title: Structural analysis of residues involving cation-pi interactions in different folding types of membrane proteins.
abstract: Cation-pi interactions play an important role to the stability of protein structures. In our earlier work, we have analyzed the influence and energetic contribution of cation-pi interactions in three-dimensional structures of membrane proteins. In this work, we investigate the characteristic features of residues that are involved in cation-pi interactions. We have computed several parameters, such as surrounding hydrophobicity, number of long-range contacts, conservation score and normalized B-factor for all these residues and identified their location, whether in the membrane or at surface. We found that the cation-pi interactions are mainly formed by long-range interactions. The cationic residues involved in cation-pi interactions have higher surrounding hydrophobicity than their average values in the whole dataset and an opposite trend is observed for aromatic residues. In transmembrane helical proteins, except Phe, all other residues that are responsible for cation-pi interactions are highly conserved with other related protein sequences whereas in transmembrane strand proteins, an appreciable conservation is observed only for Arg. The analysis on the flexibility of residues reveals that the cation-pi interaction forming residues are more stable than other residues. The results obtained in the present study would be helpful to understand the role of cation-pi interactions in the structure and folding of membrane proteins.
authors.affiliation: Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Aomi Frontier Building 17F, 2-43 Aomi, Koto-ku, Tokyo 135-0064, Japan. michael-gromiha@aist.go.jp
authors.forename: M Michael
authors.initials: MM
authors.lastname: Gromiha
authors.forename: Makiko
authors.initials: M
authors.lastname: Suwa
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D000818:Animals; D002412:Cations; D002462:Cell Membrane / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D006358:Hot Temperature; D008565:Membrane Proteins / Q000737:chemistry*; D011485:Protein Binding; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D002412:Cations; D008565:Membrane Proteins; D011506:Proteins