Biopolym. Cell. 2014; 30(2):157-162.
http://dx.doi.org/10.7124/bc.000890
Біоінформатика
Механізм взаємодії субстратів з активним центром тирозил- тРНК синтетази Mycobacterium tuberculosis за даними молекулярної динаміки
1, 2Микуляк В. В., 1, 2Корнелюк О. І.
  1. Інститут високих технологій,
    Київський національний університет імені Тараса Шевченка
    пр. Академіка Глушкова 2, кор. 5, Київ, Україна, 03022
  2. Інститут молекулярної біології і генетики НАН України
    Вул. Академіка Заболотного, 150, Київ, Україна, 03680

Abstract

Мета. Дослідити механізми взаємодії субстратів реакції аміноацилювання з активним центром тирозил-тРНК синтетази еубактерії Mycobacterium tuberculosis (MtTyrRS). Методи. Суперпозицією MtTyrRS з кристалографічними структурами бактерійних TyrRS побудовано комплекси з тирозином, тирозином, АТФ і тирозиладенілатом. Комплекси MtTyrRS з субстратами вивчали методом моделювання молекулярної динаміки (МД) у розчині. Результати. Показано водневі зв’язки між субстратами і активним центром MtTyrRS та їхню стабільність у процесі МД. Стабільність АТФ в активному центрі забезпечується водневими зв’язками, а також електростатичними взаємодіями з Lys231 та Lys 234 каталітичного мотиву KFGKS. Висновки. Ділянка зв’язування L-тирозину в активному центрі ферменту є негативно зарядженою, тоді як ділянка зв’язування АТФ має позитивно заряджені Lys231 і Lys234 каталітичної послідовності KFGKS. Процентне співвідношення тривалості існування водневих зв’язків, які формуються між субстратами та ферментом, до загального часу моделювання МД свідчить про конформаційну рухливість активного центра.
Keywords: тирозил-тРНК синтетаза, Mycobacterium tuberculosis , субстрат, водневий зв’язок, молекулярна динаміка, грид
Повний текст: (PDF, англійською)

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