화학공학소재연구정보센터
Journal of Structural Biology, Vol.207, No.2, 183-198, 2019
3D interaction homology: The hydropathic interaction environments of even alanine are diverse and provide novel structural insight
Analyses of the hydropathic environments of protein amino acid residues reveal structural information on multiple levels. The interactions made by each residue are the basis for sidechain (rotamer) conformation and ultimately for secondary, tertiary and even quaternary protein structure. By identifying and characterizing the interactions for each residue type, we are developing a basis set of environmental data that can be used to understand protein structure. This work focuses alanine and its roles. We calculated and analyzed separately backbone-to-environment and sidechain-to-environment 3D maps for over 57,000 alanines that, with respect to hydrophobic and polar interactions, show the environment around each. After binning by backbone phi and psi angles, we clustered each bin with k-means based on calculated map similarities between map-map pairs. Four bins were examined in detail: one in the beta-pleat region, two in the right-hand alpha-helix (RH alpha) region and one in the left-hand alpha-helix region of the Ramachandran plot. All regions indicated a common map motif of hydrophobic-hydrophobic interactions along the CA-CB axis, accounting for 62% in the beta-pleat bin, about one-third in the two RH alpha bins and 42% in the LH alpha bin. Another shared motif shows no interactions along the CA-CB axis; this was uncommon (8%) in beta-pleat, but > 30% elsewhere. The maps calculated for the two RH alpha bins are extremely similar (pairwise > 0.9787), which suggests that the hydropathic interaction sets or motifs found around each residue are conserved. Altogether, these results are integral to a new paradigm for understanding protein structure and function.