Molecular dynamics study of structural properties of -sheet assemblies formed by synthetic de novo oligopeptides

2007 ◽  
Vol 373 ◽  
pp. 455-476 ◽  
Author(s):  
Giovanni Bellesia ◽  
Maxim V. Fedorov ◽  
Edward G. Timoshenko
Keyword(s):  
Molecular Dynamics ◽  
Structural Properties ◽  
De Novo

Molecular dynamics study on the mechanical response and failure behaviour of graphene: performance enhancement via 5–7–7–5 defects

RSC Advances ◽  
2016 ◽  
Vol 6 (31) ◽  
pp. 26361-26373 ◽  
Author(s):  
G. Rajasekaran ◽  
Avinash Parashar
Keyword(s):  
Molecular Dynamics ◽  
Tensile Strength ◽  
Structural Properties ◽  
Elastic Moduli ◽  
Mechanical Response ◽  
Performance Enhancement ◽  
Structural Defects ◽  
Thick Sheet ◽  
Failure Behaviour ◽  
Production Techniques

A one atom-thick sheet of carbon exhibits outstanding elastic moduli and tensile strength in its pristine form but structural defects which are inevitable in graphene due to its production techniques can alter its structural properties.

scholarly journals On the dynamics of some small structural motifs in rRNA upon ligand binding

2008 ◽  
Vol 73 (1) ◽  
pp. 41-53
Author(s):  
Aleksandra Rakic ◽  
Petar Mitrasinovic
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Binding Sites ◽  
De Novo ◽  
Reference Structure ◽  
Base Pairs ◽  
Rna Sequences ◽  
Conformational Model ◽  
Thermodynamic Variables ◽  
Dynamics Simulations

The present study characterizes using molecular dynamics simulations the behavior of the GAA (1186-1188) hairpin triloops with their closing c-g base pairs in large ribonucleoligand complexes (PDB IDs: 1njn, 1nwy, 1jzx). The relative energies of the motifs in the complexes with respect to that in the reference structure (unbound form of rRNA; PDB ID: 1njp) display the trends that agree with those of the conformational parameters reported in a previous study1 utilizing the de novo pseudotorsional (?,?) approach. The RNA regions around the actual RNA-ligand contacts, which experience the most substantial conformational changes upon formation of the complexes were identified. The thermodynamic parameters, based on a two-state conformational model of RNA sequences containing 15, 21 and 27 nucleotides in the immediate vicinity of the particular binding sites, were evaluated. From a more structural standpoint, the strain of a triloop, being far from the specific contacts and interacting primarily with other parts of the ribosome, was established as a structural feature which conforms to the trend of the average values of the thermodynamic variables corresponding to the three motifs defined by the 15-, 21- and 27-nucleotide sequences. From a more functional standpoint, RNA-ligand recognition is suggested to be presumably dictated by the types of ligands in the complexes.

scholarly journals Structural Properties of G,T-Parallel Duplexes

2010 ◽  
Vol 2010 ◽  
pp. 1-11 ◽  
Author(s):  
Anna Aviñó ◽  
Elena Cubero ◽  
Raimundo Gargallo ◽  
Carlos González ◽  
Modesto Orozco ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Properties ◽  
Theoretical Calculations ◽  
Md Simulations ◽  
Theoretical Studies ◽  
Duplex Structure ◽  
Strong Stabilization ◽  
The Stability ◽  
The Impact

The structure of G,T-parallel-stranded duplexes of DNA carrying similar amounts of adenine and guanine residues is studied by means of molecular dynamics (MD) simulations and UV- and CD spectroscopies. In addition the impact of the substitution of adenine by 8-aminoadenine and guanine by 8-aminoguanine is analyzed. The presence of 8-aminoadenine and 8-aminoguanine stabilizes the parallel duplex structure. Binding of these oligonucleotides to their target polypyrimidine sequences to form the corresponding G,T-parallel triplex was not observed. Instead, when unmodified parallel-stranded duplexes were mixed with their polypyrimidine target, an interstrand Watson-Crick duplex was formed. As predicted by theoretical calculations parallel-stranded duplexes carrying 8-aminopurines did not bind to their target. The preference for the parallel-duplex over the Watson-Crick antiparallel duplex is attributed to the strong stabilization of the parallel duplex produced by the 8-aminopurines. Theoretical studies show that the isomorphism of the triads is crucial for the stability of the parallel triplex.

A computational study on cannabinoid receptors and potent bioactive cannabinoid ligands: homology modeling, docking, de novo drug design and molecular dynamics analysis

2009 ◽  
Vol 14 (2) ◽  
pp. 257-276 ◽  
Author(s):  
Serdar Durdagi ◽  
Manthos G. Papadopoulos ◽  
Panagiotis G. Zoumpoulakis ◽  
Catherine Koukoulitsa ◽  
Thomas Mavromoustakos
Keyword(s):  
Molecular Dynamics ◽  
Drug Design ◽  
Homology Modeling ◽  
Cannabinoid Receptors ◽  
De Novo ◽  
Computational Study ◽  
Dynamics Analysis ◽  
De Novo Drug Design

Molecular Dynamics Studies on the Growth and Structural Properties of Hydrogenated DLC Films

2008 ◽  
Vol 373-374 ◽  
pp. 108-112
Author(s):  
Yu Jun Zhang ◽  
Guang Neng Dong ◽  
Jun Hong Mao ◽  
You Bai Xie
Keyword(s):  
Molecular Dynamics ◽  
Structural Properties ◽  
Impact Energy ◽  
Frictional Coefficient ◽  
Carbon Films ◽  
Dynamics Simulation ◽  
Diamond Surface ◽  
Hydrogen Atoms ◽  
Molecular Configuration ◽  
The Impact

The novel frictional properties of hydrogenated DLC (Diamond-like Carbon) films have been reported for nearly ten years. But up to now, researchers still haven’t known the exact mechanism resulting in the super-low frictional performance of hydrogenated DLC films. Especially they have little knowledge on the molecular configuration and structural properties of these kinds of films. In this paper, CH3 radicals with different impact energies are selected as source species to deposit DLC films on diamond (100) by molecular dynamics simulation. Results show hydrogenated DLC films can be successfully obtained when impact energy is in an appropriate scope that is no less than 20eV. The depositing processes involve impinging diamond surface and bonding procedure. Some atoms, instead of bonding with substrate atoms, fly away from the diamond surface. Only suitable impact energy can improve the growth of the film. Within 30eV to 60eV, the maximum deposition ratio is attained. In addition, when carbon atoms act as the deposition sources, the deposition ratio is relatively higher. Furthermore, the authors find that species with higher concentration of carbon atoms in deposition sources lead to a better deposition rate. Carbon atoms are more reactive than hydrogen atoms. Then the relative densities of DLC films are calculated. The density curves indicate that the structures of the films vary obviously as the impact energy augments. The average relative density is generally monotone increase with the increment of impact energy. The hybridization of carbon atoms greatly affects the properties of hydrogenated DLC films. The transition between sp2 and sp3 will result in the graphitization and reduce the frictional coefficient when DLC films are used as tribo-pair in friction.

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