核磁共振、X射线小角散射以及计算机模拟相结合构建生物大分子复合物的结构模型（英文）

近年来,结构生物学研究越来越注重生物大分子复合物的解析,因为许多重要生物学过程都离不开复合物的参与.溶液核磁共振是目前重要的结构解析方法之一.X射线小角散射(SAXS)作为一种新的结构生物学实验手段,近年来发展迅速.SAXS能提供生物大分子复合物的较低分辨率结构信息,而核磁共振能解析复合物中各个亚基的原子分辨率结构.此外,通过核磁共振还能得到亚基之间的界面、取向以及距离信息.因此近年来通过计算机模拟,整合核磁共振和SAXS不同分辨率的结构信息,可以用来搭建生物大分子复合物的结构模型.该综述重点介绍这方面的研究进展.     

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.     

生物固体核磁共振中样品发热的研究进展

近年来,固体核磁共振被广泛应用于膜蛋白、纤维化蛋白等体系的结构和功能研究．在固体核磁共振实验中,快速魔角旋转或高功率射频场照射等实验条件将导致样品发热．生物样品发热能导致严重的后果,例如样品温度的快速升高,信号分辨率、信噪比的降低,发热严重时甚至导致样品的不可逆损坏．近年来,人们对样品发热问题进行了一些研究,发现通过优化样品制备条件或固体核磁共振实验条件,以及改进探头设计等手段,可以在一定程度上减轻样品发热．该文主要综述了生物固体核磁共振研究中导致样品发热的原因和减轻样品发热的方法．     

核磁共振波谱在药物研发中的应用进展

在现代药物的研发过程中, 能够检测药物分子化学组成、结构及其与生物分子相互作用的新方法、新技术始终是人们最关注的科学问题之一。而光谱分析(包括红外、紫外和核磁共振)是最常用的分析手段。其中, 核磁共振波谱技术通过检测组成有机化合物分子的原子核在周围化学环境影响下的跃迁规律, 来获得反映核相关性质的参数, 而这些参数包含了详尽的有机化合物分子结构和分子间相互作用的信息。核磁共振波谱能在液态、固态、气态, 甚至在生物原位环境等多种复杂条件下, 提供体系中分子组成、原子水平分辨率的三维结构、相互作用和动态过程等丰富信息, 特别是药物研发中极其重要的药物分子与生物大分子的相互作用信息。因此核磁共振波谱在药物研发中发挥了越来越重要的作用, 近年来在药物研发领域的应用是越来越广泛。而有关核磁共振波谱专门应用于药物研发方面的综述并不多见。由此, 在简单阐述核磁共振波谱基本原理的基础上, 从药物靶标生物大分子受体的结构与动力学、药物设计与筛选, 以及药物代谢三方面综述了近年来核磁共振波谱在药物研发中的最新应用进展, 以期系统的为分析工作者们提供核磁共振波谱在该领域目前的研究概貌。     

核磁共振波谱在药物研发中的应用进展

在现代药物的研发过程中,能够检测药物分子化学组成、结构及其与生物分子相互作用的新方法、新技术始终是人们最关注的科学问题之一。而光谱分析(包括红外、紫外和核磁共振)是最常用的分析手段。其中,核磁共振波谱技术通过检测组成有机化合物分子的原子核在周围化学环境影响下的跃迁规律,来获得反映核相关性质的参数,而这些参数包含了详尽的有机化合物分子结构和分子间相互作用的信息。核磁共振波谱能在液态、固态、气态,甚至在生物原位环境等多种复杂条件下,提供体系中分子组成、原子水平分辨率的三维结构、相互作用和动态过程等丰富信息,特别是药物研发中极其重要的药物分子与生物大分子的相互作用信息。因此核磁共振波谱在药物研发中发挥了越来越重要的作用,近年来在药物研发领域的应用是越来越广泛。而有关核磁共振波谱专门应用于药物研发方面的综述并不多见。由此,在简单阐述核磁共振波谱基本原理的基础上,从药物靶标生物大分子受体的结构与动力学、药物设计与筛选,以及药物代谢三方面综述了近年来核磁共振波谱在药物研发中的最新应用进展,以期系统的为分析工作者们提供核磁共振波谱在该领域目前的研究概貌。     

