Electrostatic interactions in proteins: Calculations of the electrostatic term of free energy and the electrostatic potential field

1989 ◽  
Vol 17 (5) ◽  
Author(s):  
A.D. Karshikov ◽  
R. Engh ◽  
W. Bode ◽  
B.P. Atanasov
Keyword(s):  
Free Energy ◽  
Electrostatic Potential ◽  
Potential Field ◽  
Electrostatic Interactions

scholarly journals Prediction of GluN2B-CT1290-1310/DAPK1 Interaction by Protein–Peptide Docking and Molecular Dynamics Simulation

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 3018 ◽  
Author(s):  
Gao Tu ◽  
Tingting Fu ◽  
Fengyuan Yang ◽  
Lixia Yao ◽  
Weiwei Xue ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Electrostatic Interactions ◽  
Binding Free Energy ◽  
Computational Simulation ◽  
Critical Role ◽  
Dynamics Simulation ◽  
Peptide Docking ◽  
C Terminus ◽  
Free Energy Decomposition

The interaction of death-associated protein kinase 1 (DAPK1) with the 2B subunit (GluN2B) C-terminus of N-methyl-D-aspartate receptor (NMDAR) plays a critical role in the pathophysiology of depression and is considered a potential target for the structure-based discovery of new antidepressants. However, the 3D structures of C-terminus residues 1290–1310 of GluN2B (GluN2B-CT1290-1310) remain elusive and the interaction between GluN2B-CT1290-1310 and DAPK1 is unknown. In this study, the mechanism of interaction between DAPK1 and GluN2B-CT1290-1310 was predicted by computational simulation methods including protein–peptide docking and molecular dynamics (MD) simulation. Based on the equilibrated MD trajectory, the total binding free energy between GluN2B-CT1290-1310 and DAPK1 was computed by the mechanics generalized born surface area (MM/GBSA) approach. The simulation results showed that hydrophobic, van der Waals, and electrostatic interactions are responsible for the binding of GluN2B-CT1290–1310/DAPK1. Moreover, through per-residue free energy decomposition and in silico alanine scanning analysis, hotspot residues between GluN2B-CT1290-1310 and DAPK1 interface were identified. In conclusion, this work predicted the binding mode and quantitatively characterized the protein–peptide interface, which will aid in the discovery of novel drugs targeting the GluN2B-CT1290-1310 and DAPK1 interface.

scholarly journals STUDY OF PARAMETERS OF REACTIVITY MOLECULAR IN ADDITION REACTIONS OF HYDROHALIC ACIDS WITH ETHYLENE

2011 ◽  
Vol 08 (15) ◽  
pp. 54-64
Author(s):  
Francisco José Santos LIMA ◽  
Ademir Oliveira da SILVA ◽  
Yuri Lima de BRITO ◽  
Fernanda Louise Cardoso de SOUSA
Keyword(s):  
Free Energy ◽  
Thermodynamic Parameters ◽  
Electrostatic Potential ◽  
Molecular Modelling ◽  
Quantitative Data ◽  
Addition Reactions ◽  
Partial Charge ◽  
Kinetic Behavior ◽  
Atomic Properties ◽  
Molecular Reactivity

The molecular reactivity parameters (PRM´s) have been used to quantify atomic properties that influence in the interactions among the molecules. It is possible throughout the analysis of its magnitudes and stereochemistry arrangement of the system, to foresee and/or to explain certain experimental events. The aim of this work was to establish parallel among the thermodynamic parameters (enthalpy, entropy and free energy), and the results of the simulations of theoretical molecular modelling through the geometric qualitative and semi-quantitative data (densities of coulomb of electrostatic potential and partial charge), generated by a commercial software (WebLab ViewerPro) for the obtaining of PRM´s, in the hydrohalic acids reactions with the ethylene. It can be notice that there is clearly dependence of the reactivity parameters with the thermodynamic and kinetic behavior of these reactions.

Ice Ih–Water Interfacial Free Energy of Simple Water Models with Full Electrostatic Interactions

2012 ◽  
Vol 8 (7) ◽  
pp. 2383-2390 ◽  
Author(s):  
Ruslan L. Davidchack ◽  
Richard Handel ◽  
Jamshed Anwar ◽  
Andrey V. Brukhno
Keyword(s):  
Free Energy ◽  
Electrostatic Interactions ◽  
Interfacial Free Energy ◽  
Water Models
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