scholarly journals Dynamics of the N-terminal domain of SARS-CoV-2 nucleocapsid protein drives dsRNA melting in a counterintuitive tweezer-like mechanism

2020 ◽  
Author(s):  
Ícaro P. Caruso ◽  
Karoline Sanches ◽  
Andrea T. Da Poian ◽  
Anderson S. Pinheiro ◽  
Fabio C. L. Almeida
Keyword(s):  
Molecular Dynamics ◽  
Mechanism Of Action ◽  
Md Simulations ◽  
The Body ◽  
Dynamics Simulation ◽  
Single Mutation ◽  
Base Pairing ◽  
N Protein ◽  
Terminal Domain ◽  
Major Player

ABSTRACTThe N protein of betacoronaviruses is responsible for nucleocapsid assembly and other essential regulatory functions. Its N-terminal domain (NTD) interacts and melts the double-stranded transcriptional regulatory sequences (dsTRS), regulating the discontinuous subgenome transcription process. Here, we used molecular dynamics (MD) simulations to study the binding of SARS-CoV-2 N-NTD to non-specific (NS) and TRS dsRNAs. We probed dsRNAs’ Watson and Crick (WC) base-pairing over 25 replicas of 100 ns MD simulations, showing that only one N-NTD of dimeric N is enough to destabilize dsRNAs, initiating melting. N-NTD dsRNA destabilizing activity was more efficient for dsTRS than dsNS. N-NTD dynamics, especially a tweezer-like motion of β2-β3 and 2-β5 loops, played a key role in WC base-pairing destabilization. Based on experimental information available in the literature, we constructed kinetics models for N-NTD-mediated dsRNA melting. Our results support a 1:1 stoichiometry (N-NTD:dsRNA), matching MD simulations and raising different possibilities for N-NTD action: (i) two N-NTDs of dimeric N would act independently, increasing efficiency; (ii) two N-NTDs of dimeric N would bind to two different RNA sites, bridging distant regions of the genome; and (iii) monomeric N would be active, opening up the possibility of a regulatory dissociation event.IMPORTANCECoronaviruses are among the largest positive-sense RNA viruses. They display a unique discontinous transcription mechanism, involving N protein as a major player. The N-NTD promote the dsRNA melting releasing the nascent sense negative strand via a poorly known mechanism of action. It specifically recognizes the body TRS conserved RNA motif located at the 5’ end of each ORF. N protein has the ability to transfer the nascent RNA strand to the leader TRS. The mechanism is essential and one single mutation at the RNA binding site of the N-NTD impairs the viral replication. Here, we describe a counterintuitive mechanism of action of N-NTD based on molecular dynamics simulation and kinetic modelling of the experimental melting activity of N-NTD. This data impacts directly in the understanding of the way N protein acts in the cell and will guide future experiments.

scholarly journals Understanding Covalent Grafting of Nanotubes onto Polymer Nanocomposites: Molecular Dynamics Simulation Study

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2621
Author(s):  
Seunghwa Yang
Keyword(s):  
Molecular Dynamics ◽  
Load Transfer ◽  
Cell Model ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Covalent Grafting ◽  
Modelling Strategies ◽  
Multi Walled Carbon Nanotubes ◽  
Walled Carbon Nanotubes ◽  
External Loads

Here, we systematically interrogate the effects of grafting single-walled (SWNT) and multi-walled carbon nanotubes (MWNT) to polymer matrices by using molecular dynamics (MD) simulations. We specifically investigate key material properties that include interfacial load transfer, alteration of nanotube properties, and dispersion of nanotubes in the polymer matrix. Simulations are conducted on a periodic unit cell model of the nanocomposite with a straight carbon nanotube and an amorphous polyethylene terephthalate (PET) matrix. For each type of nanotube, either 0%, 1.55%, or 3.1% of the carbon atoms in the outermost nanotubes are covalently grafted onto the carbon atoms of the PET matrix. Stress-strain curves and the elastic moduli of nanotubes and nanocomposites are determined based on the density of covalent grafting. Covalent grafting promotes two rivalling effects with respect to altering nanotube properties, and improvements in interfacial load transfer in the nanocomposites are clearly observed. The enhanced interface enables external loads applied to the nanocomposites to be efficiently transferred to the grafted nanotubes. Covalent functionalization of the nanotube surface with PET molecules can alter the solubility of nanotubes and improve dispersibility. Finally, we discuss the current limitations and challenges in using molecular modelling strategies to accurately predict properties on the nanotube and polymers systems studied here.

