Water in the Neck-Zipper Region of Kinesin

Neck linker （NL） is one of the most important mechanical elements of kinesin motors. The zipping up process of the neck-zipper （NZ） formed by NL and the related secondary structure elements is one of the major parts of kinesin＇s power stroke. All the weak interactions that are responsible for the formation of NZ are sensitive to or dependent on water. To investigate the role of water in the NZ region, a molecular dynamics （MD） model is set up with a crystal structure of kinesin 2KIN surrounded by a 10 A water layer, and minimization is performed to determine the positions of hydrogen atoms and other atoms. It is revealed that water molecules can assist the docking process of NL by forming hydrogen bonds at those positions where direct hydrogen bonding between the two sides of NZ is hindered and then acts as a constructive component of NZ at the docked state of NL. This result may improve the understanding of the mechanism for the docking of NL of kinesin wherein the function of water has not been comprehended sufficiently.     

The neck linker of kinesin 1 seems optimally designed to approach the largest stepping velocity: a simulation study of an ideal model

The neck linker is widely believed to play a critical role in the hand-over-hand walking of conventional kinesin 1. Experiments have shown that change of the neck linker length will significantly change the stepping velocity of the motor. In this paper, we studied this length effect based on a highly simplified chemically powered ratchet model. In this model, we assume that the chemical steps (ATP hydrolysis, ADP and P(i) release, ATP binding, neck linker docking) are fast enough under conditions far from equilibrium and the mechanical steps (detachment, diffusional search and re-attachment of the free head) are rate-limiting in kinesin walking. According to this model, and regarding the neck linker as a worm-like-chain polypeptide, we can calculate the steady state stepping velocity of the motor for different neck linker lengths. Our results show, under the actual values of binding energy between kinesin head and microtubule (~15k(B)T) and the persistence length of neck linker (~0.5 nm), that there is an optimal neck linker length (~14-16 a.a.) corresponding to the maximal velocity, which implies that the length of the wild-type neck linker (~15 a.a.) might be optimally designed for kinesin 1 to approach the largest stepping velocity.     

Kramers-type elastic ratchet model for ATP gating during kinesin’s mechanochemical cycle

ATP binding, acting as a gate, plays an important role in kinesin stepping. To understand the physical mechanism of the ATP gate, we propose a Kramers-type elastic ratchet model in which the free head undergoes a biased diffusive search. By first passage time analysis, we investigate the dependence of the mean dwell time on the load force for forward steps of kinesin and find that the forward dwell time varies exponentially with the backward load force which is consistent with the data of Carter and Cross, Nature 435 (2005) 308. Our work suggests that the gating mechanism triggered by ATP binding involves both Kramers-type elastic ratchet mechanism and power stroke movement.     

Biased Diffusive Search Triggered by ATP Binding During Kinesin＇s Stepping

In this paper, we present an asymmetry conformational potential with a reflecting boundary and an absorbing boundary, in which the diffusive search of the free head of kinesin motor can be biased toward its forward binding site. Under a wide range of condition, using first-passage time analysis we perform numerical simulation to the Langevin equation, and obtain the dependence of the dwell time for forward steps on the load force. And we calculate the expression for the dwell time by the Laplace transform method. Both numerical and analytical results show that the dwell times exponentially depend on the load force, which provide a simple physical explanation for experimental data. Our results suggest that ATP binding-conformation change in the neck linker plays an important role in unidirectional steps during kinesin＇s mechanochemical cycle.     

How kinesins walk,assemble and transport: A birds-eye-view of some unresolved questions

Eukaryotic cells contain an intricate network of microtubule filaments inside. It provides the mechanical support for maintaining cell shape as well as a railway for intracellular traffic. A special class of ATP hydrolyzing enzymes bind microtubule inside the cells and ‘walk’ along the filament. Kinesins constitute a subset of these so called ‘motor’ proteins. These are a diverse set of proteins capable of converting the chemical energy of ATP hydrolysis to mechanical force and move from one end of the cell to the other carrying a variety of different cargoes. Although the composition, structure and their force generating mechanism is understood in considerable detail, several questions regarding the mechanism of kinesin mediated transport remained unanswered. Here, in this review, I have provided a brief overview of kinesin structure and functions in different intracellular transports and highlighted some of the key unresolved issues.     

