Elucidating the preference of dimeric over monomeric form for thermal stability of Thermus thermophilus isopropylmalate dehydrogenase: A molecular dynamics perspective

2020 ◽  
Vol 96 ◽  
pp. 107530
Author(s):  
Reetu Sharma ◽  
Someswar Rao Sagurthi ◽  
G. Narahari Sastry
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Thermus Thermophilus ◽  
Monomeric Form ◽  
Isopropylmalate Dehydrogenase ◽  
Thermal Stability Of

Effect of polar side chains at position 172 on thermal stability of 3-isopropylmalate dehydrogenase from Thermus thermophilus

FEBS Letters ◽  
1997 ◽  
Vol 410 (2-3) ◽  
pp. 141-144 ◽  
Author(s):  
Satoshi Akanuma ◽  
Chunxu Qu ◽  
Akihiko Yamagishi ◽  
Nobuo Tanaka ◽  
Tairo Oshima
Keyword(s):  
Thermal Stability ◽  
Thermus Thermophilus ◽  
Side Chains ◽  
Isopropylmalate Dehydrogenase ◽  
Thermal Stability Of

Simulation of Thermal Stability and Friction: A Lubricant Confined Between Monolayers of Wear Inhibitors on Iron Oxide

1998 ◽  
Vol 543 ◽  
Author(s):  
T. Çağin ◽  
Y. Zhou ◽  
E. S. Yamaguchi ◽  
R. Frazier ◽  
A. Ho ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Quantum Chemical ◽  
Md Simulations ◽  
Atomic Level ◽  
The Self ◽  
Self Assembled Monolayer ◽  
Thermal Stabilities ◽  
Frictional Forces ◽  
Thermal Stability Of

AbstractTo understand antiwear phenomena in motor engines at the atomic level and provide evidence inselecting future ashless wear inhibitors, we studied the thermal stability of the self-assembled monolayer(SAM) model for dithiophosphate (DTP) and dithiocarbamate (DTC) molecules on the iron oxidesurface using molecular dynamics. The interactions for DTP, DTC and Fe2O3 are evaluated based on aforce field derived from fitting to ab initio quantum chemical calculations of dimethyl DTP (and DTC)and Fe(OH)2(H2O)2-DTP (DTC) clusters. MD simulations at constant-NPT are conducted to assesrelative thermal stabilities of the DTP and DTC with different pendant groups (n-propyl, i-propyl, npentyl.and i-pentyl). To investigate frictional process, we employ a steady state MD method, in whichone of the Fe2O3 slabs maintained at a constant linear velocity. We obtain the time averaged normaland frictional forces from the interatomic forces. Then, we calculated the friction coefficient at theinterface between SAMs of DTP and the confined lubricant, hexadecane, to assess the shear stability ofDTPs with different pendant groups.

scholarly journals A Possible Mechanism of Graphene Oxide to Enhance Thermostability of D-Psicose 3-Epimerase Revealed by Molecular Dynamics Simulations

2021 ◽  
Vol 22 (19) ◽  
pp. 10813
Author(s):  
Congcong Li ◽  
Zhongkui Lu ◽  
Min Wang ◽  
Siao Chen ◽  
Lu Han ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Graphene Oxide ◽  
Md Simulations ◽  
Strong Interactions ◽  
Limiting Factor ◽  
Active Site Residues ◽  
Detailed Mechanism ◽  
Dynamics Simulations ◽  
Thermal Stability Of

Thermal stability is a limiting factor for effective application of D-psicose 3-epimerase (DPEase) enzyme. Recently, it was reported that the thermal stability of DPEase was improved by immobilizing enzymes on graphene oxide (GO) nanoparticles. However, the detailed mechanism is not known. In this study, we investigated interaction details between GO and DPEase by performing molecular dynamics (MD) simulations. The results indicated that the domain (K248 to D268) of DPEase was an important anchor for immobilizing DPEase on GO surface. Moreover, the strong interactions between DPEase and GO can prevent loop α1′-α1 and β4-α4 of DPEase from the drastic fluctuation. Since these two loops contained active site residues, the geometry of the active pocket of the enzyme remained stable at high temperature after the DPEase was immobilized by GO, which facilitated efficient catalytic activity of the enzyme. Our research provided a detailed mechanism for the interaction between GO and DPEase at the nano–biology interface.

Thermal stability of zirconia-doped ceria surfaces: A first-principles molecular dynamics study

2020 ◽  
Vol 507 ◽  
pp. 144942
Author(s):  
Gege Zhou ◽  
Wen-Tong Geng ◽  
Wei Xiao ◽  
Lu Sun ◽  
Jianwei Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
First Principles ◽  
Doped Ceria ◽  
Thermal Stability Of ◽  
First Principles Molecular Dynamics
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