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https://www.readbyqxmd.com/read/28926766/protonation-of-%C3%AE-lactoglobulin-in-the-presence-of-strong-polyelectrolyte-chains-a-study-using-monte-carlo-simulation
#1
Paola Torres, Luciano Bojanich, Fabricio Sanchez-Varretti, Antonio Jose Ramirez-Pastor, Evelina Quiroga, Valeria Boeris, Claudio F Narambuena
In this work, the molecular interaction between the protein β-lactoglobulin and strong polyelectrolyte chains was studied using Monte Carlo simulations. Different coarse-grained models were used to represent the system components. Both net charge and protonation of the isolated dimeric protein were analyzed as a function of pH. The acid-base equilibrium of each titratable group was distinctively modified by the presence of polyanion or polycation chains. The complexation on the wrong side of pI was more evident with the polycation than with the polyanion...
September 8, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28923919/multiple-interactions-between-an-arf-gef-complex-and-charged-lipids-determine-activation-kinetics-on-the-membrane
#2
Deepti Karandur, Agata Nawrotek, John Kuriyan, Jacqueline Cherfils
Lipidated small GTPases and their regulators need to bind to membranes to propagate actions in the cell, but an integrated understanding of how the lipid bilayer exerts its effect has remained elusive. Here we focused on ADP ribosylation factor (Arf) GTPases, which orchestrate a variety of regulatory functions in lipid and membrane trafficking, and their activation by the guanine-nucleotide exchange factor (GEF) Brag2, which controls integrin endocytosis and cell adhesion and is impaired in cancer and developmental diseases...
September 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28923469/thermodynamics-and-kinetics-of-single-chain-monellin-folding-with-structural-insights-into-specific-collapse-in-the-denatured-state-ensemble
#3
Hiranmay Maity, Govardhan Reddy
Proteins, which behave as random coils in high denaturant concentrations undergo collapse transition similar to polymers on denaturant dilution. We study collapse in the denatured ensemble of single chain monellin (MNEI) using a coarse-grained protein model and molecular dynamics simulations. The model is validated by quantitatively comparing the computed Guanidinium Chloride (GuHCl) and pH-dependent thermodynamic properties of MNEI folding with the experiments. The computed properties such as the fraction of the protein in the folded state and radius of gyration (Rg) as function of [GuHCl] are in good agreement with the experiments...
September 15, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28918393/improving-membrane-protein-expression-by-optimizing-integration-efficiency
#4
Michiel J M Niesen, Stephen S Marshall, Thomas F Miller, William M Clemons
The heterologous overexpression of integral membrane proteins in Escherichia coli often yields insufficient quantities of purifiable protein for applications of interest. The current study leverages a recently demonstrated link between co-translational membrane integration efficiency and protein expression levels to predict protein sequence modifications that improve expression. Membrane integration efficiencies, obtained using a coarse-grained simulation approach, robustly predicted effects on expression of the integral membrane protein TatC for a set of 140 sequence modifications, including loop-swap chimeras and single-residue mutations distributed throughout the protein sequence...
September 16, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28918189/effects-of-temperature-and-peg-grafting-density-on-the-translocation-of-pegylated-nanoparticles-across-asymmetric-lipid-membrane
#5
Zuoheng Zhang, Xubo Lin, Ning Gu
Plasma membrane internalization of nanoparticles (NPs) is important for their biomedical applications such as drug-delivery carriers. On one hand, in order to improve their half-life in circulation, PEGylation has been widely used. However, it may hinder the NPs' membrane internalization ability. On the other hand, higher temperature could enhance the membrane permeability and may affect the NPs' ability to enter into or exit from cells. To make full use of their advantages, we systematically investigated the effects of temperature and PEG density on the translocation of PEGylated nanoparticles across the plasma asymmetric membrane of eukaryotic cells, using near-atom level coarse-grained molecular dynamics simulations...
September 6, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28918079/clogging-of-an-alpine-streambed-by-silt-sized-particles-insights-from-laboratory-and-field-experiments
#6
Jasmin Fetzer, Markus Holzner, Michael Plötze, Gerhard Furrer
Clogging of streambeds by suspended particles (SP) can cause environmental problems, as it can negatively influence, e.g., habitats for macrozoobenthos, fish reproduction and groundwater recharge. This especially applies in the case of silt-sized SP. Until now, most research has dealt with coarse SP and was carried out in laboratory systems. The aims of this study are to examine (1) whether physical clogging by silt-sized SP exhibits the same dynamics and patterns as by sand-sized SP, and (2) the comparability of results between laboratory and field experiments...
September 7, 2017: Water Research
https://www.readbyqxmd.com/read/28917842/multi-scale-simulations-of-biological-systems-using-the-opep-coarse-grained-model
#7
Fabio Sterpone, Sébastien Doutreligne, Thanh Thuy Tran, Simone Melchionna, Marc Baaden, Phuong H Nguyen, Philippe Derreumaux
Biomolecules are complex machines that are optimized by evolution to properly fulfill or contribute to a variety of biochemical tasks in the cellular environment. Computer simulations based on quantum mechanics and atomistic force fields have been proven to be a powerful microscope for obtaining valuable insights into many biological, physical, and chemical processes. Many interesting phenomena involve, however, a time scale and a number of degrees of freedom, notably if crowding is considered, that cannot be explored at an atomistic resolution...
