Biology – Quantitative Biology – Molecular Networks
Scientific paper
2008-09-22
Biology
Quantitative Biology
Molecular Networks
18 pages, 5 figures
Scientific paper
The past decade has witnessed the development and success of coarse-grained network models of proteins for predicting many equilibrium properties related to collective modes of motion. Curiously, the results are usually robust towards the different methodologies used for constructing the residue networks from knowledge of the experimental coordinates. We present a systematical study of network construction strategies, and their effect on the predicted properties. The analysis is based on the radial distribution function and the spectral dimensions of a large set of proteins as well as a newly defined quantity, the angular distribution function. By partitioning the interactions into an essential and a residual set, we show that the robustness originates from a large number of long-distance interactions belonging to the latter. These residuals have a vanishingly small effect on the force vectors on each residue. The overall force balance then translates into the Hessian as small shifts in the slow modes of motion and an invariance of the corresponding eigenvectors. Implications for the study of biologically relevant properties of proteins are discussed.
Atilgan Ali Rana
Atilgan Canan
Inanc Ibrahim
No associations
LandOfFree
Residue Network Construction and Predictions of Elastic Network Models does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.
If you have personal experience with Residue Network Construction and Predictions of Elastic Network Models, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Residue Network Construction and Predictions of Elastic Network Models will most certainly appreciate the feedback.
Profile ID: LFWR-SCP-O-299893