Molecular dynamics simulations on DNA flexibility: a comparative study of Amber bsc1 and bsc0 force fields

Abstract

The structural flexibility of DNA plays a key role in many biological processes of DNA, such as protein-DNA interactions, DNA packaging in viruses and nucleosome positioning on genomic DNA. Some experimental techniques have been employed to investigate the structural flexibility of DNA with the combination of elastic models, but these experiments could only provide the macroscopic properties of DNA, and thus, it is still difficult to understand the corresponding microscopic mechanisms. Recently, all-atom molecular dynamics (MD) simulation has emerged as a useful tool to investigate not only the macroscopic properties of DNA, but also the microscopic description of the flexibility of DNA at an atomic level. The most important issue in all-atom MD simulations of DNA is to choose an appropriate force field for simulating DNA. Very recently, a new force field for DNA has been developed based on the last generation force field of Amber bsc0, which was named Amber bsc1. In this work, all-atom MD simulations are employed to study the flexibility of a 30-bp DNA with the force fields of Amber bsc1 and Amber bsc0 in a comparative way. Our aim of the research is to examine the improvement of the new development of force field (Amber bsc1) in the macroscopic and microscopic properties of DNA, in comparison with the corresponding experimental measurements. All the MD simulations are performed with Gromacs 4.6 and lasted with a simulation time of 600 ns. The MD trajectories are analyzed with Curves+ for the last 500 ns, since the system reaches equilibrium approximately after ~100 ns. Our results show that the new force field (Amber bsc1) can lead to the improvements in the macroscopic parameters of DNA flexibility, i.e., stretch modulus S and twist-stretch coupling D become closer to experimental measurements, while bending persistence lengths lp and torsional persistence lengths C from the two force fields (bsc1 and bsc0) are both in good agreement with experimental data. Our microscopic analyses show that the microscopic structure parameters of DNA from the MD simulation with the Amber bsc1 force field are closer to the experimental values than those with the Amber bsc0 force field, except for slide, and the obvious improvements are observed in some microscopic parameters such as twist and inclination. Our further analyses show that the improvements in macroscopic flexibility from the Amber bsc1 force field are tightly related to the microscopic parameters and their fluctuations. This study would be helpful in understanding the performances of Amber bsc1 and bsc0 force fields in the description of DNA flexibility at both macroscopic and microscopic level.

Influence of temperature on bend, twist and twist–bend coupling of dsDNA

“…The simulation process adhered to the standard protocol implemented in the GROMACS 4.6 software, utilizing the Amber bsc1 force field. [70][71][72][73][74] Pre-equilibration was conducted to ensure that the MD simulations were performed under isothermal and isobaric conditions. Specifically, the simulation was started by energy-minimizing in order to ensure the stability of DNA structure.…”

A Novel Carrier Based on DNA and Exosome to Sustained Release of 5‐Fluorouracil Anticancer Drug

“…The processes were the standard simulation procedures using Gromacs 2021.5 software [20,21] with the Amber bsc1 force field. [22] A periodic boundary condition is employed in the simulation box. The particle-mesh Ewald method [23,24] was employed to compute electrostatic interactions.…”

Effect of temperature on anisotropic bending elasticity of dsRNA: an all-atom molecular dynamics simulation

“…Our MD simulations were performed using the Gromacs 4.6 soware with the Amber OL3 force elds. [49][50][51][52][53] Before the MD simulations, the system needs to be pre-equilibrated to ensure that the MD simulation is performed in an isothermal isobaric environment. 54,55 We started with an energy minimization system with a restraining force and subsequently an NVT and NPT simulations.…”