scholarly journals Influence of Oligopeptide Length and Distribution on Polyisoprene Properties

Polymers ◽  
2021 ◽  
Vol 13 (24) ◽  
pp. 4408
Author(s):  
Chang-Cheng Wang ◽  
Rong Zhang ◽  
Shiqi Li ◽  
Guangsu Huang ◽  
Maozhu Tang ◽  
...  
Keyword(s):  
Mechanical Properties ◽  
Molecular Design ◽  
Dynamics Simulation ◽  
Binding Modes ◽  
Structure And Properties ◽  
Chain Dynamics ◽  
Broadband Dielectric Spectroscopy ◽  
Polar Groups ◽  
Block Distribution ◽  
Control Samples

The tuning of binding modes of polar groups is the key step to mimicking the structure and properties of natural rubber through the molecular design of synthetic polyisoprenes. Herein, the ordering and binding distances of oligopeptides could be altered systematically by changing their lengths and distribution along the polyisoprene chain, which impose huge impacts on the mechanical properties and chain dynamics of green rubber. In detail, a series of peptide-functionalized polyisoprenes with terminal blocks (B-2A-PIP, B-3A-PIP) or random sequences (R-2A-PIP, R-3A-PIP) are fabricated by using dipeptides (2A) or tripeptides (3A) as crosslinkers to explore the mechanism of terminal interaction on mechanism properties and chain dynamics. B-4A-PIP and R-4A-PIP served as control samples. It is found that the increased oligopeptide length and the block distribution improves the mechanical properties and confine the chain movement by elevate the contents of ordered and compact microstructures, which is indicated by XRD, broadband dielectric spectroscopy (BDS) and consistent with the result of molecular dynamics simulation. New relaxation signals belonging to oligopeptide aggregates are found which showed elevated dielectric strengths upon temperatures increase. Additionally, it also reveals that the binding modes of oligopeptide do not significantly influence the entanglements of polyisoprene.

Reversibly Sampling Conformations and Binding Modes Using Molecular Darting

2020 ◽  
Author(s):  
Samuel C. Gill ◽  
David Mobley
Keyword(s):  
Monte Carlo ◽  
Ligand Binding ◽  
Binding Sites ◽  
Degrees Of Freedom ◽  
Dynamics Simulation ◽  
Hiv Integrase ◽  
Binding Modes ◽  
System A ◽  
Multiple Binding ◽  
Internal Degrees Of Freedom

<div>Sampling multiple binding modes of a ligand in a single molecular dynamics simulation is difficult. A given ligand may have many internal degrees of freedom, along with many different ways it might orient itself a binding site or across several binding sites, all of which might be separated by large energy barriers. We have developed a novel Monte Carlo move called Molecular Darting (MolDarting) to reversibly sample between predefined binding modes of a ligand. Here, we couple this with nonequilibrium candidate Monte Carlo (NCMC) to improve acceptance of moves.</div><div>We apply this technique to a simple dipeptide system, a ligand binding to T4 Lysozyme L99A, and ligand binding to HIV integrase in order to test this new method. We observe significant increases in acceptance compared to uniformly sampling the internal, and rotational/translational degrees of freedom in these systems.</div>

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo

2017 ◽  
Author(s):  
Samuel Gill ◽  
Nathan M. Lim ◽  
Patrick Grinaway ◽  
Ariën S. Rustenburg ◽  
Josh Fass ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Ligand Binding ◽  
Binding Mode ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Binding Modes ◽  
Enhanced Sampling ◽  
Recent Success ◽  
Multiple Binding ◽  
Proper Sampling

<div>Accurately predicting protein-ligand binding is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. That is, we focus on computing the dominant placement, conformation, and orientations of a relatively rigid, fragment-like ligand in a receptor, and the populations of the multiple binding modes which may be relevant. This problem is important in its own right, but is even more timely given the recent success of alchemical free energy calculations. Alchemical calculations are increasingly used to predict binding free energies of ligands to receptors. However, the accuracy of these calculations is dependent on proper sampling of the relevant ligand binding modes. Unfortunately, ligand binding modes may often be uncertain, hard to predict, and/or slow to interconvert on simulation timescales, so proper sampling with current techniques can require prohibitively long simulations. We need new methods which dramatically improve sampling of ligand binding modes. Here, we develop and apply a nonequilibrium candidate Monte Carlo (NCMC) method to improve sampling of ligand binding modes.</div><div><br></div><div>In this technique the ligand is rotated and subsequently allowed to relax in its new position through alchemical perturbation before accepting or rejecting the rotation and relaxation as a nonequilibrium Monte Carlo move. When applied to a T4 lysozyme model binding system, this NCMC method shows over two orders of magnitude improvement in binding mode sampling efficiency compared to a brute force molecular dynamics simulation. This is a first step towards applying this methodology to pharmaceutically relevant binding of fragments and, eventually, drug-like molecules. We are making this approach available via our new Binding Modes of Ligands using Enhanced Sampling (BLUES) package which is freely available on GitHub.</div>

