定量单分子检测研究进展

单分子检测是指在单分子水平上通过生物分子的构象变化、动力学、分子之间相互作用以及对单个分子进行操纵等方式进行检测.作为一种新型超灵敏检测手段,单分子检测在生物分子的定量检测领域有广阔的应用前景,尤其单分子荧光检测技术,近年来取得了很大进展,被广泛用于研究多种生物体系.本文对定量单分子检测的最新研究进展进行了系统综述,主要聚焦于定量单分子检测在生物标志物(包括DNA、酶和miRNA等)的超灵敏检测研究中的应用,及其在研究生物分子结构与动态、生物分子间相互作用、生物分子修饰和活细胞检测等方面的应用,本文也对定量单分子检测的发展方向进行了展望.     

对pluronic水溶液介观相分离的理论模拟研究

用一种新的动力学密度泛函方法(介观动力学)对pluronics(P85)水溶液的介观相分离动力学进行了模拟研究。该方法可以直接给出水溶液体系中不规则三维微观形貌的动力学形成过程。在动力学模拟中热力学参数通过平均场密度泛函方法计算得到,共聚物分子则用高斯链作为模型进行模拟研究。高斯链的最小结构单元是被抽象为键连的株子体,代表实际体系高聚物分子中的一个单体或几个单体。研究了pluronuc水溶液体系的动力学演变历程并讨论了嵌段共聚物中不同组分长短以及共聚物浓度等因素对溶液微观形貌和体系性质的影响。和其它平衡态模拟方法相比较,介观动力学方法可以给出介观相分离的时间演变过程,有助于加深对很多工业加工处理过程和生理过程机理的理解。     

精确模型化学中MPn微扰外推的一个问题

通过对ＢＨ、ＡｌＨ、ＢＦ和ＡｌＦ的高级别ａｂ ｉｎｉｔｉｏ势能曲线计算和理论分析,发现在分子的几何构型偏离平衡时,由于参考态级成不充分的问题,Ｈａｒｔｒｅｅ－Ｆｏｃｋ单参考态的ＭＰｎ微扰计算可能给出错误的能量值。从而表明,目前的精确模型化学方法（Ｇ１、Ｇ２、Ｇ３和ＣＢＳ系列）中用ＭＰｎ微扰外推的办法拟合高级别ａｂ ｉｎｉｔｉｏ,对偏离平衡构型体系（如动力学研究中的过渡态、中间体等）的能量计算,在一     

单分子/单颗粒光学显微成像研究

作为一种新型的光学显微成像手段,单分子、单颗粒光学显微成像技术具有高分辨率、高通量、高灵敏度、非接触、无损伤等优点,在各个学科领域得到了广泛应用.结合本课题组的研究方向,本文综述了单分子、单颗粒光学显微成像研究中的单分子检测,单颗粒光学显微成像追踪,超分辨成像以及单颗粒催化四个方面的重要研究进展,并展望了该成像技术在生物医学应用中的发展前景与挑战.     

生物分子的单分子检测研究

本文评述了生物单分子检测的方法及其在生物大分子结构与功能之间的关系、酶的活性、反应动力学、分子构象、DNA和RNA的转录、蛋白质折叠等生物学重要问题研究上的应用。对生物单分子检测技术这一研究领域的发展趋势作了展望。     

自组装单分子膜及其表征方法

自组装单分子膜的研究是近年来十分活跃的研究领域. 随着膜的应用领域的拓展 ,对膜的表征方法不断提出新的要求.本文综述了自组装单分子膜体系的类型和基底表面的 处理方法,着重从电化学、谱学、显微学以及表面润湿性等方面综述了近几年来自组装单分子膜的表征方法研究进展, 并对其发展前景作了展望.     

飞秒泵浦-探测实验数据分析

陈述了几种获取飞秒泵浦-探测实验数据中的光解动力学信息的解析物理模型.其中单分量和双分量模型用来解释母体分子的单通道和双通道解离过程,另一个单分量模型用来解释碎片分子的解离或去激发过程.所有模型都结合泵浦-探测实验数据予以解释.     

扫描近场光学显微镜及其在单分子探测中的应用

扫描近场光学显微镜在光学显微镜中具有独特的性能,其突破衍射光限制,具有单分子探测灵敏度,且在研究时不损伤生物样品。文中简要介绍了扫描近场光学显微镜的原理,详述近年来扫描近场光学显微镜在单分子探测中的应用,介绍了扫描近场光学显微镜结合量子点对单分子探测的进展,并对单分子探测的前景做了展望。     

聚合物单分子力谱的研究进展

在单分子水平研究聚合物体系的分子内及分子间相互作用, 对于揭示其结构-性能的关系, 进而实现对相应功能的调控极为重要. 基于原子力显微镜技术(AFM)的单分子力谱, 由于其操作简单且适用面广, 在单分子研究领域得到了广泛的应用. 本文概括了该技术在生物高分子及合成高分子体系的研究进展. 对于生物高分子体系, 主要介绍了核酸(DNA/RNA)、 蛋白质和多糖(淀粉)的单分子力谱研究及利用各自力学指纹谱对其它分子间的相互作用的研究. 对于合成高分子体系, 主要介绍了聚合物的一级结构与单链弹性的关系及溶剂和聚集态结构等对高分子单链力学性质的影响规律.     

