Investigation of changes in the arrangement of water molecules and salt ions surrounding different atoms of the DNA molecule during the melting process: a molecular dynamics simulation study

2015 ◽  
Vol 93 (3) ◽  
pp. 348-361 ◽  
Author(s):  
C. Izanloo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Double Helix ◽  
Melting Process ◽  
Minor Groove ◽  
Dynamics Simulation ◽  
Transition Curve ◽  
Water Molecules ◽  
Major Groove ◽  
Dna Duplex

A molecular dynamics simulation was performed on a B-DNA duplex (CGCGAATTGCGC) at different temperatures. The DNA was immerged in a saltwater medium with 1 mol/L NaCl concentration. The arrangements of water molecules and cations around the different atoms of DNA on the melting pathway were investigated. Almost for all atoms of the DNA by double helix → single-stranded transition, the water molecules released from the DNA duplex and cations were close to single-stranded DNA, but this behavior was not clearly seen at melting temperatures. Therefore, release of water molecules and cations approaching the DNA by the increase of temperature does not have any effect on the sharpness of the transition curve. Most of the water molecules and cations were found to be around the negatively charged phosphate oxygen atoms. The number of water molecules released from the first shell hydration upon melting in the minor groove was higher than in the major groove, and intrusion of cations into the minor groove after melting was higher than into the major groove. The hydrations of imino protons were different from each other and were dependent on DNA bases.

THE EFFECT OF THE RANGE OF THE POTENTIAL ON THE MULTI-STEP CLUSTER MELTING PROCESS

2004 ◽  
Vol 15 (05) ◽  
pp. 649-658 ◽  
Author(s):  
SHI-WEI REN
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Morse Potential ◽  
Melting Process ◽  
Dynamics Simulation ◽  
Repulsive Core ◽  
Tail Region ◽  
Step Process

By using the microcanonical molecular dynamics simulation, the melting processes of the clusters bound by Morse potential are investigated. It is found that these clusters show a multi-step melting process as long as the range of the Morse potential is a suitable value. The origins of this multi-step process are analyzed. I find that not only the repulsive core of the potential but also the attractive tail range of the potential influences the melting process. Moreover, the occurrence of the multi-step melting process is more sensitive to the tail region of the Morse potential.

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 Effects of the Temperature and the pH on the Main Protease of SARS-CoV-2: A Molecular Dynamics Simulation Study

2021 ◽  
Vol 12 (6) ◽  
pp. 7239-7248
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Root Mean Square ◽  
Dynamics Simulation ◽  
Effect Of Temperature ◽  
Water Molecules ◽  
Mean Square ◽  
Main Protease ◽  
Decreasing Ph ◽  
Increasing Temperature

The novel coronavirus, recognized as COVID-19, is the cause of an infection outbreak in December 2019. The effect of temperature and pH changes on the main protease of SARS-CoV-2 were investigated using all-atom molecular dynamics simulation. The obtained results from the root mean square deviation (RMSD) and root mean square fluctuations (RMSF) analyses showed that at a constant temperature of 25℃ and pH=5, the conformational change of the main protease is more significant than that of pH=6 and 7. Also, by increasing temperature from 25℃ to 55℃ at constant pH=7, a remarkable change in protein structure was observed. The radial probability of water molecules around the main protease was decreased by increasing temperature and decreasing pH. The weakening of the binding energy between the main protease and water molecules due to the increasing temperature and decreasing pH has reduced the number of hydrogen bonds between the main protease and water molecules. Finding conditions that alter the conformation of the main protease could be fundamental because this change could affect the virus’s functionality and its ability to impose illness.

scholarly journals Molecular Dynamics Simulation of Distribution and Diffusion Behaviour of Oil–Water Interfaces

Molecules ◽  
2019 ◽  
Vol 24 (10) ◽  
pp. 1905 ◽  
Author(s):  
Chengbin Zhang ◽  
Hanhui Dai ◽  
Pengfei Lu ◽  
Liangyu Wu ◽  
Bo Zhou ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Interface Roughness ◽  
Dynamics Simulation ◽  
Water Phase ◽  
Water Molecules ◽  
Water Interface ◽  
Oil Water ◽  
And Diffusion ◽  
Diffusion Behaviors

The distribution and diffusion behaviors of microscopic particles at fluorobenzene–water and pentanol–water interfaces are investigated using molecular dynamics simulation. The influences of Na+/Cl− ions and the steric effects of organic molecules are examined. The concentration distributions of different species, the orientations of oil molecules at the interface, and oil–water interface morphology as well as the diffusion behaviors of water molecules are explored and analyzed. The results indicate that a few fluorobenzene molecules move into the water phase influenced by Na+/Cl− ions, while the pentanol molecules at the interface prefer orientating their hydrophilic groups toward the water phase due to their large size. The water molecules more easily burst into the pentanol phase with larger molecular spaces. As the concentration of ions in the water phase increases, more water molecules enter into the pentanol molecules, leading to larger interface roughness and interface thickness. In addition, a lower diffusion coefficient for water molecules at the fluorobenzene–water interface are observed when introducing Na+/Cl− ions in the water phase, while for the pentanol–water system, the mobility of interfacial water molecules are enhanced with less ions and inhibited with more ions.

Sign in / Sign up

Export Citation Format

Share Document