A Multidomain Flexible Docking Approach to Deal with Large Conformational Changes in the Modeling of Biomolecular Complexes

SummaryBinding-induced backbone and large-scale conformational changes represent one of the major challenges in the modeling of biomolecular complexes by docking. To address this challenge, we have developed a flexible multidomain docking protocol that follows a “divide-and-conquer” approach to model both large-scale domain motions and small- to medium-scale interfacial rearrangements: the flexible binding partner is treated as an assembly of subparts/domains that are docked simultaneously making use of HADDOCK's multidomain docking ability. For this, the flexible molecules are cut at hinge regions predicted using an elastic network model. The performance of this approach is demonstrated on a benchmark covering an unprecedented range of conformational changes of 1.5 to 19.5 Å. We show from a statistical survey of known complexes that the cumulative sum of eigenvalues obtained from the elastic network has some predictive power to indicate the extent of the conformational change to be expected.

Graphical AbstractFigure optionsDownload full-size imageDownload high-quality image (155 K)Download as PowerPoint slideHighlights► A new HADDOCKing protocol to address large-scale domain rearrangements ► This divide-and-conquer approach uses HADDOCK's multidomain docking ability ► Methodology to model conformational changes as large as 19.5 Å ► Indicators are provided to predict possible large conformational changes