Multiple Substrate Binding States and Chiral Recognition in Cofactor-independent Glutamate Racemase:  A Molecular Dynamics Study†

Biochemistry ◽  
2004 ◽  
Vol 43 (30) ◽  
pp. 9685-9694 ◽  
Author(s):  
Henrik Möbitz ◽  
Thomas C. Bruice
Keyword(s):  
Molecular Dynamics ◽  
Chiral Recognition ◽  
Substrate Binding ◽  
Glutamate Racemase ◽  
Multiple Substrate

scholarly journals Simulating Multiple Substrate-Binding Events by γ-Glutamyltransferase Using Accelerated Molecular Dynamics

2020 ◽  
Vol 124 (45) ◽  
pp. 10104-10116
Author(s):  
Francesco Oliva ◽  
Jose C. Flores-Canales ◽  
Stefano Pieraccini ◽  
Carlo F. Morelli ◽  
Maurizio Sironi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Substrate Binding ◽  
Accelerated Molecular Dynamics ◽  
Multiple Substrate

scholarly journals Simulating Multiple Substrate Binding Events by γ-Glutamyltransferase using Accelerated Molecular Dynamics

2020 ◽  
Author(s):  
Francesco Oliva ◽  
Jose C. Flores-Canales ◽  
Stefano Pieraccini ◽  
Carlo F. Morelli ◽  
Maurizio Sironi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Electrostatic Interactions ◽  
Substrate Binding ◽  
Conformational Dynamics ◽  
Binding Pocket ◽  
Thermal Fluctuations ◽  
Accelerated Molecular Dynamics ◽  
Binding Cavity ◽  
Multiple Substrate ◽  
Open States

Abstractγ-glutamyltransferase (GGT) is an enzyme that uses γ-glutamyl compounds as substrate and catalyzes their transfer into a water molecule or an acceptor substrate with varied physiological-function in bacteria, plants and animals. Crystal structures of GGT are known for different species and in different states of the chemical reaction; however, structural dynamics of the substrate binding to the catalytic site of GGT is unknown. Here, we modeled Escherichia Coli GGT’s glutamine binding by using a swarm of accelerated molecular dynamics (aMD) simulations. Characterization of multiple binding events identified three structural binding motifs composed of polar residues in the binding pocket that govern glutamine binding into the active site. Simulated open and closed conformations of a lid-loop protecting the binding cavity suggests its role as a gating element by allowing or blocking substrates entry into the binding pocket. Partially open states of the lid-loop are accessible within thermal fluctuations, while the estimated free energy cost of a complete open state is 2.4 kcal/mol. Our results suggest that both specific electrostatic interactions and GGT conformational dynamics dictate the molecular recognition of substrate-GGT complexes.

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.

Using molecular dynamics simulations to identify the key factors responsible for chiral recognition by an amino acid-based molecular micelle

2018 ◽  
Vol 40 (5) ◽  
pp. 716-727 ◽  
Author(s):  
Kevin F. Morris ◽  
Eugene J. Billiot ◽  
Fereshteh H. Billiot ◽  
Jordan A. Ingle ◽  
Kevin B. Krause ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Molecular Dynamics Simulations ◽  
Chiral Recognition ◽  
Key Factors ◽  
Dynamics Simulations

scholarly journals Molecular dynamics and structure function analysis show that substrate binding and specificity are major forces in the functional diversification of Eqolisins

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Nicolás Stocchi ◽  
María Victoria Revuelta ◽  
Priscila Ailín Lanza Castronuovo ◽  
D. Mariano A. Vera ◽  
Arjen ten Have
Keyword(s):  
Molecular Dynamics ◽  
Structure Function ◽  
Function Analysis ◽  
Substrate Binding ◽  
Functional Diversification
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