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.     

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.     

蛋白质芳香基团的~1H-~(13)C HSQC信号增强研究(英文)

含芳香环的氨基酸残基多处于蛋白质的疏水内核或者是蛋白质与配体的结合部位,这些残基间的非共价键相互作用对于蛋白质结构的稳定性和生物的特异性识别有重要意义.因此,在蛋白质的核磁共振研究中,芳香基团被认为是一个研究蛋白质结构动力学的潜在探针.但是由于芳香基团的1H-13C HSQC谱的灵敏度较低,目前,利用核磁共振对其进行研究乏善可陈.造成这一现象的主要原因可能在于芳香环体积较大,往往存在慢的翻转运动,导致其NMR信号被展宽.作者利用CPMG-INEPT HSQC序列可以有效地减小慢运动影响的特征,将其应用到了GB1蛋白质芳香环的1H-13C HSQC谱中,有效的增强了芳香基团HSQC谱信号的灵敏度,得到了部分在常规HSQC中无法观测的信号.     

用异核多维NMR技术研究蛋白质动力学

蛋白质在溶液中的三维空间结构、动力学与蛋白质生物功能的关系是在分子水平上理解生命现象的重要基础. NMR技术在研究蛋白质动力学方面具有独特的优势,所能表征的运动过程相关时间尺度很广. 文章综述了异核多维NMR技术研究蛋白质动力学的实验技术和理论方法,介绍了描述蛋白质动力学的内运动参量的意义和Model-Free 方法,并举例说明¹⁵N弛豫测量实验被用于研究蛋白质及其与配体复合物的动力学.      

Molecular Dynamics Simulation on Stability of Insulin on Graphene

通过分子动力学模拟研究了胰岛素与不同尺寸石墨烯的相互作用,并比较了固定的石墨烯与不固定的石墨烯对蛋白质吸附行为及动力学的影响. 通过分析胰岛素蛋白在吸附过程中构象与取向的变化和吸附过程的动力学行为证实了石墨烯对胰岛素蛋白的有效吸附. 通过对蛋白质结构的分析发现蛋白质的三级结构在所有的体系中均有不同程度的破坏,而蛋白质二级结构的稳定性则与体系有关,其中非固定的石墨烯因其具有较大柔性而表现出对蛋白质二级结构的破坏具有一定选择性. 同时还发现石墨烯的尺寸对于胰岛素的吸附动力学过程也有较大影响.     

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.     

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.     

动力学淬火过程中的不动点及衍生拓扑现象

本文对近两年来有关淬火动力学过程中拓扑现象的研究做简要综述.这些动力学拓扑现象被动力学过程中的衍生拓扑不变量保护,与淬火前后体系的拓扑性质有密切关系.基于人工量子模拟平台的高度可控性,已在诸如超冷原子、超导量子比特、核磁共振、线性光学等众多物理体系中,通过对人工拓扑体系动力学过程的调控,观测到如动力学涡旋、动量-时间域的Hopf映射及环绕数、拓扑保护的自旋环结构、动力学量子相变、动量-时间斯格明子等诸多动力学拓扑现象.其中某些拓扑结构还可以在非幺正动力学淬火过程中稳定存在.这些研究将人们对拓扑物相的认识和研究从平衡态推广到非平衡动力学领域,具有重要的科学价值.     

有结构壁面上液滴运动特征的耗散粒子动力学模拟

本文采用耗散粒子动力学方法, 研究了恒定外力驱动下液滴在有结构壁面上的运动过程. 通过研究液滴在通过壁面结构时前缘接触点和前进角的变化, 分析了液滴的运动特征. 研究结果表明, 在不同润湿性或不同外力驱动下, 存在使液滴运动最快的“最优”壁面结构, 并对其机理进行了讨论. 本文还探讨了壁面润湿性、热涨落以及外力对液滴运动状态的影响. 关键词： 微流体 有结构壁面 润湿性 耗散粒子动力学(DPD)     

固体核磁共振研究淀粉样蛋白纤维的进展

淀粉样蛋白纤维是一类纤维状的蛋白质聚集体,与多种蛋白质沉积疾病相关. 对淀粉样蛋白纤维结构的研究,有助于人们从分子水平上阐述其形成机理, 提供相关疾病预防或治疗的依据. 由于淀粉样蛋白纤维不可溶、非结晶,因此液体核磁共振和X-射线衍射等方法对这类体系的应用受限,而固体核磁共振被认为是研究这类体系最具前景的技术. 该综述介绍了固体核磁共振解析蛋白质结构的方法及其应用于淀粉样蛋白纤维体系的研究进展.     

