以液体核磁共振波谱分析与帕金森氏病相关的I93M突变对人类泛素碳端水解酶结构的影响（英文）

人类泛素碳端水解酶(UCH-L1)是涉及帕金森氏病并且在神经元高度表达的蛋白.UCH-L1的家族性突变与转译后修饰会引起聚集倾向增加与去泛素活性损失,这二者都可能成为致病因素.作者所在实验室之前的研究指出与帕金森氏病相关的突变I93M显著降低UCH-L1的折叠稳定性并且加速其构型展开动力学.该研究使用液体核磁共振分析方法,包括侧链甲基化学位移,松弛骨干动力学和残余偶极耦合,以进一步阐明I93M突变如何影响UCH-L1的结构和动态.结果显示I93M显著影响突变位点周围的疏水核心侧链构型.然而,这样的结构扰动并不会影响在纳秒时间尺度的快速骨干动力学.透过残余偶极耦合分析显示UCH-L1在水溶液中的结构与之前报道的晶体结构有相当显著的偏离,另外I93M突变也导致超出突变位点的远距离结构扰动.这一系列水溶液结构的分析结果可补充之前已知的晶体学数据,并对UCH-L1在帕金森氏病相关的基因突变影响并提供详细的见解.     

NMR技术在蛋白质-蛋白质相互作用研究中的应用——泛素-蛋白水解酶体通路研究实例介绍

蛋白质-蛋白质相互作用在多种细胞内生理活动中发挥关键性作用,而蛋白质复合物结构信息的获得主要依赖于X-射线衍射技术和核磁共振技术2种主要技术手段的使用. 需要指出的是,虽然大部分蛋白质复合物的结构解析使用了X-射线衍射技术,然而在包括无法获得蛋白质复合物晶体、 蛋白质与蛋白质结合强度较弱以及蛋白质复合物系统具有复杂的动力学行为等几种情况下,核磁共振技术是可用于蛋白质复合物结构测定的唯一手段. 用于蛋白质-蛋白质相互作用研究的NMR技术主要有化学位移扰动分析、分子间NOE的检测、顺磁弛豫增强技术、残余偶极耦合检测技术等几种. 该文将结合这几种技术在泛素-蛋白水解酶体通路领域的应用实例对它们的工作原理以及可提供的信息做出总结介绍.     

先进固体NMR技术研究高分子结构与动力学

随着固体NMR理论和谱仪硬件技术的不断发展,近年来固体NMR技术在高分子多尺度结构与动力学研究领域中正发挥着越来越重要的作用. 多脉冲及高速魔角旋转（MAS）等质子高分辨技术的发展使得高灵敏度的¹H谱可有效地用于高分子化学结构与链间相互作用的检测;基于化学键（J-耦合）相关和通过空间（偶极耦合）相互作用的各种二维异核相关谱NMR新技术,使得复杂高分子的链结构得以严格解析. 基于MAS下同核和异核偶极-偶极相互作用、化学位移各向异性等各向异性相互作用重聚的系列新技术,使得研究者可在采用高分辨¹H或¹³C 检测信号的同时检测准静态下的各向异性相互作用,进而获得与之密切相关的结构和动力学信息. 通过质子偶极滤波技术可有效检测多相聚合物中的界面相与相区尺寸、高分子共混物中的相容性等问题. 在动力学的研究中,通过质子间自旋扩散的有效压制技术和化学位移各向异性的重聚,目前已经可以有效地获取链段上单个化学键的快速局域运动以及链段的超慢分子运动. 上述丰富的多尺度NMR技术可以使研究者在不同空间和时间尺度上对高分子聚合物的微观结构、相分离和动力学行为等进行详细的研究,进而阐明高分子微观结构与宏观性能的关联. 该文以固体NMR中最主要的2类核（¹H和¹³C）的检测技术为主线,简单介绍近年来固体NMR领域的一些最新研究进展及其在高分子结构和动力学研究中的应用.     

