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Coarse grain

Ioana M Ilie, Wouter K den Otter, Wim J Briels
We present simulations of the amyloidogenic core of α-synuclein, the protein causing Parkinson's disease, as a short chain of coarse-grain patchy particles. Each particle represents a sequence of about a dozen amino acids. The fluctuating secondary structure of this intrinsically disordered protein is modelled by dynamic variations of the shape and interaction characteristics of the patchy particles, ranging from spherical with weak isotropic attractions for the disordered state to spherocylindrical with strong directional interactions for a β-sheet...
March 21, 2017: Journal of Chemical Physics
Michiel J M Niesen, Connie Y Wang, Reid C Van Lehn, Thomas F Miller
We present a coarse-grained simulation model that is capable of simulating the minute-timescale dynamics of protein translocation and membrane integration via the Sec translocon, while retaining sufficient chemical and structural detail to capture many of the sequence-specific interactions that drive these processes. The model includes accurate geometric representations of the ribosome and Sec translocon, obtained directly from experimental structures, and interactions parameterized from nearly 200 μs of residue-based coarse-grained molecular dynamics simulations...
March 22, 2017: PLoS Computational Biology
Andrew Hill, Po-Ru Loh, Ragu B Bharadwaj, Pascal Pons, Jingbo Shang, Eva Guinan, Karim Lakhani, Iain Kilty, Scott A Jelinsky
BACKGROUND: The association of differing genotypes with disease related phenotypic traits offers great potential to both help identify new therapeutic targets and support stratification of patients who would gain the greatest benefit from specific drug classes. Development of low cost genotyping and sequencing has made collecting large scale genotyping data routine in population and therapeutic intervention studies. In addition, a range of new technologies are being used to capture numerous new and complex phenotypic descriptors...
February 28, 2017: GigaScience
Sivaramakrishnan Ramadurai, Marco Werner, Nigel K H Slater, Aaron Martin, Vladimir A Baulin, Tia E Keyes
Deeper understanding of the molecular interactions between polymeric materials and the lipid membrane is important across a range of applications from permeation for drug delivery to encapsulation for immuno-evasion. Using highly fluidic microcavity supported lipid bilayers, we studied the interactions between amphiphilic polymer PP50 and a DOPC lipid bilayer. As the PP50 polymer is pH responsive the studies were carried out at pH 6.5, 7.05 and 7.5, corresponding to fully, partly protonated (pH = pKa = 7.05) and fully ionized states of the polymer, respectively...
March 22, 2017: Soft Matter
Stanislav M Avdoshenko, Atanu Das, Rohit Satija, Garegin A Papoian, Dmitrii E Makarov
A long time ago, Kuhn predicted that long polymers should approach a limit where their global motion is controlled by solvent friction alone, with ruggedness of their energy landscapes having no consequences for their dynamics. In contrast, internal friction effects are important for polymers of modest length. Internal friction in proteins, in particular, affects how fast they fold or find their binding targets and, as such, has attracted much recent attention. Here we explore the molecular origins of internal friction in unfolded proteins using atomistic simulations, coarse-grained models and analytic theory...
March 21, 2017: Scientific Reports
Coralie Pasquier, Mario Vazdar, Jan Forsman, Pavel Jungwirth, Mikael Lund
The stability of aqueous protein solutions is strongly affected by multivalent ions, which induce ion-ion correlations beyond the scope of classical mean-field theory. Using all-atom Molecular Dynamics (MD) and coarse grained Monte Carlo (MC) simulations, we investigate the interaction between a pair of protein molecules in 3:1 electrolyte solution. In agreement with available experimental findings of "reentrant protein condensation", we observe an anomalous trend in the protein-protein potential of mean force with increasing electrolyte concentration in the order: (i) double-layer repulsion, (ii) ion-ion correlation attraction, (iii) over-charge repulsion, and in excess of 1:1 salt, (iv) non Coulombic attraction...
March 20, 2017: Journal of Physical Chemistry. B
Anatoly V Berezkin, Florian Jung, Dorthe Posselt, Detlef M Smilgies, Christine M Papadakis
Mixtures of two diblock copolymers of very different lengths may feature both macro- and microphase separation; however, not much is known about the mechanisms of separation in diblock copolymer thin films. In the present work, we study thin films of mixtures of two compositionally symmetric block copolymers, both in the one-phase and in the two-phase state, combining coarse-grained molecular simulations (dissipative particle dynamics, DPD) with scattering experiments (grazing-incidence small-angle X-ray scattering, GISAXS)...
