Modeling EphB4-EphrinB2 protein-protein interaction using flexible docking of a short linear motif.

ABSTRACT:

Background

Many protein-protein interactions are mediated by a short linear motif. Usually, amino acid sequences of those motifs are known or can be predicted. It is much harder to experimentally characterize or predict their structure in the bound form. In this work, we test a possibility of using flexible docking of a short linear motif to predict the interaction interface of the EphB4-EphrinB2 complex (a system extensively studied for its significance in tumor progression).

Methods

In the modeling, we only use knowledge about the motif sequence and experimental structures of EphB4-EphrinB2 complex partners. The proposed protocol enables efficient modeling of significant conformational changes in the short linear motif fragment during molecular docking simulation. For the

SUBMITTER: Ciemny MP 

PROVIDER: S-EPMC5568603 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature