Abstract
A method of packing of transmembrane hairpin helices in proteins is described. The procedure is based on the optimization of hydrophobic contacts calculated using the three-dimensional (3D) molecular hydrophobicity potential technique. To verify the validity of the computational scheme, we calculated relative orientations of membrane-spanning peptides in pairs L2–L3, M2–M3, and M4–M5 from L- and M-subunits of the photoreaction center ofRhodopseudomonas viridis and compared the predicted structures with those derived from atomic coordinates. The results of computer modeling agree with the X-ray data. We applied the approach proposed to study possible interhelical interactions in transmembrane hairpin structures of Na+, K+-ATPase.
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Efremov, R.G., Gulyaev, D.I. & Modyanov, N.N. Application of three-dimensional molecular hydrophobicity potential to the analysis of spatial organization of membrane protein domains. II. Optimization of hydrophobic contacts in transmembrane hairpin structures of Na+, K+-ATPase. J Protein Chem 11, 699–708 (1992). https://doi.org/10.1007/BF01024971
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DOI: https://doi.org/10.1007/BF01024971