细菌反应调节蛋白RR468磷酸化和去磷酸化关键位点的NMR研究

反应调节蛋白是细菌双组分信号转导系统的重要组分,用于传递来自组氨酸激酶的信号并产生适应性反应.在整个信号转导过程中,反应调节蛋白的磷酸化和去磷酸化最终决定了该系统的信号输出和信号转导终止,因此其磷酸化和去磷酸化作用位点是控制其功能的关键要素．我们以来源于Thermotoga maritima中的反应调节蛋白RR468作为研究对象,将其分别位于loop b3-a3和loop b4-a4上的两个关键位点M55和K85进行突变,通过功能实验验证了这两个残基突变会对蛋白磷酸化和去磷酸化产生影响,并且利用液体核磁共振（NMR）手段对两个突变体的结构和动力学性质进行了研究．     

蝎毒素LmKTT-1a 与胰蛋白酶相互作用研究

LmKTT-1a 是最近发现的一个蝎毒素，该多肽分子不仅具有钾离子通道调节剂的功能，还具有胰蛋白酶（Trypsin）抑制剂的活性，是第一个被发现的双功能蝎毒素．虽然前期工作已对LmKTT-1a 的溶液结构和钾离子通道调节剂的功能进行了研究，但未阐明LmKTT-1a 和Trypsin 的作用方式和位点．文中利用液体NMR 的手段，采用化学位移扰动分析的方法，确定了LmKTT-1a 的loop 区域V10~F17 等氨基酸位点可能参与了与Trypsin的相互作用．进一步采用定点突变的方法验证了NMR 实验的结果，并确认了LmKTT-1a与Trypsin 相互作用最关键的氨基酸位点是K14．该研究结果有助于进一步理解LmKTT-1a具有双功能活性的结构基础．     

低场固体NMR研究纳米复合凝胶结构与动力学

纳米复合水凝胶复杂的微观结构和动力学决定了其宏观性能,阐明其结构和动力学的非均匀性对揭示凝胶相变机理、认识其宏观物理和化学性质和设计新型高分子凝胶都具有重要意义.通过合成不同粘土含量的系列聚异丙基丙烯酰胺(PNIPAm)/锂藻土纳米复合水凝胶,运用多种先进的低场固体NMR技术详细研究了凝胶微观结构和动力学的非均匀性.首先建立了分析多组分凝胶体系中刚性和柔性高分子组分相对含量的计算方法,然后在不同粘土含量下,通过测量凝胶FID信号和质子T1定量研究了凝胶中刚性和柔性高分子组分的相对含量;通过偶极滤波双量子NMR实验,研究了体系中与交联密度关联的残余偶极作用参数随黏土含量的变化.结果表明:在纳米复合水凝胶中,随着粘土含量的增加,凝胶中聚合物的刚性相增加,而柔性相下降,当粘土含量达到12%(Wclay/Wwater)时体系中的刚性相含量趋于平衡.多量子实验结果表明,随着粘土含量的增加,纳米复合水凝胶中高分子链的残余偶极作用参数逐渐增大,反映了体系中高分子链的受限运动和二维无机纳米片层形成的物理交联密度增大的趋势.     

紫衫醇C13侧链的微观结构及光谱性质

本工作采用密度泛函B3LYP方法,在6-311+G*水平基组上对紫衫醇C13侧链(用M表示)分子离子基态进行了结构优化、频率、自然键原子轨道计算,得到其微观结构及相关性质,系统分析了体系的几何构型、原子的净电荷布局、前沿分子轨道特征,并对红外光谱特征峰进行了指认归属.结果表明:C13侧链分子离子稳定性顺序为:M-(1 A)M(2 A)M+(3 A),极性强弱是M+(3 A)M-(1 A)M(2 A),M+(3 A)的空间构型与M(2 A)相比在一些部位变化大,特别是在C1-C2位置,键长拉长很多而键角减小很多.净电荷、分子轨道特征分析一致确定Mn(n=0,1,-1)体系的酰胺、羟基、羧酸等基团是化学反应时的活性部位,能与亲核或亲电试剂反应,均是关键药效团的活性部位,这一结论与紫衫醇实验研究的构效关系结论一致.本研究成果为进一步研究紫衫醇C13侧链的修饰改造,合成更多高效低毒的紫衫醇类拟物提供可参考的理论基础和实验依据.     

荧光标记的聚(N-异丙基丙烯酰胺)链在水溶液中的折叠动力学

使用1.54 μm的激光脉冲(脉宽约10 ns)诱导丹磺酰基标记的热敏性线性聚N-异丙基丙烯酰胺(PNIPAM)发生线团到小球的转变．当聚合物链中NIPAM单体与丹磺酰基基团的摩尔比由110增至300时,共价键合到聚合物主链上的丹磺酰基发色团对PNIPAM相转变行为的影响会随之减小．PNIPAM链塌缩经历成核过程(伴随着初始珍珠的形成,快弛豫时间τ_fast=0.1 ms)和珍珠的增长粗化阶段(慢弛豫时间τ_slow=0.5 ms),这与之前使用水溶性的1-苯胺-8-萘磺酸铵盐作为荧光探针研究PNIPAM在水溶液中的折叠动力学得到的结果类似．τ_fast在很宽的分子量范围内都与分子量无关,而τ_slow则随链长增加而略有增大．     

