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Biophysical Journal 85:3646-3658 (2003)
© 2003 The Biophysical Society

Molecular Dynamics Simulations of the E1/E2 Transmembrane Domain of the Semliki Forest Virus

Ana Caballero-Herrera and Lennart Nilsson

Department of Biosciences at Novum, Karolinska Institutet, S-141 57 Huddinge, Sweden

Correspondence: Address reprint requests to Lennart Nilsson, E-mail: lennart.nilsson{at}biosci.ki.se.

Transmembrane (TM) helix-helix interactions are important for virus budding and fusion. We have developed a simulation strategy that reveals the main features of the helical packing between the TM domains of the two glycoproteins E1 and E2 of the {alpha}-virus Semliki Forest virus and that can be extrapolated to sketch TM helical packing in other {alpha}-viruses. Molecular dynamics simulations were performed in wild-type and mutant peptides, both isolated and forming E1/E2 complexes. The simulations revealed that the isolated wild-type E1 peptide formed a more flexible helix than the rest of peptides and that the wild-type E1/E2 complex consists of two helices that intimately pack their N-terminals. The residues located at the interhelical interface displayed the typical motif of the left-handed coiled-coils. These were small and medium residues as Gly, Ala, Ser, and Leu, which also had the possibility to form interhelical C{alpha}-H···O hydrogen bonds. Results from the mutant complexes suggested that correct packing is a compromise between these residues at both E1 and E2 interhelical interfaces. This compromise allowed prediction of E1-E2 contact residues in the TM spanning domain of other alphaviruses even though the sequence identity of E2 peptides is low in this domain.




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