Atomistic molecular dynamics simulations of tubulin heterodimers explain the motion of a microtubule

Microtubules are essential parts of the cytoskeleton that are built by polymerization of tubulin heterodimers into a hollow tube. Regardless that their structures and functions have been comprehensively investigated in a modern soft matter, it is unclear how properties of tubulin heterodimer influence and promote the self-assembly. A detailed knowledge of such structural mechanisms would be helpful in drug design against neurodegenerative diseases, cancer, diabetes etc. In this work atomistic molecular dynamics simulations were used to investigate the fundamental dynamics of tubulin heterodimers in a sheet and a short microtubule utilizing well-equilibrated structures. The breathing motions of the tubulin heterodimers during assembly show that the movement at the lateral interface between heterodimers (wobbling) dominates in the lattice. The simulations of the protofilament curvature agrees well with recently published experimental data, showing curved protofilaments at polymerization of the microtubule plus end. The tubulin heterodimers exposed at the microtubule minus end were less curved and displayed altered interactions at the site of sheet closure around the outmost heterodimers, which may slow heterodimer binding and polymerization, providing a potential explanation for the limited dynamics observed at the minus end

Finite element modeling of effective properties of nanoporous thermoelastic composites with surface effects

This investigation concerns to the determination of the material properties of nanoscale thermoelastic composites of an arbitrary anisotropy class with stochastically distributed porosity. In order to take into account nanoscale level at the borders between material and pores, the GurtinMurdoch model of surface stresses and the highly conduct- ing model are used. Finite element package ANSYS was used to simulate representative volume and to calculate the effective material properties. This approach is based on the theory of effective moduli of composite mechanics, modeling of representative volumes and the finite element method. Here, the contact boundaries between material and pores were covered by the surface membrane elastic and thermal shell elements in order to take the surface effects into account

Инфекционно-токсический шок в акушерстве и гинекологии

ШОК ТОКСИЧЕСКИЙ /ДИАГН /ПАТОФИЗИОЛ /ТЕРСЕПТИЦЕМИЯИНФЕКЦИЯ /ОСЛЖЕНСКИЕ БОЛЕЗНИ /ОСЛ /СМЕРТНАБОРТ КРИМИНАЛЬНЫЙБАКТЕРИАЛЬНЫЕ ИНФЕКЦИИ /ОСЛГИСТЕРЭКТОМИЯГИНЕКОЛОГИЧЕСКИЕ ХИРУРГИЧЕСКИЕ ОПЕРАЦИ

Tracing Molecular Conformations by X-ray Solution Scattering

In the present work the refinement of X-ray data have been used to solve different scientific problems, namely drug localization in the liposome wall, reaction kinetics of the small molecule upon excitation and resolving an ensemble of protein structures at different temperatures. The common approach included collection of X-ray scattering patterns, modelling of the system of interest in atomic level and fitting computed results to experimental data. Employed fitting algorithms varied depends on the application ranging from inverse matrix calculations to the genetic algorithm for complex tasks. Observed results broaden our understanding of investigated systems on molecular level and also lead to development faster, more effective ways to sample atomic structures by X-ray diffusion scattering

Tracing Molecular Conformations by X-ray Solution Scattering

In the present work the refinement of X-ray data have been used to solve different scientific problems, namely drug localization in the liposome wall, reaction kinetics of the small molecule upon excitation and resolving an ensemble of protein structures at different temperatures. The common approach included collection of X-ray scattering patterns, modelling of the system of interest in atomic level and fitting computed results to experimental data. Employed fitting algorithms varied depends on the application ranging from inverse matrix calculations to the genetic algorithm for complex tasks. Observed results broaden our understanding of investigated systems on molecular level and also lead to development faster, more effective ways to sample atomic structures by X-ray diffusion scattering

EnHD data

<p>X-ray scattering data collected for Engrailed Homeodomain proten (61 residue), at four different temperatures t = 20C, 30C, 40C and 55C.<br>Scattering spectra were fitted structures obtained from molecular dynamics simulations.</p> <p>Experimental data was interpreted used ensemble optimization method applying genetic algorithm. Other details could be found in REDME file.</p

Molecular insights into dipole relaxation processes in water-lysine mixtures

Dielectric spectroscopy is a robust method to investigate relaxations of molecular dipoles. It is particularly useful for studies of biological solutions because of the potential of this method to cover a broad range of dynamical time scales typical for such systems. However, this technique does not provide any information about the nature of the molecular motions, which leads to a certain underemployment of dielectric spectroscopy for gaining microscopic understanding of material properties. For such detailed understanding, computer simulations are valuable tools because they can provide information about the nature of molecular motions observed by, for example, dielectric spectroscopy and to further complement them with structural information. In this work, we acquire information about the nature of dipole relaxation, in n-lysine solutions by means of molecular dynamics simulations. Our results indicate that the experimentally observed main relaxation process of n-lysine has different origins for the single monomer and the polypeptide chains. The relaxation of 1-lysine is due to the motions of whole molecules, whereas the experimentally observed relaxation of 3-lysine and 4-lysine is due to the motions of the residues, which, in turn, are promoted by water relaxation. Furthermore, we propose a new structural model of the lysine amino acids, which can quantitatively account for the experimental dielectric relaxation data. Hydrogen bonding and the structure of water are also discussed in terms of their influence on relaxation processes.All simulations were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC) at Chalmers Center for Computational Science and Engineering (C3SE). This work was financially supported by Knut and Alice Wallenberg foundation (grant no. 2012.0106) and the Swedish Research Council (grant no. 2015-05434). S.C. is thankful to CSIC (i-Link program, Link-B 20012) and Basque Government (IT-1175-19) for financial support

Finite element modeling of effective properties of nanoporous thermoelastic composites with surface effects

This investigation concerns to the determination of the material properties of nanoscale thermoelastic composites of an arbitrary anisotropy class with stochastically distributed porosity. In order to take into account nanoscale level at the borders between material and pores, the GurtinMurdoch model of surface stresses and the highly conduct- ing model are used. Finite element package ANSYS was used to simulate representative volume and to calculate the effective material properties. This approach is based on the theory of effective moduli of composite mechanics, modeling of representative volumes and the finite element method. Here, the contact boundaries between material and pores were covered by the surface membrane elastic and thermal shell elements in order to take the surface effects into account