scholarly journals Induced fit DNA recognition by a minor groove binding analogue of Hoechst 33258: fluctuations in DNA A tract structure investigated by NMR and molecular dynamics simulations

2001 ◽  
Vol 29 (3) ◽  
pp. 693-702 ◽  
Author(s):  
C. E. Bostock-Smith
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dna Recognition ◽  
Minor Groove ◽  
Minor Groove Binding ◽  
Hoechst 33258 ◽  
Groove Binding ◽  
Induced Fit ◽  
Dynamics Simulations ◽  
A Minor

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.

A Minor Groove Binding Copper-Phenanthroline Conjugate Produces Direct Strand Breaks via β-Elimination of 2-Deoxyribonolactone

2002 ◽  
Vol 124 (31) ◽  
pp. 9062-9063 ◽  
Author(s):  
Brian C. Bales ◽  
Marguerite Pitié ◽  
Bernard Meunier ◽  
Marc M. Greenberg
Keyword(s):  
Minor Groove ◽  
Minor Groove Binding ◽  
Groove Binding ◽  
Strand Breaks ◽  
A Minor

scholarly journals Surface energy of nanoparticles – influence of particle size and structure

2018 ◽  
Vol 9 ◽  
pp. 2265-2276 ◽  
Author(s):  
Dieter Vollath ◽  
Franz Dieter Fischer ◽  
David Holec
Keyword(s):  
Molecular Dynamics ◽  
Particle Size ◽  
Surface Energy ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Definition Of ◽  
Dynamics Simulations ◽  
Classical Thermodynamics ◽  
A Minor

The surface energy, particularly for nanoparticles, is one of the most important quantities in understanding the thermodynamics of particles. Therefore, it is astonishing that there is still great uncertainty about its value. The uncertainty increases if one questions its dependence on particle size. Different approaches, such as classical thermodynamics calculations, molecular dynamics simulations, and ab initio calculations, exist to predict this quantity. Generally, considerations based on classical thermodynamics lead to the prediction of decreasing values of the surface energy with decreasing particle size. This phenomenon is caused by the reduced number of next neighbors of surface atoms with decreasing particle size, a phenomenon that is partly compensated by the reduction of the binding energy between the atoms with decreasing particle size. Furthermore, this compensating effect may be expected by the formation of a disordered or quasi-liquid layer at the surface. The atomistic approach, based either on molecular dynamics simulations or ab initio calculations, generally leads to values with an opposite tendency. However, it is shown that this result is based on an insufficient definition of the particle size. A more realistic definition of the particle size is possible only by a detailed analysis of the electronic structure obtained from initio calculations. Except for minor variations caused by changes in the structure, only a minor dependence of the surface energy on the particle size is found. The main conclusion of this work is that surface energy values for the equivalent bulk materials should be used if detailed data for nanoparticles are not available.

Identification of Potential Dual Negative Allosteric Modulators of Group I mGluR Family: A Shape Based Screening, ADME Prediction, Induced Fit Docking and Molecular Dynamics Approach Against Neurodegenerative Diseases

2019 ◽  
Vol 19 (29) ◽  
pp. 2687-2707 ◽  
Author(s):  
Sitrarasu Vijaya Prabhu ◽  
Sanjeev Kumar Singh
Keyword(s):  
Molecular Dynamics ◽  
Neurodegenerative Diseases ◽  
Molecular Dynamics Simulations ◽  
Glutamate Receptors ◽  
Allosteric Modulators ◽  
Induced Fit Docking ◽  
Induced Fit ◽  
Adme Prediction ◽  
Group I ◽  
Dynamics Simulations

Background: Glutamate is the principal neurotransmitter in the human brain that exerts its effects through ionotropic glutamate receptors (iGluRs) and metabotropic glutamate receptors (mGluRs). The mGluRs are a class of C GPCRs that play a vital role in various neurobiological functions, mGluR1 and mGluR5 are the two receptors distributed throughout the brain involved in cognition, learning, memory, and other important neurological processes. Dysfunction of these receptors can cause neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, X-fragile syndrome, anxiety, depression, etc., hence these receptors are high profile targets for pharmaceutical industries. Objective: The objective of our study is to find the novel dual negative allosteric modulators to regulate both mGluR1 and mGluR5. Methods: In this study, shape screening protocol was used to find the dual negative allosteric modulators for both mGluR1 and mGluR5 followed by ADME prediction, induced-fit docking (IFD) and molecular dynamics simulations. Further, DFT analysis and MESP studies were carried out for the selected compounds. Results: Around 247 compounds were obtained from the eMolecules database and clustered through the CANVAS module and filtered with ADME properties. Furthermore, IFD revealed that the top four compounds (16059796, 25004252, 4667236 and 11670690) having good protein-ligand interactions and binding free energies. The molecular electrostatic potential of the top compounds shows interactions in the amine group and the oxygen atom in the negative potential regions. Finally, molecular dynamics simulations were performed with all the selected as well as the reported compound 29 indicates that the screened hits have better stability of protein ligand complex. Conclusion: Hence, from the results, it is evident that top hits 16059796, 25004252, 4667236 and 11670690 could be a novel and potent dual negative allosteric modulators for mGluR1 and mGluR5.

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