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Coarse grain

Anthony R Braun, Michael M Lacy, Vanessa C Ducas, Elizabeth Rhoades, Jonathan N Sachs
α-Synuclein is the primary protein found in Lewy bodies, the protein and lipid aggregates associated with Parkinson's disease and Lewy body dementia. The protein folds into a uniquely long amphipathic α-helix (AH) when bound to a membrane, and at high enough concentrations, it induces large-scale remodeling of membranes (tubulation and vesiculation). By engineering a less hydrophobic variant of α-Synuclein, we previously showed that the energy associated with binding of α-Synuclein's AH correlates with the extent of membrane remodeling (Braun et al...
February 26, 2017: Journal of Membrane Biology
Jiawen Chen, Yinghao Wu
Intercellular contacts in multicellular organisms are maintained by membrane receptors called cell adhesion molecules (CAMs) which are expressed on cell surfaces. One interesting feature of CAMs is that almost all of their extracellular regions contain repeating copies of structural domains. It is not clear why so many extracellular domains need to be evolved through natural selection. We tackled this problem by computational modeling. A generic model of CAMs was constructed based on domain organization of neuronal cell adhesion molecule (NrCAM), which is engaged in maintaining neuron-neuron adhesion in central nervous system...
February 22, 2017: Journal of Molecular Biology
Bin Song, Nathaniel Charest, Herbert Alexander Morriss-Andrews, Valeria Molinero, Joan-Emma Shea
The conformational states adopted by a polymer chain in water are a result of a delicate balance between intra-molecular and water-mediated interactions. Using an explicit representation of the solvent is, however, computationally expensive and it is often necessary to turn to implicit representations. We present a systematic derivation of implicit models of water and study the effect of simplifying the representation of the solvent on the conformations of hydrophobic homopolymers of varying length. Starting from the explicit coarse-grained single site mW water model, we develop an implicit solvent model that reproduces the free energy of the contact pair between two hydrophobic monomers, an implicit solvent model that captures the free energy of contact pair minima, desolvation barrier, and solvent-separated minima, and finally, we consider vacuum simulations...
February 25, 2017: Journal of Computational Chemistry
Christina Schindler, Martin Zacharias
Peptide-protein interactions are abundant in the cell and form an important part of the interactome. Large-scale modeling of peptide-protein complexes requires a fully blind approach; i.e., simultaneously predicting the peptide-binding site and the peptide conformation to high accuracy. Here, we present one of the first fully blind peptide-protein docking protocols, pepATTRACT. It combines a coarse-grained ensemble docking search of the entire protein surface with two stages of atomistic flexible refinement...
2017: Methods in Molecular Biology
Alexis Lamiable, Pierre Thévenet, Stephanie Eustache, Adrien Saladin, Gautier Moroy, Pierre Tuffery
The blind identification of candidate patches of interaction on the protein surface is a difficult task that can hardly be accomplished without a heuristic or the use of simplified representations to speed up the search. The PEP-SiteFinder protocol performs a systematic blind search on the protein surface using a rigid docking procedure applied to a limited set of peptide suboptimal conformations expected to approximate satisfactorily the conformation of the peptide in interaction. All steps rely on a coarse-grained representation of the protein and the peptide...
2017: Methods in Molecular Biology
Anthony Fardet
Food health potential is not only due to the sum of its nutrients, but also to its food structure [1]. [...].
March 30, 2016: Foods (Basel, Switzerland)
Bartholomé Delort, Pedro Renault, Landry Charlier, Florent Raussin, Jean Martinez, Nicolas Floquet
In this study, we used the Martini Coarse-Grained model with no applied restraints to predict the binding mode of some peptides to G-Protein Coupled Receptors (GPCRs). Both the Neurotensin-1 and the chemokine CXCR4 receptors were used as test cases. Their ligands, NTS8-13 and CVX15 peptides, respectively, were initially positioned in the surrounding water box. Using a protocol based on Replica Exchange Molecular Dynamics (REMD), both opening of the receptors and entry of the peptides into their dedicated pockets were observed on the μs time-scale...
