Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence.

Shuhei Isami,Hiraku Nishimori,Naoaki Sakamoto,Akinori Awazu,Rafael J Najmanovich

doi:10.1371/journal.pone.0143760

Abstract

Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of temperature factors for several crystal structures of DNA. Second, we propose a coarse-grained elastic network model of DNA, where each nucleotide is described only by one node. This model could effectively reproduce the detailed dynamics obtained with the all-atom elastic network model according to the sequence-dependent geometry. Through normal-mode analysis for the coarse-grained elastic network model, we exhaustively analyzed the dynamic features of a large number of long DNA sequences, approximately ∼150 bp in length. These analyses revealed positive correlations between the nucleosome-forming abilities and the inter-strand fluctuation strength of double-stranded DNA for several DNA sequences.

Highlights

Elastic network models of proteins, including all-atom models [1, 2] and coarse-grained models [3,4,5,6,7,8,9] represent some of the simplest and most powerful types of theoretical models that can accurately reveal structure-dynamics relationships and the mechanisms underlying a protein’s functional activities [10,11,12,13,14]
We constructed a simple all-atom elastic network model that could reproduce the fluctuations of the motifs of each nucleotide of several crystal structures of short DNA sequences
We proposed a simple coarse-grained elastic network model that could reproduce the dynamic features of the long DNA sequences obtained by the allatom elastic network model

Summary

Introduction

Elastic network models of proteins, including all-atom models [1, 2] and coarse-grained models [3,4,5,6,7,8,9] represent some of the simplest and most powerful types of theoretical models that can accurately reveal structure-dynamics relationships and the mechanisms underlying a protein’s functional activities [10,11,12,13,14] Such models have been widely employed to accurately reproduce the temperature factors on the crystal structure of a protein via normal-mode analysis. DNA is no longer considered to have the sole function in the PLOS ONE | DOI:10.1371/journal.pone.0143760 December 1, 2015

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