聚氧乙烯-六氟砷酸锂复合物不同结晶结构的13C谱归属

聚氧乙烯-六氟砷酸锂复合物在不同的退火温度下会形成两种不同的结晶结构,其固体核磁共振¹³C谱具有很高的分辨率．利用二维交换¹³C谱和¹³C fp-RFDR(finite-pulse radio-frequency-driven recoupling)双量子-单量子(DQ-SQ)实验对复合物结晶的信号进行归属,为从分子水平上研究结晶区中不同-CH₂-基团的运动提供实验依据．     

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.     

以双量子谱解析胰岛素类似物中氨基酸残基质子自旋体系

氨基酸残基质子自旋体系解析,是以核磁共振方法研究蛋白质等生物大分子结构、功能、运动的基础。二维双量子谱是解析残基质子自旋体系的重要手段。对B链C端去五肽胰岛素及S-磺酸型胰岛素A链,分别在水中及重水中测定其500 MHz相敏双量子谱和300 MHz相敏双量子谱。由双量子谱的直接峰、远程峰、等价峰,解析各类残基质子自旋体系,确认了从COSY谱所作的解析,提供了可供解析的更多信息。     

蛋白质分子核磁共振谱峰的特性及其化学位移归属

尽可能完全、准确地归属蛋白质分子的核磁共振（Nuclear Magnetic Resonance,NMR）谱峰,是解析可信赖、高质量的蛋白质三维空间溶液结构的首要条件．自动归属软件的开发和应用,已经方便并加快了蛋白质分子核磁共振谱峰的归属进程．然而,对蛋白质核磁共振研究领域的新手来说,因为缺乏对蛋白质分子的核磁共振谱峰特性的系统认识而可能发生对自动归属结果的错误指认或指认不完全,从而导致蛋白质结构解析的错误或偏差．该文针对蛋白质分子中的核磁共振谱峰特性,比如同位素效应和立体异构等,结合具体的蛋白质分子的核磁共振实验图谱,进行了较为详尽的论述,期望对从事蛋白质核磁共振的研究者在理解蛋白质分子的核磁共振谱峰特性及其归属方面有所裨益．     

磁共振波谱及成像技术在纳米尺度物质生物效应研究中的应用

纳米尺度物质的生物效应研究是近年来在纳米科技发展过程中派生出来的一个崭新的、发展很快的且多学科高度交叉的领域，需要把纳米科学、物理学、化学以及生物医学等多学科的研究手段结合起来，进行综合研究．核磁共振波谱与成像，作为一种原位、无损、动态、实时、多信息的检测手段，在此领域的研究中将发挥不可或缺的重要作用．文章分3个方面简要介绍核磁共振波谱与成像技术在纳米尺度物质生物效应研究中的应用：（1）纳米尺度物质在生物组织及个体内的检测与分析；（2）纳米尺度物质与生物大分子相互作用的核磁共振波谱研究；（3）纳米尺度物质生物效应的核磁共振代谢组学研究．     

Structural modeling of proteins by integrating small-angle x-ray scattering data

Elucidating the structure of large biomolecules such as multi-domain proteins or protein complexes is challenging due to their high flexibility in solution. Recently, an "integrative structural biology" approach has been proposed, which aims to determine the protein structure and characterize protein flexibility by combining complementary high- and lowresolution experimental data using computer simulations. Small-angle x-ray scattering(SAXS) is an efficient technique that can yield low-resolution structural information, including protein size and shape. Here, we review computational methods that integrate SAXS with other experimental datasets for structural modeling. Finally, we provide a case study of determination of the structure of a protein complex formed between the tandem SH3 domains in c-Cb1-associated protein and the proline-rich loop in human vinculin.     