单氟甲基化反应的研究进展

有机氟化物在医药、农业化学等领域发挥着不可缺少的作用,其中,氟甲基官能团具有较强的的亲脂性,可以极大地改善药物分子的药代动力学性质.因此,开发各类氟化反应具有重要的价值,尤其向分子中引入单氟甲基在氟化学领域备受关注.针对不同结构分子的单氟甲基化,按照氟甲基试剂分类总结单氟甲基化反应的研究进展,并对部分反应可能的机理进行讨论.     

兔子朊蛋白结构稳定性的分子动力学研究(英文)

朊蛋白病是一种能够对人类和动物带来致命影响,并具有高度传染性的神经退行性疾病.兔子是目前已经报道的哺乳类动物中对朊蛋白病免疫的少数几个物种之一.我们将分子动力学和操控式分子动力学模拟相结合,研究了兔子正常朊蛋白的结构稳定性;同时讨论了蛋白结构的收敛性及刚性分布,并揭示了兔子朊蛋白中关键二级结构的动力学以及受力各向异性特征,证实了兔子朊蛋白结构的稳定性特征.     

Molecular Dynamics Simulations and Steered Molecular Dynamics Simulations of Glabridin Bound to Wild Type and V30A Mutant Transthyretin: Ligand-linked Perturbation of Tertiary Conformation

Transthyretin(TTR), as a tetrameric protein, functions as a neuroprotector. The native TTR homotetramer dissociates into dimers and monomers. Dimers and monomers self-assemble into amyloid fibrils, and this process can lead to some diseases. Native TTR homotetramer is a widely accepted model for TTR amyloid formation. In this study, simulations using molecular dynamics(MD) and steered MD(SMD) were performed to explore the mechanisms for glabridin(Glab), a specific inhibitor for TTR binding, for V30A mutant and wild-type(WT) TTR. MD simulation results indicate that, compared with Glab binding to WT and V30A mutant, the WT TTR could lead to the collapse of β-strands from Ser52 to His56 at chain A. This phenomenon facilitated the easy dissociation of chains A and C. Calculations of the binding free energy between the two chains showed that the V30A-Glab TTR complex displayed a lower binding energy than other systems(WT TTR and WT-Glab TTR). Then, SMD simulation was performed to explore the unbinding pathway for Glab through the WT and V30A mutant TTR. The results show that Lys15(chain A) produced a hydrogen bond with Glab at the force peak via the WT TTR tunnel. Meanwhile, in the V30A TTR mutant, the hydrogen bond between Lys15(chain A) and Glab was broken at the force peak. This condition was beneficial for Glab to be taken off from the protein. Our theoretical results will be useful in designing a new specific inhibitor of TTR protein to control the TTR homotetramer dissociation.     

Approximating nonequilibrium processes using a collection of surrogate diffusion models

The surrogate process approximation (SPA) is applied to model the nonequilibrium dynamics of a reaction coordinate (RC) associated with the unfolding and refolding processes of a deca-alanine peptide at 300 K. The RC dynamics, which correspond to the evolution of the end-to-end distance of the polypeptide, are produced by steered molecular dynamics (SMD) simulations and approximated using overdamped diffusion models. We show that the collection of (estimated) SPA models contain structural information "orthogonal" to the RC monitored in this study. Functional data analysis ideas are used to correlate functions associated with the fitted SPA models with the work done on the system in SMD simulations. It is demonstrated that the shape of the nonequilibrium work distributions for the unfolding and refolding processes of deca-alanine can be predicted with functional data analysis ideas using a relatively small number of simulated SMD paths for calibrating the SPA diffusion models.     

Introduction of steered molecular dynamics into UNRES coarse‐grained simulations package

In this article, an implementation of steered molecular dynamics (SMD) in coarse‐grain UNited RESidue (UNRES) simulations package is presented. Two variants of SMD have been implemented: with a constant force and a constant velocity. The huge advantage of SMD implementation in the UNRES force field is that it allows to pull with the speed significantly lower than the accessible pulling speed in simulations with all‐atom representation of a system, with respect to a reasonable computational time. Therefore, obtaining pulling speed closer to those which appear in the atomic force spectroscopy is possible. The newly implemented method has been tested for behavior in a microcanonical run to verify the influence of introduction of artificial constrains on keeping total energy of the system. Moreover, as time dependent artificial force was introduced, the thermostat behavior was tested. The new method was also tested via unfolding of the Fn3 domain of human contactin 1 protein and the I27 titin domain. Obtained results were compared with Gø‐like force field, all‐atom force field, and experimental results. © 2017 Wiley Periodicals, Inc.     

