Search for rigid sub domains in DNA from molecular dynamics simulations

Area of Science:

• Computational Biology
• Biophysics
• Molecular Dynamics

Background:

• Molecular Dynamics (MD) simulations are crucial for understanding biopolymer dynamics.
• Identifying rigid sub-units within biopolymers can simplify complex simulations and analysis.
• Current methods may not efficiently capture the dynamic nature of these sub-units.

Purpose of the Study:

• To develop and present a novel strategy for identifying and grouping atoms into rigid sub-units during MD simulations of biopolymers.
• To establish a criterion based on root mean square fluctuations of interatomic distances for defining rigidity.
• To investigate the impact of different tolerance values (rc) on the number and composition of identified rigid sub-units.

Main Methods:

• Utilizing root mean square fluctuations (RMSF) of interatomic distances as a primary criterion for defining atomic rigidity.
• Implementing a tolerance parameter (rc) to quantify acceptable fluctuations for grouping atoms into rigid bodies.
• Applying the developed method to analyze two B-form self-complementary oligonucleotides.

Main Results:

• The method successfully identified rigid sub-units within the oligonucleotides, with the number and composition dependent on the chosen tolerance (rc).
• At rc = 0.027 nm, each nucleotide was consistently resolved into three rigid sub-units: sugar ring, base, and backbone (PO4 + C5' atoms).
• At a stricter tolerance (rc = 0.01 nm), the C5' atoms were no longer grouped with PO4, indicating finer structural resolution.

Conclusions:

• The developed strategy effectively identifies dynamic rigid sub-units in biopolymers during MD simulations.
• The choice of tolerance (rc) critically influences the level of detail in sub-unit identification.
• Deformation-induced variations in coulombic potential are comparable to force field parameter inaccuracies, highlighting the significance of sub-unit dynamics.