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．     

牛奶蛋白质含量的SSA-SVM高光谱预测模型

牛奶中包含着很多人体需要的营养元素,如脂肪、蛋白质、钙等;对牛奶营养元素进行分析是牛奶安全检测关键的一部分。高光谱技术可以有效地结合图像和光谱数据识别牛奶种营养元素。为了实现对牛奶中蛋白质含量快速、精确的预测,采用竞争性自适应重加权(CARS)算法选取特征波长,并提出一种基于麻雀搜索算法(SSA)优化支持向量机(SVM)实现对牛奶蛋白质含量预测。利用高光谱仪获取牛奶反射光谱(400～1 000 nm)。通过选取归一化(N)、标准化(Standardization)和多元散射校正(MSC)对原始的牛奶数据进行光谱降噪处理提高光谱利用率;利用竞争性自适应重加权算法和连续投影算法(SPA)对经过处理的牛奶光谱数据提取特征波长,求取蛋白质和光谱间的相关系数并进行重要性排序,获取重要的特征波段;最后,通过遗传算法(GA)优化SVM, 粒子群算法(PSO)优化SVM和偏最小二乘法(PLS)算法对牛奶蛋白质进行预测并比较预测结果,为了提高蛋白质预测的精度和模型稳定性,提出利用SSA对SVM的核函数g和惩罚参数c进行优化,以均方根误差(RMSE)作为适应度函数,通过迭代选择最优的回归参数训练模型。牛奶数据预测结果表明最优组合模型为：MSC-CARS-SSA-SVM。模型测试集的决定系数R2为0.999 6,均方根误差RMSE为0.001 1,耗时4.112 1 s。结果表明：使用CARS算法能实现特征波段的提取和冗余信息的剔除,从而提高模型效率,简化了算法的复杂度;SSA算法优化SVM的参数,通过迭代更新麻雀最优位置,可以快速得到全局最优解,与SVM,GA-SVM,PSO-SVM和PLS相比,牛奶蛋白质的预测准确度和模型稳定性都得到了明显提高,满足了对乳品检测的精确度要求,是快速检测牛奶蛋白质的一个可行新方法。为光谱模型的优化及预测模型精度的提高提供参考。     

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     

Self-organization of five species in a cyclic competition game

Cyclic competition game models, particularly the “rock–paper–scissors” model, play important roles in exploring the problem of multi-species coexistence in spatially ecological systems. We propose an extended “rock–paper–scissors” game to model cyclic interactions among five species, and find that two of the five can coexistent when biodiversity disappears, which is different from the “rock–paper–scissors” game. As the number of fingers is five, we named the new model the “fingers” game, where the thumb, forefinger, middle finger, ring finger, and little finger cyclically dominate their subsequent species and are dominated by their former species. We investigate the “fingers” model in two ways: direct simulations and nonlinear partial differential equations. An important finding is that the number of species in a cyclic competition game has an influence on the emergence of biodiversity. To be specific, the “rock–paper–scissors” model is in favor of maintaining biodiversity in comparison with the “fingers” model when the variables (population size, reproduction rate, selection rate, and migration rate) are the same. It is also shown that the mobility and reproduction rate can promote or jeopardize biodiversity.     

Contrastive analysis on tone between Putonghua and Taiwan Mandarin

The differences of the pitch and duration of Chinese syllables between Putonghua （PTH） and Taiwan Mandarin （TM） were studied. The speech materials to be used are not only isolated syllables, but also sentences. The results reveal that： For the isolated syllables, T1 and T2 in TM are influenced by Minnan dialect, therefore their pitch are lower than those in PTH. T3 is fall-rise in PTH, while it is fall in TM. Moreover, the syllable duration sequence for different tone is T3〉T2〉T1〉T4 in PTH, while it is T1〉T2〉T3〉T4 in TM. For the syllables in sentences, T2 is mid-rise in PTH, while it is mid-level in TM. And the T3 is longer than T4 but shorter than T1 or T2 in PTH, while it is the shortest in TM. Furthermore the effects of prosodic phrase boundary on duration for different tones are almost the same in PTH, but the lengthening part of T1 or T2 is longer than that of T3 or T4 in TM.     

