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Bio-energy in s-Helix protein molecules with Three Properties of Soliton-Transported Channels

Communications in Theoretical Physics 2007年第2X期48卷 369-376页

作者： PANG Xiao-Feng LIU Mei-Jie Institute of Life Science and Technology University of Electronic Science and Technology of China Chengdu 610054 China International Center for Material Physics the Chinese Academy of Sciences Shenyang 110015 China

We study numerically the propagating properties of soliton-transported bio-energy excited in the a-helix protein molecules with three channels in the cases of the short-time and long-time motions and its features of collision at temperature T = 0 and biological temperature T = 300 K by the dynamic equations in the improved Davydov theory and fourth-order Runge-Kutta method, respectively. From these simulation experiments we see that the new solitons in the improved model can move without dispersion at a constant speed retaining its shape and energy in the cases of motion of both short-time or T = 0 and long time or T = 300 K and can go through each other without scattering in their collisions. In these cases its lifetime is, at least, 120 ps at 300 K, in which the soliton can travel over about 700 amino acid residues. This result is consistent with analytic result obtained by quantum perturbed theory in this model. In the meanwhile, the influences of structure disorder of a-helix protein molecules, including the inhomogeneous distribution of amino acids with different masses and fluctuations of spring constant, dipole-dipole interaction, exciton-phonon coupling constant and diagonal disorder, on the solitons are also studied by the fourth-order Runge-Kutta method. The results show that the soliton still is very robust against the structure disorders and thermal perturbation of proteins at biological temperature 300 K. Therefore we can conclude that the new soliton in the a-helix protein molecules with three channels is a possible carrier of bio-energy transport and the improved model is possibly a candidate for the mechanism of this transport.

关键词： bio-energy transport soliton protein molecule Runge-Kutta method thermal stabilization

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Probability Properties of Multi-contact in protein molecules

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Chemical Research in Chinese Universities 2003年第3期19卷 370-375页

作者： WANGXiang-hong KEJian-hong HUMin-xiao ZHANGLin-xi DepartmentofPhysics WenzhouNormalCollegeWenzhou325000P.R.China DepartmentofPhysics ZhejiangUniversityHangzhou310028P.R.China

The compact conformations of polymers are important because the native conformations of all bio-polymers with certain function are highly compact. The properties of mutil-contact bio-polymer chains were studied by Gaussian statistics of the random-flight chain. The theoretical expressions(were given, also), the calculations of probability distributions and correlation functions for different topologic cases were derived and made respectively. Comparison between single, double and triple contacts was also made. By means of setting the parameters, the results of the current calculations of the multiple contacts are just the same as those calculated by single, double or tripe contacts separately. It is a useful method to investigate native conformations of biopolymers. The probabilities of multi contacts and correlation functions between chain 's contacts were calculated for the Gaussian chains. Because the bond probability distributions are Gaussian 's distributions, the probability distributions of the separations of various points along the chains are always consecutive. All the contacts may break up into several groups, and each group consists of many contacts. Here we investigated the probability distribution from one group to three groups of contacts.

关键词： Random-flight model protein molecule Correlation function

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Properties of Soliton-Transported Bio-energy in c~-Helix protein molecules with Three Channels

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Communications in Theoretical Physics 2007年第8期48卷 369-376页

作者： PANG Xiao-Feng(1,2) LIU Mei-Jie11 Institute of Life Science and Technology,Uniersity of Electronic Science and Technology of China,Chengdu 610054,China2 International Center for Material Physics,the Chinese Academy of Sciences,Shenyang 110015,China

We study numerically the propagating properties of soliton-transported bio-energy excited in the α-helixprotein molecules with three channels in the cases of the short-time and long-time motions and its features of collisionat temperature T=0 and biological temperature T=300 K by the dynamic equations in the improved Davydov theoryand fourth-order Runge-Kutta method,*** these simulation experiments we see that the new solitonsin the improved model can move without dispersion at a constant speed retaining its shape and energy in the cases ofmotion of both short-time or T=0 and long time or T=300 K and can go through each other without scattering in *** these cases its lifetime is,at least,120 ps at 300 K,in which the soliton can travel over about 700 aminoacid *** result is consistent with analytic result obtained by quantum perturbed theory in this *** themeanwhile,the influences of structure disorder of α-helix protein molecules,including the inhomogeneous distribution ofamino acids with different masses and fluctuations of spring constant,dipole-dipole interaction,exciton-phonon couplingconstant and diagonal disorder,on the solitons are also studied by the fourth-order Runge-Kutta *** resultsshow that the soliton still is very robust against the structure disorders and thermal perturbation of proteins at biologicaltemperature 300 *** we can conclude that the new soliton in the α-helix protein molecules with three channelsis a possible carrier of bio-energy transport and the improved model is possibly a candidate for the mechanism of thistransport.

关键词： bio-energy transport soliton protein molecule Runge-Kutta method thermal stabilization

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Sub-molecular features of single proteins in solution resolved with scanning tunneling microscopy

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Nano Research 2016年第9期9卷 2551-2560页

作者： Jihao Wang Lei Zhang Chen Hu Qingsong Liu Yubin Hou Xin Zhang Qingyou Lu High Magnetic Field Laboratory Chinese Academy of Sciences and University of Science and Technology of ChinaHefei 230026China Hefei National Laboratory for Physical Sciences at the Microscale University of Science and Technology of ChinaHefei 230026China Collaborative Innovation Center of Advanced Microstructures Nanjing UniversityNanjing 210093China

Scanning tunneling microscopy (STM) can be used to image individual biological molecules, such as proteins, in vacuum or air. This requires sample dehydration and thus may not reflect the native state of the molecule. Extensive efforts have been made to image single proteins in solution using STM; however, the images have revealed only round or oval shapes with no sub-molecular details. Here, we present the sub-molecular features of streptavidin proteins under physiological conditions using a homebuilt low-leakage-current and highstability liquid phase STM. The N-lobe, C-lobe, and C-terminal tail of the epidermal growth factor receptor kinase domains were also resolved in solution. Our results demonstrate that the structure, morphology, and dynamics of a protein molecule can be examined under physiological conditions by the STM. [Figure not available: see fulltext.] © 2016, Tsinghua University Press and Springer-Verlag Berlin Heidelberg.

关键词： liquid-phase scanning tunneling microscopy (STM) STM imaging under physiological conditions protein molecule sub-molecular resolution

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