PREDICTION OF MEMBRANE PROTEIN STRUCTURES WITH COMPLEX TOPOLOGIES USING LIMITED

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 可靠的膜蛋白结构预测方法是非常重要的，因为高分辨率膜蛋白结构的实验测定仍然非常困难，特别是对于真核蛋白。然而，膜蛋白通常长于200aa，对于结构预测来说是一个巨大的挑战。我们开发了一种预测大膜蛋白结构的方法，通过限制根据序列预测或实验确定的特定位置的螺旋-螺旋堆积排列来预测大分子膜蛋白的结构。我们对12种不同结构和功能的膜蛋白进行了测试，其长度在190到300个残基之间。在折叠模拟过程中实施单一约束，丰富了9种蛋白质的近天然模型。在根据序列预测约束的4种情况下，5个最低能量模型中有1个在4A内可在自然结构上重叠。通过分别限制一对保守的组氨酸螯合血红素和一个实验确定的盐桥的模拟，也可以选择近天然的结构来结合血红素和形成孔洞。这些结果表明，如果从蛋白质结构数据库或实验中获得关于残基-残基相互作用的有限信息，就可以在天然结构的4A范围内对复杂的膜蛋白进行建模。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Reliable structure-prediction methods for membrane proteins are important because the experimental determination of high-resolution membrane protein structures remains very difficult, especially for eukaryotic proteins. However, membrane proteins are typically longer than 200 aa and represent a formidable challenge for structure prediction. We have developed a method for predicting the structures of large membrane proteins by constraining helix-helix packing arrangements at particular positions predicted from sequence or identified by experiments. We tested the method on 12 membrane proteins of diverse topologies and functions with lengths ranging between 190 and 300 residues. Enforcing a single constraint during the folding simulations enriched the population of near-native models for 9 proteins. In 4 of the cases in which the constraint was predicted from the sequence, 1 of the 5 lowest energy models was superimposable within 4 A on the native structure. Near-native structures could also be selected for heme-binding and pore-forming domains from simulations in which pairs of conserved histidine-chelating hemes and one experimentally determined salt bridge were constrained, respectively. These results suggest that models within 4 A of the native structure can be achieved for complex membrane proteins if even limited information on residue-residue interactions can be obtained from protein structure databases or experiments.