Protein subunit interfaces: A statistical analysis of hot spots in Sm proteins.

Journal of Molecular Modeling
Srđan D StojanovićSnežana D Zarić

Abstract

The distinguishing property of Sm protein associations is very high stability. In order to understand this property, we analyzed the interfaces and compared the properties of Sm protein interfaces with those of a test set, the Binding Interface Database (BID). The comparison revealed that the main differences between the interfaces of Sm proteins and those of the BID set are the content of charged residues, the coordination numbers of the residues, knowledge-based pair potentials, and the conservation scores of hot spots. In Sm proteins, the interfaces have more hydrophobic and fewer charged residues than the surfaces, which is also the case for the BID test set and other proteins. However, in the interfaces, the content of charged residues in Sm proteins (26%) is substantially larger than that in the BID set (22%). Hot spots are residues that make up a small fraction of the interfaces, but they contribute most of the binding energy. These residues are critical to protein-protein interactions. Analyses of knowledge-based pair potentials of hot spot and non-hot spot residues in Sm proteins show that they are significantly different; their mean values are 31.5 and 11.3, respectively. In the BID set, this difference is smaller; in...Continue Reading

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Citations

Nov 26, 2010·Journal of Theoretical Biology·Božidarka L ZarićSrđan Đ Stojanović
Nov 20, 2014·Protoplasma·Ivana D MucićSrđan D Stojanović
Dec 17, 2014·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Luka M BreberinaSrđan Đ Stojanović
May 16, 2011·Molecular Informatics·Srđan Đ StojanovićBožidarka L Zarić
Sep 20, 2019·Molecular Informatics·Luka M BreberinaSrđan Đ Stojanović

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