The harmonic analysis of cylindrically symmetric proteins: a comparison of Dronpa and a DNA sliding clamp.
The harmonic analysis of two types of proteins with cylindrical symmetry is performed by the Standard Force Field Normal Mode Analysis and by the elastic network model. For both proteins the global elastic modes are assigned to their characteristic topologies. Dronpa is a rigid β-barrel structure, presenting the twisting, bending and breathing motion of a cylindrical rod. The β sliding clamp of Escherichia coli is a hexagonal β-wheel, consisting of rigid segments. In its spectrum four classes of vibrations are identified which are characteristic of an elastic torus. Correlation diagrams and RMSF analysis are compared. The results provide not only a comprehensive validation of the use of both methods to describe the elastic behavior according to the low-frequency normal modes, but also depict the correlated motions of β-barrel and β-wheel proteins. The harmonic flexibility of the Dronpa protein is compared to the principal components of molecular dynamics (MD) simulation. A functionally important localized cleft opening mode is found, which is not detected by harmonic analysis.
Department of Chemistry and INPAC Institute for Nanoscale Physics and Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
Guang
G
Hu
Servaas
S
Michielssens
Samuel L C
SL
Moors
Arnout
A
Ceulemans
D000465:Algorithms; D000818:Animals; D037421:Anthozoa; D004258:DNA Polymerase III / Q000737:chemistry*; D004548:Elasticity; D004926:Escherichia coli / Q000201:enzymology; D029968:Escherichia coli Proteins / Q000737:chemistry*; D049452:Green Fluorescent Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D025341:Principal Component Analysis; D017434:Protein Structure, Tertiary
D029968:Escherichia coli Proteins; D049452:Green Fluorescent Proteins; C101139:beta subunit, DNA polymerase III; D004258:DNA Polymerase III