A New Cooperation Mechanism of Kinesin Motors when Extracting Membrane Tube

Membrane tubes are important functional elements for living cells. Experiments have found that membrane tubes can be extracted from giant lipid vesicles by groups of kinesin. How these motors cooperate in extracting the membrane tube is a very important issue but still unclear so far. In this paper, we propose a cooperation mechanism called two-track-dumbbell model, in which kinesin is regarded as a dumbbell with an end (tail domain) tethered on the fluid-like membrane and the other end (head domain) stepping on the microtubule. Taking account of the elasticity of kinesin molecule and the excluded volume effect of both the head domain and the tail domain of kinesin, which are not considered in previous models, we simulate the growth process of the membrane tube pulled by kinesin motors. Our results indicate that in the case of strong or moderate exclusion of motor tails, the average number of motors pulling the tube can be as high as 9 and thus motors moving along a single microtubule protofilament can generate enough force to extract membrane tubes from vesicles. This result is different from previous studies and may be tested by future experiments.     

A New Cooperation Mechanism of Kinesin Motors when Extracting Membrane Tube

Membrane tubes are important functional elements for riving cells. Experiments have found that membrane tubes can be extracted from giant lipid vesicles by groups of kinesin. How these motors cooperate in extracting the membrane tube is a very important issue but still unclear so far. In this paper, we propose a cooperation mechanism called two-track-dumbbell model, in which kinesin is regarded as a dumbbell with an end （tail domain） tethered on the fluid-like membrane and the other end （head domain） stepping on the microtubule. Taking account of the elasticity of kinesin molecule and the excluded volume effect of both the head domain and the tail domain of kinesin, which are not considered in previous models, we simulate the growth process of the membrane tube pulled by kinesin motors. Our results indicate that in the case of strong or moderate exclusion of motor tails, the average number of motors pulling the tube can be as high as 9 and thus motors moving along a single microtubule protofilament can generate enough force to extract membrane tubes from vesicles. This result is different from previous studies and may be tested by future experiments.     

光谱法和分子对接法研究和比较两种全氟羧酸与人血清白蛋白的结合模式

全氟羧酸(PFCAs)由于具有既亲水又疏水的表面活性剂特性,被广泛应用于工业和生活产品中。全氟十一酸(PFUnA)和全氟十三酸(PFTriA)是长链PFCAs类的典型代表,但近年来它们越来越频繁的在人体中检测到,并且发现表现出内分泌干扰效应、发育毒性和致畸性。本文以光谱学和分子对接为基础,探索PFUnA和PFTriA与人体最丰富的蛋白人血清白蛋白(HSA)的结合模式。结果表明,PFUnA和PFTriA均通过动静态猝灭过程猝灭HSA的内源荧光,与HSA只有一个强亲和位点,且PFUnA与HSA的结合比PFTriA更紧密。根据热力学计算结果,可知PFUnA与HSA结合的焓变、熵变分别为-26.32 kJ·mol-1和21.76 J·mol-1·K-1,其结合作用主要依靠静电引力,而PFTriA主要通过范德华力和卤键与HSA结合,是放热熵减过程,其焓变和熵变分别为-39.69 kJ·mol-1和-25.66 J·mol-1·K-1。计算得到的结合距离(r<8 nm)显示从HSA到PFUnA和PFTriA发生了非辐射能量转移。三维荧光光谱和圆二色谱表明,PFUnA和PFTriA与HSA的结合不仅可以改变HSA的构象和微环境,还可以引起α-螺旋稳定性降低。取代实验和分子对接进一步显示PFUnA 和PFTriA通过极性键、疏水作用力和卤键等与HSA的亚域ⅡA疏水腔有高亲和性,且荧光团Trp残基处于结合位置中,进一步证明PFUnA和PFTriA可以猝灭HSA的荧光。本文研究结果为阐明长链PFCAs在机体内与血清蛋白的结合机理提供了完整可靠的数据,并为长链PFCAs的毒性评价和毒理学研究提供了理论依据。     

