Stability analysis of CBD3 peptide predictsA1R2 dipeptide as a suitable target for small molecule peptidomimetics
Underlying molecular recognition is the ability of a ligand to present a suitable structural motif for at least a few nanoseconds to efficiently engage its receptor (Rajamani, Thiel, Vajda & Camacho, 2004). In the far-western assay using 15-mer peptides (overlapping by 12 amino acids) of full-length CRMP2 revealed that the highest binding to Cav2.2 was attained by peptide ARSRLAELRGVPRGL(CBD3) (Brittain et al., 2011b). Subsequent work showed that the first six amino acids ARSRLA were critical for binding, mutagenesis suggested that two residues (Ala1 and Arg4) were important for binding (Moutal et al., 2018). To predict the recognition motif in CBD3, we performed three independent molecular dynamics simulations (MDS) of the full peptide and of the TAT conjugated peptide and scanned the trajectories for the most stable dipeptide conformation (Figure 1A; see also Figure S1 ), as well as assessed whether the corresponding side chains are blocked by intra-peptide contacts or are exposed to solvent and free to interact (Figure 1B ). Simulations showed thatA1R2 dipeptide, formed the most stable solvent exposed motif, while the rest of the peptide was mostly cluttered (Figure 1A, B ).