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

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．     

固体核磁共振谱学研究层状双氢氧化物

层状双氢氧化物(LDHs)作为一类非常重要的无机超分子材料,已经被广泛应用于催化、离子交换、生命科学等众多领域．固体核磁共振谱学是研究层状双氢氧化
物局域结构和动态特征的一种强有力手段,提供了非常丰富的信息．特别是最近,借助固体核磁共振在探索层状双氢氧化物的结构方面取得了非常重要的进展（如：阳离子的有序性信息）．该文主要介绍了最近40 年来固体核磁共振研究层状双氢氧化物方面的重要进展．     

Machine learning for collective variable discovery and enhanced sampling in biomolecular simulation

Classical molecular dynamics simulates the time evolution of molecular systems through the phase space spanned by the positions and velocities of the constituent atoms. Molecular-level thermodynamic, kinetic, and structural data extracted from the resulting trajectories provide valuable information for the understanding, engineering, and design of biological and molecular materials. The cost of simulating many-body atomic systems makes simulations of large molecules prohibitively expensive, and the high-dimensionality of the resulting trajectories presents a challenge for analysis. Driven by advances in algorithms, hardware, and data availability, there has been a flare of interest in recent years in the applications of machine learning – especially deep learning – to molecular simulation. These techniques have demonstrated great power and flexibility in both extracting mechanistic understanding of the important nonlinear collective variables governing the dynamics of a molecular system, and in furnishing good low-dimensional system representations with which to perform enhanced sampling or develop long-timescale dynamical models. It is the purpose of this article to introduce the key machine learning approaches, describe how they are married with statistical mechanical theory into domain-specific tools, and detail applications of these approaches in understanding and accelerating biomolecular simulation.     

If "discrete breathers" is the answer,what is the question?

Intense work on discrete breathers or intrinsic localized modes in recent years has revealed a wealth of new properties of classical energy localization. Relaxation and mobility in particular may be two of the critical links with biomolecular processes. We review some of the basic discrete breather properties that we think are pertinent to biomolecules and make conjectures as to their possible biological utility.     

Direct measurement of internal energy of fragmented C60

A new experimental approach has been investigated to measure directly the internal energy of fragmented C60. Doubly charged C60{2+*} prepared in collisions H++C60-->H- +C60{2+*} decay by evaporation of C2 units. We have measured the internal energy distribution of the transient C60{2+*} for each decay channel by analyzing the kinetic energy loss of the scattered anion H-. This method offers an experimental opportunity for studying the fragmentation dynamics of more complex systems such as larger clusters and biomolecules under internal energy controlled conditions.     

增强采样分子动力学模拟在生物分子研究中的进展

分子动力学模拟能够描述蛋白质分子在行使生物学功能过程中涉及的构象变化,已发展成为中物学研究中重要的计算工具.由于生物分子的构象分布存在崎岖的自由能面,在较为复杂的生物体系的模拟中,传统的分子动力学模拟的构象采样能力受到极大限制,模拟的时间尺度与真实的生物学过程之间仍存在差距.增强采样是解决这一问题的有效手段.本文综述了两类增强采样方法即约束型和无约束型增强采样算法的理论基础、最新进展及其在生物分子中的典型应用,同时也简要总结了组合型增强采样算法近些年的发展.     

Ferrihydrite modification by boron doping

Application of the electrostatic ion storage ring ELISA to studies of clusters and biomolecules is discussed. Ions injected from a plasma source or a sputter source are hot, and at short times the yield of neutrals is usually dominated by decay of metastable ions. We have demonstrated that the decay function is close to a 1/t dependence when the internal energy of the ions is conserved, i.e., when photon emission can be ignored. Deviations from a 1/t distribution therefore gives information about the radiative lifetime or, for larger systems, about the intensity of the emitted radiation. Systematic measurements have been carried out for fullerene anions C _N ^?, for even values of N from 36 to 96, to test a classical dielectric model. Recently we have installed an electrospray ion source with a Paul trap for bunching, which can be used to inject biomolecular ions from solution, and the first experiments on laser spectroscopy of biomolecules have been carried out. Also lifetimes of excited states have been measured for stored biomolecular ions excited by a laser pulse.

