Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein

International Physics Conference at the Anatolian Peak 2016

Asafi, M.S.^1 ; Yildirim, A.^2 ; Tekpinar, M.^1

Yuzuncu Yil University, Van, Turkey^1

Siirt University, Siirt, Turkey^2

关键词: Biological implications;    Elastic network models;    Molecular dynamics methods;    Molecular dynamics simulations;    Motion direction;    Normal mode analysis;    Principal Components;    Spatial fluctuation;   

Others  :  https://iopscience.iop.org/article/10.1088/1742-6596/707/1/012036/pdf
DOI  :  10.1088/1742-6596/707/1/012036

来源: IOP

【 摘 要 】

Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated.