An improved loopless mounting method for cryocrystallography

Based on a recent loopless mounting method, a simplified loopless and bufferless crystal mounting method is developed for macromolecular crystallography. This simplified crystal mounting system is composed of the following components: a home-made glass capillary, a brass seat for holding the glass capillary, a flow regulator, and a vacuum pump for evacuation. Compared with the currently prevalent loop mounting method, this simplified method has almost the same mounting procedure and thus is compatible with the current automated crystal mounting system. The advantages of this method include higher signal-to-noise ratio, more accurate measurement, more rapid flash cooling, less x-ray absorption and thus less radiation damage to the crystal. This method can be extended to the flash-freeing of a crystal without or with soaking it in a lower concentration of cryoprotectant, thus it may be the best option for data collection in the absence of suitable cryoprotectant. Therefore, it is suggested that this mounting method should be further improved and extensively applied to cryocrystallographic experiments.     

蛋白质空间结构的实验技术和理论方法

文章主要介绍几种蛋白质空间结构的实验测定方法，在现代生物学研究中，最常用的方法包括X射线晶体学、二维核磁共振（2D-NMR）和低温冷冻电镜，近几年发展起来的单分子技术在生物大分子动态结构的研究中应用越来越多，这些方法都有它们特定的时间和空间分辨率，所测定的结构及其动力学受环境热运动涨落的影响也非常不同，文章对这些问题作了较详细的分析，在蛋白质结构的理论方法方面，介绍了一个新的折叠理论及其与现有折叠模型的关系．讨论了模拟计算在研究蛋白质构象变化和动力学方面的应用，同时强调了分子动力学和蒙特卡罗方法．指出粗粒化模型是研究的热点之一，对生物学中经常遇到的多长度多时问尺度问题提供了一个可行的解决方案。     

The balance of flexibility and rigidity in the active site residues of hen egg white lysozyme

The crystallographic temperature factors(B factor) of individual atoms contain important information about the thermal motion of the atoms in a macromolecule.Previously the theory of flexibility of active site has been established based on the observation that the enzyme activity is sensitive to low concentration denaturing agents.It has been found that the loss of enzyme activity occurs well before the disruption of the three-dimensional structural scaffold of the enzyme.To test the theory of conformational flexibility of enzyme active site,crystal structures were perturbed by soaking in low concentration guanidine hydrochloride solutions.It was found that many lysozyme crystals tested could still diffract until the concentration of guanidine hydrochloride reached 3 M.It was also found that the B factors averaged over individually collected data sets were more accurate.Thus it suggested that accurate measurement of crystal temperature factors could be achieved for medium-high or even medium resolution crystals by averaging over multiple data sets.Furthermore,we found that the correctly predicted active sites included not only the more flexible residues,but also some more rigid residues.Both the flexible and the rigid residues in the active site played an important role in forming the active site residue network,covering the majority of the substrate binding residues.Therefore,this experimental prediction method may be useful for characterizing the binding site and the function of a protein,such as drug targeting.     

Phasing of lysozyme using one－wavelength anomalous scattering of sulphur atoms through the combination of direct methods and density modification

A new method of combining one-wavelength anomalous scattering (OAS) phasing and density modification has been described, in which the improved phases from density modification axe re-introduced into OAS phasing. In this way, the phases could be improved iteratively until convergence. The OAS phasing method is based on the previously established sign-probability formula, which breaks the phase ambiguity in the OAS phasing. The implementation of this method has been available in CCP4 as OASIS. This method, although based on direct-methods, could also incorporate known phases and figures of merit into its sign-probability formula. In the implementation of OASIS, the known phases axe from the positions of the anomalous scatters. In the current method, the known phases are from the density modification. The current method was tested on phasing a lysozyme crystal using anomalous scattering of sulphur atoms with diffraction data collected on an in-house x-ray source. The resulting map was well connected for the backbone atoms and clearly traceable, with an average map correlation coefficient of 0.6622 for the backbone atoms.     