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo

2018 ◽  
Author(s):  
Samuel Gill ◽  
Nathan M. Lim ◽  
Patrick Grinaway ◽  
Ariën S. Rustenburg ◽  
Josh Fass ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Ligand Binding ◽  
Binding Mode ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Binding Modes ◽  
Enhanced Sampling ◽  
Recent Success ◽  
Multiple Binding ◽  
Proper Sampling

<div>Accurately predicting protein-ligand binding is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. That is, we focus on computing the dominant placement, conformation, and orientations of a relatively rigid, fragment-like ligand in a receptor, and the populations of the multiple binding modes which may be relevant. This problem is important in its own right, but is even more timely given the recent success of alchemical free energy calculations. Alchemical calculations are increasingly used to predict binding free energies of ligands to receptors. However, the accuracy of these calculations is dependent on proper sampling of the relevant ligand binding modes. Unfortunately, ligand binding modes may often be uncertain, hard to predict, and/or slow to interconvert on simulation timescales, so proper sampling with current techniques can require prohibitively long simulations. We need new methods which dramatically improve sampling of ligand binding modes. Here, we develop and apply a nonequilibrium candidate Monte Carlo (NCMC) method to improve sampling of ligand binding modes.</div><div><br></div><div>In this technique the ligand is rotated and subsequently allowed to relax in its new position through alchemical perturbation before accepting or rejecting the rotation and relaxation as a nonequilibrium Monte Carlo move. When applied to a T4 lysozyme model binding system, this NCMC method shows over two orders of magnitude improvement in binding mode sampling efficiency compared to a brute force molecular dynamics simulation. This is a first step towards applying this methodology to pharmaceutically relevant binding of fragments and, eventually, drug-like molecules. We are making this approach available via our new Binding Modes of Ligands using Enhanced Sampling (BLUES) package which is freely available on GitHub.</div>

Structure and properties of compact articles from high-alloyed iron powder with adding of boron nitride

2020 ◽  
pp. 39-48
Author(s):  
B. O. Bolshakov ◽  
◽  
R. F. Galiakbarov ◽  
A. M. Smyslov ◽  
◽  
...  
Keyword(s):  
Mechanical Properties ◽  
Boron Nitride ◽  
Grain Boundary ◽  
Bending Strength ◽  
Physical And Mechanical Properties ◽  
Operating Conditions ◽  
Structure And Properties ◽  
Steam Turbines ◽  
Friction Forces ◽  
Wide Range

The results of the research of structure and properties of a composite compact from 13 Cr – 2 Мо and BN powders depending on the concentration of boron nitride are provided. It is shown that adding boron nitride in an amount of more than 2% by weight of the charge mixture leads to the formation of extended grain boundary porosity and finely dispersed BN layers in the structure, which provides a high level of wearing properties of the material. The effect of boron nitride concentration on physical and mechanical properties is determined. It was found that the introduction of a small amount of BN (up to 2 % by weight) into the compacts leads to an increase in plasticity, bending strength, and toughness by reducing the friction forces between the metal powder particles during pressing and a more complete grain boundary diffusion process during sintering. The formation of a regulated structure-phase composition of powder compacts of 13 Cr – 2 Mо – BN when the content of boron nitride changes in them allows us to provide the specified physical and mechanical properties in a wide range. The obtained results of studies of the physical and mechanical characteristics of the developed material allow us to reasonably choose the necessary composition of the powder compact for sealing structures of the flow part of steam turbines, depending on their operating conditions.

scholarly journals Computational Investigations on the Binding Mode of Ligands for the Cannabinoid-Activated G Protein-Coupled Receptor GPR18

Biomolecules ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 686 ◽  
Author(s):  
Alexander Neumann ◽  
Viktor Engel ◽  
Andhika B. Mahardhika ◽  
Clara T. Schoeder ◽  
Vigneshwaran Namasivayam ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
G Protein ◽  
Phenyl Ring ◽  
Binding Mode ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Binding Modes ◽  
G Protein Coupled Receptor ◽  
G Protein Coupled