Cooperativity of multiple kinesin-1 motors mechanically coupled through a shared load

Recent experiments using single-molecule techniques have characterized the mechanical properties of single kinesin molecules in vitro at a range of loads and ATP concentrations. These experiments have shown that kinesin moves processively along microtubules by alternately advancing each of its motor domains in a hand-over-hand fashion, using Brownian motion and the energy from ATP hydrolysis. We have extended the theoretical analysis of kinesin through a mechanistic model that is capable of describing transient and steady-state behavior. Transient dynamics are needed to describe the effect of external perturbations (e.g. interactions with other kinesin molecules). Quantitative metrics are tailored to characterize the synchronization of nonlinear, nonsmooth systems such as kinesin. These metrics are employed to analyze the simulation results and to quantify the effect of the cargo linker stiffness, the load, and the difference in intrinsic velocity on the synchronization of two coupled motor proteins. Herein, the mechanistic model and the new analysis techniques are demonstrated for the case of two coupled kinesin motors.     

驱动蛋白单向运动机理

驱动蛋白马达在实验和理论上已被进行了广泛的研究. 然而, 其行进运动的微观机理仍未确定. 在本文中我们基于化学、力学和电学耦合提出了一个交臂模型来描述这种行进运动. 在该模型中，驱动蛋白两个头的ATP水解化学反应速率由作用在其颈上的力（包括内部弹性力和外部负荷）来调控. 在低外部负荷情况下, 驱动蛋白的后头的ATP水解化学反应速率远大于前头的速率, 因而两个头在ATP水解化学反应和力学周期循环中是协调的且马达以每步消耗一个ATP的方式的行走. 在大的前向负荷情况下, 两个头的ATP水解化学反应速率变得可比拟, 因而两个头在ATP水解化学反应和力学周期循环中不再很好地协调. 该模型与驱动蛋白的结构研究结果以及ATP水解化学反应路径一致. 利用此模型所估算的驱动力（约5.8 pN）与实验结果（5~7.5 pN）一致. 所估算的每步中的运动时间（约10）也与实验测量值（0~50）符合. 解释了已观察到的每步（8nm）分为两个半步的现象. 所得到的运动速度-负荷曲线与已有的实验结果一致.     

三种肉桂酰胺衍生物的制备及其与人血清白蛋白的结合

基于临床上肉桂酰胺类药物的广泛应用及优异性能, 以间羟基肉桂酸为母体, 分别与不同氨基酸反应, 设计合成了3种未见报道的肉桂酰胺类衍生物, 并用MS、IR、¹H NMR、¹³C NMR进行结构表征.采用分子对接技术和荧光光谱法、同步荧光光谱法、紫外-可见光谱法共同研究了3种衍生物分别和人血清白蛋白(HSA)相结合的机理.AutoDock对接显示, 这3种衍生物结合在HSA亚结构域ⅡA(即site Ⅰ)的疏水腔内, 维系衍生物与HSA的主要作用力为氢键和范德华力, 同时还存在着疏水作用.光谱实验结果表明, 在体外生理条件下, 衍生物都与HSA形成复合物, 对HSA内源荧光产生静态猝灭, 且对其构象产生影响.根据不同温度下的热力学函数, 确定主要作用力均是氢键和范德华力.分子对接与实验获得了一致的结果.     

