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Coarse grain

Ramachandra Moorthy Bhaskara, Stephanie M Linker, Martin Vögele, Juergen Koefinger, Gerhard Hummer
The fusion of lipid membranes is opposed by high energetic barriers. In living organisms, complex protein machineries carry out this biologically essential process. Here we show that membrane-spanning carbon nanotubes (CNTs) can trigger spontaneous fusion of small lipid vesicles. In coarse-grained molecular dynamics simulations, we find that a CNT bridging between two vesicles locally perturbs their lipid structure. Their outer leaflets merge as the CNT pulls lipids out of the membranes, creating an hourglass-shaped fusion intermediate with still intact inner leaflets...
January 19, 2017: ACS Nano
Cheng-Dong Li, Qin Xu, Ruo-Xu Gu, Jing Qu, Dong-Qing Wei
It is generally believed that the etiology of Alzheimer's disease (AD) is closely related to the amyloid-β polypeptides, produced from γ-secretase cleavage of C99. There is preliminary evidence that cholesterol directly activates γ-secretase cleavage of C99 through mechanisms that have not been understood so far. In this article, coarse-grained (CG) and all-atom (AT) simulations were employed to investigate the association between C99 and cholesterol, which is essential for our understanding of the role of cholesterol in the amyloidogenic pathway...
January 19, 2017: Physical Chemistry Chemical Physics: PCCP
Michael D Ward, Shivangi Nangia, Eric R May
The PACE force field presents an attractive model for conducting molecular dynamics simulations of membrane-protein systems. PACE is a hybrid model, in which lipids and solvents are coarse-grained consistent with the MARTINI mapping, while proteins are described by a united atom model. However, given PACE is linked to MARTINI, which is widely used to study membranes, the behavior of proteins interacting with membranes has only been limitedly examined in PACE. In this study, PACE is used to examine the behavior of several peptides in membrane environments, namely WALP peptides, melittin and influenza hemagglutinin fusion peptide (HAfp)...
January 19, 2017: Journal of Computational Chemistry
Hyun Woo Cho, Bong June Sung
We investigate the glass transition and interfacial dynamics of single strand fibers of flexible polymers by employing molecular dynamics (MD) simulations along with a coarse grained model. While the polymer fiber has drawn significant attention due to its applicability in tissue engineering and stretchable electronics, its dynamic properties, especially the glass transition temperature (Tg), are yet to be understood at the molecular level. For example, there has been a controversy on the effect of the polymer fiber radius (R) on Tg: Tg decreased with a decrease in R for some polymer fibers, whereas Tg of other polymer fibers was not sensitive to R...
January 18, 2017: Soft Matter
Ana Rojas, Nika Maisuradze, Khatuna Kachlishvili, Harold A Scheraga, Gia G Maisuradze
Fibrils formed by the β-amyloid (Aβ) peptide play a central role in the development of Alzheimer's disease. In this study, the principles governing their growth and stability are investigated by analyzing canonical and replica-exchange molecular dynamics trajectories of Aβ(9-40) fibrils. In particular, an unstructured monomer was allowed to interact freely with an Aβ fibril template. Trajectories were generated with the coarse-grained united-residue force field, and one- and two-dimensional free-energy landscapes (FELs) along the backbone virtual-bond angle θ and backbone virtual-bond-dihedral angle γ of each residue and principal components, respectively, were analyzed...
January 18, 2017: ACS Chemical Neuroscience
Gabrielle Stetz, Gennady M Verkhivker
Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions...
January 2017: PLoS Computational Biology
Jan-Michael Y Carrillo, John Katsaras, Bobby G Sumpter, Rana Ashkar
Biological cell membranes are responsible for a range of structural and dynamical phenomena crucial to a cell's well-being and its associated functions. Due to the complexity of cell membranes, lipid bilayer systems are often used as biomimetic models. These systems have led to significant insights into vital membrane phenomena such as domain formation, passive permeation and protein insertion. Experimental observations of membrane structure and dynamics are, however, limited in resolution, both spatially and temporally...
