Identification of the most significant amphipathic helix with application to HIV and MHV envelope proteins.
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.
Auger
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Laboratory of Biometrics, Wadsworth Center for Laboratories and Research, New York State Department of Health, Albany 12201.
Lawrence
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CE
D000465:Algorithms; D015699:HIV Envelope Protein gp120 / Q000737:chemistry; D015700:HIV Envelope Protein gp41 / Q000737:chemistry; D015497:HIV-1 / Q000032:analysis*; D008956:Models, Chemical; D006517:Murine hepatitis virus / Q000032:analysis*; D011487:Protein Conformation; D014759:Viral Envelope Proteins / Q000737:chemistry*
D015699:HIV Envelope Protein gp120; D015700:HIV Envelope Protein gp41; D014759:Viral Envelope Proteins