级联环境下双原子的纠缠动力学

文献Phys.Rev.A 90,042108(2014)提出了一种级联环境模型,即单量子系统与光学腔作用,而腔又级联着一个有结构的零温玻色热库。本文在此基础上,研究两个二能级原子在该级联环境下的纠缠动力学,考察原子与腔场的耦合强度、原子间的偶极-偶极相互作用、热库的谱宽度、腔场与库间的失谐对原子间纠缠以及两原子与腔组成的三体纠缠动力学的影响。结果表明,在一定条件下两原子间的二体纠缠和原子-腔的三体纠缠在长时极限下都趋于稳定值,且随着偶极-偶极相互作用增加而增大,而无论腔场与热库耦合强弱,失谐量的增加都可以抑制纠缠的衰减。     

光谱及分子探针方法研究番茄Metacaspase蛋白与Ca~(2+)的相互作用

Metacaspases(MCPs)是发现于植物、真菌、原生动物体内的一种结构上类似多细胞动物Caspase的半胱氨酸蛋白酶家族,其大多数成员的激活依赖于钙离子,但钙离子如何影响MCPs的激活机制有待深入研究。借助圆二色谱技术、Terbium/Stains-all探针技术以及荧光光谱技术,以番茄Ⅱ型Metacaspase(LeMCA1)重要位点突变的三种体外原核表达重组蛋白,包括LeMCA1C139A(活性催化位点突变体)、LeMCA1K223G(自降解位点突变体)以及预测的Ca2+结合位点突变体LeMCA1D116A/D117A为研究材料,探究了MCPs与Ca2+相互作用机制。实验结果表明,Ca2+与LeMCA1之间既不存在强烈的结合作用,也不影响蛋白的二级结构,但Ca2+通过相互作用改变LeMCA1的三级结构来实现对LeMCA1的酶原激活过程。其中,LeMCA1蛋白的Asp-116,Asp-117氨基酸残基作为预测的与Ca2+作用的重要位点,其缺失将导致蛋白与Ca2+相互作用能力下降。利用圆二色谱、荧光光谱结合离子探针技术研究了典型茄科植物番茄中Ca2+与LeMCA1的相互作用特性,结合之前同源序列比对、位点突变结果确定了LeMCA1中的Asp-116,Asp-117氨基酸残基影响着Ca2+与蛋白质的相互作用。该结果对后续LeMCA1的生化特性及晶体结构的解析研究有着重要的参考价值。     

Efficient and accurate estimation of relative order tensors from λ-maps

The rapid increase in the availability of RDC data from multiple alignment media in recent years has necessitated the development of more sophisticated analyses that extract the RDC data’s full information content. This article presents an analysis of the distribution of RDCs from two media (2D-RDC data), using the information obtained from a λ-map. This article also introduces an efficient algorithm, which leverages these findings to extract the order tensors for each alignment medium using unassigned RDC data in the absence of any structural information. The results of applying this 2D-RDC analysis method to synthetic and experimental data are reported in this article. The relative order tensor estimates obtained from the 2D-RDC analysis are compared to order tensors obtained from the program REDCAT after using assignment and structural information. The final comparisons indicate that the relative order tensors estimated from the unassigned 2D-RDC method very closely match the results from methods that require assignment and structural information. The presented method is successful even in cases with small datasets. The results of analyzing experimental RDC data for the protein 1P7E are presented to demonstrate the potential of the presented work in accurately estimating the principal order parameters from RDC data that incompletely sample the RDC space. In addition to the new algorithm, a discussion of the uniqueness of the solutions is presented; no more than two clusters of distinct solutions have been shown to satisfy each λ-map.     

Rapid classification of protein structure models using unassigned backbone RDCs and probability density profile analysis (PDPA)

A method of identifying the best structural model for a protein of unknown structure from a list of structural candidates using unassigned 15N1H residual dipolar coupling (RDC) data and probability density profile analysis (PDPA) is described. Ten candidate structures have been obtained for the structural genomics target protein PF2048.1 using ROBETTA. 15N1H residual dipolar couplings have been measured from NMR spectra of the protein in two alignment media and these data have been analyzed using PDPA to rank the models in terms of their ability to represent the actual structure. A number of advantages in using this method to characterize a protein structure become apparent. RDCs can easily and rapidly be acquired, and without the need for assignment, the cost and duration of data acquisition is greatly reduced. The approach is quite robust with respect to imprecise and missing data. In the case of PF2048.1, a 79 residue protein, only 58 and 55 of the total RDC data were observed. The method can accelerate structure determination at higher resolution using traditional NMR spectroscopy by providing a starting point for the addition of NOEs and other NMR structural data.     