January 12, 2017: Journal of Chemical Theory and Computation
Govardhan Reddy, Dave Thirumalai
The folding of small protein Ubiquitin (Ub), which plays an indispensable role in targeting proteins for degradation and DNA damage response is complex. A number of experiments on Ub folding have reached differing conclusions regarding the relation between collapse and folding, and whether intermediates are populated. In order to resolve these vexing issues, we elucidate the denaturant-dependent thermodynamics and kinetics of Ub folding at low and neutral pH as a function of Guanidinium chloride and Urea using coarse-grained molecular simulations...
January 11, 2017: Journal of Physical Chemistry. B
Adam K Sieradzan, Rafał Jakubowski
In this article, an implementation of steered molecular dynamics (SMD) in coarse-grain UNited RESidue (UNRES) simulations package is presented. Two variants of SMD have been implemented: with a constant force and a constant velocity. The huge advantage of SMD implementation in the UNRES force field is that it allows to pull with the speed significantly lower than the accessible pulling speed in simulations with all-atom representation of a system, with respect to a reasonable computational time. Therefore, obtaining pulling speed closer to those which appear in the atomic force spectroscopy is possible...
January 11, 2017: Journal of Computational Chemistry
Manaswee Suttipong, Brian P Grady, Alberto Striolo
Using coarse-grained dissipative particle dynamics (DPD) simulations, we systematically study the effect of surface heterogeneity on surfactant adsorption. Here we investigate the adsorption and aggregation of surfactants on hydrophobic stripes crossing each other perpendicularly (i.e., crossing stripes) and on hydrophobic steps. The results are compared with those obtained for isolated stripes. We find that on crossing stripes of moderate stripe widths (e.g., L = 0.61LS, 1.22LS and 1.83LS, where LS is the length of one surfactant molecule) the crossing region hinders the formation of defect-free adsorbed surfactant structures...
January 11, 2017: Soft Matter
Dudu Tong, Sichun Yang, Lanyuan Lu
Structure modelling via small-angle X-ray scattering (SAXS) data generally requires intensive computations of scattering intensity from any given biomolecular structure, where the accurate evaluation of SAXS profiles using coarse-grained (CG) methods is vital to improve computational efficiency. To date, most CG SAXS computing methods have been based on a single-bead-per-residue approximation but have neglected structural correlations between amino acids. To improve the accuracy of scattering calculations, accurate CG form factors of amino acids are now derived using a rigorous optimization strategy, termed electron-density matching (EDM), to best fit electron-density distributions of protein structures...
August 1, 2016: Journal of Applied Crystallography
Xavier Periole
G protein-coupled receptors (GPCRs) are central to many fundamental cellular signaling pathways. They transduce signals from the outside to the inside of cells in physiological processes ranging from vision to immune response. It is extremely challenging to look at them individually using conventional experimental techniques. Recently, a pseudo atomistic molecular model has emerged as a valuable tool to access information on GPCRs, more specifically on their interactions with their environment in their native cell membrane and the consequences on their supramolecular organization...
January 11, 2017: Chemical Reviews
Paolo Calligari, Marco Gerolin, Daniel Abergel, Antonino Polimeno
In this article, we present a clustering method of atoms in proteins based on the analysis of the correlation times of interatomic distance correlation functions computed from MD simulations. The goal is to provide a coarse-grained description of the protein in terms of fewer elements that can be treated as dynamically independent subunits. Importantly, this domain decomposition method does not take into account structural properties of the protein. Instead, the clustering of protein residues in terms of networks of dynamically correlated domains is defined on the basis of the effective correlation times of the pair distance correlation functions...
January 10, 2017: Journal of Chemical Theory and Computation
Jibao Lu, Liam C Jacobson, Yamila A Perez Sirkin, Valeria Molinero
Molecular simulations provide a versatile tool to study the structure, anion conductivity, and stability of anion-exchange membrane (AEM) materials and can provide a fundamental understanding of the relation between structure and property of membranes that is key for their use in fuel cells and other applications. The quest for large spatial and temporal scales required to model the multiscale structure and transport processes in the polymer electrolyte membranes, however, cannot be met with fully atomistic models, and the available coarse-grained (CG) models suffer from several challenges associated with their low-resolution...
