p53活性四聚体全原子分子动力学分析

p53是一种肿瘤抑制蛋白,对阻碍癌症发展、维持遗传完整性起着至关重要的作用.在细胞核内,4个p53分子通过高度协同的方式、通过DNA结合域与DNA结合,形成稳定的四聚体活性结构,并转录激活或抑制其靶向基因.然而,大多数肿瘤细胞中存在大量p53的突变,其中绝大部分突变发生在p53的DNA结合域,而p53的DNA结合域又是p53形成四聚体活性结构、调控下游靶基因转录的重要区域.本文通过全原子分子动力学模拟,研究了野生型p53四聚体内分子间的相互作用机制.结果表明,位于DNA两侧的对称二聚体是一个稳定的二聚体,在与DNA结合前后都能维持稳定的结构.位于DNA同侧的两个单体依靠两个接触面提供的蛋白-蛋白相互作用和DNA的骨架作用使四聚体活性结构保持稳定,这些相互作用为四聚体的形成机制提供了重要支撑.该工作厘清了p53四聚体在动力学过程中的内部相互作用机制和关键残基,揭示了四聚化过程中各个相互作用界面的关键位点,对于理解p53的抑癌机制、探索有效治癌策略、发展治癌药物具有重要意义.

复杂环境下矿用巡检机器人的路径规划方法

针对传统机器人路径规划方法效率低、实时性差等不足,提出了一种新的矿用巡检机器人路径规划方法,以保证复杂环境下的巡检要求。通过栅格法构建巡检地形的矩阵地图,利用蚁群算法(ACO)来完成巡检路径的规划,并对标准ACO算法的信息素更新规则和期望启发式因子进行了优化,解决算法收敛速度慢,易陷入局部最优等问题。MATLAB仿真实验结果表明:相较于标准ACO算法,优化后算法的稳定性良好,收敛速度加快了59.09%,最优路径缩短了11.98%,满足复杂环境机器人巡检实时规划的需求,进一步提升机器人的环境适应能力。

Nutlin-3a对p53-MDM2复合物稳定性影响

p53蛋白是一种与细胞周期停滞和细胞凋亡有关的蛋白质.在受到细胞压力或环境扰动后,p53促进下游多个靶基因的转录,介导肿瘤抑制.MDM2是主要的E3泛素连接酶,也是p53的负调控因子.MDM2可促进p53的泛素化和核输出,抑制p53的抑癌活性.因此MDM2对p53的负调控始终是肿瘤治疗中急切需要解决的问题.Nutlin-3a是被证明可以有效抑制p53-MDM2相互作用的小分子抑制剂.本文使用全原子分子动力学模拟,研究Nutlin-3a对p53-MDM2复合物的稳定性的影响.结果表明,通过引起p53和MDM2间Phe19-Gln72的氢键和Glu17-Lys94的盐桥发生的断裂,Nutlin-3a可以削弱p53和MDM2间的相互作用.我们的工作对Nutlin-3a小分子抑制剂的作用机制进行了说明,揭示了抗癌药物Nutlin-3a介导的p53-MDM2复合物亲和力降低的分子机制,并为针对p53蛋白的有效抗癌治疗提供了理论基础.

配电网作业机器人协调控制动力学模型研究

针对配电网人工检修作业风险高、效率低的特点,提出一种新型配电网检修作业机器人的结构模型。在该机器人结构基础上,建立工作机器人与工作物体之间闭合链的关节动力学模型,分别得到不同工作模式下的系统动力学方程;设计机器人的力-位置混合协调控制系统,提出闭环内力的动态分配方法,并通过仿真实验和现场运行验证了力-位置混合协调控制可以有效降低机器人操作过程中的闭环内力,表明该机器人能有效实现机器人的剥线、修线、连线等配电检修功能。

驱动蛋白力产生机制的研究

驱动蛋白颈链对接过程及其力产生机制的研究,是揭示驱动蛋白结构与功能的关系,认识生物体蛋白质中普遍存在的、高效的能量转化机制和精确的构象变化调控机制的一个基础性课题。本文中,我们对驱动蛋白颈链对接的过程及其力产生机制进行了系统地分析研究。通过分子动力学模拟,得到了处于空态的马达头部的合理结构。在此结构的基础上,通过对颈链对接的启动机制以及具体实现过程、ATP结合引起的马达头部转动到颈链对接过程力传递路径的分析,从动力学上实现了驱动蛋白颈链对接;澄清了颈链对接的启动机制、颈链向马达头部对接的实现机制、驱动蛋白向前行走时的力产生机制、以及驱动蛋白双头力学化学循环调控机制。对文中所讨论的一些关键问题,给出了实验验证的可能方案。本文的研究结果对理解驱动蛋白结构与功能关系、分子马达的力产生机制、做功原理和高效的能量转换机制有重要的参考价值。