September 13, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28917669/knowledge-driven-computational-modeling-in-alzheimer-s-research-current-state-and-future-trends
#8
Hugo Geerts, Martin Hofmann-Apitius, Thomas J Anastasio
Neurodegenerative diseases such as Alzheimer's disease (AD) follow a slowly progressing dysfunctional trajectory, with a large presymptomatic component and many comorbidities. Using preclinical models and large-scale omics studies ranging from genetics to imaging, a large number of processes that might be involved in AD pathology at different stages and levels have been identified. The sheer number of putative hypotheses makes it almost impossible to estimate their contribution to the clinical outcome and to develop a comprehensive view on the pathological processes driving the clinical phenotype...
September 14, 2017: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/28915764/sequence-dependent-aggregation-of-peptides-and-fibril-formation
#9
Nguyen Ba Hung, Duy-Manh Le, Trinh X Hoang
Deciphering the links between amino acid sequence and amyloid fibril formation is key for understanding protein misfolding diseases. Here we use Monte Carlo simulations to study the aggregation of short peptides in a coarse-grained model with hydrophobic-polar (HP) amino acid sequences and correlated side chain orientations for hydrophobic contacts. A significant heterogeneity is observed in the aggregate structures and in the thermodynamics of aggregation for systems of different HP sequences and different numbers of peptides...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915762/on-the-relationship-between-the-local-segmental-dynamics-and-the-tagged-monomer-dynamics-in-lamellar-phases-of-diblock-copolymers
#10
Vaidyanathan Sethuraman, Venkat Ganesan
In this brief article, we present results from coarse-grained molecular dynamics simulations which probed the relationship between the local segmental dynamics and the tagged monomer dynamics in lamellar phases of diblock copolymers. Our results demonstrate that monomer relaxation times do not provide directly a quantitatively accurate measure of the spatial variations in segmental dynamics. However, a convolution of the monomer density distributions with their corresponding relaxation times is shown to provide an approximate, but accurate, quantitative characterization of the average local segmental dynamics...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915745/non-local-effects-of-point-mutations-on-the-stability-of-a-protein-module
#11
Mateusz Chwastyk, Andrés M Vera, Albert Galera-Prat, Melissabye Gunnoo, Damien Thompson, Mariano Carrión-Vázquez, Marek Cieplak
We combine experimental and theoretical methods to assess the effect of a set of point mutations on c7A, a highly mechanostable type I cohesin module from scaffoldin CipA from Clostridium thermocellum. We propose a novel robust and computationally expedient theoretical method to determine the effects of point mutations on protein structure and stability. We use all-atom simulations to predict structural shifts with respect to the native protein and then analyze the mutants using a coarse-grained model. We examine transitions in contacts between residues and find that changes in the contact map usually involve a non-local component that can extend up to 50 Å...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28911866/molecular-dynamics-simulations-of-stratum-corneum-lipid-mixtures-a-multiscale-perspective
#12
Timothy C Moore, Christopher R Iacovella, Anne Leonhard, Annette L Bunge, Clare McCabe
The lipid matrix of the stratum corneum (SC) layer of skin is essential for human survival; it acts as a barrier to prevent rapid dehydration while keeping potentially hazardous material outside the body. While the composition of the SC lipid matrix is known, the molecular-level details of its organization are difficult to infer experimentally, hindering the discovery of structure-property relationships. To this end, molecular dynamics simulations, which give molecular-level resolution, have begun to play an increasingly important role in understanding these relationships...
September 11, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28911864/multiscale-approach-to-the-activation-and-phosphotransfer-mechanism-of-cpxa-histidine-kinase-reveals-a-tight-coupling-between-conformational-and-chemical-steps
#13
Franco Marsico, Osvaldo Burastero, Lucas A Defelipe, Elias Daniel Lopez, Mehrnoosh Arrar, Adrián G Turjanski, Marcelo A Marti
Sensor histidine kinases (SHKs) are an integral component of the molecular machinery that permits bacteria to adapt to widely changing environmental conditions. CpxA, an extensively studied SHK, is a multidomain homodimeric protein with each subunit consisting of a periplasmic sensor domain, a transmembrane domain, a signal-transducing HAMP domain, a dimerization and histidine phospho-acceptor sub-domain (DHp) and a catalytic and ATP-binding subdomain (CA). The key activation event involves the rearrangement of the HAMP-DHp helical core and translation of the CA towards the acceptor histidine, which presumably results in a autokinase-competent complex...