A Study on the Uniaxial Tension of FCC Metals at Nano Level Using MD

2008 ◽  
Vol 32 ◽  
pp. 255-258
Author(s):  
Bohayra Mortazavi ◽  
Akbar Afaghi Khatibi
Keyword(s):  
Molecular Dynamics ◽  
Uniaxial Tension ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Face Centered Cubic ◽  
Engineering Strain ◽  
Fcc Metals ◽  
Engineering Stress ◽  
Nano Science ◽  
Face Centered

Molecular Dynamics (MD) are now having orthodox means for simulation of matter in nano-scale. It can be regarded as an accurate alternative for experimental work in nano-science. In this paper, Molecular Dynamics simulation of uniaxial tension of some face centered cubic (FCC) metals (namely Au, Ag, Cu and Ni) at nano-level have been carried out. Sutton-Chen potential functions and velocity Verlet formulation of Noise-Hoover dynamic as well as periodic boundary conditions were applied. MD simulations at different loading rates and temperatures were conducted, and it was concluded that by increasing the temperature, maximum engineering stress decreases while engineering strain at failure is increasing. On the other hand, by increasing the loading rate both maximum engineering stress and strain at failure are increasing.

Molecular Dynamics Simulation of a Pullout Test on a Carbon Nanotube in a Polymer Matrix

2014 ◽  
Vol 1700 ◽  
pp. 61-66
Author(s):  
Guttormur Arnar Ingvason ◽  
Virginie Rollin
Keyword(s):  
Molecular Dynamics ◽  
Polymer Matrix ◽  
Large Scale ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Atomistic Simulations ◽  
Polymer Molecules ◽  
Molecular Potential ◽  
Pull Out ◽  
Walled Carbon Nanotubes

ABSTRACTAdding single walled carbon nanotubes (SWCNT) to a polymer matrix can improve the delamination properties of the composite. Due to the complexity of polymer molecules and the curing process, few 3-D Molecular Dynamics (MD) simulations of a polymer-SWCNT composite have been run. Our model runs on the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), with a COMPASS (Condensed phase Optimized Molecular Potential for Atomistic Simulations Studies) potential. This potential includes non-bonded interactions, as well as bonds, angles and dihedrals to create a MD model for a SWCNT and EPON 862/DETDA (Diethyltoluenediamine) polymer matrix. Two simulations were performed in order to test the implementation of the COMPASS parameters. The first one was a tensile test on a SWCNT, leading to a Young’s modulus of 1.4 TPa at 300K. The second one was a pull-out test of a SWCNT from an originally uncured EPON 862/DETDA matrix.

scholarly journals An Analysis Based on Molecular Docking and Molecular Dynamics Simulation Study of Bromelain as Anti-SARS-CoV-2 Variants

2021 ◽  
Vol 12 ◽  
Author(s):  
Trina Ekawati Tallei ◽  
Fatimawali ◽  
Afriza Yelnetty ◽  
Rinaldi Idroes ◽  
Diah Kusumawaty ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Three Dimensional ◽  
Md Simulations ◽  
Inhibitory Effect ◽  
Dynamics Simulation ◽  
Novel Coronavirus

The rapid spread of a novel coronavirus known as SARS-CoV-2 has compelled the entire world to seek ways to weaken this virus, prevent its spread and also eliminate it. However, no drug has been approved to treat COVID-19. Furthermore, the receptor-binding domain (RBD) on this viral spike protein, as well as several other important parts of this virus, have recently undergone mutations, resulting in new virus variants. While no treatment is currently available, a naturally derived molecule with known antiviral properties could be used as a potential treatment. Bromelain is an enzyme found in the fruit and stem of pineapples. This substance has been shown to have a broad antiviral activity. In this article, we analyse the ability of bromelain to counteract various variants of the SARS-CoV-2 by targeting bromelain binding on the side of this viral interaction with human angiotensin-converting enzyme 2 (hACE2) using molecular docking and molecular dynamics simulation approaches. We have succeeded in making three-dimensional configurations of various RBD variants using protein modelling. Bromelain exhibited good binding affinity toward various variants of RBDs and binds right at the binding site between RBDs and hACE2. This result is also presented in the modelling between Bromelain, RBD, and hACE2. The molecular dynamics (MD) simulations study revealed significant stability of the bromelain and RBD proteins separately up to 100 ns with an RMSD value of 2 Å. Furthermore, despite increases in RMSD and changes in Rog values of complexes, which are likely due to some destabilized interactions between bromelain and RBD proteins, two proteins in each complex remained bonded, and the site where the two proteins bind remained unchanged. This finding indicated that bromelain could have an inhibitory effect on different SARS-CoV-2 variants, paving the way for a new SARS-CoV-2 inhibitor drug. However, more in vitro and in vivo research on this potential mechanism of action is required.

