Comparative analysis of structure and sequence based methods for the prediction of linear motif binding energies

FERNÁNDEZ-BALLESTER, GREGORIO; GIBSON, TOBY J.; GLAVINA, JULIANA; SEHR, PETER; SÁNCHEZ, IGNACIO E.; ÁLVAREZ, LUCÍA; LEWIS, JOE; CHEMES, LUCIA B

Mendoza

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

Asociación Argentina de Bioinformática y Biología Computacional

BACKGROUND: Linear motifs (LMs) are ubiquitous short sequence elements that participate in protein-protein interactions. The LxCxE motif is a 9-residue sequence that interacts with the retinoblastoma protein (pRb), which plays a key role in cell cycle progression. Viruses mimic the LxCxE motif to hijack pRb inducing proliferation and thus promoting the synthesis of the viral genome. However, the mechanism by which viruses outcompete the host interactions is stillunclear. One main hypothesis is that viral motifs evolve higher affinities than cellular motifs. A predictor that represents LMs mediated interactions properly would facilitate the understanding of these mechanisms. Here, we used sequence- and structure-based approaches to obtain predictions of binding affinities of cellular, viral and mutant sequences of the LxCxE motif, which allowed us to compare different methods and describe their reliability in predicting the true binding affinities measured from the sequences.RESULTS: Structure-based calculations used the empirical force field FoldX under different conditions. Using available LxCxE-pRb structures, we used FoldX to study the binding energy of each LxCxE peptide to pRb. Sequence-based calculations used molecular information theory, which makes use of residue statistics at an alignment of known LMs. We used an alignment of LxCxE motifs to compute a position specific scoring matrix. The different methods were able to reproduce the experimental data with different accuracy. For instance, we found major differences at a conserved hydrophobic position (L28 in the E7 protein) after the LxCxE core that associates to a pRb groove. Experimental data indicated the broad hydrophobic groove in pRb accommodates a wide range of amino acids. However, the marginal decrease in affinity (0.6x) of the L28W mutation was poorly captured by all structure-based calculations, where the tryptophan was highly penalized in that position.DISCUSSION: The structure-based methods reflected almost all the sequence variability in the dataset but they are biased. The sequence-based method reflected the sequence variability, but they were highly dependent on the initial dataset and did not reflect the structural flexibility. However, both approaches were able to reproduce quantitative binding experiments to an acceptable degree, suggesting they constitute useful tools to predict LMs binding energetics.