Substrate Binding Mechanism of HIV-1 Protease from Explicit-Solvent Atomistic Simulations

2009 ◽  
Vol 131 (33) ◽  
pp. 11811-11818 ◽  
Author(s):  
Fabio Pietrucci ◽  
Fabrizio Marinelli ◽  
Paolo Carloni ◽  
Alessandro Laio
Keyword(s):  
Substrate Binding ◽  
Atomistic Simulations ◽  
Binding Mechanism ◽  
Explicit Solvent ◽  
Hiv 1

scholarly journals Binding Ensembles of p53-MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations

Molecules ◽  
2021 ◽  
Vol 26 (1) ◽  
pp. 198
Author(s):  
Lijun Lang ◽  
Alberto Perez
Keyword(s):  
Bayesian Inference ◽  
Virtual Screening ◽  
Statistical Mechanics ◽  
Small Molecules ◽  
Rational Design ◽  
Driving Forces ◽  
Peptide Inhibitors ◽  
Atomistic Simulations ◽  
Binding Mechanism ◽  
Intrinsically Disordered

Designing peptide inhibitors of the p53-MDM2 interaction against cancer is of wide interest. Computational modeling and virtual screening are a well established step in the rational design of small molecules. But they face challenges for binding flexible peptide molecules that fold upon binding. We look at the ability of five different peptides, three of which are intrinsically disordered, to bind to MDM2 with a new Bayesian inference approach (MELD × MD). The method is able to capture the folding upon binding mechanism and differentiate binding preferences between the five peptides. Processing the ensembles with statistical mechanics tools depicts the most likely bound conformations and hints at differences in the binding mechanism. Finally, the study shows the importance of capturing two driving forces to binding in this system: the ability of peptides to adopt bound conformations (ΔGconformation) and the interaction between interface residues (ΔGinteraction).

scholarly journals Atomistic Simulations of the HIV-1 Protease Folding Inhibition

2008 ◽  
Vol 95 (2) ◽  
pp. 550-562 ◽  
Author(s):  
Gennady Verkhivker ◽  
Guido Tiana ◽  
Carlo Camilloni ◽  
Davide Provasi ◽  
Ricardo A. Broglia
Keyword(s):  
Atomistic Simulations ◽  
Hiv 1

Molecular basis of P450 OleTJE: an investigation of substrate binding mechanism and major pathways

2017 ◽  
Vol 31 (5) ◽  
pp. 483-495 ◽  
Author(s):  
Juan Du ◽  
Lin Liu ◽  
Li Zhong Guo ◽  
Xiao Jun Yao ◽  
Jian Ming Yang
Keyword(s):  
Molecular Basis ◽  
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 A Cryptic Polyreactive Antibody Recognizes Distinct Clades of HIV-1 Glycoprotein 120 by an Identical Binding Mechanism

2014 ◽  
Vol 289 (25) ◽  
pp. 17767-17779 ◽  
Author(s):  
Jordan D. Dimitrov ◽  
Cyril Planchais ◽  
Tobias Scheel ◽  
Delphine Ohayon ◽  
Stephane Mesnage ◽  
...  
Keyword(s):  
Binding Mechanism ◽  
Hiv 1
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