基于NMR自旋弛豫技术的蛋白质动力学研究

蛋白质的三维结构在很多情况下不能很好地解释其在生理过程中的作用机制. 动力学研究能够获悉蛋白质在不同时间尺度下的内运动信息,建立起动态结构和生物功能的联系. 该文综述了通过NMR自旋弛豫技术研究蛋白质动力学的原理和方法：ps~ns的快运动分析主要采用约化谱密度函数映射和Modelfree方法;μs~ms的慢运动涉及化学/构象交换过程,常借助CPMG和R_1ρ弛豫色散手段. 基于NMR的蛋白质动力学研究,将蛋白质科学从三维空间结构推进到四维时空结构的新层面.     

高压NMR在蛋白质结构和动力学研究中的应用

与温度一样,压力是基本的热力学变量.蛋白质在溶液中是多种构象的热力学平衡体.在不同的温度和压力等条件下,蛋白质包括折叠构象、变性构象以及各种中间体在内的不同构象的存在频率各不相同.当用压力作为扰动时,由于这些构象的偏摩尔体积不同,它们的存在频率便会因而发生变化,加压可将平衡向具有较小偏摩尔体积的方向移动.因此,利用高压核磁共振(NMR)技术,不仅可以研究高压对蛋白质结构和动力学的影响,还可以通过改变压力,在更为广泛的构象空间研究蛋白质结构和动力学.例如,利用平衡体系在加压时向体积小的构象方向移动这一特性,能够对在常压下因其存在频率低而难于检测、但在高压下因其体积小而存在频率增加了的构象进行深入研究,而这些构象往往与蛋白质的功能密切相关.该篇综述首先介绍了高压在蛋白质科学研究中的历史、有关概念和高压NMR技术;其次,结合实例,阐述高压NMR技术在蛋白质结构、折叠以及动力学研究中的应用;最后,对高压NMR技术在蛋白质研究中的应用前景进行展望.     

高聚物微观结构的固体NMR研究

核磁共振波谱是研究高聚物结构和动力学的有效手段,特别是固体高分辨NMR实验方法的不断发展及谱仪技术的进步,使这方面的研究不断深入. 文中简述了若干固体高分辨NMR技术在固态高聚物结构研究中的应用和重要进展. 部分实验工作在Varian UNITYplus 400MHz NMR谱仪的固体单元上完成.     

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.     

用NMR技术研究蛋白质-配体相互作用

蛋白质-配体相互作用的研究对理解生命过程、药物设计和药物筛选具有相当重要的科学意义和巨大的经济价值. NMR是研究蛋白质-配体相互作用的最有用的技术之一,有着显著的优势. 本文综述了近年来国际上用NMR技术研究蛋白质-配体相互作用的发展状况和趋势,先介绍表征蛋白质-配体相互作用的重要参数,然后介绍如何判断蛋白质或配体与复合物的化学交换类型以及所能获得的有关蛋白质-配体相互作用的信息,最后介绍具体用于研究蛋白质-配体相互作用的若干NMR技术以及基于NMR的药物筛选技术.     

高分子软物质动力学与NMR

高分子熔体或浓溶液中链段扩散和链的弛豫模式满足普适的物理定律,这些定律代表了高分子链动力学的普遍特征.核磁共振(NMR)则为我们直接验证这些物理定律或揭示高分子运动的基本规律提供了强有力的实验手段.本文介绍三个基本的高分子动力学模型(即Rouse模型,蛇行/管道模型和重整化Rouse模型)和以这三个理论模型为基础的NMR实验原理和技术.最后对相关的NMR实验结果进行了综述,并着重与理论模型所期待的结果进行了比较.     

19F NMR技术在蛋白质研究中的应用

因为¹⁹F核自身的特性,如自旋为1/2;丰度高(100%),具有与¹H相当的灵敏度;化学位移分布广且对环境敏感;绝大部分生物体内都不含¹⁹F因而无背景干扰等;¹⁹F NMR自诞生以来就成为非常有吸引力的研究手段. 现在,¹⁹F NMR已被广泛用于核磁共振成像、药物化学及生物大分子的研究,各个方面均有较多的相关文献综述. 该综述将集中讨论¹⁹F NMR在蛋白质研究中的应用,包括蛋白质¹⁹F标记方法,¹⁹F NMR在蛋白质结构、 动力学、蛋白质折叠、蛋白质与药物的相互作用及In-cell NMR中的应用.     

非天然氨基酸在蛋白质动态特性核磁共振研究中的应用

核磁共振（NMR）是蛋白质结构解析的主要方法之一.除可获得蛋白质的高分辨结构外,NMR还可用于观测最接近生理条件的蛋白质动态构象,获得蛋白质行使生物学功能的详细机制.非天然氨基酸定点标记方法可显著减少大分子量蛋白质的信号数目,降低数据采集和分析难度,已广泛运用于蛋白质结构和功能研究.本文介绍了常用的在蛋白质中引入非天然氨基酸的实验方法,包括蛋白质化学合成法、蛋白质化学修饰法、氟代芳香族氨基酸插入和基因密码子编辑的位点特异性插入等方法,并介绍了部分应用非天然氨基酸结合NMR研究大分子量蛋白的成功案例.此外,此篇综述讨论了目前非天然氨基酸标记在蛋白质研究中的局限性及发展方向.     

四卤化锡混合物中受扩散控制的卤原子交换动力学研究

以¹¹⁹Sn NMR 方法研究了四氯化锡和四溴化锡混合物（1∶1, 摩尔比）交换体系在不同条件下的动力学性质. 测定了在不同浓度的氘代氯仿溶液中5个交换组份的表观纵向弛豫时间（T¹）及5个组份相互间的交换速率常数（k）,结果表明交换速率常数与表观纵向弛豫速率成正比关系;同时,根据¹¹⁹Sn 1D NMR信号的线宽估测了有效横向弛豫时间（T^*₂）,并由T₁/T^*₂推断在所研究的体系中分子的运动属NMR慢运动极限. 从实验结果可推断在所研究的复杂交换体系中5个组份间的交换与分子自扩散运动有关,即化学交换与交换主体的扩散运动有必然的联系.     

蛋白质溶液结构及动力学的核磁共振研究

高场液相核磁共振技术作为解析高分辨率蛋白质结构的两大主要手段之一,在近二十几年的时间里得到了迅猛的发展. 一方面,随着谱仪硬件技术、核磁脉冲技术和蛋白质标记技术的不断发展,液相核磁共振技术所能够研究的蛋白质不断突破分子量的限制,可以达到几万,甚至几十万. 另一方面,液相核磁共振技术成功地应用于蛋白质分子动力学的研究中,是目前唯一能够对蛋白质多个位点同时进行动力学研究的实验方法,并且仍在不断地创新、发展和完善中. 本文从蛋白质溶液结构的解析和动力学的研究两个主要方面对液相核磁共振研究的基本方法进行简要的介绍,并结合实例介绍一些最新的研究进展.     

利用CαH系统的零量子-双量子混合相干的弛豫测量研究蛋白质动力学(英文)

越来越多的证据说明,"传统"的弛豫测量(T1, T2, NOE)不足以完整描述蛋白质的复杂动态,如化学交换、构型交换或相互作用导致的动态改变.涉及到多量子相干弛豫机制可以提供额外的动态信息.该文测量2个蛋白质的CαH系统的混合零量子和双量子弛豫速率随CPMG序列中脉冲间隔及温度的变化来探讨蛋白质中的动态及温度的影响.发现2种蛋白之质中均存在可观的交换效应,且与残基位置有关.进一步的分析表明,两位点交换模型不足以解释蛋白质的复杂动态.     

Measurement of dipole-dipole cross-correlated relaxation in fast rotating CH2D groups

Studies of protein dynamics are key to understanding their biological function. NMR relaxation studies of proteins to date have focused primarily on characterizing backbone dynamics. In this paper, we focus on the aliphatic side-chains (Ala, Thr, Val, Leu, and Ile) with the goal of deriving dynamical information on the motion of terminal methyl groups. Dipole-dipole cross-correlated cross-relaxation is analyzed in a fast rotating CH(2)D group, as found in partially deuteriated proteins. In comparison with previous studies on AMX spin systems (methylene C(beta)H(2) groups), the fast rotation of the methyl group makes a number of relaxation pathways efficient, through the coherence C(+)H(1)(+)H(2)(-)+C(+)H(1)(-)H (2)(+). Several pulse schemes were designed to evaluate these relaxation rates: the measured values are small and well predicted by taking into account the complete relaxation network, but they remain strongly influenced by 1H-1H relaxation with all protons in the neighborhood of the CH(2)D moiety. The prospects and limitations of this method are discussed in comparison with 2H relaxation measurements.     

