Deciphering general characteristics of residues constituting allosteric communication paths

Girik Malik; Anirban Banerji; Maksim Kouza; Irina A. Buhimschi; Andrzej Kloczkowski

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arXiv · 1802.10207

Deciphering general characteristics of residues constituting allosteric communication paths

Girik Malik·Anirban Banerji·Maksim Kouza·Irina A. Buhimschi·Andrzej Kloczkowski

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Abstract

Considering all the PDB annotated allosteric proteins (from ASD - AlloSteric Database) belonging to four different classes (kinases, nuclear receptors, peptidases and transcription factors), this work has attempted to decipher certain consistent patterns present in the residues constituting the allosteric communication sub-system (ACSS). The thermal fluctuations of hydrophobic residues in ACSSs were found to be significantly higher than those present in the non-ACSS part of the same proteins, while polar residues showed the opposite trend. The basic residues and hydroxyl residues were found to be slightly more predominant than the acidic residues and amide residues in ACSSs, hydrophobic residues were found extremely frequently in kinase ACSSs. Despite having different sequences and different lengths of ACSS, they were found to be structurally quite similar to each other - suggesting a preferred structural template for communication. ACSS structures recorded low RMSD and high Akaike Information Criterion(AIC) scores among themselves. While the ACSS networks for all the groups of allosteric proteins showed low degree centrality and closeness centrality, the betweenness centrality magnitudes revealed nonuniform behavior. Though cliques and communities could be identified within the ACSS, maximal-common-subgraph considering all the ACSS could not be generated, primarily due to the diversity in the dataset. Barring one particular case, the entire ACSS for any class of allosteric proteins did not demonstrate "small world" behavior, though the sub-graphs of the ACSSs, in certain cases, were found to form small-world networks.

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Girik Malik, Anirban Banerji, Maksim Kouza, Irina A. Buhimschi, Andrzej Kloczkowski. 2018-02-27. Deciphering general characteristics of residues constituting allosteric communication paths. https://arxiv.org/abs/1802.10207

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