Biopolym. Cell. 2002; 18(2):117-123.
Конформационные изменения ВИЧ-1 протеазы в области «флэпов»: изучение методом молекулярной динамики в пико- и наносекундном временных интервалах
1Ковальский Д. Б., 1Корнелюк А. И.
  1. Институт молекулярной биологии и генетики НАН Украины
    ул. Академика Заболотного, 150, Киев, Украина, 03680

Abstract

Изучена молекулярная динамика (МД) ВИЧ-J протеазы в воде и вакууме в пико- и наносекундном временных интервалах. Получены конформации, обеспечивающие расстояние между двумя анти­параллельными β-стрэндами («флэпами»), необходимое для вхождения субстрата в активный центр. Использование различных параметров для учета дальних электростатических взаимодей­ствий при симуляции МД в воде свидетельствует о значительном их вкладе в стабилизацию пространственной структуры протеазы. Как в пико-, так и в наносекундном временных интервалах наблюдается формирование «динамического» кармана с объемом –0,85 нм3. Карман образован, в основном, гидрофобными остатками аминокислот Val32, Lys45, Ile47, Gly48, Gly49, Ile50, Gly51, Gly52, Ile54, Val56, Leu76, Gly78, Pro79, Thr80 и Pro81. «Динамический» структурный карман может являться мишенью при создании ингибиторов ВИЧ-1 протеазы нового поколения.

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