Ordered Water and Ligand Mobility in the HIV-1 Integrase-5CITEP Complex:  A Molecular Dynamics Study

2001 ◽  
Vol 44 (19) ◽  
pp. 3043-3047 ◽  
Author(s):  
Ni ◽  
Christoph A. Sotriffer ◽  
J. Andrew McCammon
Keyword(s):  
Molecular Dynamics ◽  
Ordered Water ◽  
Hiv 1

Molecular Docking and Molecular Dynamics Simulation Based Approach to Explore the Dual Inhibitor Against HIV-1 Reverse Transcriptase and Integrase

2017 ◽  
Vol 20 (8) ◽  
Author(s):  
Subhash Chander ◽  
Rajan Kumar Pandey ◽  
Ashok Penta ◽  
Bhanwar Singh Choudhary ◽  
Manish Sharma ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Reverse Transcriptase ◽  
Dynamics Simulation ◽  
Dual Inhibitor ◽  
Simulation Based ◽  
Hiv 1

scholarly journals Identifying binding hot spots on protein surfaces by mixed-solvent molecular dynamics: HIV-1 protease as a test case

Biopolymers ◽  
2015 ◽  
Vol 105 (1) ◽  
pp. 21-34 ◽  
Author(s):  
Peter M. U. Ung ◽  
Phani Ghanakota ◽  
Sarah E. Graham ◽  
Katrina W. Lexa ◽  
Heather A. Carlson
Keyword(s):  
Molecular Dynamics ◽  
Hot Spots ◽  
Mixed Solvent ◽  
Test Case ◽  
Protein Surfaces ◽  
Hiv 1

scholarly journals Activities, Crystal Structures, and Molecular Dynamics of Dihydro-1H-isoindole Derivatives, Inhibitors of HIV-1 Integrase

2012 ◽  
Vol 8 (1) ◽  
pp. 209-217 ◽  
Author(s):  
Mathieu Métifiot ◽  
Kasthuraiah Maddali ◽  
Barry C. Johnson ◽  
Stephen Hare ◽  
Steven J. Smith ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Crystal Structures ◽  
Hiv 1

scholarly journals Molecular Dynamics Simulations of the First Steps of the Reaction Catalyzed by HIV-1 Protease

2002 ◽  
Vol 83 (2) ◽  
pp. 794-807 ◽  
Author(s):  
Joanna Trylska ◽  
Piotr Bała ◽  
Maciej Geller ◽  
Paweł Grochowski
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
Hiv 1

Investigating potency of TMC-126 against wild-type and mutant variants of HIV-1 protease: a molecular dynamics and free energy study

2021 ◽  
Vol 32 (11) ◽  
pp. 941-962
Author(s):  
M.F. Sk ◽  
S. Haridev ◽  
R. Roy ◽  
P. Kar
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Wild Type ◽  
Hiv 1

scholarly journals Dynamic regulation of HIV-1 capsid interaction with the restriction factor TRIM5α identified by magic-angle spinning NMR and molecular dynamics simulations

2018 ◽  
Vol 115 (45) ◽  
pp. 11519-11524 ◽  
Author(s):  
Caitlin M. Quinn ◽  
Mingzhang Wang ◽  
Matthew P. Fritz ◽  
Brent Runge ◽  
Jinwoo Ahn ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Building Blocks ◽  
Magic Angle Spinning ◽  
Magic Angle ◽  
Capsid Assembly ◽  
Dynamic Regulation ◽  
Angle Spinning ◽  
Dynamics Simulations ◽  
Hiv 1

The host factor protein TRIM5α plays an important role in restricting the host range of HIV-1, interfering with the integrity of the HIV-1 capsid. TRIM5 triggers an antiviral innate immune response by functioning as a capsid pattern recognition receptor, although the precise mechanism by which the restriction is imposed is not completely understood. Here we used an integrated magic-angle spinning nuclear magnetic resonance and molecular dynamics simulations approach to characterize, at atomic resolution, the dynamics of the capsid’s hexameric and pentameric building blocks, and the interactions with TRIM5α in the assembled capsid. Our data indicate that assemblies in the presence of the pentameric subunits are more rigid on the microsecond to millisecond timescales than tubes containing only hexamers. This feature may be of key importance for controlling the capsid’s morphology and stability. In addition, we found that TRIM5α binding to capsid induces global rigidification and perturbs key intermolecular interfaces essential for higher-order capsid assembly, with structural and dynamic changes occurring throughout the entire CA polypeptide chain in the assembly, rather than being limited to a specific protein-protein interface. Taken together, our results suggest that TRIM5α uses several mechanisms to destabilize the capsid lattice, ultimately inducing its disassembly. Our findings add to a growing body of work indicating that dynamic allostery plays a pivotal role in capsid assembly and HIV-1 infectivity.

scholarly journals Pressure induced structural changes and dimer destabilization of HIV-1 protease studied by molecular dynamics simulations

2014 ◽  
Vol 16 (47) ◽  
pp. 25906-25915 ◽  
Author(s):  
Eva Kutálková ◽  
Josef Hrnčiřík ◽  
Marek Ingr
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structural Changes ◽  
Dynamics Simulations ◽  
Hiv 1

A Combination of Molecular Dynamics and Docking Calculation to Explore the Binding Mode of ADS-J1, a Polyanionic Compound Endowed with anti-HIV-1 Activity.

ChemInform ◽  
2006 ◽  
Vol 37 (31) ◽  
Author(s):  
Fabrizio Manetti ◽  
Cristina Tintori ◽  
Mercedes Armand-Ugon ◽  
Imma Clotet-Codina ◽  
Silvio Massa ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Binding Mode ◽  
Docking Calculation ◽  
Anti Hiv ◽  
Hiv 1
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