The role of continuous and discrete water structures in protein function

Proteins have evolved to perform numerous roles as specific catalysts and nano-machines. Some of the mechanisms exploited by evolution are clear. Hydrophobicity drives the stabilization energy of folding, charges mediate long-range interactions and facilitate catalysis, and specific geometries and hydrogen bonding patterns facilitate molecular recognition and catalysis. In this work, we examine the energy landscape of protein dynamics in terms of the continuous and discrete water structures that control protein dynamics. We observe that the internal structures at the active site of proteins are constantly shaped by strong interactions with hydration shell and bulk water motions. By describing the energy landscape of proteins in terms of its three component motions; conformational, hydration and protonation, and electronic structure, it is possible to systematically understand protein function.     

Identification of key residues in protein functional movements by using molecular dynamics simulations combined with a perturbation-response scanning method

The realization of protein functional movement is usually accompanied by specific conformational changes, and there exist some key residues that mediate and control the functional motions of proteins in the allosteric process. In the present work, the perturbation-response scanning method developed by our group was combined with the molecular dynamics (MD) simulation to identify the key residues controlling the functional movement of proteins. In our method, a physical quantity that is directly related to protein specific function was introduced, and then based on the MD simulation trajectories, the perturbation-response scanning method was used to identify the key residues for functional motions, in which the residues that highly correlated with the fluctuation of the function-related quantity were identified as the key residues controlling the specific functional motions of the protein. Two protein systems, i.e., the heat shock protein 70 and glutamine binding protein, were selected as case studies to validate the effectiveness of our method. Our calculated results are in good agreement with the experimental results. The location of the key residues in the two proteins are similar, indicating the similar mechanisms behind the performance of their biological functions.     

Fluorescence methods for studying molecular motions

The characteristics of photoluminescence are affected by the molecular motions in the local environment of the excited molecule. Hence, by knowing the lifetime of the excited state, various relaxation times of the molecular motions can be estimated from the emission characteristics. In the present paper the effect of the molecular motions manifested in the fluorescence emission, such as the rotational depolarization of fluorescence, the internal quenching of fluorescence due to internal rotation, and the inter-and intramolecular excimer formation, are reviewed and the possible applications of such phenomena to the study of molecular motions in polymer systems are discussed. The application of fluorescence methods provide unique information about the molecular motions in the nanosecond range in polymer solutions, melts, and solids.     

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.     

A Bayesian statistical method for the detection and quantification of rotational diffusion anisotropy from NMR relaxation data

It has recently become more widely appreciated that the presence of rotational diffusional anisotropy in proteins and other macromolecules can have a significant affect on the interpretation of NMR relaxation data in terms of molecular motion. In this paper, we show how commonly used NMR relaxation data (R(1), R(2), and NOE) obtained at two spectrometer frequencies can be analyzed using a Bayesian statistical approach to reliably detect and quantify the degree of rotational diffusion anisotropy. Our approach differs from previous methods in that it does not make assumptions concerning the internal motions experienced by the residues which are used to quantify the diffusion anisotropy, but rather averages the results over all internal motions consistent with the data. We demonstrate our method using synthetic data corresponding to isotropic, axially symmetric anisotropic, and fully asymmetric anisotropic rotational diffusion, as well as experimental NMR data. We compare the Bayesian statistical approach with a widely used method for extracting tumbling parameters using both synthetic and experimental data. While it can be difficult to separate the effects of chemical exchange from rotational anisotropy using this "standard" method, these effects are readily separated using Bayesian statistics. In addition, we find that the Bayesian statistical approach requires considerably less CPU time than an equivalent standard analysis.     

Correlated dynamics determining x-ray diffuse scattering from a crystalline protein revealed by molecular dynamics simulation

The dynamical origin of the x-ray diffuse scattering by crystals of a protein, Staphylococcal nuclease, is determined using molecular dynamics simulation. A smooth, nearly isotropic scattering shell at originates from equal contributions from correlations in nearest-neighbor water molecule dynamics and from internal protein motions, the latter consisting of -helix pitch and inter--strand fluctuations. Superposed on the shell are intense, three-dimensional scattering features that originate from a very small number of slowly varying (>10 ns) collective motions. The individual three-dimensional features are assigned to specific collective motions in the protein, and some of these explicitly involve potentially functional active-site deformations.     

Effects of Internal Rotations on the Time-Resolved Fluorescence in a Bichromophoric Protein System Under the Energy Transfer Interaction

Effects of internal rotations of chromophores under the energy transfer interaction in proteins on the time-resolved fluorescence were examined by numerical calculations. Expressions used for the calculations are based on the approximations that the energy transfer takes place according to Foöurster's mechanism and the rotational motions of the energy donor and acceptor along the surfaces of cones are described by a set of rotational diffusion equations. The intensity decay of the donor depended a little on the rotational diffusion coefficient of the donor in some cases, while that of the acceptor did very little. Anisotropy of the donor decayed faster as the diffusion coefficient of the donor increased. Anisotropy decay of the acceptor markedly depended not only on the mutual configuration of the pair in the protein, but also on the diffusion coefficient of the donor. The dependence of the time-resolved fluorescence on the diffusion coefficient of the acceptor was not as great as that of the donor.