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

GLAVINA JULIANA; GONZÁLEZ FOUTEL, NICOLÁS S; FERNÁNDEZ-BALLESTER GREGORIO; BORCHERDS, WADE; DAUGHDRILL GARY; IGNACIO E SANCHEZ; CHEMES LUCIA BEATRIZ

Mendoza

Conferencia; 10CAB2C. 10mo Congreso Argentino de Bioinformática y Biologı́a Computacional; 2019

Asociacion Argentina de Bioinformática y Biología Computacional

BACKGROUND: Viruses hijack the host cell cycle through i nteraction with key host proteins. Manyof these protein-protein i nteractions (PPIs) are mediated by short protein sequences named l inearmotifs (LMs). Viruses mimic host LMs to disrupt PPIs. However, the mechanism by which virusesoutcompete host i nteractions i s still unclear and there are no straightforward methods to predict thebinding affinity of PPIs i nvolving more than one LM. The adenovirus E1A protein uses two LMsjoined by a disordered l inker to bind to the Retinoblastoma protein (pRb) l eading to cell cyclederegulation. We used E1A as a model system to study the role played by flexible l inkers i ndetermining the binding strength to the host target.RESULTS: To probe the role of flexibility i n E1A-pRb i nteractions, we used the known bindingaffinities of the E2F-like and LxCxE E1A motifs and a worm-like chain model (WLC) i nspired onpolymer physics which describes the l inker as an entropic chain and yields an effectiveconcentration (C eff) to calculate compound binding affinities. The agreement between thepredicted and experimental binding affinities demonstrated that flexibility within the l inker i s criticalfor maximal enhancement of binding strength. These results are supported by experimentalevidence that shows the disordered nature of the l inker. The polymer-like behavior was l argelydetermined by extension, sequence composition and predicted disorder, features highly conservedacross 110 E1A sequences. Using the empirical FoldX force field and the E2F-pRb andLxCxE-pRb structures, we computed position specific scoring matrices to predict the bindingenergy of i ndividual LMs i n those sequences. Combining these binding affinities with the predictedCeff for each l inker, we found that the global affinity for pRb was highly conserved acrossevolution.DISCUSSION: Using polymer theory we show that E1A l inkers behave as entropic chains thatposition two LMs to maximize pRb binding affinity. Our results suggest that E1A l inker sequencecomposition was optimized throughout evolution to maintain an extended and flexibleconformation, with l inker extension being the main feature under selection to enhance effectiveconcentration, maximizing the competition with host i nteractions while providing a platform forprotein complex assembly, essential for E1A hub function.