Time resolved velocity measurements of unsteady systems using spiral imaging

Although biomolecular dynamics has been investigated using NMR for at least 40 years, only in the past 20 years have internal motions been characterized at atomic resolution throughout proteins and nucleic acids. This development was made possible by multidimensional heteronuclear NMR approaches that provide near complete sequential signal assignments of uniformly labeled biomolecules. Recent methodological advances have enabled characterization of internal dynamics on timescales ranging from picoseconds to seconds, both in solution and in the solid state. The size, complexity and functional significance of biomolecules investigated by NMR continue to grow, as do the insights that have been obtained about function. In this article I review a number of recent advances that have made such studies possible, and provide a few examples of where NMR either by itself or in combination with other approaches has paved the way to a better understanding of the complex relationship between dynamics and biomolecular function. Finally, I discuss prospects for further advances in this field.     

15N chemical shift anisotropy in protein structure refinement and comparison with NH residual dipolar couplings

Recent methods of aligning proteins which were developed in order to measure residual dipolar couplings (RDCs) in solution can also be used for additional applications such as measuring the 15N CSA in the form of chemical shift differences, Deltadelta. A new XPLOR-NIH module has been developed and implemented for NMR structure refinement using the 15N Deltadelta data as restraints. The results of this refinement are shown using the protein Bax. This method should be amenable to any protein which can be studied by NMR. An analysis comparing the structural information provided by NH RDCs and the 15N Deltadelta is included.     

Structure solution of network materials by solid-state NMR without knowledge of the crystallographic space group

An algorithm is presented for solving the structures of silicate network materials such as zeolites or layered silicates from solid-state ²⁹Si double-quantum NMR data for situations in which the crystallographic space group is not known. The algorithm is explained and illustrated in detail using a hypothetical two-dimensional network structure as a working example. The algorithm involves an atom-by-atom structure building process in which candidate partial structures are evaluated according to their agreement with SiOSi connectivity information, symmetry restraints, and fits to ²⁹Si double quantum NMR curves followed by minimization of a cost function that incorporates connectivity, symmetry, and quality of fit to the double quantum curves. The two-dimensional network material is successfully reconstructed from hypothetical NMR data that can be reasonably expected to be obtained for real samples. This advance in “NMR crystallography” is expected to be important for structure determination of partially ordered silicate materials for which diffraction provides very limited structural information.     

水化磷脂层中蛋白质和多肽的高分辨固体核磁共振波谱学

有序样品的固体核磁共振(NMR)已快速发展成测定蛋白质和多肽在“仿真”水化磷脂层中高分辨结构的重要谱学方法. 由于与膜相连的蛋白质和多肽的结构、动力学和功能往往都和其周边自然环境密切相关,因此人们把蛋白质和多肽有序排列于水化磷脂层中进行固体NMR测量, 从而获得与取向相关的各向异性自旋相互作用. 这些取向约束可作为结构参数重构蛋白质在水化磷脂层中的高分辨三维结构. 近十年来在样品制备,NMR探头和实验方法方面的显著发展,极大地促进了有序样品的固体NMR的发展,并使之成为测定与膜相连的蛋白质和多肽结构的有效方法. 该综述介绍有序样品的固体NMR谱学方法,并总结此领域里的最新研究进展.     

Software for the high-throughput collection of SAXS data using an enhanced Blu-Ice/DCS control system

Biological small-angle X-ray scattering (SAXS) provides powerful complementary data for macromolecular crystallography (MX) by defining shape, conformation and assembly in solution. Although SAXS is in principle the highest throughput technique for structural biology, data collection is limited in practice by current data collection software. Here the adaption of beamline control software, historically developed for MX beamlines, for the efficient operation and high-throughput data collection at synchrotron SAXS beamlines is reported. The Blu-Ice GUI and Distributed Control System (DCS) developed in the Macromolecular Crystallography Group at the Stanford Synchrotron Radiation Laboratory has been optimized, extended and enhanced to suit the specific needs of the biological SAXS endstation at the SIBYLS beamline at the Advanced Light Source. The customizations reported here provide a potential route for other SAXS beamlines in need of robust and efficient beamline control software. As a great deal of effort and optimization has gone into crystallographic software, the adaption and extension of crystallographic software may prove to be a general strategy to provide advanced SAXS software for the synchrotron community. In this way effort can be put into optimizing features for SAXS rather than reproducing those that have already been successfully implemented for the crystallographic community.     

