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.

scholarly journals Structure and Thermal Stability of wtRop and RM6 Proteins through All-Atom Molecular Dynamics Simulations and Experiments

2021 ◽  
Vol 22 (11) ◽  
pp. 5931
Author(s):  
Maria Arnittali ◽  
Anastassia N. Rissanou ◽  
Maria Amprazi ◽  
Michael Kokkinidis ◽  
Vagelis Harmandaris
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Structural Integrity ◽  
Md Simulations ◽  
Effect Of Temperature ◽  
Key Factors ◽  
Loop Region ◽  
Dynamics Simulations ◽  
Experimental Findings ◽  
Thermal Stability Of

In the current work we study, via molecular simulations and experiments, the folding and stability of proteins from the tertiary motif of 4-α-helical bundles, a recurrent motif consisting of four amphipathic α-helices packed in a parallel or antiparallel fashion. The focus is on the role of the loop region in the structure and the properties of the wild-type Rop (wtRop) and RM6 proteins, exploring the key factors which can affect them, through all-atom molecular dynamics (MD) simulations and supporting by experimental findings. A detailed investigation of structural and conformational properties of wtRop and its RM6 loopless mutation is presented, which display different physical characteristics even in their native states. Then, the thermal stability of both proteins is explored showing RM6 as more thermostable than wtRop through all studied measures. Deviations from native structures are detected mostly in tails and loop regions and most flexible residues are indicated. Decrease of hydrogen bonds with the increase of temperature is observed, as well as reduction of hydrophobic contacts in both proteins. Experimental data from circular dichroism spectroscopy (CD), are also presented, highlighting the effect of temperature on the structural integrity of wtRop and RM6. The central goal of this study is to explore on the atomic level how a protein mutation can cause major changes in its physical properties, like its structural stability.

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 study of the structural properties and thermal stability of human Bcl-2 by molecular dynamics simulations

2013 ◽  
Vol 32 (11) ◽  
pp. 1707-1719 ◽  
Author(s):  
Ian Ilizaliturri-Flores ◽  
José Correa-Basurto ◽  
Claudia G. Benítez-Cardoza ◽  
Absalom Zamorano-Carrillo
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Molecular Dynamics Simulations ◽  
Structural Properties ◽  
Dynamics Simulations ◽  
Thermal Stability Of

scholarly journals Molecular dynamics simulations of nanoscale engravings on an alkanethiol monolayer

RSC Advances ◽  
2017 ◽  
Vol 7 (56) ◽  
pp. 35537-35542 ◽  
Author(s):  
Zhengqing Zhang ◽  
Yoonho Ahn ◽  
Joonkyung Jang
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
Thermal Stability Of

Thermal stability of nanoscale engravings on alkanethiol monolayer.

Molecular dynamics simulations reveal how graphene oxide stabilizes and activates lipase in an anhydrous gas

2019 ◽  
Vol 21 (45) ◽  
pp. 25425-25430 ◽  
Author(s):  
Zhongwang Fu ◽  
Weina Xu ◽  
Gong Chen ◽  
Zheyu Wang ◽  
Diannan Lu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Graphene Oxide ◽  
Simulated Annealing ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Candida Antarctica ◽  
Lipase B ◽  
Annealing Procedure ◽  
Dynamics Simulations ◽  
Simulated Annealing Procedure

The interaction between Candida antarctica lipase B (CALB) and graphene oxide (GO) in an anhydrous gas was studied using molecular dynamics (MD) simulations augmented with a simulated annealing procedure to accelerate relaxation towards equilibrium.

scholarly journals Thermal Stability of Globins: Implications of Flexibility and Heme Coordination Studied by Molecular Dynamics Simulations

2018 ◽  
Vol 59 (1) ◽  
pp. 441-452 ◽  
Author(s):  
Laia Julió Plana ◽  
Alejandro D. Nadra ◽  
Dario A. Estrin ◽  
F. Javier Luque ◽  
Luciana Capece
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
Thermal Stability Of
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