Nonlinear dynamics of specific DNA-protein interactions

13th South-East Asian Congress of Medical Physics 2015

物理学;医药卫生

Dwiputra, D.^1 ; Hidayat, W.^1,2 ; Khairani, R.^1 ; Zen, F.P.^1,2

Departement of Physics, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung

40132, Indonesia^1

Indonesian Center of Theoretical and Mathematical Physics (ICTMP), Indonesia^2

关键词: Biological information;    Coupled nonlinear Schrodinger equation;    Coupled oscillators;    DNA-binding protein;    DNA-protein interaction;    Intermolecular interactions;    Nonlinear travelling waves;    Perturbative approach;   

Others  :  https://iopscience.iop.org/article/10.1088/1742-6596/694/1/012076/pdf
DOI  :  10.1088/1742-6596/694/1/012076

学科分类：卫生学

来源: IOP

【 摘 要 】

Interactions between DNA binding protein and specific base pairs of nucleic acid is critical for biological process. We propose a new model of DNA-protein interactions to depict the dynamics of specific DNA-protein interactions. Hydrogen bonds (H-bonds) are, among the other intermolecular interactions in DNA, the most distinctive in term of specificity of molecular bonds. As H-bonds account for specificity, we only consider the dynamics affected by H-bonds between DNA base pairs and H-bonds connecting protein side chains and DNA. The H-bonds are modelled by Morse potentials and coupling terms in the Hamiltonian of coupled oscillators resembling a coupling between planar DNA chain and a protein molecule. In this paper we give a perturbative approach as an attempt for a soliton solution. The solution is in the form of nonlinear travelling wave having the amplitudes satisfying coupled nonlinear Schrodinger equations and is interpreted as the mediator for nonlocal transmittance of biological information in DNA.