March 20, 2017: ACS Applied Materials & Interfaces
Tomaz Urbic, Sara Najem, Cristiano L Dias
In this manuscript we use a two-dimensional coarse-grained model to study how amyloid fibrils grow towards an equilibrium state where they coexist with proteins dissolved in a solution. Free-energies to dissociate proteins from fibrils are estimated from the residual concentration of dissolved proteins. Consistent with experiments, the concentration of proteins in solution affects the growth rate of fibrils but not their equilibrium state. Also, studies of the temperature dependence of the equilibrium state can be used to estimate thermodynamic quantities, e...
March 7, 2017: Biophysical Chemistry
Chenyi Liao, Xiaochuan Zhao, Jiyuan Liu, Severin T Schneebeli, John C Shelley, Jianing Li
The structures and dynamics of protein complexes are often challenging to model in heterogeneous environments such as biological membranes. Herein, we meet this fundamental challenge at attainable cost with all-atom, mixed-resolution, and coarse-grained models of vital membrane proteins. We systematically simulated five complex models formed by two distinct G protein-coupled receptors (GPCRs) in the lipid-bilayer membrane on the ns-to-μs timescales. These models, which suggest the swinging motion of an intracellular loop, for the first time, provide the molecular details for the regulatory role of such a loop...
March 20, 2017: Physical Chemistry Chemical Physics: PCCP
Shilpa Yadahalli, Shachi Gosavi
Comparative studies of proteins from a family have been used to understand the factors that determine the folding routes of proteins. It has been conjectured that the folding mechanism of ribonuclease-H (RNase-H) proteins is determined by the topology of their fold. To test this hypothesis, we computationally studied the folding of four proteins from the RNase-H family, which have the overall RNase-H fold, but whose topologies differ in the region termed CORE in E. coli RNase-H. We simulated the folding of these proteins using molecular dynamics (MD) simulations of a coarse-grained structure-based model (SBM) which captures the effects of topology and found that the four proteins had similar folding routes...
March 20, 2017: Physical Chemistry Chemical Physics: PCCP
Vishal Maingi, Jonathan R Burns, Jaakko J Uusitalo, Stefan Howorka, Siewert J Marrink, Mark S P Sansom
Recently developed DNA-based analogues of membrane proteins have advanced synthetic biology. A fundamental question is how hydrophilic nanostructures reside in the hydrophobic environment of the membrane. Here, we use multiscale molecular dynamics (MD) simulations to explore the structure, stability and dynamics of an archetypical DNA nanotube inserted via a ring of membrane anchors into a phospholipid bilayer. Coarse-grained MD reveals that the lipids reorganize locally to interact closely with the membrane-spanning section of the DNA tube...
March 20, 2017: Nature Communications
Zhaojun Li, Qiuxian Cai, Xuanqi Zhang, Guangwei Si, Qi Ouyang, Chunxiong Luo, Yuhai Tu
We study cell navigation in spatiotemporally complex environments by developing a microfluidic racetrack device that creates a traveling wave with multiple peaks and a tunable wave speed. We find that while the population-averaged chemotaxis drift speed increases with wave speed for low wave speed, it decreases sharply for high wave speed. This reversed dependence of population-averaged chemotaxis drift speed on wave speed is caused by a "barrier-crossing" phenomenon, where a cell hops backwards from one peak attractant location to the peak behind by crossing an unfavorable (barrier) region with low attractant concentrations...
March 3, 2017: Physical Review Letters
Lijun Liu, Issei Nakamura
We illustrate the effects of chain connectivity on the solvation energy of ions immersed in polymer liquids by developing a new coarse-grained molecular dynamics simulation. Our theory accounts for the dielectric response of the polymers through the connection of dipolar, monomeric units with nonlinear springs. In stark contrast to the standard Born solvation energy of ions, our results depend substantially on the chain length of the polymers. We also demonstrate the marked difference in the solvation energies of the ions immersed in non-polymeric particle mixtures, single-component polymers, polymer blends, and block copolymers...