驱动蛋白的研究进展

驱动蛋白是一类典型的分子马达蛋白,它在胞内运输、有丝分裂、细胞形成、细胞功能等方面起着至关重要的作用.驱动蛋白不仅负责运输各种膜细胞器、蛋白复合体、mRNA等以保证细胞的基本活性,还在大脑的发育、记忆功能以及神经元的活性等方面扮演着极其重要的角色,可以说驱动蛋白是生命体系赖以生存的基础之一.

驱动蛋白的颈链结构与功能关系

驱动蛋白的颈链是驱动蛋白力产生的关键元件。颈链与驱动蛋白马达结构域的对接过程为驱动蛋白沿着微管的向前运动提供了驱动力。驱动蛋白的颈链由14～18个氨基酸组成，它连接着马达结构域和由缠绕螺旋组成的茎部。颈链与驱动蛋白马达结构域的对接过程是通过多种弱键相互作用实现的，这些弱键相互作用多数都直接或间接与水分子有关。颈链及其相关区域的极为巧妙的氨基酸结构使得这些弱键能够在细胞环境下有效地发挥作用。对颈链的结构与功能关系的认识大大提高了我们对驱动蛋白运动机制的理解。

Kinesin-microtubule interaction reveals the mechanism of kinesin-1 for discriminating the binding site on microtubule

Microtubule catalyzes the mechanochemical cycle of kinesin,a kind of molecular motor,through its crucial roles in kinesin's gating,ATPase and force-generation process.These functions of microtubule are realized through the kinesin-microtubule interaction.The binding site of kinesin on the microtubule surface is fixed.For most of the kinesin-family members,the binding site on microtubule is in the groove betweenα-tubulin andβ-tubulin in a protofilament.The mechanism of kinesin searching for the appropriate binding site on microtubule is still unclear.Using the molecular dynamics simulation method,we investigate the interactions between kinesin-1 and the different binding positions on microtubule.The key non-bonded interactions between the motor domain and tubulins in kinesin's different nucleotide-binding states are listed.The differences of the amino-acid sequences betweenα-andβ-tubulins make kinesin-1 binding to theα–βgroove much more favorable than to theβ–αgroove.From these results,a two-step mechanism of kinesin-1 to discriminate the correct binding site on microtubule is proposed.Most of the kinesin-family members have the conserved motor domain and bind to the same site on microtubule,the mechanism may also be shared by other family members of kinesin.

驱动蛋白的结构与功能

驱动蛋白是一类蛋白质超家族的总称,其中驱动蛋白-1(以下简称驱动蛋白)是目前已知的有机体内最小的马达蛋白.驱动蛋白能够催化三磷酸腺苷(adenosine triphosphate,ATP)分子的水解反应,将贮藏在ATP中的化学能转变为自身机械运动所需的机械能.驱动蛋白能够沿着微管连续定向运动,在细胞的有丝分裂和胞内物质运输中发挥重要作用.在真核细胞中,驱动蛋白主要以二聚体的形式存在,其结构主要包括4个部分,即马达头部、茎部、连接头部与茎部的颈链以及与"货物"相结合的尾部.驱动蛋白二聚体独特的结构特征以及各个组成部分协调的构象变化,保证了其沿微管的连续行走.目前,驱动蛋白的结构与功能之间的关系的研究取得了重要的进展.随着实验和计算水平的不断提高,彻底了解驱动蛋白的运动机理已经为期不远了.

