Electron density calculations as an extension of protein structure refinement. Streptomyces griseus protease A at 1.5 A resolution.
Electron density calculations as an extension of protein structure refinement. Streptomyces griseus protease A at 1.5 A resolution.
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DOI：
10.1016/0022-2836(85)90241-4
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发表时间：
1983-04
影响因子：
5.6
通讯作者：
J. Moult;F. Sussman;M. James
中科院分区：
文献类型：
--
作者：
J. Moult;F. Sussman;M. James
Ab initioquantum mechanical calculations have been used to obtain details of the electron density distribution in a high-resolution refined protein structure. It is shown that with accurate atomic co-ordinates, electron density may be calculated with a quality similar to that which can be obtained directly from crystallographic studies of small organic molecules, and that this density contains information relevant to the understanding of catalysis.Atomic co-ordinates from the 1.8 Å and 1.5 Å resolution refinements of the crystal structure of protease A fromStreptomyces griseushave been used to examine the influence of the environment on the electron density in the side-chain of the active site histidine (His57). The neighbouring aspartic acid 102 is the dominant factor in the environment, and quantum mechanical calculations have been performed on these two residues. Most interesting from the point of view of understanding the catalytic process is the effect that Asp102 has on the electron density in the region of the imidazole nitrogen (Nε2) adjacent to the active site serine 195. In the positively charged imidazolium species, there is a polarization of the Nε2H bond, reducing the bonding density in a manner that may lower the height of the energy barrier for proton transfer. In the uncharged imidazole species, the proximity of Asp102 causes a movement of density from the lone pair region of the Nε2 into the π bonding region above and below the plane of the ring. Although it is shown that the primary effect of the aspartic acid is electrostatic, this movement is perpendicular to the direction of the electric field inducing it.