February 23, 2017: Journal of Chemical Information and Modeling
C Xu, T Nakata, X G Qiao, M Y Zheng, K Wu, S Kamado
The effect of long period stacking ordered (LPSO) phase and γ' precipitates on the ageing behavior and mechanical properties of the extruded Mg-8.2Gd-3.8Y-1.0Zn-0.4Zr (wt.%) alloy was investigated. The results show that more β' phases precipitate during ageing treatment in the LPSO phase containing alloy so that the LPSO phase containing alloy exhibits a higher age-hardening response than the γ' precipitates containing alloy. The precipitation strengthening induced by β' precipitates is the greatest contributor to the strength of the peak-aged LPSO-containing alloys...
February 23, 2017: Scientific Reports
Claire A Lemarchand, Marc Couty, Bernard Rousseau
We apply the dissipative particle dynamics strategy proposed by Hijón et al. [Faraday Discuss. 144, 301-322 (2010)] and based on an exact derivation of the generalized Langevin equation to cis- and trans-1,4-polybutadiene. We prove that it is able to reproduce not only the structural but also the dynamical properties of these polymers without any fitting parameter. A systematic study of the effect of the level of coarse-graining is done on cis-1,4-polybutadiene. We show that as the level of coarse-graining increases, the dynamical properties are better and better reproduced while the structural properties deviate more and more from those calculated in molecular dynamics (MD) simulations...
February 21, 2017: Journal of Chemical Physics
Hamed Azami, Keith Smith, Javier Escudero, Hamed Azami, Keith Smith, Javier Escudero, Javier Escudero, Keith Smith, Hamed Azami
Multivariate multiscale entropy (mvMSE) has been proposed as a combination of the coarse-graining process and multivariate sample entropy (mvSE) to quantify the irregularity of multivariate signals. However, both the coarse-graining process and mvSE may not be reliable for short signals. Although the coarse-graining process can be replaced with multivariate empirical mode decomposition (MEMD), the relative instability of mvSE for short signals remains a problem. Here, we address this issue by proposing the multivariate fuzzy entropy (mvFE) with a new fuzzy membership function...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Lauren Samy, Paul M Macey, Majid Sarrafzadeh, Lauren Samy, Paul M Macey, Majid Sarrafzadeh, Majid Sarrafzadeh, Lauren Samy
Obstructive sleep apnea (OSA) is a prevalent sleep disorder characterized by repeated episodes of complete or partial blockage of the upper airway. These episodes can interfere with sound sleep and have fatal health consequences. They can also reduce the flow of oxygen to vital organs, like the brain, and lead to brain damage. In this paper, we leverage the correlation between brain damage and OSA to design a prediction framework that can assess the severity level of the OSA condition, as well as estimate the Apnea-Hypopnea Index (AHI) using only features obtained during wakefulness...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Xueming Tang, Weizhong Zou, Peter H Koenig, Shawn D McConaughy, Michael R Weaver, David Michael Eike, Michael J Schmidt, Ronald G Larson
We link micellar structures to rheological properties for two surfactant body-wash formulations at various concentrations of salts and perfume raw materials (PRMs) using molecular simulations and micellar-scale modeling as well as traditional surfactant packing arguments. The two body washes, named BW-1EO and BW-3EO, are composed of sodium lauryl ethylene glycol ether sulfate (SLEnS, where n is the average number of ethylene glycol repeat units), cocamidopropyl betaine (CAPB), ACCORD (which is a mixture of six PRMs), and NaCl salt...
February 22, 2017: Journal of Physical Chemistry. B
Guanhua Zhu, Wuan Geok Saw, Anjaiah Nalaparaju, Gerhard Grüber, Lanyuan Lu
An ensemble modeling scheme incorporating coarse-grained simulations with experimental small-angle X-ray scattering (SAXS) data is applied to the dengue virus 2 (DENV2) non-structural protein 5 (NS5). NS5 serves a key role in viral replication through its two domains that are connected by a ten-residue polypeptide segment. A set of representative structures are generated from a simulated structure pool using SAXS data fitting by the non-negativity least squares (NNLS) or the standard Ensemble Optimization Method (EOM) based on a genetic algorithm (GA)...
February 22, 2017: Journal of Physical Chemistry. B
Ramesh Adhikari, Dmitrii E Makarov
A common approach to inducing selective mechanochemical transformations relies on embedding the target molecules (called mechanophores) within elastomeric polymer networks. Mechanical properties of such elastomers can also be modulated through the mechanochemical response of the constituent polymer chains. The inherent randomness in the molecular structure of such materials leads to heterogeneity of the local forces exerted on individual mechanophores. Here we use coarse-grained simulations to study the force distributions within random elastomeric networks and show that those distributions are close to exponential regardless of the applied macroscopic load, entanglement effects and/or network parameters...