AssignFit: a program for simultaneous assignment and structure refinement from solid-state NMR spectra

AssignFit is a computer program developed within the XPLOR-NIH package for the assignment of dipolar coupling (DC) and chemical shift anisotropy (CSA) restraints derived from the solid-state NMR spectra of protein samples with uniaxial order. The method is based on minimizing the difference between experimentally observed solid-state NMR spectra and the frequencies back calculated from a structural model. Starting with a structural model and a set of DC and CSA restraints grouped only by amino acid type, as would be obtained by selective isotopic labeling, AssignFit generates all of the possible assignment permutations and calculates the corresponding atomic coordinates oriented in the alignment frame, together with the associated set of NMR frequencies, which are then compared with the experimental data for best fit. Incorporation of AssignFit in a simulated annealing refinement cycle provides an approach for simultaneous assignment and structure refinement (SASR) of proteins from solid-state NMR orientation restraints. The methods are demonstrated with data from two integral membrane proteins, one α-helical and one β-barrel, embedded in phospholipid bilayer membranes.     

Gamma-resonance and X-ray investigations of slow motions in macromolecular systems

Information on slow motions of atomic complexes in proteins and other large molecules can be obtained from X-ray and from Mössbauer type experiments. This paper deals with the information on the motional behavior within macromolecular systems, which is contained in the line intensities and in the line widths observed in such experiments. The particular suitability of the gamma resonance method for studies of structural fluctuations in biomolecules is emphasized.     

NMR spectroscopy reveals common structural features of the birch pollen allergen Bet v 1 and the cherry allergen Pru a 1

A high percentage of birch pollen allergic patients also experience food hypersensitivity which results from common epitopes on the corresponding allergens. In order to analyze whether this observed cross-reactivity can be attributed to common structural features, the major birch pollen allergen Bet v 1 and the cherry allergen Pru a 1 were investigated by multidimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy. For the 17 kDa Bet v 1 a three-dimensional structure was calculated on the basis of 1344 experimental restraints. The structure is well defined showing average root mean square deviations of 0.67 and 1.15 Å for the backbone heavy atoms and all heavy atoms of residues 1–154, respectively. The major structural features include a seven-stranded antiparallel β-sheet that wraps around a long C-terminal α-helix, thereby forming a large cavity in the interior of the protein. This structure served as template for the generation of an NMR-based model of Pru a 1 by homology modelling in conjunction with 277 experimentally derived distance restraints. Comparison to the structure of Bet v 1 proves both structures to be highly similar concerning the elements of secondary structure as well as the shape and charge distribution of the protein surface. This finding is consistent with the observed cross-reactivity between both proteins and allows the delineation of common cross-reactive B-cell epitopes.     

Phase transitions in 8CB liquid crystal confined to a controlled-pore glass: Deuteron NMR and small angle X-ray scattering studies

We present results of the deuteron nuclear magnetic resonance (NMR) and small-angle X-ray scattering (SAXS) study of ordering and phase transition behavior of octylcyanobiphenyl (8CB) liquid crystal confined to a controlled-pore glass (CPG) with nontreated and silanes-treated pore surfaces. The deuteron NMR spectra allowed to determine the degree of nematic liquid crystal ordering and also provided an indirect information on the confined 8CB smectic ordering via its influence on the nematic ordering. For the smectic phase these data are supplemented with measurements of the temperature dependence of the first-order SAXS diffraction pattern. The NMR results indicate that the average nematic and smectic order parameters of 8CB in the nontreated CPG are only weakly perturbed by the confinement. The SAXS data further suggest that in confined 8CB for both nontreated and silane-treated CPG a domainlike pattern appears in accordance with the Imry-Ma theorem.