de Groot B L, Amadei A, Scheek R M, van Nuland N A, Berendsen H J
Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Department of Biophysical Chemistry, University of Groningen, The Netherlands.
Proteins. 1996 Nov;26(3):314-22. doi: 10.1002/(SICI)1097-0134(199611)26:3<314::AID-PROT7>3.0.CO;2-D.
Recently, we developed a method (Amadei et al., J. Biomol. Str. Dyn. 13: 615-626; de Groot et al., J. Biomol. Str. Dyn. 13: 741-751, 1996) to obtain an extended sampling of the configurational space of proteins, using an adapted form of molecular dynamics (MD) simulations, based on the essential dynamics (ED) (Amadei et al., Proteins 17:412-425, 1993) method. In the present study, this ED sampling technique is applied to the histidine-containing phosphocarrier protein HPr from Escherichia coli. We find a cluster of conformations that is an order of magnitude larger than that found for a usual MD simulation of comparable length. The structures in this cluster are geometrically and energetically comparable to NMR structures. Moreover, on average, this large cluster satisfies nearly all NMR-derived distance restraints.
最近，我们开发了一种方法（阿马代伊等人，《生物分子结构与动力学杂志》13: 615 - 626；德格鲁特等人，《生物分子结构与动力学杂志》13: 741 - 751，1996），基于主成分动力学（ED）（阿马代伊等人，《蛋白质》17: 412 - 425，1993）方法，通过采用一种改进形式的分子动力学（MD）模拟来对蛋白质的构象空间进行扩展采样。在本研究中，这种ED采样技术应用于来自大肠杆菌的含组氨酸的磷酸载体蛋白HPr。我们发现了一个构象簇，其大小比长度相当的常规MD模拟所发现的构象簇大一个数量级。该簇中的结构在几何和能量上与核磁共振（NMR）结构相当。此外，平均而言，这个大的构象簇几乎满足所有基于NMR得出的距离限制。
