Comparative modelling of major house dust mite allergen Der p I : structure validation using an extended environmental amino acid propensity table

A model of the 3-D structure of a major house dust mite allergen Dar p I associated with hypersensitivity reactions in humans was built from its amino acid sequence and its homology to three known structures, papain, actinidin and papaya proteinase Ω of the cysteine proteinase family. Comparative model using COMPOSER was used to arrive at an initial model. Thi was refined using interactive graphics and energy minimization with the AMBER force field incorporated in SYBYL (Tripos Associates). Compatibility of the Dar p I amino acid sequence with the cysteine proteinase fold was checked using an environment-dependent amino acid propensity table incorporated into a new program HARMONY with a variable length windowing facility