Molecular Dynamics Simulations and Thermodynamics Analysis of DNA−Drug Complexes. Minor Groove Binding between 4‘,6-Diamidino-2-phenylindole and DNA Duplexes in Solution

2003 ◽  
Vol 125 (7) ◽  
pp. 1759-1769 ◽  
Author(s):  
Nad'a Špačková ◽  
Thomas E. Cheatham ◽  
Filip Ryjáček ◽  
Filip Lankaš ◽  
Luc van Meervelt ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Minor Groove ◽  
Minor Groove Binding ◽  
Dna Duplexes ◽  
Groove Binding ◽  
Thermodynamics Analysis ◽  
Dynamics Simulations

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 Positively and Negatively Hydrated Counterions in Molecular Dynamics Simulations of DNA Double Helix

2020 ◽  
Vol 65 (6) ◽  
pp. 510
Author(s):  
S. Perepelytsya
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Double Helix ◽  
Dipole Moments ◽  
Hydration Shell ◽  
Minor Groove ◽  
Water Molecules ◽  
Negative Hydration ◽  
Dynamics Simulations ◽  
Dna Double Helix

The DNA double helix is a polyanionic macromolecule that is neutralized in water solutions by metal ions (counterions). The property of counterions to stabilize the water network (positive hydration) or to make it friable (negative hydration) is important in terms of the physical mechanisms of stabilization of the DNA double helix. In the present research, the effects of positive hydration of Na+ counterions and negative hydration of K+ and Cs+ counterions incorporated into the hydration shell of the DNA double helix have been studied using molecular dynamics simulations. The results have shown that the dynamics of the hydration shell of counterions depends on the region of the double helix: minor groove, major groove, and outside the macromolecule. The longest average residence time has been observed for water molecules contacting with the counterions localized in the minor groove of the double helix (about 50 ps for Na+ and lower than 10 ps for K+ and Cs+). The estimated potentials of the mean force for the hydration shells of counterions show that the water molecules are constrained too strongly, and the effect of negative hydration for K+ and Cs+ counterions has not been observed in the simulations. The analysis has shown that the effects of counterion hydration can be described more accurately with water models having lower dipole moments.

scholarly journals Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations

2006 ◽  
Vol 12 (6) ◽  
pp. 781-791 ◽  
Author(s):  
Hongwei Jin ◽  
Suxin Zheng ◽  
Zhanli Wang ◽  
Cheng Luo ◽  
Jianhua Shen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dna Duplexes ◽  
Dynamics Simulations ◽  
Structural Insights

Berenil [1,3-Bis(4'-amidinophenyl)triazene] Binding to DNA Duplexes and to a RNA Duplex: Evidence for Both Intercalative and Minor Groove Binding Properties

Biochemistry ◽  
1995 ◽  
Vol 34 (31) ◽  
pp. 9962-9976 ◽  
Author(s):  
Daniel S. Pilch ◽  
Michael A. Kirolos ◽  
Xiaoyan Liu ◽  
G. Eric Plum ◽  
Kenneth J. Breslauer
Keyword(s):  
Minor Groove ◽  
Minor Groove Binding ◽  
Dna Duplexes ◽  
Groove Binding ◽  
Binding Properties
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