蛋白质顺磁标记技术与生物核磁共振中的赝接触位移

未配对电子与蛋白质分子自旋核的作用能提供丰富的长程结构信息,这些顺磁信息通常可用顺磁弛豫增强、赝接触位移和残余偶极耦合描述,其中赝接触位移包含生物大分子内重要的距离和角度信息.稀土离子具有相似的配位化学性质和不同的顺磁物理特性,而大多稀土离子具有磁各向异性,在与大分子作用过程中会产生赝接触位移.由于大多数蛋白质没有顺磁中心,获得这些顺磁信息需要通过定点选择标记蛋白质来实现.该文旨在对近年来蛋白质顺磁标记的方法和进展进行介绍,在顺磁标记基础上阐述赝接触位移在结构生物学中的应用.     

Effect of the deletion of the C region on the structure and hydration of insulin-like growth factor 1: a molecular dynamics investigation

The structure and hydration of insulin-like growth factor 1 and an inactive mutant lacking the C region have been investigated in aqueous solution by molecular dynamics simulation. The overall structures of the two polypeptide resemble those determined by NMR spectroscopy. The deletion of the C region in the wild polypeptide introduces structural stability in the mutant, leading to a better definition of the secondary structure elements. A detailed hydration analysis was performed using the radial distribution functions and energy distributions. The backbone of the mutant is in general more solvent accessible than the wild polypeptide backbone. The structural rearrangements induced in the mutant led to changes in the solvent exposition of Tyr24 and Tyr60, which are residues important for ligand—receptor complex formation. Tyr24 exhibited a similar degree of solvent exposition in both IGF-I and in the mutant; however, its hydroxyl group in the wild polypeptide is better solvated than in the mutant. Tyr60 was found to be solvent exposed in the wild protein, while in the mutant the involvement of its hydroxyl group in intramolecular hydrogen bonds led to it being buried away from the solvent.     

Interpretation of NMR data on proteins by molecular dynamics simulations

The stability and the internal mobility of the recently determined solution structure of the activation domain of porcine procarboxypeptidase B (ADB; Vendrell J., Billeter M., Wider G., Avilés F.X., Wüthrich K.: EMBO J.10, 11–15 (1991)) was studied by unrestrained molecular dynamics. A 66 residue long polypeptide corresponding to the structurally well-defined fragment of ADB was immersed in a water bath and carefully equilibrated. A trajectory of 90 ps was then recorded at room temperature, using no constraints deduced from NMR distance measurements. The averages of the inverse third power of the proton-proton distances, for which NMR distance measurements are available, were calculated and converted to time averages of the distances. Comparison of these time averaged distances with the corresponding distance constraints used in the determination of the solution structure show that the dynamic structure described by the molecular dynamics trajectory is consistent with the NMR data for the polypeptide backbone and for most side chains. In the course of the 90 ps trajectory, the ß-sheet of ADB remains intact and well-defined. The last helix of the protein domain is also stable, but moves with respect to the rest of the protein, while the first helix shows increased instability. The structural fluctuations of the side chain do in general not exceed those observed among the 20 conformers describing the solution structure.     

REDCRAFT: a tool for simultaneous characterization of protein backbone structure and motion from RDC data

REDCRAFT, a new open source software tool that accommodates the analysis of RDC data for simultaneous structure and dynamics characterization of proteins is presented in this article. Simultaneous consideration of structure and motion is believed to be necessary for accurate representation of the solution-state of a protein. REDCRAFT is designed to primarily utilize RDC data from multiple alignment media in two stages. During Stage-I, a list of possible torsion angles joining any two neighboring peptide planes is ranked based on their fitness to experimental constraints; in Stage-II, a dipeptide fragment is extended by addition of one peptide plane at a time. The algorithm adopted by REDCRAFT is very efficient and can produce a structure for an 80 residue protein within two hours on a typical desktop computer. REDCRAFT exhibits robustness with respect to noise and missing data. REDCRAFT describes the overall alignment of the molecule in the form of an order tensor matrix and is capable of identifying peptide fragments with internal dynamics. Identification of the location of internal motion will permit a more accurate structural representation. Experimental data from two proteins as well as simulated data are presented to illustrate the capabilities of REDCRAFT in both structure determination and identification of the dynamical regions.     

