scholarly journals Molecular Dynamics Investigation of the Substrate Binding Mechanism in Carboxylesterase

Biochemistry ◽  
2015 ◽  
Vol 54 (9) ◽  
pp. 1841-1848 ◽  
Author(s):  
Qi Chen ◽  
Zheng-Jiao Luan ◽  
Xiaolin Cheng ◽  
Jian-He Xu
Keyword(s):  
Molecular Dynamics ◽  
Substrate Binding ◽  
Binding Mechanism

Molecular dynamics insights into the structure, function, and substrate binding mechanism of mucin desulfating sulfatase of gut microbe Bacteroides fragilis

2018 ◽  
Vol 119 (4) ◽  
pp. 3618-3631 ◽  
Author(s):  
Ardhendu Bhusan Praharaj ◽  
Budheswar Dehury ◽  
Namita Mahapatra ◽  
Shantanu Kumar Kar ◽  
Santosh Kumar Behera
Keyword(s):  
Molecular Dynamics ◽  
Structure Function ◽  
Substrate Binding ◽  
Bacteroides Fragilis ◽  
Binding Mechanism ◽  
Gut Microbe

scholarly journals Binding mechanism of naringenin with monoamine oxidase – B enzyme: QM/MM and molecular dynamics perspective

Heliyon ◽  
2021 ◽  
Vol 7 (4) ◽  
pp. e06684
Author(s):  
Hunday Govindasamy ◽  
Sivanandam Magudeeswaran ◽  
Saravanan Kandasamy ◽  
Kumaradhas Poomani
Keyword(s):  
Molecular Dynamics ◽  
Monoamine Oxidase ◽  
Monoamine Oxidase B ◽  
Binding Mechanism

A molecular dynamics study of the complete binding process of meropenem to New Delhi metallo-β-lactamase 1

2018 ◽  
Vol 20 (9) ◽  
pp. 6409-6420 ◽  
Author(s):  
Juan Duan ◽  
Chuncai Hu ◽  
Jiafan Guo ◽  
Lianxian Guo ◽  
Jia Sun ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Substrate Binding ◽  
New Delhi ◽  
Binding Process ◽  
Dynamics Simulations

We have investigated the substrate-binding pathways of NDM-1 via unbiased molecular dynamics simulations and metadynamics.

Exploring the binding mechanism of positive allosteric modulators in human metabotropic glutamate receptor 2 using molecular dynamics simulations

2021 ◽  
Author(s):  
Panpan Wang ◽  
Xiaonan Gao ◽  
Ke Zhang ◽  
Qinglan Pei ◽  
Xiaobo Xu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Glutamate Receptor ◽  
Metabotropic Glutamate Receptor ◽  
Binding Mode ◽  
Allosteric Modulators ◽  
Binding Mechanism ◽  
Metabotropic Glutamate ◽  
High Affinity ◽  
Dynamics Simulations ◽  
High Electronegativity

Based on the binding mode and electrostatics, the features of high affinity PAMs were the reduced hydrophobicity with low electronegativity of R1, increased hydrophobicity with low electronegativity of R2 and with high electronegativity of linker.

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