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.     

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.     

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.     

Molecular modeling of oscillating GHz electric field influence on the kinesin affinity to microtubule

Kinesin is a microtubule-associated motor protein which can respond to the external electric field due to its polarity.Using a molecular dynamics simulation method, the effect of such a field on the affinity of kinesin to the αβ-tubulin is investigated in this study. To consider kinesin affinity, the system is exposed to an electric field of 0.03 V/nm with frequency values of 1, 2,..., 9, and 10 GHz. It is found that the applied electric field can change kinesin affinity to the microtubule.These changes could perturb the normal operation of kinesin, such as the processive motility of kinesin on the microtubule.     

Effects of rebinding rate and asymmetry in unbinding rate on cargo transport by multiple kinesin motors

Many intracellular transports are performed by multiple molecular motors in a cooperative manner.Here,we use stochastic simulations to study the cooperative transport by multiple kinesin motors,focusing mainly on effects of the form of unbinding rate versus force and the rebinding rate of single motors on the cooperative transport.We consider two forms of the unbinding rate.One is the symmetric form with respect to the force direction,which is obtained according to Kramers theory.The other is the asymmetric form,which is obtained from the prior studies for the single kinesin motor.With the asymmetric form the simulated results of both velocity and run length of the cooperative transport by two identical motors and those by a kinesin-1 motor and a kinesin-2 motor are in quantitative agreement with the available experimental data,whereas with the symmetric form the simulated results are inconsistent with the experimental data.For the cooperative transport by a faster motor and a much slower motor,the asymmetric form can give both larger velocity and longer run length than the symmetric form,giving an explanation for why kinesin adopts the asymmetric form of the unbinding rate rather than the symmetric form.For the cooperative transport by two identical motors,while the velocity is nearly independent of the rebinding rate,the run length increases linearly with the rebinding rate.For the cooperative transport by two different motors,the increase of the rebinding rate of one motor also enhances the run length of the cooperative transport.The dynamics of transport by N(N=3,4,5,6,7 and 8)motors is also studied.     

Locking Function of a Key Residue in Kinesin＇s Gating Mechanism

In kinesin＇s mechanochemical cycle, ATP＇s binding to the nucleotide-free leading head is exquisitely gated so that futile hydrolysis is effectively avoided, Experiments show that, when both kinesin heads bind to a microtubule~ ATP cannot bind to kinesin＇s leading head when the neck linker （NL） of this head has a backward orientation. How NL＇s backward orientation is maintained needs understanding on a structural basis. By using steered molecular dynamics and rrmtation simulations, we investigate the backward-pointing conformation of the leading head＇s NL under different inter-head tensions. We find that the NL cannot keep in a strict backward orientation solely by the inter-head tension. LYS325 （amino acid sequence in 2KIN） has an assistant locking function which locks the NL and β0 to the β-domain. This locking function has an enhanced positive cooperation with the inter-head tension. When the inter-head tension is weakened, this locking function can be broken, resulting in a loose backward orientation of the NL. The difference between the strict and loose backward orientation of the NL might be a crucial factor in the gating mechanism. These results are consistent with relevant experiments and proposals.     

Effect of multiple rescattering processes on harmonic emission in spatially inhomogeneous field

The effect of multiple rescattering processes on the harmonic emission from He atom in a spatially inhomogeneous field is discussed by solving the one-dimensional time-dependent Schr?dinger equation and the classical equation of motion.By establishing the physical model of the harmonic emission in the inhomogeneous field, we discuss the related characters of the multiple rescatterings process in the harmonic generation process. It shows that the second rescattering rather than the first rescattering tends to determine the harmonic cutoff energy when the inhomogeneous parameter is larger than 0.0055.Additionally, with the classical simulation, the underlying physical mechanism of the continuum–continuum harmonics is also revealed. Moreover, this work may provide new physical insight into the harmonic generation in an inhomogeneous field, and is beneficial to further extract the harmonic emission from molecular systems.     