麋鹿朊蛋白结构稳定性的分子动力学研究

朊蛋白病是一种致命且具有高度传染性的神经退行性疾病.糜鹿是目前已经报道的哺乳类动物中较易发生朊蛋白病的物种之一.作者使用分子动力学和操控式分子动力学模拟相结合的方法对糜鹿正常朊蛋白的结构稳定性进行了研究.发现了麋鹿朊蛋白结构中的不稳定结构域分布以及热动力学性质,揭示了糜鹿朊蛋白稳定性的分子结构基础以及力学特征.     

Mechanically untying a protein slipknot: multiple pathways revealed by force spectroscopy and steered molecular dynamics simulations

Protein structure is highly diverse when considering a wide range of protein types, helping to give rise to the multitude of functions that proteins perform. In particular, certain proteins are known to adopt a knotted or slipknotted fold. How such proteins undergo mechanical unfolding was investigated utilizing a combination of single molecule atomic force microscopy (AFM), protein engineering, and steered molecular dynamics (SMD) simulations to show the mechanical unfolding mechanism of the slipknotted protein AFV3-109. Our results reveal that the mechanical unfolding of AFV3-109 can proceed via multiple parallel unfolding pathways that all cause the protein slipknot to untie and the polypeptide chain to completely extend. These distinct unfolding pathways proceed via either a two- or three-state unfolding process involving the formation of a well-defined, stable intermediate state. SMD simulations predict the same contour length increments for different unfolding pathways as single molecule AFM results, thus providing a plausible molecular mechanism for the mechanical unfolding of AFV3-109. These SMD simulations also reveal that two-state unfolding is initiated from both the N- and C-termini, while three-state unfolding is initiated only from the C-terminus. In both pathways, the protein slipknot was untied during unfolding, and no tightened slipknot conformation was observed. Detailed analysis revealed that interactions between key structural elements lock the knotting loop in place, preventing it from shrinking and the formation of a tightened slipknot conformation. Our results demonstrate the bifurcation of the mechanical unfolding pathway of AFV3-109 and point to the generality of a kinetic partitioning mechanism for protein folding/unfolding.     

Behavior regulation of adsorbed proteins via hydroxyapatite surface texture control

The influence of nanometer-scale interfaces on proteins has received much attention in recent years. The dynamic behaviors of bone morphogenetic protein-7 (BMP-7) on a series of hydroxyapatite (HAP) surface textures were investigated to explore the influence of different surface textures using molecular dynamics (MD), steered molecular dynamics simulations (SMD), and quantum mechanics calculations. It is observed that the interaction energy curve from SMD simulations can exhibit the dynamic behavior of BMP-7 in detail. Both the type and the number difference of the adsorptive residues and the intensity discrepancy of interaction, which is induced by the specific texture of the HAP surface, could be uncovered from the energy curve qualitatively and semiquantitatively in this study. The largest conformational change occurs in the system 010+a. The quantum mechanics calculations suggest that there is a phenomenon of electron transfer from HAP to the groups of BMP-7 during the adsorption process. These findings suggest that surface-engineering techniques could be employed to directly control the texture of HAP surfaces in order to regulate the behavior of a protein adsorbed onto the nanometer-scale interface.     

Calculating potentials of mean force from steered molecular dynamics simulations

Steered molecular dynamics (SMD) permits efficient investigations of molecular processes by focusing on selected degrees of freedom. We explain how one can, in the framework of SMD, employ Jarzynski's equality (also known as the nonequilibrium work relation) to calculate potentials of mean force (PMF). We outline the theory that serves this purpose and connects nonequilibrium processes (such as SMD simulations) with equilibrium properties (such as the PMF). We review the derivation of Jarzynski's equality, generalize it to isobaric--isothermal processes, and discuss its implications in relation to the second law of thermodynamics and computer simulations. In the relevant regime of steering by means of stiff springs, we demonstrate that the work on the system is Gaussian-distributed regardless of the speed of the process simulated. In this case, the cumulant expansion of Jarzynski's equality can be safely terminated at second order. We illustrate the PMF calculation method for an exemplary simulation and demonstrate the Gaussian nature of the resulting work distribution.     

A gate mechanism indicated in the selectivity filter of the potassium channel KscA

Classical molecular dynamics (MD) and non-equilibrium steered molecular dynamics (SMD) simulations were performed on the molecular structure of the potassium channel KcsA using the GROMOS 87 force fields. Our simulations focused on mechanistic and dynamic properties of the permeation of potassium ions through the selectivity filter of the channel. According to the SMD simulations a concerted movement of ions inside the selectivity filter from the cavity to extracellular side depends on the conformation of the peptide linkage between Val76 and Gly77 residues in one subunit of the channel. In SMD simulations, if the carbonyl oxygen of Val76 is positioned toward the ion bound at the S3 site (gate-opened conformation) the net flux of ions through the filter is observed. When the carbonyl oxygen leaped out from the filter (gate-closed conformation), ions were blocked at the S3 site and no flux occurred. A reorientation of the Thr75-Val76 linkage indicated by the CHARMM-based MD simulations performed Berneche and Roux [(2005) Structure 13:591–600; (2000) Biophys J 78:2900–2917] as a concomitant process of the Val76-Gly77 conformational interconversion was not observed in our GROMOS-based MD simulations.