Experimental study on downstep in Chinese intonation

Downstep in pitch contour of Chinese Putonghua is examined using subtly designed sentences by controlling tone combinations. The results show both automatic and nonautomatic downstep phenomena exist in Chinese. In non-automatic downstep, low tones compress downwards the pitch range of the following syllables. and the main influence of downstep is on topline. Low tone not only lower the topline behind it, but also raise the high tones before it, the effects are compatible with each other. In automatic downstep, the topline of pitch contour in intonational phrase is presented as a linear downtrend, but it differs among speakers due to the effect of personal stress practice. In comparison with downstep phenomenon in other tone or non-tone languages, the downstep ratio in Chinese is not constant, and the domain of downstep is not limited within the adjacent tones.     

Abelian-Higgs phase of SU(2) QCD and glueball energy

It is shown that SU(2) QCD admits an dual Abelian-Higgs phase, with a Higgs vacuum of a type-Ⅱ superconductor. This is done by using a connection decomposition for the gluon field and the random-direction approximation. Using a bag picture with soft wall, we presented a calculational procedure for the glueball energy based on the recent proof for wall-vortices [Nucl. Phys. B 741(2006)1].     

Signal generation in an isotropic medium in scanning electron acoustic microscope

Based on the research in Ref. [5][Materials Science and Engineering, 1989; A122： 57 63], an improved model of heat source is set up, the different modes of Lamb wave in an isotropic sample generated by a chopped electron beam at frequency f are obtained with integral transform and normal function expansion method, and the output signal of PZT coupled at the back surface of the sample is found out. The generation mechanism of SEAM （Scanning Electron Acoustic Microscopy） signal is discussed. It shows that the SEAM is a near field imaging technique with high spatial resolution and its best lateral spatial resolution is about 2√2α （α is the radius of the focused electron beam）. Some of experimental results of SEAM images are presented in the paper and it shows that the spatial resolution of SEAM is better than 0.5 μm and smaller than the thermal diffusion length of the sample. Therefore the character of near field imaging in SEAM is also proved experimentally.     

High efficiency filtering using two-dimensional photonic crystal coupled cavity structures

Transmission spectra of coupled cavity structures (CCSs) in two-dimensional (2D) photonic crystals (PCs) are investigated using a coupled mode theory, and an optical filter based on CCS is proposed. The performance of the filter is investigated using finite-difference time-domain (FDTD) method, and the results show that within a very short coupling distance of about 3λ, where λ is the wavelength of signal in vacuum, the incident signals with different frequencies are separated into different channels with a contrast ratio of 20 dB. The advantages of this kind of filter are small size and easily tunable operation frequencies.     

Real-time restoration of rotational blurred image using gradient-loading

The key to the restoration of rotational motion blurred image is how to restore the image under a low cost and to correct the irreversibility of the degradation function matrix.Based on the special qualities of degradation function matrix and precise deduction in space-domain, we present a new approach using gradient-loading for restoration of rotational blurred image.By easily adding a gradient operator, the irreversibility of the original matrix is corrected and can be applied for inverse filtering then.Gradientloading is the optimized approach which combines the advantages of both the approaches using constrained least square filtering and traditional diagonal-loading.Compared with the approach using least square filtering, its peak signal-to-noise ratio (PSNR) is improved from 3.18 to 6.46dB, while the computing time is reduced to 1/2-1/3.Experimental results demonstrate the effectiveness, noise-resistibility, robustness, and low complexity of this approach, which make it more suitable for real-time environment.     

All-Optical Logic Device Using Bent Nonlinear Tapered Y-Junction Waveguide Structure

We propose an all-optical logic device made of a bent tapered Y-junction waveguide with a Kerr-type nonlinear interface. It could provide an AND gate, OR gate, and exclusive-OR (XOR) gate. We could obtain different transmission results by adjusting the bending angle. The numerical simulation results show that the device functions as AND, OR, and XOR gates.     

Real-time, continuous-wave terahertz imaging by a pyroelectric camera

Real-time, continuous-wave terahertz (THz) imaging is demonstrated. A 1.89-THz optically-pumped farinfrared laser is used as the illumination source, and a 124 × 124 element room-temperature pyroelectric camera is adopted as the detector. With this setup, THz images through various wrapping materials are shown. The results show that this imaging system has the potential applications in real-time mail and security inspection.