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Red fluorescent protein DsRed: Parametrization of its chromophore as an amino acid residue for computer modeling in the OPLS-AA force fieldстатья
Информация о цитировании статьи получена из
Web of Science,
Scopus
Статья опубликована в журнале из списка Web of Science и/или Scopus
Дата последнего поиска статьи во внешних источниках: 7 октября 2013 г.
- Авторы: Dmitrienko D.V., Vrzheshch E.P., Drutsa V.L., Vrzheshch P.V.
- Журнал: Biochemistry (Moscow)
- Том: 71
- Номер: 10
- Год издания: 2006
- Издательство: Pleiades Publishing, Ltd
- Местоположение издательства: Road Town, United Kingdom
- Первая страница: 1133
- Последняя страница: 1152
- DOI: 10.1134/S0006297906100129
- Аннотация: Topology of the neutral form of the DsRed fluorescent protein chromophore as a residue of [(4-cis)-2-[(1-cis)-4-amino-4-oxobutanimidoyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid was calculated with OPLS-AA force field. Use of this topology and molecular dynamics simulation allows calculating the parameters of proteins that contain such residue in their polypeptide chains. The chromophore parameters were obtained by ab initio (RHF/6-31G**) quantum chemical calculations applying density functional theory (B3LYP). Using this chromophore, we have calculated the molecular dynamics trajectory of tetrameric fluorescent protein DsRed in solution at 300 K (4 nsec). Correctness of the chromophore parametrization was revealed by comparison of quantitative characteristics of the chromophore structure obtained from the molecular dynamic simulations of DsRed protein with the quantitative characteristics of the chromophore based on the crystallographic X-ray data of fluorescent protein DsRed (PDB ID: 1ZGO, 1G7K, and 1GGX), and also with the quantitative characteristics of the chromophore obtained by quantum chemical calculations. Inclusion of the neutral form of DsRed protein chromophore topology into the OPLS-AA force field yielded the extended force field OPLS-AA/DsRed. This force field can be used for molecular dynamics calculations of proteins containing the DsRed chromophore. The parameter set presented in this study can be applied for similar extension in any other force fields.
- Добавил в систему: Друца Валерий Львович
Прикрепленные файлы
| № | Имя | Описание | Имя файла | Размер | Добавлен |
|---|---|---|---|---|---|
| 1. | Полный текст | Red fluorescent protein DsRed: Parametrization of its chromophore as an amino acid residue for computer modeling in the OPLS-AA force field | 2006_bcm_1133_1152_Dmitrienko_Vrzheshch_Drutsa_Vrzheshch.pdf | 280,0 КБ | 17 сентября 2014 [VrzheshchPV] |