Incorporation of side chain flexibility into protein binding pockets using MTflex

2016 ◽  
Vol 24 (20) ◽  
pp. 4978-4987 ◽  
Author(s):  
Nupur Bansal ◽  
Zheng Zheng ◽  
Kenneth M. Merz
Keyword(s):  
Protein Binding ◽  
Side Chain ◽  
Chain Flexibility ◽  
Binding Pockets

scholarly journals RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases

2009 ◽  
Vol 37 (Database) ◽  
pp. D369-D373 ◽  
Author(s):  
A. Shulman-Peleg ◽  
R. Nussinov ◽  
H. J. Wolfson
Keyword(s):  
Protein Binding ◽  
Binding Pockets ◽  
Nucleotide Bases

Side-chain flexibility in proteins upon ligand binding

2000 ◽  
Vol 39 (3) ◽  
pp. 261-268 ◽  
Author(s):  
Rafael Najmanovich ◽  
Josef Kuttner ◽  
Vladimir Sobolev ◽  
Marvin Edelman
Keyword(s):  
Ligand Binding ◽  
Side Chain ◽  
Chain Flexibility

scholarly journals Computational Analysis of HIV-1 Protease Protein Binding Pockets

2010 ◽  
Vol 50 (10) ◽  
pp. 1759-1771 ◽  
Author(s):  
Gene M. Ko ◽  
A. Srinivas Reddy ◽  
Sunil Kumar ◽  
Barbara A. Bailey ◽  
Rajni Garg
Keyword(s):  
Protein Binding ◽  
Computational Analysis ◽  
Binding Pockets ◽  
Hiv 1

scholarly journals Substituted polyfluoroaryl interactions with an arginine side chain in galectin-3 are governed by steric-, desolvation and electronic conjugation effects

2019 ◽  
Vol 17 (5) ◽  
pp. 1081-1089 ◽  
Author(s):  
Rohit Kumar ◽  
Kristoffer Peterson ◽  
Majda Misini Ignjatović ◽  
Hakon Leffler ◽  
Ulf Ryde ◽  
...  
Keyword(s):  
Protein Binding ◽  
Binding Affinity ◽  
Binding Sites ◽  
Binding Pocket ◽  
Side Chain ◽  
Complex Interplay ◽  
Protein Binding Sites ◽  
Arginine Side Chain ◽  
Galectin 3 ◽  
Insight Into

Analysis of a ligand induced-aglycone-binding pocket in galectin-3 provides detailed insight into interactions of fluorinated phenyl moieties with arginine-containing protein binding sites and the complex interplay of different energetic components in defining the binding affinity.

scholarly journals Free enthalpies of replacing water molecules in protein binding pockets

2012 ◽  
Vol 26 (12) ◽  
pp. 1293-1309 ◽  
Author(s):  
Sereina Riniker ◽  
Luzi J. Barandun ◽  
François Diederich ◽  
Oliver Krämer ◽  
Andreas Steffen ◽  
...  
Keyword(s):  
Protein Binding ◽  
Water Molecules ◽  
Binding Pockets

scholarly journals Structural Impacts of Drug-Resistance Mutations Appearing in HIV-2 Protease

Molecules ◽  
2021 ◽  
Vol 26 (3) ◽  
pp. 611
Author(s):  
Pierre Laville ◽  
Michel Petitjean ◽  
Leslie Regad
Keyword(s):  
Drug Resistance ◽  
Binding Pocket ◽  
Antiretroviral Drugs ◽  
Side Chain ◽  
Resistance Mutations ◽  
Structural Deformations ◽  
Binding Pockets ◽  
Structural Impacts ◽  
Backbone Atoms ◽  
Structural Shifts

The use of antiretroviral drugs is accompanied by the emergence of HIV-2 resistances. Thus, it is important to elucidate the mechanisms of resistance to antiretroviral drugs. Here, we propose a structural analysis of 31 drug-resistant mutants of HIV-2 protease (PR2) that is an important target against HIV-2 infection. First, we modeled the structures of each mutant. We then located structural shifts putatively induced by mutations. Finally, we compared wild-type and mutant inhibitor-binding pockets and interfaces to explore the impacts of these induced structural deformations on these two regions. Our results showed that one mutation could induce large structural rearrangements in side-chain and backbone atoms of mutated residue, in its vicinity or further. Structural deformations observed in side-chain atoms are frequent and of greater magnitude, that confirms that to fight drug resistance, interactions with backbone atoms should be favored. We showed that these observed structural deformations modify the conformation, volume, and hydrophobicity of the binding pocket and the composition and size of the PR2 interface. These results suggest that resistance mutations could alter ligand binding by modifying pocket properties and PR2 stability by impacting its interface. Our results reinforce the understanding of the effects of mutations that occurred in PR2 and the different mechanisms of PR2 resistance.

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