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.     

Spin-lattice relaxation and intramolecular motions in transferrin on the Mössbauer spectroscopy data

A new approach for the investigation of intramolecular motions in proteins, based on the study of spin-lattice relaxation of the iron atom of the protein active centres, has been developed. The gamma-resonance spectra have been obtained for the globules of transferrin enriched with⁵⁷Fe. They possessed a paramagnetic hyperfine structure up to room temperature. This afforded the opportunity to experimentally investigate high temperature conformational motions in proteins and to study their influence on the spin-lattice relaxation. A theoretical model of relaxational spectra calculations has been developed, which enabled us to extract the frequency distribution of the spin-lattice relaxation from the shape of the spectra. The approach developed for the study of intramolecular dynamics of proteins based on the examination of spin-lattice relaxation in gamma-resonance spectra increases the frequency scale by at least one order in comparison with conventional methods.     

Role of protein-water hydrogen bond dynamics in the protein dynamical transition

The role of water in protein dynamics has been investigated using molecular dynamics simulations of crystals and a dehydrated powder. On the 100 ps time scale, the anharmonic and diffusive motions involved in the protein structural relaxation are correlated with the protein-water hydrogen bond dynamics. The complete structural relaxation of the protein requires relaxation of the hydrogen bond network via solvent translational displacement. Inhibiting the solvent translational mobility, and therefore the protein-water hydrogen bond dynamics, has an effect on the protein relaxation similar to dehydration.     

Comparing continuous wave progressive saturation EPR and time domain saturation recovery EPR over the entire motional range of nitroxide spin labels

The measurement of spin-lattice relaxation rates from spin labels, such as nitroxides, in the presence and absence of spin relaxants provides information that is useful for determining biomolecular properties such as nucleic acid dynamics and the interaction of proteins with membranes. We compare X-band continuous wave (CW) and pulsed or time domain (TD) EPR methods for obtaining spin-lattice relaxation rates of spin labels across the entire range of rotational motion to which relaxation rates are sensitive. Model nitroxides and spin-labeled biological species are used to illustrate the potential complications that arise in extracting relaxation data under conditions typical to biological experiments. The effect of super hyperfine (SHF) structure is investigated for both CW and TD spectra. First and second harmonic absorption and dispersion CW spectra of the nitroxide spin label, TEMPOL, are all fit simultaneously to a model of SHF structure over a range of microwave amplitudes. The CW spectra are novel because all harmonics and microwave phases were acquired simultaneously using our homebuilt CW/TD spectrometer. The effect of the SHF structure on the pulsed free induction decay (FID) and pulsed saturation recovery spectrum is shown for both protonated and deuterated TEMPOL. We present novel pulsed saturation recovery measurements on biological molecules, including spin-lattice relaxation rates of spin-labeled proteins and spin-labeled double-stranded DNA. The impact of structure and dynamics on relaxation rates are discussed in the context of each of these examples. Collisional relaxation rates with oxygen and transition metal paramagnetic relaxants are extracted using both continuous wave and time domain methods. The extent of the errors inherent in the CW method and the advantages of pulsed methods for unambiguously measuring collisional relaxation rates are discussed. Spin-lattice relaxation rates, determined by both CW and pulsed methods, are used to determine the electrostatic potential on the surface of a protein.     

Evidence of internal protein dynamics in transferrins from TDPAC experiments

The relaxation in liquid transferrin and ovotransferrin samples has been studied at different temperatures using the TDPAC method. Information about reorientation and internal dynamics has been obtained from immobilized protein samples. Characteristic differences between the two proteins will be discussed.     

Probing protein-protein interactions by dynamic force correlation spectroscopy

We develop a formalism for single molecule dynamic force spectroscopy to map the energy landscape of protein-protein complex (P(1)P(2)). The joint distribution P(tau(1),tau(2)) of unbinding lifetimes tau(1) and tau(2), measurable in a compression-tension cycle, which accounts for the internal relaxation dynamics of the proteins under tension, shows that the histogram of tau(1) is not Poissonian. The theory is applied to the forced unbinding of protein P1, modeled as a wormlike chain, from P(1)P(2). We propose a new class of experiments which can resolve the effect of internal protein dynamics on the unbinding lifetimes.