Calculation of centralities in protein kinase A

Abstract

Topological analysis of amino acid networks is a common method that can help to understand the roles of individual residues. The most popular approach for network construction is to create a connection between residues if they interact. These interactions are usually weighted by absolute values of correlation coefficients or mutual information. Here we argue that connections in such networks have to reflect levels of cohesion within the protein instead of a simple fact of interaction between residues. If this is correct, an indiscriminate combination of correlation and anti-correlation, as well as the all-inclusive nature of the mutual information metrics, should be detrimental for the analysis. To test our hypothesis, we studied amino acid networks of the protein kinase A created by Local Spatial Pattern alignment, a method that can detect conserved patterns formed by Cα-Cβ vectors. Our results showed that, in comparison with the traditional methods, this approach is more efficient in detecting functionally important residues. Out of four studied centrality metrics, Closeness centrality was the least efficient measure of residue importance. Eigenvector centrality proved to be ineffective as the spectral gap values of the networks were very low due to the bilobal structure of the kinase. We recommend using joint graphs of Betweenness centrality and Degree centrality to visualize different aspects of amino acid roles.

Temperature-dependent hydrogen deuterium exchange shows impact of analog binding on adenosine deaminase flexibility but not embedded thermal networks

“…HDX mass spectrometry is increasingly applied to a wide variety of biological questions ( 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 ). Traditionally, an HDX experiment is performed at a single temperature to examine changes triggered in the targeted protein by ligand binding or protein–protein complex formation.…”

“…Then a volume of 45 µL preequilibrated D2O buffer (50 mM potassium phosphate buffer, pD 7.3) was mixed with the preheated 2.5 µL protein solution and 2.5 µL 1-deaza-adenosine or pentostatin. The samples were incubated at five different temperatures (10,20,25,30, and 40 ˚C) for different times spanning from seconds to hours (0, 10, 30, 45, 60, 180, 600, 1200, 1800, 2700, 3600, 7200, 10800, 14400 s). Upon the completion of the exchange reaction, the sample was first quenched in a -20 ˚C ice bath with salt and the subsequent addition J o u r n a l P r e -p r o o f of 20 µL acid (0.32 M citric acid, pH 2.4).…”