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.

scholarly journals Substrate Binding at the Qo-Site of the Bacterial Cytochrome bc1 Complex Predicted by Atomistic Molecular Dynamics Simulations

2013 ◽  
Vol 104 (2) ◽  
pp. 490a
Author(s):  
Pekka A. Postila ◽  
Karol Kaszuba ◽  
Marcin Sarewicz ◽  
Artur Osyczka ◽  
Ilpo Vattulainen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Substrate Binding ◽  
Cytochrome Bc1 ◽  
Bc1 Complex ◽  
Cytochrome Bc1 Complex ◽  
Qo Site ◽  
Dynamics Simulations

scholarly journals Exploration of gated ligand binding recognizes an allosteric site for blocking FABP4–protein interaction

2015 ◽  
Vol 17 (48) ◽  
pp. 32257-32267 ◽  
Author(s):  
Yan Li ◽  
Xiang Li ◽  
Zigang Dong
Keyword(s):  
Molecular Dynamics ◽  
Ligand Binding ◽  
Molecular Dynamics Simulations ◽  
Small Molecule ◽  
Protein Interaction ◽  
Allosteric Site ◽  
Binding Process ◽  
Dynamics Simulations

The binding process of a drug-like small molecule through a conformational gate is illustrated by extensive molecular dynamics simulations.

scholarly journals ROLE OF SUBSTRATE BINDING ON THE PROTEIN DYNAMICS OF AN ENDOGLUCANASE FROM FUSARIUM OXYSPORUM AT DIFFERENT TEMPERATURES

2018 ◽  
Vol 19 (1) ◽  
pp. 307-314
Author(s):  
ABDUL AZIZ AHMAD ◽  
Hamzah Mohd. Salleh ◽  
IBRAHIM ALI NOORBATCHA
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Fusarium Oxysporum ◽  
Protein Dynamics ◽  
Substrate Binding ◽  
Solvent Accessible Surface Area ◽  
Enzyme Complex ◽  
Different Temperatures ◽  
Endoglucanase I ◽  
Dynamics Simulations

: Thermostability is an important requirement for protein function, and one goal of protein engineering is improvement of activity of the enzymes at higher temperatures, particularly for industrial applications. Computational approaches to investigate factors influencing thermostability of proteins are becoming researchers’ choice. This study investigates the influence of substrate binding on the protein dynamics by comparing the molecular dynamics simulations of substrate-enzyme complex against un-bound enzyme, using endoglucanase I from Fusarium oxysporum. Endoglucanase-substrate complex was prepared by docking and molecular dynamics simulations were carried out at three different temperatures, 313 K, 333 K and 353 K. Our finding shows that the secondary structures for substrate-enzyme complex show more fluctuations relative to un-complexed structure. The same trend was observed for solvent accessible surface area and radius of gyration. At the highest temperature studied (353 K), the substrate-enzyme complex form showed the highest fluctuations. The fluctuations around the active site regions reach a minimum at the optimum temperature, compared to the other structural regions and other temperatures. ABSTRAK: Kestabilan (ketahanan) terhadap haba merupakan keperluan yang penting untuk fungsi protin, salah satu matlamat kejuruteraan protin adalah penambahbaikan aktiviti enzim pada suhu yang tinggi khususnya untuk aplikasi industri. Kini para penyelidik memilih kaedah komputasi, bagi mengkaji faktor yang mempengaruhi kestabilan terhadap haba. Kajian ini menyelidik pengaruh ikatan substrat pada protin dengan membandingkan simulasi molekular dinamik diantara substrat-enzim kompleks dan enzim sahaja, menggunakan endoglucanase I dari Fusarium oxysporum. Kompleks endoglucanase-substrat disediakan melalui kaedah docking dan simulasi molekular dinamik dilakukan pada suhu 313 K, 333 K dan 353 K. Kajian kami menunjukkan struktur sekunder bagi substrat-enzim kompleks kurang stabil berbanding enzim sahaja. Pola yang sama bagi luas permukaan boleh dicapai pelarut (SASA) dan jejari gyrasi. Pada suhu tertinggi dikaji (353 K), substrat-enzim kompleks paling tidak stabil. Pada suhu optimum, kadar ubah-ubah sekitar amino asid aktif adalah minimum berbanding struktur dan suhu lain.  

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