Molecular Dynamics Simulation of Neutron Damage in β-SIC

1998 ◽  
Vol 540 ◽  
Author(s):  
J.M. Perlado ◽  
L. Malerba ◽  
T. Diaz De La Rubia
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Point Defects ◽  
Damage Accumulation ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Temperature Sensitive ◽  
Neutron Damage ◽  
Preliminary Study ◽  
Threshold Displacement

AbstractMolecular Dynamics (MD) simulations of neutron damage in β-SiC have been performed using a modified version of the Tersoff potential. The Threshold Displacement Energy (TDE) for Si and C atoms at 300 K has been determined along directions [001], [110], [111] and [ 1 1 1 ]. The existence of recombination barriers, which allow the formation of metastable, temperature-sensitive defects even below the threshold, has been observed. Displacement cascades produced by both C- and Si-recoils of energies spanning from 0.5 keV up to, respectively, 5 keV and 8 keV have also been simulated at 300 K and 1300 K. Their analysis, together with the analysis of damage accumulation (∼3.4×10-3 DPA) at 1300 K, reveals that the two sub-lattices exhibit opposite responses to irradiation: whereas only a little damage is produced on the “ductile” Si sub-lattice, many point-defects accumulate on the much more “fragile” C sub-lattice. A preliminary study of the nature and clustering tendency of these defects is performed. The possibility of disorder-induced amorphization is considered and the preliminary result is that no amorphization takes place at the dose and temperature simulated.

Influence of Carbon Nanotube Aspect Ratio on Glass Transition Temperature of Polymers: A Molecular Dynamics Simulation Study

2015 ◽  
Vol 817 ◽  
pp. 797-802 ◽  
Author(s):  
Cai Jiang ◽  
Jian Wei Zhang ◽  
Shao Feng Lin ◽  
Su Ju ◽  
Da Zhi Jiang
Keyword(s):  
Molecular Dynamics ◽  
Glass Transition ◽  
Carbon Nanotube ◽  
Transition Temperature ◽  
Glass Transition Temperature ◽  
Aspect Ratio ◽  
Epoxy Resin ◽  
Md Simulations ◽  
Diglycidyl Ether ◽  
Dynamics Simulation

Molecular dynamics (MD) simulations on three single walled carbon nanotube (SWCNT) reinforced epoxy resin composites were conducted to study the influence of SWCNT type on the glass transition temperature (Tg) of the composites. The composite matrix is cross-linked epoxy resin based on the epoxy monomers bisphenol A diglycidyl ether (DGEBA) cured by diaminodiphenylmethane (DDM). MD simulations of NPT (constant number of particles, constant pressure and constant temperature) dynamics were carried out to obtain density as a function of temperature for each composite system. The Tg was determined as the temperature corresponding to the discontinuity of plot slopes of the densityvsthe temperature. In order to understand the motion of polymer chain segments above and below the Tg, various energy components and the MSD at various temperatures of the composites were investigated and their roles played in the glass transition process were analyzed. The results show that the Tg of the composites increases with increasing aspect ratio of the embedded SWCNT

A Molecular Dynamics Simulation Study of the Mechanical Properties of Carbon-Nanotube Reinforced Polystyrene Composite

2014 ◽  
pp. 466-477
Author(s):  
Nabila Tahreen ◽  
K. M. Masud
Keyword(s):  
Molecular Dynamics ◽  
Carbon Nanotube ◽  
Longitudinal Direction ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Minimization Method ◽  
Polymer Properties ◽  
Polystyrene Matrix ◽  
Nanotube Composites ◽  
Strain Energy Minimization

