Influence of cation-pi interactions in different folding types of membrane proteins.
Cation-pi interactions play an important role to the stability of protein structures. In this work, we analyze the influence of cation-pi interactions in three-dimensional structures of membrane proteins. We found that transmembrane strand (TMS) proteins have more number of cation-pi interactions than transmembrane helical (TMH) proteins. In TMH proteins, both the positively charged residues Lys and Arg equally experience favorable cation-pi interactions whereas in TMS proteins, Arg is more likely than Lys to be in such interactions. There is no relationship between number of cation-pi interactions and number of residues in TMH proteins whereas a good correlation was observed in TMS proteins. The average cation-pi interaction energy for TMH proteins is -16 kcal/mol and that for TMS proteins is -27 kcal/mol. The pair-wise cation-pi interaction energy between aromatic and positively charged residues showed that Lys-Trp energy is stronger in TMS proteins than TMH proteins; Arg-Phe, Arg-Tyr and Lys-Phe have higher energy in TMH proteins than TMS proteins. The decomposition of energies into electrostatic and van der Waals revealed that the contribution from electrostatic energy is twice as that from van der Waals energy in both TMH and TMS proteins. The results obtained in the present study would be helpful to understand the contribution of cation-pi interactions to the stability of membrane proteins.
Gromiha
M Michael
MM
Computational Biology Research Center, AIST, 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan. michael-gromiha@aist.go.jp
D024322:Amino Acids, Aromatic / Q000737:chemistry*; D001120:Arginine / Q000737:chemistry; D002412:Cations; D008239:Lysine / Q000737:chemistry; D008565:Membrane Proteins / Q000737:chemistry*; D055672:Static Electricity; D013816:Thermodynamics
D024322:Amino Acids, Aromatic; D002412:Cations; D008565:Membrane Proteins; D001120:Arginine; D008239:Lysine