Molecular Dynamics Modeling of the Interaction of Cationic Fluorescent Lipid Peroxidation-Sensitive Probes with the Mitochondrial Membrane

2019 ◽  
Vol 486 (1) ◽  
pp. 220-223
Author(s):  
A. M. Nesterenko ◽  
E. G. Kholina ◽  
K. G. Lyamzaev ◽  
A. Ya. Mulkidjanian ◽  
B. V. Chernyak
2019 ◽  
Vol 486 (4) ◽  
pp. 509-513
Author(s):  
A. M. Nesterenko ◽  
E. G. Kholina ◽  
K. G. Lyamzaev ◽  
A. Y. Mulkidzhanyan ◽  
B. V. Chernyak

Cardiolipin (CL) plays a central role in lipid peroxidation (LPO) of the mitochondrial inner membrane due to higher content of unsaturated fatty acids in CL in comparison with the other phospholipids. CL oxidation plays an important role in the regulation of various intracellular signaling pathways and its excessive oxidation contributes to the development of various pathologies and, possibly, participates in the aging process. Mitochondria-targeted antioxidants containing triphenylphosphonium cation (TPP+) effectively protect CL from oxidation. It is assumed that fluorescent probes on the basis of the C11-BODIPY fluorophore sensitive to LPO and containing TPP+ can selectively register CL oxidation. To test this possibility, we carried out a molecular dynamic simulation of such probes in a model mitochondrial membrane. It is shown that the probes are located in the membrane at the same depth as the unsaturated bonds in CL molecules sensitive to oxidation. Increasing the length of the linker that binds the fluorophore and TPP+ residue has little effect on the position of the probe in the membrane. This indicates the possibility of modifying the linker to increase the selectivity of the probes to CL.


Author(s):  
Peiqiang Yang ◽  
Xueping Zhang ◽  
Zhenqiang Yao ◽  
Rajiv Shivpuri

Abstract Titanium alloys’ excellent mechanical and physical properties make it the most popular material widely used in aerospace, medical, nuclear and other significant industries. The study of titanium alloys mainly focused on the macroscopic mechanical mechanism. However, very few researches addressed the nanostructure of titanium alloys and its mechanical response in Nano-machining due to the difficulty to perform and characterize nano-machining experiment. Compared with nano-machining, nano-indentation is easier to characterize the microscopic plasticity of titanium alloys. This research presents a nano-indentation molecular dynamics model in titanium to address its microstructure alteration, plastic deformation and other mechanical response at the atomistic scale. Based on the molecular dynamics model, a complete nano-indentation cycle, including the loading and unloading stages, is performed by applying Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). The plastic deformation mechanism of nano-indentation of titanium with a rigid diamond ball tip was studied under different indentation velocities. At the same time, the influence of different environment temperatures on the nano-plastic deformation of titanium is analyzed under the condition of constant indentation velocity. The simulation results show that the Young’s modulus of pure titanium calculated based on nano-indentation is about 110GPa, which is very close to the experimental results. The results also show that the mechanical behavior of titanium can be divided into three stages: elastic stage, yield stage and plastic stage during the nano-indentation process. In addition, indentation speed has influence on phase transitions and nucleation of dislocations in the range of 0.1–1.0 Å/ps.


2016 ◽  
Vol 711 ◽  
pp. 1061-1068
Author(s):  
Yang Zhou ◽  
Guo Dong Xu

Molecular Dynamics was employed to investigate the interaction of calcium silicate hydrate (C-S-H), the primary hydration product of cement based materials, and chloride, causing severe durable problems of concrete. The 11Å tobermorite structure was chosen to describe the C-S-H structure and the CLAYFF force field was used. It is observed in the simulation that there are no bound chlorides at 303K, while a fraction of chlorides appear in the adsorption district of tobermorite/solution interface at 323K indicating the temperature increase can improve chloride sorption capacity of C-S-H. The formation of Ca-Cl cluster is found on the surface of tobermorite, which is assumed to promote the chloride sorption. The experimental results of sorption isotherms of C-S-H in CaCl2 and NaCl aqueous solutions with the same chloride concentration have proved this point. Other researchers have made the same conclusion by means of molecular dynamics modeling, NMR tests or zeta potential experiments.


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