Continuum electrostatic approach for evaluating positions and interactions of proteins in a bilayer membrane.
Orientations of proteins in the membranes are crucial to their function and stability. Unfortunately the exact positions of these proteins in the lipid bilayer are mostly undetermined. Here, the spatial orientation of membrane proteins within the lipid membrane was evaluated using a Poisson-Boltzmann solvent continuum approach to calculate the electrostatic free energy of the protein solvation at various orientations in an implicit bilayer. The solvation energy was obtained by computing the difference in electrostatic energies of the protein in water and in lipid/water environments, treating each as an implicit solvent model. The optimal position of transmembrane proteins (TMP) in a lipid bilayer is identified by the minimum in the "downhill" pathway of the solvation energy landscape. The energy landscape pattern was considerably conserved in various TMP classes. Evaluation of the position of 1060 membrane proteins from the orientations of proteins in membranes (OPM) database revealed that most of the polytopic and β-barrel proteins were in good agreement with those of the OPM database. The study provides a useful scheme for estimating the membrane solvation energy made by lipid-exposed amino acids in membrane proteins. In addition, our results tested with the bacterial potassium channel model demonstrated the potential usefulness of the approach in assessing the quality of membrane protein models. The present approach should be applicable for constructing transmembrane proteins-lipid configuration suitable for membrane protein simulations and will have utility for the structural modeling of membrane proteins.
Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Rd. Prathumwan, Bangkok 10330, Thailand.
Chirayut
C
Supunyabut
Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Rd. Prathumwan, Bangkok 10330, Thailand.
Sunit
S
Fuklang
Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Rd. Prathumwan, Bangkok 10330, Thailand. Electronic address: Pornthep.S@chula.ac.th.
Pornthep
P
Sompornpisut
D003198:Computer Simulation; D030562:Databases, Protein; D008051:Lipid Bilayers / Q000737:chemistry*; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D011487:Protein Conformation; D055672:Static Electricity; D014867:Water / Q000737:chemistry
D008051:Lipid Bilayers; D008565:Membrane Proteins; D014867:Water
Electrostatic energy of membrane solvation; Implicit solvent model; Orientations of proteins in membranes database; Poisson–Boltzmann; Transmembrane protein