封面说明

北京正负电子对撞机（BEPC）于1988建成后，成为τ-粲能区国际领先的对撞机，在1.89GeV的亮度为1．2×10^31cm^-2s^-1，取得了诸如τ轻子质量精确测量、R值测量和新粒子X（1835）的发现等举世瞩目的物理成果。为了争夺在τ-粲能区的物理成果，美国康奈尔大学于2000年提出了CESRc／CLEOc的计划，把束流能量从原来的5．6Gev降低到1．55-2．5GeV，在1．89GeV时的亮度达到6×10^-31cm^-2s^-1，超过了BEPC。     

Improvement of a new rotation function for molecular replacement by designing new scoring functions and dynamic correlation coefficient

A previously published new rotation function has been improved by using a dynamic correlation coefficient as well as two new scoring functions of relative entropy and mean-square-residues to make the rotation function more robust and independent of a specific set of weights for scoring and ranking. The previously described new rotation function calculates the rotation function of molecular replacement by matching the search model directly with the Patterson vector map. The signal-to-noise ratio for the correct match was increased by averaging all the matching peaks. Several matching scores were employed to evaluate the goodness of matching. These matching scores were then combined into a single total score by optimizing a set of weights using the linear regression method. It was found that there exists an optimal set of weights that can be applied to the global rotation search and the correct solution can be ranked in the top 100 or less. However, this set of optimal weights in general is dependent on the search models and the crystal structures with different space groups and cell parameters. In this work, we try to solve this problem by designing a dynamic correlation coefficient. It is shown that the dynamic correlation coefficient works for a variety of space groups and cell parameters in the global search of rotation function. We also introduce two new matching scores: relative entropy and mean-square-residues. Last but not least, we discussed a valid method for the optimization of the adjustable parameters for matching vectors.     

新型硒二唑衍生物荧光分子的合成及光电性能研究

为了增大前期工作开发中Hg²⁺荧光探针分子TBBA在近红外区间的吸收范围,降低分子的生物组织损耗,本研究在保持三苯胺为给电子单元不变的情况下,将苯并噻二唑分子换成吸电子能力更强的苯并硒二唑和吡啶硒二唑单元,并通过Suzuki偶联反应合成了两种新型荧光分子TBSeBA和TPSeBA。经过核磁共振氢谱、碳谱和ESI质谱确认了两种分子的结构,在DMSO溶液中TBSeBA和TPSeBA的吸收峰分别位于465.00 nm和520.00 nm。 TBSeBA的HOMO和LUMO能级分别为-5.00 eV和-2.82 eV; TPSeBA的HOMO和LUMO能级分别为-5.17 eV和-2.77 eV。硒原子的引入为荧光分子的光学性质和电化学性质调控提供了一种有效策略。     

蛋白质晶体结构刚体优化的新方法

将多元函数的变尺度法与两电子密度图的相关系数相结合,得到一种能够对蛋白质晶体结构进行刚体优化的新方法.初步测试结果表明,该方法能够明显地改善待测晶体的初始模型在晶胞中的取向和位置.而与最大似然方法相比,该方法可能更适用于搜索空间中存在大量局域极值点的情况. 关键词： 蛋白质晶体结构 刚体优化 多元函数的变尺度方法 电子密度图的相关系数     

Protein structural codes and nucleation sites for protein folding

One of the long-standing controversial arguments in protein folding is Levinthal's paradox. We have recently proposed a new nucleation hypothesis and shown that the nucleation residues are the most conserved sequences in protein. To avoid the complicated effect of tertiary interactions, we limit our search for structural codes to the nucleation residues. Starting with the hypotheses of secondary structure nucleation and conservation of residues important for folding, we have analysed 762 folds classified as unique by SCOP. Segments of 17 residues around the top 20% conserved amino acids are analysed, resulting in approximately 100 clusters each for the main secondary structure classes of helix, sheet and coil. Helical clusters have the longest correlation range, coils the shortest (four residues). Strong specific sequence-structure correlation is observed for coil but not for helix and sheet, suggesting a mapping relationship between the sequence and the structure for coil. We propose that the central sequences in these clusters form `structural codes', a useful basis set for identifying nucleation sites, protein fragments stable in isolation, and secondary structural patterns in proteins (particularly turns and loops).