In-situ measurement of the surface temperature during holographic recording

Photo-induced processes in organic materials mostly occur on molecular levels. Excited molecules may split to form radicals, starting a polymerization process with diffusing monomers. The azo-dyes perform an optically induced cis-trans isomerization. During pattern formation like a holographic grating, the local temperature increase, especially in thin films, is up to date a subject of estimation from absorption and dissipation data. However, the exact knowledge of the surface temperature would help a lot in understanding the resulting refractive index and thickness patterns during holographic exposure. In this paper, in-situ pyrometer measurements are presented. As examples, different photosensitive materials, varying from a photopolymer to polycrystalline azo dyes, are used in order to outline the magnitude of this effect and demonstrate the feasibility of this technique.     

Correlation mechanism between force chains and friction mechanism during powder compaction

The relation between friction mechanism and force chains characteristics has not yet been fully studied in the powder metallurgy research area.In this work,a uniaxial compression discrete element model is established based on the compaction process of ferrous powder.Furthermore,the correlation mechanism between force chains and the friction mechanism during powder compaction is investigated.The simulation results reveal a strong correlation between the variation of the friction coefficient and the evolution of force chains.During the powder compaction,the friction coefficient would eventually tend to be stable,a feature which is also closely related to the slip ratio between particles.The side wall friction and the friction between particles would have an important effect on the direction of force chain growth in about one-third of the area near the side wall.The research results provide theoretical guidance for improving the densification process of the powder according to the force chain and friction.     

Collisional quantum interference on rotational energy transfer： physical interpretation of the differential interference angle

Collisional quantum interference （CQI） on the intramolecular rotational energy transfer is observed in an experiment with a static cell, and the integral interference angles are measured. To obtain more accurate information, an experiment with a molecular beam is carried out, and thereby the relationship between the differential interference angle and the scattering angle is obtained. Based on the first-Born approximation of time-dependent perturbation theory, the theoretical model of CQI is developed in an atom-diatom system in the condition of the molecular beam, with the long-range interaction potential taken into account. The method of measuring correctly the differential interference angle is presented. The tendencies of the differential interference angle changing with the impact parameter and rel- ative velocity are discussed. The theoretical model presented here is important for understanding or performing the experiment in the molecular beam.     

DNA based molecular motors

Most of the essential cellular processes such as polymerisation reactions, gene expression and regulation are governed by mechanical processes. Controlled mechanical investigations of these processes are therefore required in order to take our understanding of molecular biology to the next level. Single-molecule manipulation and force spectroscopy have over the last 15 years been developed into extremely powerful techniques. Applying these techniques to the investigation of proteins and DNA molecules has led to a mechanistic understanding of protein function on the level of single molecules. As examples for DNA based molecular machines we will describe single-molecule experiments on RNA polymerases as well as on the packaging of DNA into a viral capsid—a process that is driven by one of the most powerful molecular motors.     

Transport in a fluctuating potential

We study the overdamped motion of a particle in a fluctuating one-dimensional periodic potential. The potential has no inversion symmetry, and the fluctuations are correlated in time. At finite temperatures, a stationary current is induced. The amplitude and the direction of the current depend on the details of the noise process that is responsible for the potential fluctuations. We discuss several limiting situations for a general case. Furthermore we calculate the current in the case of a piecewise linear potential for different noise processes and parameters. A detailed discussion of the results is given, including a discussion of the mechanism that is responsible for the current reversal. We compare the present results with results for transport in a ratchet-like potential due to a fluctuating force. We also discuss the biological relevance of the present models for molecular motors. We present a model for the motion of molecular motors that explains why similar molecular motors can move in different directions.     