肌肉力量的微观起源

人体实现机械运动所需的力量是由肌肉产生的。理解肌肉的力产生机理是目前科学研究的最前沿课题之一。肌肉的最基本单元是肌小节。肌小节是一个设计极为精巧的力学装置,其中负责产生力的是一种叫做肌球蛋白的分子马达。通过介绍肌小节和肌球蛋白的结构和工作原理,可以看到生命如何利用蛋白质分子巧妙地实现了复杂的力学功能。此外,对于肌球蛋白马达研究中有待理解的相关问题也进行了简要介绍。

驱动蛋白的能量转换过程——从ATP分子结合到颈链对接

驱动蛋白是一种分子马达,同时也是一种核苷酸酶,它能够将ATP分子所携带的化学能转化为其沿微管蛋白行走的机械能,每消耗一个ATP分子行走一步。对于驱动蛋白如何将ATP的化学能转化为构象变化的机械能的研究一直是生物物理学研究的热点问题。本文从3个方面对此问题的研究进展进行了综述:ATP分子与驱动蛋白结合;ATP结合引起驱动蛋白头部产生转动;驱动蛋白头部转动引起驱动蛋白颈链向头部的对接。将这三个方面的内容合并起来就构成了驱动蛋白的能量传递路径。

Initial conformation of kinesin's neck linker

How ATP binding initiates the docking process of kinesin＇s neck linker is a key question in understanding kinesin mechanisms. By exploiting a molecular dynamics method, we investigate the initial conformation of kinesin＇s neck linker in its docking process. We find that, in the initial conformation, the neck linker has interactions with /30 and forms a ＇cover-neck bundle＇ structure with/30. From this initial structure, the formation of extra turns and the docking of the cover- neck bundle structure can be achieved. The motor head provides a forward force on the initial cover-neck bundle structure through ATP-induced rotation. This force, together with the hydrophobic interaction of ILE327 with the hydrophobic pocket on the motor head, drives the formation of the extra turn and initiates the neck linker docking process. Based on these findings, a pathway from ATP binding-induced motor head rotation to neck linker docking is proposed.

Initiation Mechanism of Kinesin's Neck Linker Docking Process

The neck linker （NL） docking to the motor domain is the key force generation process of a kinesin motor. In the initiation step of NL docking the first three residues （LYS325, THR326 and ILE327 in 2KIN） of the NL must form an ＇extra turn＇, thus the other parts of the NL could dock to the motor domain. How the extra turn is formed remains elusive. We investigate the extra turn formation mechanism using structure-based mechanical analysis via molecular dynamics simulation. We find that the motor head rotation induced by ATP binding first drives ILE327 to move towards a hydrophobic pocket on the motor domain. The driving force, together with the hydrophobic interaction of ILE327 with the hydrophobic pocket, then causes a clockwise rotation of THR326, breaks the locking of LYS325, and finally drives the extra turn formation. This extra turn formation mechanism provides a clear pathway from ATP binding to NL docking of kinesin.

Protection-against-water-attack determined difference between strengths of backbone hydrogen bonds in kinesin＇s neck zipper region

Docking of the kinesin＇s neck linker （NL） to the motor domain is the key force-generation process of the kinesin. In this process, NL＇sβ10 portion forms four backbone hydrogen bonds （HBs） with the motor domain. These backbone hydrogen bonds show big differences in their effective strength. The origins of these strength differences are still unclear. Using molecular dynamics method, we investigate the stability of the backbone HBs in explicit water environment. We find that the strength differences of these backbone HBs mainly arise from their relationships with water molecules which are controlled by arranging the surrounding residue sidechains. The arrangement of the residues in the C-terminal part of /310 results in the existence of the water-attack channels around the backbone HBs in this region. Along these channels the water molecules can directly attack the backbone HBs and make these HBs relatively weak. In contrast, the backbone HB at the N-terminus ofβ 10 is protected by the surrounding hydrophobic and hydrophilic residues which cooperate positively with the central backbone HB and make this HB highly strong. The intimate relationship between the effective strength of protein backbone HB and water revealed here should be considered when performing mechanical analysis for protein conformational changes.

Oscillation of S5 helix under different temperatures in determination of the open probability of TRPV1 channel

Transient receptor potential vanilloid subtype 1 (TRPV1) is a polymodel sensory receptor and can be activated by moderate temperature (≥ 43 ℃). Though extensive researches on the heat-activation mechanism revealed some key elements that participate in the heat-sensation pathway, the detailed thermal-gating mechanism of TRPV1 is still unclear. We investigate the heat-activation process of TRPV1 channel using the molecular dynamics simulation method at different temperatures. It is found that the favored state of the supposed upper gate of TRPV1 cannot form constriction to ion permeation. Oscillation of S5 helix originated from thermal fluctuation and forming/breaking of two key hydrogen bonds can transmit to S6 helix through the hydrophobic contact between S5 and S6 helix. We propose that this is the pathway from heat sensor of TRPV1 to the opening of the lower gate. The heat-activation mechanism of TRPV1 presented in this work can help further functional study of TRPV1 channel.