September 11, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28905963/coarse-grained-molecular-dynamics-studies-of-the-structure-and-stability-of-peptide-based-drug-amphiphile-filaments
#14
Myungshim Kang, Honggang Cui, Sharon M Loverde
Peptide-based supramolecular filaments, in particular filaments self-assembled by drug amphiphiles (DAs), possess great potential in the field of drug delivery. These filaments possess one hundred percent drug loading, with a release mechanism that can be tuned based on the dissociation of the supramolecular filaments and the degradation of the DAs [Cheetham et al., J. Am. Chem. Soc., 2013, 135(8), 2907]. Recently, much attention has been drawn to the competing intermolecular interactions that drive the self-assembly of peptide-based amphiphiles into supramolecular filaments...
September 14, 2017: Soft Matter
https://www.readbyqxmd.com/read/28905417/investigating-the-structural-dynamics-of-the-piezo1-channel-activation-and-inactivation-by-coarse-grained-modeling
#15
Wenjun Zheng, Frederick Sachs
The PIEZO channels, a family of mechanosensitive channels in vertebrates, feature a fast activation by mechanical stimuli (e.g., membrane tension) followed by a slower inactivation. Although a medium-resolution structure of the trimeric form of PIEZO1 was solved by cryo-electron microscopy (cryo-EM), key structural changes responsible for the channel activation and inactivation are still unknown. Toward decrypting the structural mechanism of the PIEZO1 activation and inactivation, we performed systematic coarse-grained modeling using an elastic network model and related modeling/analysis tools (i...
September 14, 2017: Proteins
https://www.readbyqxmd.com/read/28905203/adaptive-resolution-simulations-of-biomolecular-systems
#16
Julija Zavadlav, Staš Bevc, Matej Praprotnik
In this review article, we discuss and analyze some recently developed hybrid atomistic-mesoscopic solvent models for multiscale biomolecular simulations. We focus on the biomolecular applications of the adaptive resolution scheme (AdResS), which allows solvent molecules to change their resolution back and forth between atomistic and coarse-grained representations according to their positions in the system. First, we discuss coupling of atomistic and coarse-grained models of salt solution using a 1-to-1 molecular mapping-i...
September 13, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28904383/effects-of-coarse-graining-and-saturation-of-hydrocarbon-chains-on-structure-and-dynamics-of-simulated-lipid-molecules
#17
Pavel Buslaev, Ivan Gushchin
Molecular dynamics simulations are used extensively to study the processes on biological membranes. The simulations can be conducted at different levels of resolution: all atom (AA), where all atomistic details are provided; united atom (UA), where hydrogen atoms are treated inseparably of corresponding heavy atoms; and coarse grained (CG), where atoms are grouped into larger particles. Here, we study the behavior of model bilayers consisting of saturated and unsaturated lipids DOPC, SOPC, OSPC and DSPC in simulations performed using all atom CHARMM36 and coarse grained Martini force fields...
September 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28902500/stratified-uwham-and-its-stochastic-approximation-for-multicanonical-simulations-which-are-far-from-equilibrium
#18
Bin W Zhang, Nanjie Deng, Zhiqiang Tan, Ronald M Levy
We describe a new analysis tool called Stratified unbinned Weighted Histogram Analysis Method (Stratified-UWHAM), which can be used to compute free energies and expectations from a multicanonical ensemble when a subset of the parallel simulations are far from being equilibrated because of barriers between free energy basins which are only rarely (or never) crossed at some states. The Stratified-UWHAM equations can be obtained in the form of UWHAM equations but with an expanded set of states. We also provide a stochastic solver, Stratified RE-SWHAM, for Stratified-UWHAM to remove its computational bottleneck...
September 13, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28895608/surfactant-effects-on-droplet-dynamics-and-deposition-patterns-a-lattice-gas-model
#19
Narina Jung, Hae Won Seo, Perry H Leo, Jaeup Kim, Pilwon Kim, Chun Sang Yoo
A coarse-grained lattice gas model is developed to study pattern forming processes in drying drops containing surfactant. By performing Monte Carlo simulations of the model, the coupled dynamics of surfactant and liquid evaporation and the resulting oscillatory dynamics at the contact line are elucidated. We show that the coupled drop dynamics and the resulting final deposition patterns can be altered by adsorption kinetics. For slow adsorption rates, surfactant molecules recirculate along with colloidal particles and the area covered by the surfactant on the surface grows from the contact line as the initial concentration of the surfactant increases...
September 12, 2017: Soft Matter
https://www.readbyqxmd.com/read/28892618/consistent-integration-of-experimental-and-ab-initio-data-into-effective-physical-models
#20
Lukas Vlcek, Rama K Vasudevan, Stephen Jesse, Sergei V Kalinin
We describe and test theoretical principles for consistent integration of experimental and ab initio data from diverse sources into a single statistical mechanical model. The approach is based on the recently introduced concept of statistical distance between partition functions, uses a simple vector algebra formalism to describe measurement outcomes and coarse-graining operations, and takes advantage of thermodynamic perturbation expressions for fast exploration of the model parameter space. The methodology is demonstrated on a combination of thermodynamic, structural, spectroscopic, and imaging pseudo-experimental data along with ab initio-type trajectories, which are incorporated into models describing the behavior of a near-critical fluid, liquid water, thin-film mixed oxides, and binary alloys...
September 11, 2017: Journal of Chemical Theory and Computation
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