单分子荧光检测在生命科学中的应用

文章对单分子荧光检测在分子马达、离子通道、信号分子、蛋白折叠、蛋白构象变化动力学、酶活性反应、细胞过程实时观察等生命科学领域中的应用进行了介绍.这些研究结果表明,单分子荧光检测在研究生物大分子的活动规律与机制方面不但有着无法替代的优越性,而且有着广阔的发展空间.     

Stochastic mechano-chemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist’s perspective

A molecular motor is made of either a single macromolecule or a macromolecular complex. Just like their macroscopic counterparts, molecular motors “transduce” input energy into mechanical work. All the nano-motors considered here operate under isothermal conditions far from equilibrium. Moreover, one of the possible mechanisms of energy transduction, called Brownian ratchet, does not even have any macroscopic counterpart. But, molecular motor is not synonymous with Brownian ratchet; a large number of molecular motors execute a noisy power stroke, rather than operating as Brownian ratchet. We review not only the structural design and stochastic kinetics of individual single motors, but also their coordination, cooperation and competition as well as the assembly of multi-module motors in various intracellular kinetic processes. Although all the motors considered here execute mechanical movements, efficiency and power output are not necessarily good measures of performance of some motors. Among the intracellular nano-motors, we consider the porters, sliders and rowers, pistons and hooks, exporters, importers, packers and movers as well as those that also synthesize, manipulate and degrade “macromolecules of life”. We review mostly the quantitative models for the kinetics of these motors. We also describe several of those motor-driven intracellular stochastic processes for which quantitative models are yet to be developed. In part I, we discuss mainly the methodology and the generic models of various important classes of molecular motors. In part II, we review many specific examples emphasizing the unity of the basic mechanisms as well as diversity of operations arising from the differences in their detailed structure and kinetics. Multi-disciplinary research is presented here from the perspective of physicists.     

Ligand diffusion in proteins via enhanced sampling in molecular dynamics

Computational simulations in biophysics describe the dynamics and functions of biological macromolecules at the atomic level. Among motions particularly important for life are the transport processes in heterogeneous media. The process of ligand diffusion inside proteins is an example of a complex rare event that can be modeled using molecular dynamics simulations. The study of physical interactions between a ligand and its biological target is of paramount importance for the design of novel drugs and enzymes. Unfortunately, the process of ligand diffusion is difficult to study experimentally. The need for identifying the ligand egress pathways and understanding how ligands migrate through protein tunnels has spurred the development of several methodological approaches to this problem. The complex topology of protein channels and the transient nature of the ligand passage pose difficulties in the modeling of the ligand entry/escape pathways by canonical molecular dynamics simulations. In this review, we report a methodology involving a reconstruction of the ligand diffusion reaction coordinates and the free-energy profiles along these reaction coordinates using enhanced sampling of conformational space. We illustrate the above methods on several ligand–protein systems, including cytochromes and G-protein-coupled receptors. The methods are general and may be adopted to other transport processes in living matter.     

The Efficiency of Molecular Motors

Molecular motors convert chemical energy into mechanical work while operating in an environment dominated by Brownian motion. The aim of this paper is to explore the flow of energy between the molecular motors and its surroundings, in particular, its efficiency. Based on the Fokker-Planck equation with either N or infinite chemical states, we find that the energy efficiency of molecular motors, whether the Stokes efficiency or the usual thermodynamic efficiency, is strictly less than one, because of the dissipation of the energy in both the overdamped surroundings and in the process of the chemical reaction.     

An introduction to the physics of the bacterial flagellar motor: a nanoscale rotary electric motor

Biological molecular motors show us how directed motion can be generated by nanometre-scale devices that work at the energy scale of the thermal bath. Direct and indirect observations of functioning single molecule motors allow us to see fundamental processes of statistical physics unfolding in microscopic detail at room temperature, something that was unimaginable only a few decades ago. In this review, we introduce molecular motors and the physics relevant to their mechanisms before focusing on our recent experiments on the bacterial flagellar motor, the rotary device responsible for bacterial locomotion.     

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.