Dipole moment analysis of membrane proteins suggests role in orientation in the membrane.
The position independent dipole membrane proteins need to be oriented in the membrane in order to function as channels, transporters or recognition systems. Membrane proteins can be broadly classified as either predominantly alpha helical or beta barrel in nature. All the different types of thirteen beta barrel membrane proteins (2OMF, 2POR, 1PRN, 1PHO, 1IIV, 1AF6, 1AOT, 2MPR, 1OSM, 1QJ8, 1BXW, 2FCP and 1FEP) and six alpha helical membrane proteins (1BL8, 1MSL, 1QLB, 1AR1, 1PSS and 1QHJ) from the Protein Data Bank were analyzed. Dipole moment was calculated for both classes of proteins. In all the oligomers, the orientation of the dipole was found to be parallel to direction of insertion that is perpendicular to the possible membrane layer. Monomers do not show a similar orientation. In all the alpha helical oligomers, the dipole points from the intra-cellular to the extra-cellular side. In the oligomeric beta barrel proteins, the direction of the dipole is from the extra-cellular to the intra-cellular side, except for OmpF from E.coli, Omp36 from Klebsiella pneumonia and LamB from E.coli where the situation is reversed. However, the dipole moments of the monomeric proteins and the monomers of the oligomers themselves are not oriented parallel to the molecular axis and the insertion orientation, but they are almost parallel to the membrane surface. It is possible that the quaternary oligomeric association is necessary for the correct orientation in the membrane and this is aided by the dipole orientation. The electrostatic potential surface calculated with all atoms, which also do not show clear separation of charge surfaces. Calculations suggest that backbone structure and oligomer are sufficient for providing the dipole orientation.
Bioinformatics Center, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India.
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Vasanthi
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Krishnaswamy
D000900:Anti-Bacterial Agents / Q000737:chemistry; D001425:Bacterial Outer Membrane Proteins / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry; D001671:Biochemistry / Q000379:methods; D001692:Biological Transport; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D004926:Escherichia coli / Q000378:metabolism*; D007711:Klebsiella pneumoniae / Q000378:metabolism; D008565:Membrane Proteins / Q000737:chemistry*; D008968:Molecular Conformation; D018272:Porins / Q000378:metabolism; D017433:Protein Structure, Secondary; D011991:Receptors, Virus / Q000378:metabolism
D000900:Anti-Bacterial Agents; D001425:Bacterial Outer Membrane Proteins; D001426:Bacterial Proteins; D008565:Membrane Proteins; C109237:OmpF protein; D018272:Porins; D011991:Receptors, Virus; C016532:maltoporins