100ps Molecular Dynamic Simulation of d(TATCACC)2

Abstract

A heptanucleotide sequence d(TATCACC)2 from OR3 region of bacteriophage lambda is considered sufficient for the recognition of Cro protein. We present here results on molecular dynamic simulations on this sequence for 100 ps in 0.02 ps interval. The simulations are done using computer program GROMOS. The conformational results are averaged over each ps. The IUPAC torsional parameters for 100 conformations are illustrated using a wheal and a dial systems. Several other stereochemical parameters such as H-bonding lengths and angles, sugar puckers, helix twist and roll angles as also distances between opposite strand phosphorus are depicted graphically. We find that there is rupture of terminal H-bonds. The bases are tilted and shifted away from the helix axis giving rise to bifurcated H-bonds. H-bonds are seen even in between different base pairs. The role of these dynamic structural changes in the recognition of OR3 operator by Cro protein is discussed in the paper.

Using Molecular Dynamics Simulation To Reinforce Student Understanding of Intermolecular Forces

“…Fourteen years later, MDS was used to explore a heptanucleotide portion of a bacteriophage. From that study stereochemical parameters such as hydrogen bond lengths and angles, helix twist, and roll angles were determined (9). More recently, as modeling techniques have improved, the use of MDS has played an important role in studying the properties of single-wall carbon nanotubes (10) and the interaction of metallic clusters (11).…”