Journal:JBSD:12
From Proteopedia
Analysis of Delta–Notch interaction by molecular modeling and molecular dynamic simulation studiesRiddhi Majumder, Sujata Roy, Ashoke Ranjan Thakur ^{[1]} Molecular Tour Further in both models the interactions are Van der Waal’s with one or two strong electrostatic interactions. The interface of ModelX, analyzed by PROTORP server is more planar (Planarity =2.2 Å) than ModelI (Planarity =3.8 Å). It has been suggested that heterocomplexes have interfaces that are more planar than the homodimers thus from the analysis ModelX is preferred. In ModelI the solvation energy gain is 0.1 Kcal/mol for Delta and 0.0 Kcal/mol for Notch which increases to 1.5 Kcal/mol and 1.8 Kcal/mol respectively after MD simulation. On the other hand, solvation energy gain on complex formation in ModelX (after docking) is 4.6 Kcal/mol for Delta and 4.3 Kcal/mol for Notch which decreases to 3.3 Kcal/mol and 3.2 Kcal/mol respectively after MD simulation. (Structure of and after simulation) In conclusion from planarity of the docked structure, distances between Delta and Notch residues, favorable solvation energy gain, it appears that ModelX is a better fit and provides a compact structure for DeltaNotch interaction. This in turn will help understand the easy packing of these structures in a membrane pit during endocytosis.

 ↑ Majumder R, Roy S, Thakur AR. Analysis of DeltaNotch interaction by molecular modeling and molecular dynamic simulation studies. J Biomol Struct Dyn. 2012 May;30(1):1329. PMID:22571430 doi:10.1080/07391102.2012.674184