Investigation of the structural and dynamic basis of kinesin dissociation from microtubule by atomistic molecular dynamics simulations

Kinesin is a molecular motor that can step processively on microtubules via the hydrolysis of ATP molecules. An important factor characterizing the processivity of the kinesin motor is its dissociation from the microtubule. Here, using all-atom molecular dynamics simulations, we studied the dissociation process of the kinesin head in weak-microtubule-binding or ADP state from tubulin on the basis of the available high-resolution structural data for the head and tubulin. By analyzing the simulated snapshots of the structure of the head-tubulin complex we provided detailed structural and dynamic information for the dissociation process. We found that the dissociation of the head along different directions relative to the tubulin exhibits very different dynamic behaviors. Moreover, the potential forms or energy landscapes of the interaction between the head and tubulin along different directions were determined. The studies have important implications for the detailed molecular mechanism of the dissociation of the kinesin motor and thus are critical to the mechanism of its processivity.     

Theoretical Analysis of Kinesin KIF1A Transport Along Microtubule

Recently, a three-state model is presented to describe the intracellular traffic of unconventional (single-headed) kinesin KIF1A (Phys. Rev. Lett. 95:118101, 2005), in which each motor can bind strongly or weakly to its microtubule track, and each binding site of the track might be empty or occupied by one motor. As the usual two-state model, i.e. the totally asymmetric simple exclusion process (TASEP) with motor detachment and attachment, in steady state of the system, this three-state model also exhibits shock (or domain wall separating the high-density and low density phases) and boundary layers. In this study, using mean-field analysis, the conditions of existence of shock and boundary layers are obtained theoretically. Combined with numerical calculations, the properties of shock are also studied. This study will be helpful to understand the biophysical properties of the collective transport of kinesin KIF1A.     

血管紧张素转化酶抑制肽Leu-Lys-Pro(LKP)抑制机理的研究

血管紧张素转化酶(ACE)是一种含锌离子的羧二肽酶,通过肾素-血管紧张素系统和激肽释放酶-激肽系统进行血压调节。食源血管紧张素转化酶抑制肽(ACEIP)可抑制ACE的活性对高血压控制有利。以鲣鱼蛋白分离出的ACE抑制肽Leu-Lys-Pro(LKP)为原料,采用荧光光谱法、紫外-可见光谱法、圆二色谱法、等温滴定量热法(ITC)以及分子对接技术研究了LKP对ACE的抑制机理。荧光光谱结果表明,LKP能够有效猝灭ACE的内源荧光,猝灭机制为静态猝灭,两者结合可形成较稳定的复合物,ACE中色氨酸和酪氨酸残基所处的微环境疏水性减小,导致极性增强。紫外、圆二色谱结果表明,LKP与ACE结合会导致ACE构象发生改变,ACE与LKP结合后二级结构比未结合时松散,为紧密-松散-稍紧密的变化过程。ITC测得LKP与ACE结合的焓变(ΔH)、熵变(ΔS)、化学计量比(n)以及结合常数(K_a)等热力学参数,结果表明两者结合反应是由熵驱动的自发吸热过程,结合力主要为疏水作用,确定LKP与ACE相互作用的结合位点数约为1,且随温度升高而增加。LKP与ACE的结合常数K_a     

基于片段的核磁共振筛选方法识别NSD1 SET结构域的全新苗头化合物

包含SET结构域的核受体结合蛋白1（NSD1）是一种组蛋白甲基转移酶,它能够特异性的甲基化组蛋白H3赖氨酸第36位（H3K36）.异常表达的NSD1主要发现于Sotos综合症患者体内,但它同样也能导致其他多种人类疾病的发生.目前已有靶向组蛋白甲基转移酶DOT1L和EZH2的小分子抑制剂报道,然而,靶向NSD1的化学探针分子尚未被发现.本文使用基于片段的核磁共振（NMR）筛选方法寻找到3个以NSD1蛋白作为靶点的苗头化合物,利用化学位移扰动分析技术测定了这些化合物与NSD1的结合亲和力.另外,利用分子对接方法选择获得苗头化合物与NSD1蛋白的最可能的结合模型.结果显示苗头化合物1结合于NSD1天然底物S-腺苷酸甲硫氨酸（SAM）的结合口袋中.我们的研究成果为进一步以结构为指导的从苗头化合物到先导化合物的衍化奠定了基础.     

