Fig. 2: Clustering of the H3K36 and ssK36 peptide solution conformations observed in MD simulations reveals a hairpin conformation preference for ssK36.
A total of 350,000 conformations from MD simulations of H3K36 and ssK36 were clustered by Enspara21 based on backbone atom RMSD into 2 (a) or 3 (b) groups. Because of trajectory pooling prior to clustering, the combined conformational space of both peptides was accessible for clustering. Centroid structures of cluster 1 and 2 show the conformation, which most accurately represents the corresponding cluster. a Clustering the conformations in two groups revealed major differences between H3K36 and ssK36. Cluster 1 is represented by an almost extended peptide conformation, which consists to 66% of conformations observed in simulations with H3K36. Cluster 2 is represented by a bent hairpin structure, with 67% of the conformations coming from ssK36 simulations. b By using three groups for clustering, the different conformational preferences of H3K36 were even more distinct. The extended structure consists to 70% of conformations from H3K36 simulations, whereas the sharply bound hairpin conformation to 69% of conformations observed in ssK36 simulations. Cluster 3 is represented by a mixture of an extended and bent centroid structure and shows an almost equal contribution of H3K36 and ssK36 conformations (H3K36: 47%, ssK36: 53%). The bars represent the mean of three independent clustering replicates. Error bars represent the standard error of the mean (SEM). c The ssK36 specific residues F32F and R31 form contacts with Y41 and R40 supporting the formation of a hairpin conformation. Shown is the ssK36 peptide in hairpin conformation taken from one MD simulation with the target lysine, the two specific residues and their interactions partners represented as sticks. d For further analysis, structures were assigned as hairpin conformations based on two parameters, a stem loop distance (G33 Cα–P38 Cα) < 7 Å and an end-to-end distance (A29 Cα–P43 Cα) < 15 Å. e Distribution of the lifetimes of hairpin conformations, determined by the number of consecutive frames with the peptide in hairpin conformation in all peptide in solution simulations (50 × 70 ns for each peptide). Note the strong overrepresentation of long-living hairpin conformations of ssK36 (highlighted by the red box).