Stochastic Nature in Cellular Processes

The importance of stochasticity in cellular processes is increasingly recognized in both theoretical andexperimental studies.General features of stochasticity in gene regulation and expression are briefly reviewed in thisarticle,which include the main experimental phenomena,classification,quantization and regulation of noises.Thecorrelation and transmission of noise in cascade networks are analyzed further and the stochastic simulation methodsthat can capture effects of intrinsic and extrinsic noise are described.

Covalent intermolecular interaction of the nitric oxide dimer (NO)_2

Covalent bonds arise from the overlap of the electronic clouds in the internucleus region, which is a pure quantum effect and cannot be obtained in any classical way. If the intermolecular interaction is of covalent character, the result from direct applications of classical simulation methods to the molecular system would be questionable. Here, we analyze the special intermolecular interaction between two NO molecules based on quantum chemical calculation. This weak intermolecular interaction, which is of covalent character, is responsible for the formation of the NO dimer,（NO）2, in its most stable conformation, a cis conformation. The natural bond orbital（NBO） analysis gives an intuitive illustration of the formation of the dimer bonding and antibonding orbitals concomitant with the breaking of the πbonds with bond order 0.5of the monomers. The dimer bonding is counteracted by partially filling the antibonding dimer orbital and the repulsion between those fully or nearly fully occupied nonbonding dimer orbitals that make the dimer binding rather weak. The direct molecular mechanics（MM） calculation with the UFF force fields predicts a trans conformation as the most stable state, which contradicts the result of quantum mechanics（QM）. The lesson from the investigation of this special system is that for the case where intermolecular interaction is of covalent character, a specific modification of the force fields of the molecular simulation method is necessary.

Radiation-induced robust oscillation and non-Gaussian fluctuation

There have been many recent studies devoted to the consequences of stochasticity in protein circuitry. Stress conditions, including DNA damage, hypoxia, heat shock, nutrient deprivation, and oncogene activation, can result in the activation and accumulation of p53. Several experimental studies show that oscillations can be induced by DNA damage following nuclear irradiation. To explore the underlying dynamical features and the role of stochasticity, we discuss the oscillatory dynamics in the well-studied regulatory network motif. The fluctuations around the fixed point of a delayed system are Gaussian in the limit of sufficiently weak delayed feedback, and remain Gaussian along a limit cycle when viewed tangential to the trajectory. The experimental results are recapitulated in this study. We illustrate several features of the p53 activities, which are robust when the parameters change. Furthermore, the distribution in protein abundance can be characterized by its non-Gaussian nature.

驱动蛋白颈链对接机制的研究进展

驱动蛋白能够携带"货物"沿微管高速连续行走,在行走过程中,将ATP结合与水解释放的化学能转化为机械能。驱动蛋白的由十几个氨基酸组成的颈链周期性地与驱动蛋白头部对接和分离是其行走的关键步骤,也是驱动蛋白发力做功的关键环节。现结合本课题组最新的研究结果,对驱动蛋白颈链3个部分不同的对接机制的研究进展进行综述。驱动蛋白颈链对接机制的阐明,加深了人们对于驱动蛋白沿微管行走机制的理解,同时也为其他分子马达工作机理的研究提供了参考。

驱动蛋白MCAK的微管解聚机制研究进展

有丝分裂着丝粒相关驱动蛋白(MCAK)是驱动蛋白-13家族的代表性成员,在细胞分裂的多个过程中起作用。与传统的驱动蛋白不同,MCAK蛋白的生物学功能不是通过沿微管轨道的连续行走实现物质输运,而是从微管末端解聚微管蛋白,从而实现对微管动力学的调控。因此,MCAK蛋白是一种微管解聚蛋白,其沿微管轨道的运动过程以及解聚微管蛋白时的力学-化学循环过程都与其他驱动蛋白家族有很大的差异。该文对MCAK蛋白微管解聚过程的研究进展进行综述,尤其对高分辨率分子结构展现的MCAK蛋白在解聚微管末端蛋白时的1:2复合物模型进行了详细讨论。