Comparative molecular dynamics simulations of histone deacetylase-like protein: Binding modes and free energy analysis to hydroxamic acid inhibitors

2008 ◽  
Vol 73 (1) ◽  
pp. 134-149 ◽  
Author(s):  
Chunli Yan ◽  
Zhilong Xiu ◽  
Xiaohui Li ◽  
Shenmin Li ◽  
Ce Hao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Protein Binding ◽  
Molecular Dynamics Simulations ◽  
Histone Deacetylase ◽  
Hydroxamic Acid ◽  
Energy Analysis ◽  
Binding Modes ◽  
Dynamics Simulations ◽  
Free Energy Analysis

Molecular dynamics simulations and binding free energy analysis of DNA minor groove complexes of curcumin

2011 ◽  
Vol 17 (11) ◽  
pp. 2805-2816 ◽  
Author(s):  
Mathew Varghese Koonammackal ◽  
Unnikrishnan Viswambharan Nair Nellipparambil ◽  
Chellappanpillai Sudarsanakumar
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Energy Analysis ◽  
Binding Free Energy ◽  
Minor Groove ◽  
Dna Minor Groove ◽  
Dynamics Simulations ◽  
Free Energy Analysis

scholarly journals Dynamics and Thermodynamics of Transthyretin Association from Molecular Dynamics Simulations

2018 ◽  
Vol 2018 ◽  
pp. 1-14 ◽  
Author(s):  
Cedrix J. Dongmo Foumthuim ◽  
Alessandra Corazza ◽  
Rodolfo Berni ◽  
Gennaro Esposito ◽  
Federico Fogolari
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Energy Analysis ◽  
Wild Type ◽  
Triple Mutant ◽  
Energy Functions ◽  
Dimer Interface ◽  
Dynamics Simulations ◽  
Free Energy Analysis ◽  
Effective Energy Functions

Molecular dynamics simulations are used in this work to probe the structural stability and the dynamics of engineered mutants of transthyretin (TTR), i.e., the double mutant F87M/L110M (MT-TTR) and the triple mutant F87M/L110M/S117E (3M-TTR), in relation to wild-type. Free energy analysis from end-point simulations and statistical effective energy functions are used to analyze trajectories, revealing that mutations do not have major impact on protein structure but rather on protein association, shifting the equilibria towards dissociated species. The result is confirmed by the analysis of 3M-TTR which shows dissociation within the first 10 ns of the simulation, indicating that contacts are lost at the dimer-dimer interface, whereas dimers (formed by monomers which pair to form two extended β-sheets) appear fairly stable. Overall the simulations provide a detailed view of the dynamics and thermodynamics of wild-type and mutant transthyretins and a rationale of the observed effects.

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