussian pulses. The experimental results give a minimum pulse duration of 233 fs, which is in good agreement with the model. Shorter and coherent pulses, down to 90 fs, have been obtained by inserting an interference filter at the optical output.     

Effect ofγ-radiation on the spectral luminescence characteristics of impure cadmium tungstate crystals

Results of a study of the effect of γ-radiation on the spectral luminescence properties of cadmium tungstate crystals doped with silver, bismuth, and molybdenum cations are presented. Spectral characteristics of the nondnnnoped crystals are briefly described. Absorption and photo and X-ray luminescence spectra of the crystals taken before and after exposure to γ-radiation (5.5·10⁴ Gy) are compared. It is found that the spectral characteristics of the crystals doped with silver, bismuth, and molybdenum cations do not change markedly after the exposure. The relation between the type of impurity-induced defects, individual characteristics of the impurity cations, and the character of the effect of γ-radiation on the spectral luminescence properties of impure crystals is analyzed (preliminarily). Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 64, No. 1, pp. 55–60, January–February, 1997.     

Theoretical analysis and simulation of conjugate heights for dual-conjugate AO system in lidar

A multi-conjugate adaptive optics （MCAO） can offer a possibility of widening field of view （FOV） characterized by the isoplanatic angle, and the choose of conjugate height becomes a basic problem for MCAO, which influences the size of iosplanatic angle. Considering the application of lidar, the isoplanatic angle＇s expressions of two deformable mirrors （DMs） MCAO for uplink and downlink are deduced. The effects of conjugate heights for dual-conjugate AO are thoughtfully discussed, and the isoplanatic angles are further analyzed. The results show that the isopanatic angle varies with the conjugate height and reaches the maximum as the conjugate height is at the optimal altitude. Moreover, the optimal conjugate height changes with the propagation distance.     

Quick single-photon detector with many avalanche photo diodes working on the time division

Due to the limit of response speed of the present single-photon detector, the code rate is still too low to come into practical use for the present quantum key distribution (QKD) system.A new idea is put up to design a quick single-photon detector.This quick single-photon detector is composed of a multi-port optic-fiber splitter and many avalanche photo diodes (APDs).Au of the ports with APDs work on the time division and cooperate with a logic discriminating and deciding unit driven by the clock signal.The operation frequency lies on the number N of ports, and can reach N times of the conventional single-photon detector.The single-photon prompt detection can come true for high repetition-rate pulses.The applying of this detector will largely raise the code rate of the QKD, and boost the commercial use.     

Research on beamforming method for dual-line array with space mismatch between the two line arrays

The performance of port/starboard discrimination of dual-line array will be seriously degraded when the space between the two line arrays of the dual-line array is mismatched. The directivity function of the delay-sum and delay-subtract beamforming is deduced and the port/starboard discrimination of the delay-sum and delay-subtract beamforming is also studied both under the ideal status and the status under which the space between the two line arrays of the dual-line array is mismatched. Analysis results show the delay-subtract beamforming has better performance of port/starboard discrimination. At last, the sea trial results demonstrate the theoretical results.     

Sorting of bending magnets for the SSRF booster

The Shanghai Synchrotron Radiation Facility(SSRF)booster ring,a full energy injector for the storage ring,is deigned to accelerate the electron beam energy from 150MeV to 3.5GeV that demands high extraction efficiency at the extraction energy with low beam loss rate when electrons are ramping.Closed orbit distortion(COD)caused by bending magnet field uniformity errors which affects the machine performance harmfully could be effectively reduced by bending magnet location sorting.Considering the affections of random errors in measurement,both ideal sorting and realistic sorting are studied based on measured bending magnet field uniformity errors and one reasonable combination of bending magnets which can reduce the horizontal COD by a factor of 5is given as the final installation sequence of the booster bending magnets in this paper.     

Retrieval of ultraviolet skylight radiances and O3 slant column densities from balloon-borne limb spectrometer

With a novel light-weight and absolutely calibrated ultraviolet （UV） spectrometer, UV skylight radiances and O3 slant column densities are measured by balloon-borne limb measurements in Xinjiang area, China. UV skylight radiances measured at the height of 31 km are compared with the results from Modtran in the wavelength range from 290 to 420 nm. O3 slant column densities are derived from radiance spectra in the Huggins bands （320 - 335 nm） using differential optical absorption spectroscopy method. And the parameter exhibits a good correlation with the same value simulated by radiative transfer model （Tracy）. The O3 profile simultaneously measured by an O3 sonde is used as input in Tracy calculations. The O3 sonde is launched on the same balloon.