In recent years, polymer/carbon nanotube composites have attracted increased attention because the polymer properties have significantly improved. In this paper, a single walled carbon nanotube (SWCNT) is used to reinforce polystyrene matrix. Molecular dynamics (MD) simulations are used to study two periodic systems - a long CNT-reinforced polystyrene composite and amorphous polystyrene matrix itself. The axial and transverse elastic moduli of the amorphous polystyrene matrix and nanocomposites are evaluated using constant-strain energy minimization method. The results from MD simulations are compared with corresponding rule-of-mixture predictions. The simulation results show that CNTs significantly improve the stiffness of polystyrene/CNT composite, especially in the longitudinal direction of the nanotube. Polystyrene posses a strong attractive interaction with the surface of the SWCNT and therefore play an important role in providing effective adhesion. The conventional rule-of-mixture predicts a smaller value than MD simulation where there are strong interfacial interactions. Here the authors report a study on the interfacial characteristics of a CNT-PS composite system through MD simulations and continuum mechanics.

scholarly journals Molecular Dynamics Simulation of Homo-DNA: The Role of Crystal Packing in Duplex Conformation

Crystals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 532
Author(s):  
Jonathan H. Sheehan ◽  
Jarrod A. Smith ◽  
Pradeep S. Pallan ◽  
Terry P. Lybrand ◽  
Martin Egli
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Nucleic Acid ◽  
Base Pair ◽  
Crystal Packing ◽  
Md Simulations ◽  
Conformational Flexibility ◽  
Dynamics Simulation ◽  
Dna Duplex ◽  
Solution Studies

The (4′→6′)-linked DNA homolog 2′,3′-dideoxy-β-D-glucopyranosyl nucleic acid (dideoxy-glucose nucleic acid or homo-DNA) exhibits stable self-pairing of the Watson–Crick and reverse-Hoogsteen types, but does not cross-pair with DNA. Molecular modeling and NMR solution studies of homo-DNA duplexes pointed to a conformation that was nearly devoid of a twist and a stacking distance in excess of 4.5 Å. By contrast, the crystal structure of the homo-DNA octamer dd(CGAATTCG) revealed a right-handed duplex with average values for helical twist and rise of ca. 15° and 3.8 Å, respectively. Other key features of the structure were strongly inclined base-pair and backbone axes in the duplex with concomitant base-pair slide and cross-strand stacking, and the formation of a dimer across a crystallographic dyad with inter-duplex base swapping. To investigate the conformational flexibility of the homo-DNA duplex and a potential influence of lattice interactions on its geometry, we used molecular dynamics (MD) simulations of the crystallographically observed dimer of duplexes and an isolated duplex in the solution state. The dimer of duplexes showed limited conformational flexibility, and key parameters such as helical rise, twist, and base-pair slide exhibited only minor fluctuations. The single duplex was clearly more flexible by comparison and underwent partial unwinding, albeit without significant lengthening. Thus, base stacking was preserved in the isolated duplex and two adenosines extruded from the stack in the dimer of duplexes were reinserted into the duplex and pair with Ts in a Hoogsteen mode. Our results confirmed that efficient stacking in homo-DNA seen in the crystal structure of a dimer of duplexes was maintained in the separate duplex. Therefore, lattice interactions did not account for the different geometries of the homo-DNA duplex in the crystal and earlier models that resembled inclined ladders with large base-pair separations that precluded efficient stacking.

Constant-Temperature Molecular-Dynamics Simulation of the 2D Melting Transition of Rb and K

1992 ◽  
Vol 291 ◽  
Author(s):  
J. D. Fan ◽  
Zhi-Xiong Cai
Keyword(s):  
Molecular Dynamics ◽  
Constant Temperature ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Melting Transition ◽  
Histogram Method ◽  
Graphite Intercalation ◽  
2D System ◽  
Incommensurate Structures ◽  
First Time

ABSTRACTThe energy histogram method, introduced by Ferrenberg and Swendsen [Phys. Rev. Lett., 61, 2635, (1988) and 63, 1195, (1989)], was applied for the first time to the constant temperature molecular dynamics (MD) simulation of a two-dimensional (2D) system with incommensurate structures. We performed MD simulations for the stage-2 graphite intercalation compounds (GIC's) with Rb or K being the intercalants (Rb-GIC's and K- GIC's). The temperature dependence of the specific heat, Cv, is calculated for various sizes up to 864 atoms. The melting temperature was found to be 158 K for Rb-GIC's and 119 K for K-GIC's, respectively, which are in agreement with the experimental observations.

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