January 10, 2017: Journal of Chemical Theory and Computation
David Ando, Ajay Gopinathan
Nucleocytoplasmic transport is highly selective, efficient, and is regulated by a poorly understood mechanism involving hundreds of disordered FG nucleoporin proteins (FG nups) lining the inside wall of the nuclear pore complex (NPC). Previous research has concluded that FG nups in Baker's yeast (S. cerevisiae) are present in a bimodal distribution, with the "Forest Model" classifying FG nups as either di-block polymer like "trees" or single-block polymer like "shrubs". Using a combination of coarse-grained modeling and polymer brush modeling, the function of the di-block FG nups has previously been hypothesized in the Di-block Copolymer Brush Gate (DCBG) model to form a higher-order polymer brush architecture which can open and close to regulate transport across the NPC...
2017: PloS One
Ming Tang, Tong Li, Neha S Gandhi, Kevin Burrage, YuanTong Gu
Collagen is an abundant structural biopolymer in mammal vertebrates, providing structural support as well as mechanical integrity for connective tissues such as bone, ligament, and tendon. The mechanical behaviours of these tissues are determined by the nanomechanics of their structures at different hierarchies and the role of collagen structures in the extracellular matrix. Some studies revealed that there is significant microstructural difference in the longitudinal direction of the collagen fibril, which challenges the conventional rod-like assumption prevalently adopted in the existing studies...
January 7, 2017: Biomechanics and Modeling in Mechanobiology
Abelardo Ramírez-Hernández, Brandon L Peters, Ludwig Schneider, Marat Andreev, Jay D Schieber, Marcus Müller, Juan J de Pablo
Coarse grained simulation approaches provide powerful tools for the prediction of the equilibrium properties of polymeric systems. Recent efforts have sought to develop coarse-graining strategies capable of predicting the non-equilibrium behavior of entangled polymeric materials. Slip-link and slip-spring models, in particular, have been shown to be capable of reproducing several key aspects of the linear response and rheology of polymer melts. In this work, we extend a previously proposed multi-chain slip-spring model in a way that correctly incorporates the effects of the fluctuating environment in which polymer segments are immersed...
January 7, 2017: Journal of Chemical Physics
Zhen Li, Hee Sun Lee, Eric Darve, George Em Karniadakis
Memory effects are often introduced during coarse-graining of a complex dynamical system. In particular, a generalized Langevin equation (GLE) for the coarse-grained (CG) system arises in the context of Mori-Zwanzig formalism. Upon a pairwise decomposition, GLE can be reformulated into its pairwise version, i.e., non-Markovian dissipative particle dynamics (DPD). GLE models the dynamics of a single coarse particle, while DPD considers the dynamics of many interacting CG particles, with both CG systems governed by non-Markovian interactions...
January 7, 2017: Journal of Chemical Physics
Sima Hashemi Nemati, Afra Hadjizadeh
Titanium (Ti)-based materials is the most appropriate choices for the applications as orthopedic and dental implants. In this regard, ultrafine-grained (UFG) titanium with an enhanced mechanical properties and surface energy has attracted more attention. Titanium dioxide (TiO2) nanotubes grown on the titanium could enhance bone bonding, cellular response and are good reservoirs for loading drugs and antibacterial agents. This article investigates gentamicin loading into and release from the TiO2 nanotubes, grown on the UFG compared to coarse-grained (CG) titanium substrate surfaces...
January 6, 2017: AAPS PharmSciTech
Y S Zhang, Y H Zhao, W Zhang, J W Lu, J J Hu, W T Huo, P X Zhang
Multifunctional materials with more than two good properties are widely required in modern industries. However, some properties are often trade-off with each other by single microstructural designation. For example, nanostructured materials have high strength, but low ductility and thermal stability. Here by means of spark plasma sintering (SPS) of nitrided Ti particles, we synthesized bulk core-shell structured Ti alloys with isolated soft coarse-grained Ti cores and hard Ti-N solid solution shells. The core-shell Ti alloys exhibit a high yield strength (~1...
January 6, 2017: Scientific Reports
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