Nonlinear Model of the Specificity of DNA-Protein Interactions and Its Stability

6th Asian Physics Symposium

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

Theoretical Physics Laboratory, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha no. 10, Bandung

40132, Indonesia^1

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

关键词: Coupled oscillators;    Coupling terms;    DNA base pairs;    DNA-protein interaction;    Non-linear model;    Peptide groups;    Site-specificity;    Specific binding;   

Others  :  https://iopscience.iop.org/article/10.1088/1742-6596/739/1/012030/pdf
DOI  :  10.1088/1742-6596/739/1/012030

来源: IOP

【 摘 要 】

Specific DNA-protein interactions are fundamental processes of living cells. We propose a new model of DNA-protein interactions to explain the site specificity of the interactions. The hydrogen bonds between DNA base pairs and between DNA-protein peptide groups play a significant role in determination of the specific binding site. We adopt the Morse potential with coupling terms to construct the Hamiltonian of coupled oscillators representing the hydrogen bonds in which the depth of the potentials vary in the DNA chain. In this paper we investigate the stability of the model to determine the conditions satisfying the biological circumstances of the DNA-protein interactions.