Berlin 2015 – scientific programme

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BP: Fachverband Biologische Physik

BP 17: Posters: Protein structure and dynamics

BP 17.12: Poster

Monday, March 16, 2015, 17:30–19:30, Poster A

Investigating interactions of anions with selectins using molecular dynamics simulations — •Sadra Kashef Ol Gheta and Ana Vila Verde — Max Planck Institute of Colloids and Interfaces

Selectins are well known for their role in the adhesion of leukocytes and platelets to the endothelium that takes place, e.g., during inflammation. Because of the important biological role played by selectins, much effort has been put into finding artificial ligands that effectively compete with the natural ones. Recently, dendrimeric polyglycerol (dPG) polymers functionalized with various anionic functional groups were investigated for their potential as L-selectin inhibitors. It was found that the affinity of dendrimers for selectin depends strongly on the nature of the anionic group, increasing in the order carboxylate < phosphate < phosphonate, sulfonate < bisphosphonate <<< sulfate. To understand the molecular origin of this anionic series, we use classical all-atom models based on the CHARMM36 force field for proteins and explicit water to characterize the intrinsic interactions between various anionic functional groups and positively charged amino acids using small molecule analogues, e.g., methylsulfate, methylamine. The results from classical simulations are compared against those from ab initio calculations, to assess the quality of the classical models.