February 21, 2017: Journal of Physical Chemistry. B
Ming Yang, Henry Chan, Gongpu Zhao, Joong Hwan Bahng, Peijun Zhang, Petr Král, Nicholas A Kotov
Nanoscale compartments are one of the foundational elements of living systems. Capsids, carboxysomes, exosomes, vacuoles and other nanoshells easily self-assemble from biomolecules such as lipids or proteins, but not from inorganic nanomaterials because of difficulties with the replication of spherical tiling. Here we show that stabilizer-free polydispersed inorganic nanoparticles (NPs) can spontaneously organize into porous nanoshells. The association of water-soluble CdS NPs into self-limited spherical capsules is the result of scale-modified electrostatic, dispersion and other colloidal forces...
March 2017: Nature Chemistry
Daniel Rodriquez, Jae-Han Kim, Samuel E Root, Zhuping Fei, Pierre Boufflet, Martin Heeney, Taek-Soo Kim, Darren J Lipomi
This paper describes a comparison of two characterization techniques for determining the mechanical properties of thin-film organic semiconductors for applications in soft electronics. In the first method, the film is supported by water (film-on-water, FOW), and a stress-strain curve is obtained using a direct tensile test. In the second method, the film is supported by an elastomer (film-on-elastomer, FOE), and is subjected to three tests to reconstruct the key features of the stress-strain curve: the buckling test (tensile modulus), the onset of buckling (yield point), and the crack-onset strain (strain at fracture)...
February 21, 2017: ACS Applied Materials & Interfaces
Zhongyu Li, Dimitris N Metaxas, Aidong Lu, Shaoting Zhang
This paper proposes a novel framework to help biologists explore and analyze neurons based on retrieval of data from neuron morphological databases. In recent years, the continuously expanding neuron databases provide a rich source of information to associate neuronal morphologies with their functional properties. We design a coarse-to-fine framework for efficient and effective data retrieval from large-scale neuron databases. In the coarse-level, for efficiency in large-scale, we employ a binary coding method to compress morphological features into binary codes of tens of bits...
February 17, 2017: Methods: a Companion to Methods in Enzymology
Irene Adroher-Benítez, Alberto Martín-Molina, Silvia Ahualli, Manuel Quesada-Pérez, Gerardo Odriozola, Arturo Moncho-Jordá
In this work the equilibrium distribution of ions around a thermo-responsive charged nanogel particle in an electrolyte aqueous suspension is explored using coarse-grained Monte Carlo computer simulations and the Ornstein-Zernike integral equation theory. We explicitly consider the ionic size in both methods and study the interplay between electrostatic and excluded-volume effects for swollen and shrunken nanogels, monovalent and trivalent counterions, and for two different nanogel charges. We find good quantitative agreement between the ionic density profiles obtained using both methods when the excluded repulsive force exerted by the cross-linked polymer network is taken into account...
February 20, 2017: Physical Chemistry Chemical Physics: PCCP
Joshua E Condon, Tyler B Martin, Arthi Jayaraman
Using atomistic and coarse-grained molecular dynamics (MD) simulations, we explain the shifts in lower critical solution temperature (LCST)-like phase transitions exhibited by elastin-like peptides (ELPs) upon conjugation to other macromolecules (e.g. collagen-like peptides or CLPs). First, using atomistic simulations, we study ELP oligomers with the sequence (VPGFG)6 in explicit water, and characterize the LCST-like transition temperature as one at which the ELP oligomers undergo a change in "hydration state"...
February 20, 2017: Soft Matter
Elena Ermakova, Yuriy Zuev
Plant defensins are a part of the innate immune system of plants that acts against a broad range of pathogens. Many plant defensins, including pine defensins, show strong antifungal activity that is associated with their ability to penetrate into the fungal cell membrane. However, the exact molecular mechanism of their action remains poorly defined. To obtain insight into the mechanism of protein-membrane interaction, we applied a coarse-grained molecular dynamics simulation to study the interaction of pine defensin with two model membranes: the first consisted of zwitterion-neutral POPC molecules and the second was composed of combined anionic POPG and POPC...
February 18, 2017: Journal of Membrane Biology
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