Conservation of high affinity binding between the viral adenovirus E1A and host Retinoblastoma proteins requires a flexible and disordered linker.

GLAVINA, JULIANA; BORCHERDS, WADE; CHEMES, LUCIA B; GONZÁLEZ FOUTEL, NICOLAS SEBASTIAN; DAUGHDRILL, GARY; FERNÁNDEZ-BALLESTER, GREGORIO; SÁNCHEZ, IGNACIO E.

Mendoza

Congreso; 10CAB2C. 10th Argentinian Congress of Bioinformatics and Computational Biology; 2019

Asociación Argentina de Bioinformática y Biología Computacional

BACKGROUND: Viruses hijack the host cell cycle through interaction with key host proteins. Many of these protein-protein interactions (PPIs) are mediated by short protein sequences named linear motifs (LMs). Viruses mimic host LMs to disrupt PPIs. However, the mechanism by which viruses outcompete host interactions is still unclear and there are no straightforward methods to predict the binding affinity of PPIs involving more than one LM. The adenovirus E1A protein uses two LMs joined by a disordered linker to bind to the Retinoblastoma protein (pRb) leading to cell cycle deregulation. We used E1A as a model system to study the role played by flexible linkers in determining the binding strength to the host target.RESULTS: To probe the role of flexibility in E1A-pRb interactions, we used the known binding affinities of the E2F-like and LxCxE E1A motifs and a worm-like chain model (WLC) inspired on polymer physics which describes the linker as an entropic chain and yields an effective concentration (Ceff) to calculate compound binding affinities. The agreement between the predicted and experimental binding affinities demonstrated that flexibility within the linker is critical for maximal enhancement of binding strength. These results are supported by experimental evidence that shows the disordered nature of the linker. The polymer-like behavior was largely determined by extension, sequence composition and predicted disorder, features highly conserved across 110 E1A sequences. Using the empirical FoldX force field and the E2F-pRb and LxCxE-pRb structures, we computed position specific scoring matrices to predict the binding energy of individual LMs in those sequences. Combining these binding affinities with the predicted Ceff for each linker, we found that the global affinity for pRb was highly conserved across evolution.DISCUSSION: Using polymer theory we show that E1A linkers behave as entropic chains that position two LMs to maximize pRb binding affinity. Our results suggest that E1A linker sequence composition was optimized throughout evolution to maintain an extended and flexible conformation, with linker extension being the main feature under selection to enhance effective concentration, maximizing the competition with host interactions while providing a platform for protein complex assembly, essential for E1A hub function.