Modulation of structure and folding homologs of Amb a 6 allergen of Ambrosia artemisiifolia

Abstract

Amb a 6 allergen of Ambrosia artemisiifolia is a ragweed allergen (a principle cause of late summer hayfever in North America and Europe). The weed has recently become spreading as a neophyte in Europe, while climate change may also affect on the growth of the plant and additionally may also influence pollen allergenicity. In Ukraine, the number of diseases caused by this allergen has recently increased. Still the three-dimensional structure of Amb a 6 allergen has been yet undescribed. The aims of our study were the modulation of the three-dimensional structure and the search of folding-homologs of Amb a 6 allergen of A. artemisiifolia by bioinformatics methods. Material and Methods. Template search with Blast and HHBlits has been performed by the SWISSMODEL template library. Models are built based on the target-template alignment using ProMod3. Coordinates which are conserved between the target and the template are copied from the template to the model. Insertions and deletions are remodelled using a fragment library. Side chains are then rebuilt. Finally, the geometry of the resulting model is regularized by a force field. In case loop modelling with ProMod3 fails, an alternative model is built with PROMOD-II. Results and Discussion. Three-dimensional structure of Amb a 6 allergen has been successfully built. As folding-homologs of Amb a 6 allergen the maize nonspecific-lipid transfer protein was found. This protein has ability to bind and transfer lipids. Information about the three-dimensional structure and partial analogy with nonspecific-lipid transfer protein may help to thoroughly understand the properties and the spatial configuration of Amb a 6 allergen.

Amb a 6 аллерген Ambrosia artemisiifolia является одной из главных причин аллергических заболеваний в Северной Америке и Европе. Структура данного аллергена неизвестна. Целью нашего исследования была модуляция трехмерной структуры и поиск фолдинговых гомологов аллергена Amb a 6 A. artemisiifolia биоинформатическими методами. Материал и методы. Моделирование структуры и поиск гомологов проводили при помощи программ SWISS-MODEL и ProMod3. Результаты и обсуждение. Создана трехмерная структура аллергена Amb a 6. В качестве фолдинговых гомологов аллергена Amb a 6 был обнаружен белок неспецифического переноса липидов кукурузы.