     

Low energy electron-driven damage in biomolecules

The damage induced by the impact of low energy electrons (LEE) on biomolecules is reviewed from a radiobiological perspective with emphasis on transient anion formation. The major type of experiments, which measure the yields of fragments produced as a function of incident electron energy (0.1-30 eV), are briefly described. Theoretical advances are also summarized. Several examples are presented from the results of recent experiments performed in the gas-phase and on biomolecular films bombarded with LEE under ultra-high vacuum conditions. These include the results obtained from DNA films and those obtained from the fragmentation of elementary components of the DNA molecule (i.e., the bases, sugar and phosphate group analogs and oligonucleotides) and of proteins (e.g. amino acids). By comparing the results from different experiments and theory, it is possible to determine fundamental mechanisms that are involved in the dissociation of the biomolecules and the production of single- and double-strand breaks in DNA. Below 15 eV, electron resonances (i.e., the formation of transient anions) play a dominant role in the fragmentation of all biomolecules investigated. These transient anions fragment molecules by decaying into dissociative electronically excited states or by dissociating into a stable anion and a neutral radical. These fragments can initiate further reactions within large biomolecules or with nearby molecules and thus cause more complex chemical damage. Dissociation of a transient anion within DNA may occur by direct electron attachment at the location of dissociation or by electron transfer from another subunit. Damage to DNA is dependent on the molecular environment, topology, type of counter ion, sequence context and chemical modifications.     

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.     

Dynamical response of nanomechanical oscillators in immiscible viscous fluid for in vitro biomolecular recognition

Dynamical response of nanomechanical cantilever structures immersed in a viscous fluid is important to in vitro single-molecule force spectroscopy, biomolecular recognition of disease-specific proteins, and the study of microscopic protein dynamics. Here we study the stochastic response of biofunctionalized nanomechanical cantilever beams in a viscous fluid. Using the fluctuation-dissipation theorem we derive an exact expression for the spectral density of displacement and a linear approximation for resonance frequency shift. We find that in a viscous solution the frequency shift of the nanoscale cantilever is determined by surface stress generated by biomolecular interaction with negligible contributions from mass loading due to the biomolecules.     

Some perspectives on dispersion and the use of ensemble-averaged PGSE NMR

Magnetic resonance methodology has made a significant impact in helping us understand the physics of porous media. Among an important class of experiments is that set of techniques designed to measure fluid dispersion. This paper provides some background on some of the underlying physics of dispersion, and outlines some of the NMR approaches that have proven successful. The local and nonlocal dispersion tensors are described and the prospects for future NMR advances considered.     

Nuclear magnetic resonance for quantum computing: Techniques and recent achievements

Rapid developments in quantum information processing have been made, and remarkable achievements have been obtained in recent years, both in theory and experiments. Coherent control of nuclear spin dynamics is a powerful tool for the experimental implementation of quantum schemes in liquid and solid nuclear magnetic resonance(NMR) system,especially in liquid-state NMR. Compared with other quantum information processing systems, the NMR platform has the advantages such as the long coherence time, the precise manipulation, and well-developed quantum control techniques,which make it possible to accurately control a quantum system with up to 12-qubits. Extensive applications of liquid-state NMR spectroscopy in quantum information processing such as quantum communication, quantum computing, and quantum simulation have been thoroughly studied over half a century. This article introduces the general principles of NMR quantum information processing, and reviews the new-developed techniques. The review will also include the recent achievements of the experimental realization of quantum algorithms for machine learning, quantum simulations for high energy physics, and topological order in NMR. We also discuss the limitation and prospect of liquid-state NMR spectroscopy and the solid-state NMR systems as quantum computing in the article.     

Application of 15N NMR Spectroscopy to Studies of the Intermolecular Interaction of Biomolecules

