THE INFLUENCES OF THE TEMPERATURE ON THE SOLITONS EXCITED IN THE PROTEIN MOLECULES

The thermal stability of the soliton excited in the protein molecular system which work at finite temperature and a nonlinear vibration of the molecular chain have beed studied in our theory. The results obtained show that the soliton moves in supersonic velocity and the amplitude of soliton depends on the temperature and the strengthen of nonlinear vibration. but the soliton excited is thermal stable in the case of the physiologic temperature 310K.

Bio-energy in s-Helix Protein Molecules with Three Properties of Soliton-Transported Channels

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.

Probability Properties of Multi-contact in Protein Molecules

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.

Distribution of Vibrational Energy Levels of Protein Molecular Chains

The distributions of the quantum vibrational energy levels of the protein molecular chain are found by the discretely nonlinear Schr?dinger equation appropriate to protein obtained from the Davydov theory. The results calculated by this method are basically consistent with the experimental values. Furthermore, the energy spectra at high excited states have also been obtained for the molecular chain which is helpful in researching the properties of infrared absorption and Raman scattering of the protein molecules.

Influences of Temperature on Proton Conductivity in the Hydrogen-Bond Molecular Systems with Damping

Influences of temperature of medium on proton conductivity in hydrogen-bonded systems exposed in an electricfield are numerically studied by the fourth-order Runge-Kutta method with our model. The results obtained show that the proton soliton is very robust against thermal perturbation and damping of medium, and is thermally stable in the temperature range T ≤ 273 K. From the simulation we find out that the mobility （or velocity） of proton conduction in ice crystal is a nonmonotonic function of temperature in the temperature range 170-273 K： i.e., it increases initially, reaches a maximum at about 191 K, subsequently decreases to a minimum at about 211 K, and then increases again. This changed rule of mobility is qualitatively consistent with its experimental data in ice in the same temperature range. This result provides an evidence for existence of solitons in the hydrogen-bonded systems.

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

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.

Voyage inside the cell:Microsystems and nanoengineering for intracellular measurement and manipulation

Properties of organelles and intracellular structures play important roles in regulating cellular functions,such as gene expression,cell motility and metabolism.The ability to directly interrogate intracellular structures inside a single cell for measurement and manipulation has significant implications in the understanding of subcellular and suborganelle activities,diagnosing diseases,and potentially developing new therapeutic approaches.In the past few decades,a number of technologies have been developed to study single-cell properties.However,methods of measuring intracellular properties and manipulating subcellular structures have been largely underexplored.Due to the even smaller size of intracellular targets and lower signal-to-noise ratio than that in wholecell studies,the development of tools for intracellular measurement and manipulation is challenging.This paper reviews emerging microsystems and nanoengineered technologies for sensing and quantitative measurement of intracellular properties and for manipulating structures inside a single cell.Recent progress and limitations of these new technologies as well as new discoveries and prospects are discussed.

MiR-3653 blocks autophagy to inhibit epithelial-mesenchymal transition in breast cancer cells by targeting the autophagy-regulatory genes ATG12 and AMBRA1

Background:Metastasis is the main cause of tumor-associated death and mainly responsible for treatment failure of breast cancer.Autophagy accelerates tumor metastasis.In our work,we aimed to investigate the possibility of microRNAs(miRNAs)which participate in the regulation of autophagy to inhibit tumor metastasis.Methods:MiRNA array and comprehensive analysis were performed to identify miRNAs which participated in the regulation of autophagy to inhibit tumor metastasis.The expression levels of miR-3653 in breast cancer tissues and cells were detected by quantitative real-time polymerase chain reaction.In vivo and in vitro assays were conducted to determine the function of miR-3653.The target genes of miR-3653 were detected by a dual luciferase reporter activity assay and Western blot.The relationship between miR-3653 and epithelial-mesenchymal transition(EMT)was assessed by Western blot.Student’s t-test was used to analyze the difference between any two groups,and the difference among multiple groups was analyzed with one-way analysis of variance and a Bonferroni post hoc test.Results:miR-3653 was downregulated in breast cancer cells with high metastatic ability,and high expression of miR-3653 blocked autophagic flux in breast cancer cells.Clinically,low expression of miR-3653 in breast cancer tissues(0.054±0.013 vs.0.131±0.028,t=2.475,P=0.014)was positively correlated with lymph node metastasis(0.015±0.004 vs.0.078±0.020,t=2.319,P=0.023)and poor prognosis(P<0.001).miR-3653 ameliorated the malignant phenotypes of breast cancer cells,including proliferation,migration(MDA-MB-231:0.353±0.013 vs.1.000±0.038,t=16.290,P<0.001;MDA-MB-468:0.200±0.014 vs.1.000±0.043,t=17.530,P<0.001),invasion(MDA-MB-231:0.723±0.056 vs.1.000±0.035,t=4.223,P=0.013;MDA-MB-468:0.222±0.016 vs.1.000±0.019,t=31.050,P<0.001),and colony formation(MDA-MB-231:0.472±0.022 vs.1.000±0.022,t=16.620,P<0.001;MDA-MB-468:0.650±0.040 vs.1.000±0.098,t=3.297,P=0.030).The autophagy-associated genes autophagy-related gene 12(ATG12)and activating molecule in beclin 1-regulated autophagy protein 1(AMBRA1)are target genes of miR-3653.Further studies showed that miR-3653 inhibited EMT by targeting ATG12 and AMBRA1.Conclusions:Our findings suggested that miR-3653 inhibits the autophagy process by targeting ATG12 and AMBRA1,thereby inhibiting EMT,and provided a new idea and target for the metastasis of breast cancer.