GPR18 is an orphan G protein-coupled receptor (GPCR) expressed in cells of the immune system. It is activated by the cannabinoid receptor (CB) agonist ∆9-tetrahydrocannabinol (THC). Several further lipids have been proposed to act as GPR18 agonists, but these results still require unambiguous confirmation. In the present study, we constructed a homology model of the human GPR18 based on an ensemble of three GPCR crystal structures to investigate the binding modes of the agonist THC and the recently reported antagonists which feature an imidazothiazinone core to which a (substituted) phenyl ring is connected via a lipophilic linker. Docking and molecular dynamics simulation studies were performed. As a result, a hydrophobic binding pocket is predicted to accommodate the imidazothiazinone core, while the terminal phenyl ring projects towards an aromatic pocket. Hydrophobic interaction of Cys251 with substituents on the phenyl ring could explain the high potency of the most potent derivatives. Molecular dynamics simulation studies suggest that the binding of imidazothiazinone antagonists stabilizes transmembrane regions TM1, TM6 and TM7 of the receptor through a salt bridge between Asp118 and Lys133. The agonist THC is presumed to bind differently to GPR18 than to the distantly related CB receptors. This study provides insights into the binding mode of GPR18 agonists and antagonists which will facilitate future drug design for this promising potential drug target.

Determination of mechanical properties of two-phase and hybrid nanocomposites: experimental determination and multiscale modeling

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Mahmoud Haghighi ◽  
Hossein Golestanian ◽  
Farshid Aghadavoudi
Keyword(s):  
Mechanical Properties ◽  
Ultimate Strength ◽  
Multiscale Modeling ◽  
Filler Content ◽  
Hybrid Nanocomposites ◽  
Dynamics Simulation ◽  
Strength Increase ◽  
Two Phase ◽  
Macro Scale ◽  
Elongation To Failure

Abstract In this paper, the effects of filler content and the use of hybrid nanofillers on agglomeration and nanocomposite mechanical properties such as elastic moduli, ultimate strength and elongation to failure are investigated experimentally. In addition, thermoset epoxy-based two-phase and hybrid nanocomposites are simulated using multiscale modeling techniques. First, molecular dynamics simulation is carried out at nanoscale considering the interphase. Next, finite element method and micromechanical modeling are used for micro and macro scale modeling of nanocomposites. Nanocomposite samples containing carbon nanotubes, graphene nanoplatelets, and hybrid nanofillers with different filler contents are prepared and are tested. Also, field emission scanning electron microscopy is used to take micrographs from samples’ fracture surfaces. The results indicate that in two-phase nanocomposites, elastic modulus and ultimate strength increase while nanocomposite elongation to failure decreases with reinforcement weight fraction. In addition, nanofiller agglomeration occurred at high nanofiller contents especially higher than 0.75 wt% in the two-phase nanocomposites. Nanofiller agglomeration was observed to be much lower in the hybrid nanocomposite samples. Therefore, using hybrid nanofillers delays/prevents agglomeration and improves mechanical properties of nanocomposite at the same total filler content.

scholarly journals Tentative Peptide‒Lipid Bilayer Models Elucidating Molecular Behaviors and Interactions Driving Passive Cellular Uptake of Collagen-Derived Small Peptides

Molecules ◽  
2021 ◽  
Vol 26 (3) ◽  
pp. 710
Author(s):  
Pathomwat Wongrattanakamon ◽  
Wipawadee Yooin ◽  
Busaban Sirithunyalug ◽  
Piyarat Nimmanpipug ◽  
Supat Jiranusornkul
Keyword(s):  
Lipid Bilayer ◽  
Lipid Bilayers ◽  
Mean Square Displacement ◽  
Dynamics Simulation ◽  
Coordinate Frame ◽  
Mean Square ◽  
Binding Modes ◽  
Small Peptides ◽  
Collagen Peptides ◽  
Electron Density Profiles

Collagen contains hydroxyproline (Hyp), which is a unique amino acid. Three collagen-derived small peptides (Gly-Pro-Hyp, Pro-Hyp, and Gly-Hyp) interacting across a lipid bilayer (POPC model membrane) for cellular uptakes of these collagen-derived small peptides were studied using accelerated molecular dynamics simulation. The ligands were investigated for their binding modes, hydrogen bonds in each coordinate frame, and mean square displacement (MSD) in the Z direction. The lipid bilayers were evaluated for mass and electron density profiles of the lipid molecules, surface area of the head groups, and root mean square deviation (RMSD). The simulation results show that hydrogen bonding between the small collagen peptides and plasma membrane plays a significant role in their internalization. The translocation of the small collagen peptides across the cell membranes was shown. Pro-Hyp laterally condensed the membrane, resulting in an increase in the bilayer thickness and rigidity. Perception regarding molecular behaviors of collagen-derived peptides within the cell membrane, including their interactions, provides the novel design of specific bioactive collagen peptides for their applications.

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