应用~(15)N-~1H残留偶极偶合验证刪除肝癌2(DLC2-SAM)不育-α-基序域的螺旋间的取向(英文)

刪除肝癌2(DLC2),一种经常发现在原发性肝癌过低表达的肿瘤抑制基因,编码一种含有不育-α-基序多域蛋白质(DLC2-SAM).以前SAM域蛋白(DLC2-SAM)核磁共振结构显示此蛋白是由独特的四螺旋束组成,与其它已知SAM域结构截然不同.在该研究中,作者运用了15N-1H残留偶极偶合(RDC)作为附加约束连同NOE和TA-LOS数据进一步优化了DLC2-SAM的结构.由此所得的结构与没有15N-1H残留偶极偶合约束比较显示改善了结构的质量并且有较低的Q值.螺旋的取向,尤其是螺旋4,被残留偶极偶合数据所验证.RDC-优化的人类DLC2-SAM的结构与小鼠的DLC2-SAM很相像.DLC家庭独特的SAM域结构表明该域可能还具有没被发现的新功能.     

Effects of concentrated NaCl and KCl solutions on the behaviour of aqueous peptide bond environment: single-particle dynamics and H-bond structural relaxation

The effects of salt concentrations on the structure, dynamics and hydrogen bond structural relaxation properties of ～1.10 M aqueous N-methylacetamide (NMA) solution at 308 K are studied by classical molecular dynamics simulations. We have considered the concentration range of salts solution from 0.222 to 3.756 M to investigate the behaviour of aqueous environment of peptide bonds in the presence of concentrated NaCl and KCl solution. It is found that the addition of salt solution facilitates the structural breaking of aqueous NMA hydrogen bonds, as a result the number of hydrogen bonds per NMA molecule and their stability decreases. The water and NMA molecule shows slower translational and rotational dynamics with increasing salt concentrations due to additional ion atmospheric friction. Our result shows that the cation–O_NMA radial distribution function decreases whereas the Cl^?─H_NMA radial distribution function increases with ion concentration. On the other hand, the cation–O_water and Cl^?─H_water radial distribution function shows very negligible change with respect to ion concentration. We have also calculated NMA–water and water–water hydrogen bond structural relaxation times. It is observed that the hydrogen bond structural relaxation of O_NMA─H_water is comparatively slower than the H_NMA─O_water hydrogen bond, which can be attributed to higher number and greater stability of the former hydrogen bond than the latter. The change of the dynamical quantities observed here is more prominent in addition of NaCl rather than the KCl solution.     

Mesogenic polybutadiene diols with thiol side-chain units: synthesis and thermal behaviour

Several types of the chiral thiols with two aromatic rings have been synthesised and grafted on polybutadiene diols backbone. The resulting functional polymers possess the OH end groups for the possible preparation of liquid crystal ordered networks. The thermal and mesomorphic properties of the synthesised side-chain units and resulting polymers have been studied by polarising optical microscopy, differential scanning calorimetry and X-ray scattering. Some of the resulting polymers possess a mesomorphic behaviour. The effects of the side-chain structure, number of the chiral groups and density of grafting on the polybutadiene diols have been studied.     

Analysis of cold denaturation mechanism of β‐lactoglobulin and comparison with thermal denaturation from Raman spectroscopy investigations

Cold‐ and heat‐induced β‐lactoglobulin (BLG) transformations have been analyzed in the presence of 4 M urea, from Raman spectroscopy investigations carried out simultaneously in the low wavenumber range (10–400 cm⁻¹) and in the amide I region (1500–1800 cm⁻¹). These investigations show common features between the denaturation processes at low and high temperatures. The denatured states are reached via an intermediate state characterized by a soft tertiary structure without detectable conformational changes. This intermediate is intimately connected with a tetrahedral hydrogen‐bond structure of water which extends over a limited range. It is shown that the disruption of the hydrogen‐bond network of D₂O has an important consequence on the solvent dynamics, which controls protein dynamics and is characterized by an anharmonic behavior. By monitoring the amide I mode, conformational changes are detected at low temperature (below 5 °C) and determined to be similar to those detected at high temperature in the presence of urea near 65 °C, and in the absence of urea near 80 °C. The conformational changes are described as a loss of α‐helix structures and a concomitant formation of β‐sheets. The temperature dependence of the amide I wavenumber in BLG dissolved in the 4 M urea aqueous solution was interpreted on the basis of a two‐state model, leading to the protein stability curve related to its molecular conformation. Copyright © 2011 John Wiley & Sons, Ltd.