March 17, 2017: Journal of Physical Chemistry. B
Ningning Liang, Yonghao Zhao, Jingtao Wang, Yuntian Zhu
Nanostructured (NS) and ultrafine-grained (UFG) materials have high strength and relatively low ductility. Their toughness has not been comprehensively investigated. Here we report the Charpy impact behavior and the corresponding microstructural evolutions in UFG Cu with equi-axed and elongated grains which were prepared by equal channel angular pressing (ECAP) for 2 and 16 passes at room temperature. It is found that their impact toughness (48 J/cm(2)) is almost comparable to that of coarse grained (CG) Cu: 55 J/cm(2)...
March 17, 2017: Scientific Reports
Huw Colin-York, Christian Eggeling, Marco Fritzsche
Cells continuously exert or respond to mechanical force. Measurement of these nanoscale forces is a major challenge in cell biology; yet such measurement is essential to the understanding of cell regulation and function. Current methods for examining mechanical force generation either necessitate dedicated equipment or limit themselves to coarse-grained force measurements on the micron scale. In this protocol, we describe stimulated emission depletion traction force microscopy-STED-TFM (STFM), which allows higher sampling of the forces generated by the cell than conventional TFM, leading to a twofold increase in spatial resolution (of up to 500 nm)...
April 2017: Nature Protocols
Subhadip Ghosh, Ignacio Pagonabarraga, Sudipto Muhuri
We study a two-filament driven lattice gas model with oppositely directed species of particles moving on two parallel filaments with filament-switching processes and particle inflow and outflow at filament ends. The filament-switching process is correlated with the occupation number of the adjacent site such that particles switch filaments with finite probability only when oppositely directed particles meet on the same filament. This model mimics some of the coarse-grained features observed in context of microtubule-(MT) based intracellular transport, wherein cellular cargo loaded and off-loaded at filament ends are transported on multiple parallel MT filaments and can switch between the parallel microtubule filaments...
February 2017: Physical Review. E
Somajit Dey, Jayashree Saha
Aggregation mesophases of self-assembling amphiphiles in water are highly important in the context of biology (biomembranes), therapy (liposomes), industry (polymer surfactants), and condensed-matter physics (lyotropic liquid crystals). Besides helping to increase fundamental understanding of collective molecular behavior, simulations of these lyotropic phases are pivotal to technological and medical developments such as smart drug carriers for gene therapy. Implicit-solvent, coarse-grained, low resolution modeling with a simple pair potential is the key to realizing the larger length and time scales associated with such mesoscopic phenomena during a computer simulation...
February 2017: Physical Review. E
Marc Lämmel, Kamil Dzikowski, Klaus Kroy, Luc Oger, Alexandre Valance
The collision of a spherical grain with a granular bed is commonly parametrized by the splash function, which provides the velocity of the rebounding grain and the velocity distribution and number of ejected grains. Starting from elementary geometric considerations and physical principles, like momentum conservation and energy dissipation in inelastic pair collisions, we derive a rebound parametrization for the collision of a spherical grain with a granular bed. Combined with a recently proposed energy-splitting model [Ho et al...
February 2017: Physical Review. E
Eirik G Flekkøy, Steven R Pride, Renaud Toussaint
Onsager reciprocity relations derive from the fundamental time reversibility of the underlying microscopic equations of motion. This gives rise to a large set of symmetric cross-coupling phenomena. We here demonstrate that different reciprocity relations may arise from the notion of mesoscopic time reversibility, i.e., reversibility of intrinsically coarse-grained equations of motion. We use Brownian dynamics as an example of such a dynamical description and show how it gives rise to reciprocity in the hydrodynamic dispersion tensor as long as the background flow velocity is reversed as well...
February 2017: Physical Review. E
Valeri V Smirnov, Leonid I Manevitch
We present an analytical description of the large-amplitude stationary oscillations of the finite discrete system of harmonically coupled pendulums without any restrictions on their amplitudes (excluding a vicinity of π). Although this model has numerous applications in different fields of physics, it was studied earlier in the infinite limit only. The discrete chain with a finite length can be considered as a well analytical analog of the coarse-grain models of flexible polymers in the molecular dynamics simulations...
February 2017: Physical Review. E
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