Molecular Dynamics Exploration of the Growth Mechanism of Hydroxyapatite Nanoparticles Regulated by Glutamic Acid

2021 ◽  
Author(s):  
Wentian Wang ◽  
Zhiyu Xue ◽  
Ruihan Wang ◽  
Xin Wang ◽  
Dingguo Xu
Keyword(s):  
Molecular Dynamics ◽  
Glutamic Acid ◽  
Growth Mechanism ◽  
Hydroxyapatite Nanoparticles

WHICH IS THE PROTON-SHUTTLE IN ISOXANTHOPTERIN DEAMINASE? QM/MM MD UNDERSTANDING

2013 ◽  
Vol 12 (08) ◽  
pp. 1341002 ◽  
Author(s):  
XIN ZHANG ◽  
MING LEI
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Glutamic Acid ◽  
Active Site ◽  
Nucleophilic Attack ◽  
Zinc Ions ◽  
Initial Model ◽  
Dynamics Simulations

The deamination process of isoxanthopterin catalyzed by isoxanthopterin deaminase was determined using the combined QM(PM3)/MM molecular dynamics simulations. In this paper, the updated PM3 parameters were employed for zinc ions and the initial model was built up based on the crystal structure. Proton transfer and following steps have been investigated in two paths: Asp336 and His285 serve as the proton shuttle, respectively. Our simulations showed that His285 is more effective than Aap336 in proton transfer for deamination of isoxanthopterin. As hydrogen bonds between the substrate and surrounding residues play a key role in nucleophilic attack, we suggested mutating Thr195 to glutamic acid, which could enhance the hydrogen bonds and help isoxanthopterin get close to the active site. The simulations which change the substrate to pterin 6-carboxylate also performed for comparison. Our results provide reference for understanding of the mechanism of deaminase and for enhancing the deamination rate of isoxanthopterin deaminase.

scholarly journals Growth mechanism of hydrogenated carbon films: molecular dynamics simulations of the effects of low energy CH radical

2012 ◽  
Vol 61 (3) ◽  
pp. 030701
Author(s):  
Song Qing ◽  
Ji Li ◽  
Quan Wei-Long ◽  
Zhang Lei ◽  
Tian Miao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Growth Mechanism ◽  
Carbon Films ◽  
Low Energy ◽  
Dynamics Simulations ◽  
Ch Radical

NMR and Molecular Dynamics Study of the Binding Mode of Naphthalene-N-sulfonyl-d-glutamic Acid Derivatives: Novel MurD Ligase Inhibitors

2009 ◽  
Vol 52 (9) ◽  
pp. 2899-2908 ◽  
Author(s):  
Mihael Simčič ◽  
Milan Hodošček ◽  
Jan Humljan ◽  
Katja Kristan ◽  
Uroš Urleb ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Glutamic Acid ◽  
Binding Mode ◽  
Glutamic Acid Derivatives ◽  
Murd Ligase

Molecular dynamics study of active-site interactions with tetracoordinate transients in acetylcholinesterase and its mutants

2001 ◽  
Vol 353 (3) ◽  
pp. 645-653 ◽  
Author(s):  
Istvan J. ENYEDY ◽  
Ildiko M. KOVACH ◽  
Akos BENCSURA
Keyword(s):  
Molecular Dynamics ◽  
Glutamic Acid ◽  
Active Site ◽  
Indole Ring ◽  
Active Site Residues ◽  
Parallel Simulations ◽  
Electrostatic Stabilization ◽  
Carbenium Ion ◽  
Dynamics Simulations

The role of active-site residues in the dealkylation reaction in the PSCS diastereomer of 2-(3,3-dimethylbutyl)methylphosphonofluoridate (soman)-inhibited Torpedo californicaacetylcholinesterase (AChE) was investigated by full-scale molecular dynamics simulations using CHARMM: > 400ps equilibration was followed by 150–200ps production runs with the fully solvated tetracoordinate phosphonate adduct of the wild-type, Trp84Ala and Gly199Gln mutants of AChE. Parallel simulations were carried out with the tetrahedral intermediate formed between serine-200 Oγ of AChE and acetylcholine. We found that the NεH in histidine H+-440 is positioned to protonate the oxygen in choline and thus promote its departure. In contrast, NεH in histidine H+-440 is not aligned for a favourable proton transfer to the pinacolyl O to promote dealkylation, but electrostatic stabilization by histidine H+-440 of the developing anion on the phosphonate monoester occurs. Destabilizing interactions between residues and the alkyl fragment of the inhibitor enforce methyl migration from Cβ to Cα concerted with C—O bond breaking in soman-inhibited AChE. Tryptophan-84, phenyalanine-331 and glutamic acid-199 are within 3.7–3.9 Å (1 Å=10-10 m) from a methyl group in Cβ, 4.5–5.1 Å from Cβ and 4.8–5.8 Å from Cα, and can better stabilize the developing carbenium ion on Cβ than on Cα. The Trp84Ala mutation eliminates interactions between the incipient carbenium ion and the indole ring, but also reduces its interactions with phenylalanine-331 and aspartic acid-72. Tyrosine-130 promotes dealkylation by interacting with the indole ring of tryptophan-84. Glutamic acid-443 can influence the orientation of active-site residues through tyrosine-421, tyrosine-442 and histidine-440 in soman-inhibited AChE, and thus facilitate dealkylation.

Study of growth mechanism of TiC cluster in ferrite via molecular dynamics simulation

2015 ◽  
Vol 159 ◽  
pp. 389-391 ◽  
Author(s):  
Yanan Lv ◽  
Peter Hodgson ◽  
Lingxue Kong ◽  
Weimin Gao
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Growth Mechanism ◽  
Dynamics Simulation

Growth Mechanism of Si Dimer Rows on Si(001)

1995 ◽  
Vol 408 ◽  
Author(s):  
T. Yamasaki ◽  
T. Uda ◽  
K. Terakura
Keyword(s):  
Molecular Dynamics ◽  
High Temperatures ◽  
Growth Mechanism ◽  
First Principles ◽  
Activation Energies ◽  
Molecular Dynamics Method ◽  
Perpendicular Direction ◽  
Condensation Process ◽  
Growth Processes ◽  
Dynamics Method

AbstractInitial processes of Si dimer row growth on Si(001) surface is studied by the first principles molecular dynamics method. We optimize several different ad-Si clusters composed of one to four atoms on the surface and estimate activation energies for some important growth processes. At lower temperatures, a metastable ad-Si dimer in the trough between substrate dimer rows attracts monomers and tends to grow into a short diluted-dimer row in the perpendicular direction to the substrate dimer rows. In high temperatures as ad-Si dimers can diffuse, a direct dimer condensation process is possible to elongate the dense-dimer rows also in the perpendicular direction.

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