Search results for "molecular dynamics simulation"

Pearl-necklace structures of molecular brushes with rigid backbone under poor solvent conditions: A simulation study

2010

Bottle-brush polymers, where flexible side chains containing N=20 to 50 effective monomers are grafted to a rigid backbone, are studied by molecular dynamics simulations, varying the grafting density σ and the solvent quality. Whereas for poor solvents and large enough σ the molecular brush is a cylindrical object, homogeneous in axial direction, for intermediate values of σ an axially inhomogeneous structure of "pearl-necklace" type is formed. The "pearls," however, have a strongly nonspherical ellipsoidal shape, due to the fact that several side chains cluster together in one pearl, qualitatively consistent with predictions of Sheiko et al. [Eur. Phys. J. E 13, 125 (2004)] We analyze the …

Structure of bottle-brush brushes under good solvent conditions: a molecular dynamics study.

2011

We report a simulation study for bottle-brush polymers grafted on a rigid backbone. Using a standard coarse-grained bead-spring model extensive molecular dynamics simulations for such macromolecules under good solvent conditions are performed. We consider a broad range of parameters and present numerical results for the monomer density profile, density of the untethered ends of the grafted flexible backbones and the correlation function describing the range that neighboring grafted bottle-brushes are affected by the presence of the others due to the excluded volume interactions. The end beads of the flexible backbones of the grafted bottle-brushes do not access the region close to the rigid…

Enzyme molecular mechanism as a starting point to design new inhibitors: a theoretical study of O-GlcNAcase.

2011

O-Glycoprotein 2-acetamino-2-deoxy-β-d-glucopyranosidase (O-GlcNAcase) hydrolyzes O-linked 2-acetamido-2-deoxy-β-d-glucopyranoside (O-GlcNAc) residues from post-translationally modified serine/threonine residues of nucleocytoplasmic protein. The chemical process involves substrate-assisted catalysis, where two aspartate residues have been identified as the two key catalytic residues of O-GlcNAcase. In this report, the first step of the catalytic mechanism used by O-GlcNAcase involving substrate-assisted catalysis has been studied using a hybrid quantum mechanical/molecular mechanical (QM/MM) Molecular Dynamics (MD) calculations. The free energy profile shows that the formation of the oxazol…

Hydrodynamic mechanisms of spinodal decomposition in confined colloid-polymer mixtures: A multiparticle collision dynamics study

2013

A multiscale model for a colloid-polymer mixture is developed. The colloids are described as point particles interacting with each other and with the polymers with strongly repulsive potentials, while polymers interact with each other with a softer potential. The fluid in the suspension is taken into account by the multiparticle collision dynamics method (MPC). Considering a slit geometry where the suspension is confined between parallel repulsive walls, different possibilities for the hydrodynamic boundary conditions (b.c.) at the walls (slip versus stick) are treated. Quenching experiments are considered, where the system volume is suddenly reduced (keeping the density of the solvent flui…

Structural behaviour differences in low methoxy pectin solutions in the presence of divalent cations (Ca 2+ and Zn 2+ ): a process driven by the bind…

2014

International audience; In this paper, we compare the interactions between low methoxy pectin (LMP) and either Ca2+ or Zn2+ in semi-dilute solutions. Intrinsic viscosity and turbidity measurements reveal that pectin-calcium solutions are more viscous, but yet less turbid, than pectin-zinc ones. To get a molecular understanding on the origin of this rather unexpected behavior, we further performed isothermal titration calorimetry, small angle neutron scattering experiments, as well as molecular dynamics simulations. Our results suggest that calcium cations induce the formation of a more homogeneous network of pectin than zinc cations do. The molecular dynamics simulations indicate that this …

HSV-1 Glycoprotein D and Its Surface Receptors: Evaluation of Protein–Protein Interaction and Targeting by Triazole-Based Compounds through In Silico…

2023

Protein–protein interactions (PPI) represent attractive targets for drug design. Thus, aiming at a deeper insight into the HSV-1 envelope glycoprotein D (gD), protein–protein docking and dynamic simulations of gD-HVEM and gD-Nectin-1 complexes were performed. The most stable complexes and the pivotal key residues useful for gD to anchor human receptors were identified and used as starting points for a structure-based virtual screening on a library of both synthetic and designed 1,2,3-triazole-based compounds. Their binding properties versus gD interface with HVEM and Nectin-1 along with their structure-activity relationships (SARs) were evaluated. Four [1,2,3]triazolo[4,5-b]pyridines were i…

Molecular dynamics simulations of a new model of human a7 nicotinic receptor

2014

Structural Origin of Metal Specificity in Isatin Hydrolase from Labrenzia aggregata Investigated by Computer Simulations.

2017

We performed quantum-chemical calculations, ab initio molecular dynamics, hybrid quantum mechanics/molecular mechanics (QM/MM) and enhanced sampling metadynamics simulations to investigate the origin of metal specificity in isatin hydrolase from Labrenzia aggregata. The peculiar octahedral binding geometry of the Mn2+ ion in the Michaelis complex includes both the isatin substrate and the catalytic water within the first coordination shell of the cation. Our calculations show that the same arrangement of the ligands cannot be efficiently achieved in the presence of other small divalent metal cations such as Zn2+ or Cu2+ . On the contrary, bulkier alkaline-earth cations such as Mg2+ , which …

Hydration dependence of myoglobin dynamics studied with elastic neutron scattering, differential scanning calorimetry and broadband dielectric spectr…

2014

In this work we present a thorough investigation of the hydration dependence of myoglobin dynamics. The study is performed on D2O-hydrated protein powders in the hydration range 0<h<0.5 (h≡gr[D2O]/gr[protein]) and in the temperature range 20-300K. The protein equilibrium fluctuations are investigated with Elastic Neutron Scattering using the spectrometer IN13 at ILL (Grenoble), while the relaxations of the protein + hydration water system are investigated with Broadband Dielectric Spectroscopy; finally, Differential Scanning Calorimetry is used to obtain a thermodynamic description of the system. The effect of increasing hydration is to speed up the relaxations of the myoglobin + hydration …

The Photocycle of Bacteriophytochrome Is Initiated by Counterclockwise Chromophore Isomerization.

2022

Photoactivation of bacteriophytochrome involves a cis–trans photoisomerization of a biliverdin chromophore, but neither the precise sequence of events nor the direction of the isomerization is known. Here, we used nonadiabatic molecular dynamics simulations on the photosensory protein dimer to resolve the isomerization mechanism in atomic detail. In our simulations the photoisomerization of the D ring occurs in the counterclockwise direction. On a subpicosecond time scale, the photoexcited chromophore adopts a short-lived intermediate with a highly twisted configuration stabilized by an extended hydrogen-bonding network. Within tens of picoseconds, these hydrogen bonds break, allowing the c…