Binding of an Anti-inflammatory Drug Lornoxicam with Blood Proteins: Insights from Spectroscopic Investigations

The interaction between an anti-inflammatory drug, lornoxicam (LXM) and protein (human serum albumin and bovine serum albumin) was studied by spectroscopic techniques (Fluorescence, synchronous, FT-IR, UV-vis absorption and circular dichroism). The quenching mechanism of fluorescence of the protein by the drug was discussed. Based on the interaction studies carried out at different temperatures by spectrofluorometry, the binding constant and the number of binding sites for drug on protein have been evaluated. The nature of binding force operating between the drug and protein was proposed to be electrostatic and hydrophobic based on thermodynamic parameters. The distance r between the donor (protein) and acceptor (drug) was determined based on the Förster’s theory of non-radiation energy transfer and found to be 2.38 nm and 2.56 nm for LXM-BSA and LXM-HSA respectively. Displacement studies with different site probes revealed that the drug bound to the hydrophobic pocket located in sub domain IIA; that is to say, Trp-214 was near or within the binding site. Circular dichroism data of protein in the presence of drug revealed the decreased α-helicity and hence changes in secondary structure of protein. The effects of some common ions were also investigated.     

Mechanochemical Coupling of Kinesin Studied with a Neck-Linker Swing Model

A neck-linker swing model has been proposed in this work to investigate the mechanochemical coupling of kinesin. The difference between force-velocity curves given by force clamp and fixed trap respectively has been satisfactorily interpreted by this model. The study implies that ADP releasing and ATP hydrolysis are much less forcedependent in force clamp experiments than that in fixed trap experiments in the regime of moderate loading force, which might be a consequence of the delayed response of servo system in force clamp experiments.     

Monte Carlo Simulation of Kinesin Movement with a Lattice Model

Kinesin is a processive double-headed molecular motor that moves along a microtubule by taking about 8nm steps. It generally hydrolyzes one ATP molecule for taking each forward step. The processive movement of the kinesin molecular motors is numerically simulated with a lattice model. The motors are considered as Brownian particles and the ATPase processes of both heads are taken into account. The Monte Carlo simulation results agree well with recent experimental observations, especially on the relation of velocity versus ATP and ADP concentrations.     

Structural characterization and angiotensin-converting enzyme (ACE) inhibitory mechanism of Stropharia rugosoannulata mushroom peptides prepared by ultrasound

To reveal the structural characteristics and angiotensin-converting enzyme (ACE) inhibition mechanism of Stropharia rugosoannulata mushroom peptides prepared by multifrequency ultrasound, the peptide distribution, amino acid sequence composition characteristics, formation pathway, and ACE inhibition mechanism of S. rugosoannulata mushroom peptides were studied. It was found that the peptides in S. rugosoannulata mushroom samples treated by multifrequency ultrasound (probe ultrasound and bath ultrasound mode) were mainly octapeptides, nonapeptides, and decapeptides. Hydrophobic amino acids were the primary amino acids in the peptides prepared by ultrasound, and the amino acid dissociation of the peptide bonds at the C-terminal under the action of ultrasound was performed mainly to produce hydrophobic amino acids. Pro and Val (PV), Arg and Pro (RP), Pro and Leu (PL), and Asp (D) combined with hydrophobic amino acids were the characteristic amino acid sequence basis of the active peptides of the S. rugosoannulata mushroom. The docking results of active peptides and ACE showed that hydrogen bond interaction remained the primary mode of interaction between ACE and peptides prepared by ultrasound. The peptides can bind to the amino acid residues in the ACE active pocket, zinc ions, or key amino acids in the domain, and this results in inhibition of ACE activity. Cation–pi interactions also played an important role in the binding of mushroom peptides to ACE. This study explains the structural characteristics and ACE inhibition mechanism used by S. rugosoannulata mushroom peptides prepared by ultrasound, and it will provide a reference for the development and application of S. rugosoannulata mushroom peptides.