MP:PD-a data base of internal packing densities, internal packing defects and internal waters of helical membrane proteins
MP:PD-a data base of internal packing densities, internal packing defects and internal waters of helical membrane proteins
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DOI：
10.1093/nar/gkt1062
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发表时间：
2014-01-01
影响因子：
14.9
通讯作者：
Hildebrand, Peter W.
中科院分区：
文献类型：
--
作者：
Rose, Alexander;Theune, Dominic;Hildebrand, Peter W.
膜蛋白堆积数据库（MP：PD）（http：//proteinformatics.charite.de/mppd）是螺旋膜蛋白的数据库，其特征在于内部原子堆积密度、空腔和沃茨。膜蛋白不是紧密堆积的，而是含有相当数量的内部空腔，这些空腔在体积、极性和溶剂可及性以及它们填充有内部水方面不同。内部空腔被认为是高物理压缩性的区域。通过充当移动的氢键供体或受体，内部沃茨可能促进不同功能状态之间的转变。尽管有这些不同的功能作用，螺旋膜蛋白的内腔尚未得到很好的表征，主要是因为大多数内部沃茨水无法通过晶体结构分析来解析。在这里，我们结合了各种计算生物物理技术来表征内部空腔，重新分配内部沃茨的位置，并计算所有可用的螺旋膜蛋白结构的内部堆积密度，并将它们存储在MP：PD中。可以使用关键字搜索数据库，并可以下载条目。每个条目都可以在Provi中可视化，Provi是一个基于Jmol的蛋白质查看器，它提供了沿着膜平面、内部堆积密度、疏水空腔和氢键的低能沃茨的综合显示。
The membrane protein packing database (MP:PD) (http://proteinformatics.charite.de/mppd) is a database of helical membrane proteins featuring internal atomic packing densities, cavities and waters. Membrane proteins are not tightly packed but contain a considerable number of internal cavities that differ in volume, polarity and solvent accessibility as well as in their filling with internal water. Internal cavities are supposed to be regions of high physical compressibility. By serving as mobile hydrogen bonding donors or acceptors, internal waters likely facilitate transition between different functional states. Despite these distinct functional roles, internal cavities of helical membrane proteins are not well characterized, mainly because most internal waters are not resolved by crystal structure analysis. Here we combined various computational biophysical techniques to characterize internal cavities, reassign positions of internal waters and calculate internal packing densities of all available helical membrane protein structures and stored them in MP: PD. The database can be searched using keywords and entries can be downloaded. Each entry can be visualized in Provi, a Jmol-based protein viewer that provides an integrated display of low energy waters alongside membrane planes, internal packing density, hydrophobic cavities and hydrogen bonds.