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© IRL Press at Oxford University Press

Identification of the most significant amphipathic helix with application to HIV and MHV envelope proteins

Ivan E. Auger * and Charles E. Lawrence

Laboratory of Biometrics PO Box 509
Wadsworth Center for Laboratories and Research, New York State Department of Health Albany. NY 12201, USA

*To whom reprint requests should be sent

Amphipathic helices, which play important roles in protein structure, occur in a wide variety of lengths. Yet existing methods employ fixed window lengths. We present a hierarchical procedure that identifies the Q most significant amphipathic helices regardless of length. Since the observed hydrophobicities are not normally distributed, test statistics usually employed for least-squares regression are inappropriate for assessing statistical significance of amphipathic helices. We show that an adjusted F statistic provides a good test. An application to the envelope protein of HIV finds an unexpected long amphipathic helix in gp41.

Received on July 12, 1989; accepted on February 28, 1990

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