Abstract

Nitrogen nuclei are frequently located at the interaction sites of biomolecules; for example, amide nitrogens in the peptide are the key to maintaining the peptide backbone conformation by hydrogen bonding. Histidine, tryptophan, and arginine side chains contain nitrogen atoms which are often located at the active sites of enzymes. Heterocyclic compounds like purine and pyrimidine bases are substances essential to information transfer by base pair formation of nucleic acids. Also some other co-factors and dyes, such as flavins, porphyrins and chlorophylls, are nitrogen-containing substances which regulate energy tranduction in biological systems. Lecithin and phosphatidylethanolamine are the principal components of the phospholipids from biomembranes. To detect interaction sites and to study the interaction mechanism of these biomolecules, the use of nitrogen NMR seems promising. Although more than 99% of naturally occurring nitrogen element has the ¹⁴N nuclei, a disadvantage of the use of ¹⁴N magnetic resonance has been recognized. It has a spin quantum number I = 1 and the associated quadrupole moment provides a very broad resonance signal of about 100～1000 Hz. Thus, for detection of small changes of the chemical environment, use of ¹⁴N magnetic resonance is not adequate. The natural abundance of ¹⁵N nuclei with a spin quantum number I = 1/2 (which give a sharp resonance signal) is only 0.3% (Table 1). But recent developments in the instrumentation of NMR spectroscopy have made it possible to observe the resonance of the nuclei with low natural abundance. Fourier transform (FT) NMR can save thousands of times the accumulation time to improve the signal to noise ratio of ¹⁵N spectra [1-3]. Also superconducting magnets with wide bores have made possible the use of thick sample tubes of 25 mmΦ and observation of the ¹⁵N resonance of substances of low solubility [4]. In spite of such instrumental development, the observation of the 15N resonance is still not easy because of its low sensitivity; about of proton magnetic resonance. In the application of ¹⁵N NMR in biological systems, we often encounter quite low solubility of biomacromolecules and also sometimes need to measure the concentration dependency of ¹⁴N chemical shifts. For such experiments, enrichment of ¹⁵N nuclei in the molecules is required. Chemical syntheses starting from the simple ¹⁵N containing compounds as an ¹⁵N source and also biological syntheses by bacterial fermentation using the ¹⁵N source in culture media are employed for ¹⁵N enrichment. Enrichment at specific positions of biomolecules is useful for spectral assignments and also for analyses of the pathways of biosyntheses [5].     

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.     

High resolution 2D 1H-13C correlation of cholesterol in model membrane

High resolution 2D NMR MAS spectra of liposomes, in particular 1H-13C chemical shifts correlations have been obtained on fluid lipid bilayers made of pure phospholipids for several years. We have investigated herein the possibility to obtain high resolution 2D MAS spectra of cholesterol embedded in membranes, i.e. on a rigid molecule whose dynamics is characterized mainly by axial diffusion without internal segmental mobility. The efficiency of various pulse sequences for heteronuclear HETCOR has been compared in terms of resolution, sensitivity and selectivity, using either cross polarization or INEPT for coherence transfer, and with or without MREV-8 homonuclear decoupling during t1. At moderately high spinning speed (9 kHz), a similar resolution is obtained in all cases (0.2 ppm for 1H(3,4), 0.15 ppm for 13C(3,4) cholesterol resonances), while sensitivity increases in the order: INEPT < CP(x4) < CP + MREV. At reduced spinning speed (5 kHz), the homonuclear dipolar coupling between the two geminal protons attached to C(4) gives rise to spinning sidebands from which one can estimate a H-H dipolar coupling of 10 kHz which is in good agreement with the known dynamics of cholesterol in membranes.     

Comparing proteins by their internal dynamics: Exploring structure–function relationships beyond static structural alignments

The growing interest for comparing protein internal dynamics owes much to the realisation that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional structural elements, those aspects of protein flexibility and dynamics that are functionally oriented should be subject to evolutionary conservation. Accordingly, dynamics-based protein comparisons or alignments could be used to detect protein relationships that are more elusive to sequence and structural alignments. Here we provide an account of the progress that has been made in recent years towards developing and applying general methods for comparing proteins in terms of their internal dynamics and advance the understanding of the structure–function relationship.     

Applications of laser-polarized 129Xe to biomolecular assays

The chemical shift sensitivity and significant signal enhancement afforded by laser-polarized ¹²⁹Xe have motivated the application of ¹²⁹Xe NMR to biological imaging and spectroscopy. Recent research done by our group has used laser-polarized ¹²⁹Xe in biomolecular assays that detect ligand-binding events and distinguish protein conformations. The successful application of unfunctionalized and functionalized ¹²⁹Xe NMR to in vitro biomolecular assays suggests the potential future use of a functionalized xenon biosensor for in vivo imaging.