Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions

摘要

We perform a mixed coarse-graining approach in a normal mode analysis of protein motions,which enables the modeling of a protein's nativge conformation with different regions having low and high resolution.As a result,the dynamics of the interesting functioal parts within a supramolecular assmblage can be analyzed at high resolution,while the remainder of the tructure is represented at poorer resoluton,thus keeping the total number of nodes in the system sufficiently low for computational tractability.Our results indicate that the vibrational dynamics of specific components in a large multi-subunit protein are best described by retaining all the components of the structure,whether at higher or lower resolution.It is also shown that similar frequency distributions are obtained for different proteins and at different levels of coarse-grainign,at the lower end of the spectrum,where the most significant slowest motions occur.