Herzyk P, Hubbard R E
Department of Chemistry, University of York, Heslington, England.
Biophys J. 1998 Mar;74(3):1203-14. doi: 10.1016/S0006-3495(98)77835-X.
Molecular models of the transmembrane domain of the phospholamban pentamer have been generated by a computational method that uses the experimentally measured effects of systematic single-site mutations as a guiding force in the modeling procedure. This method makes the assumptions that 1) the phospholamban transmembrane domain is a parallel five-helix bundle, and 2) nondisruptive mutation positions are lipid exposed, whereas 3) disruptive or partially disruptive mutations are not. Our procedure requires substantially less computer time than systematic search methods, allowing rapid assessment of the effects of different experimental results on the helix arrangement. The effectiveness of the approach is investigated in test calculations on two helix-dimer systems of known structure. Two independently derived sets of mutagenesis data were used to define the restraints for generating models of phospholamban. Both resulting models are left-handed, highly symmetrical pentamers. Although the overall bundle geometry is very similar in the two models, the orientation of individual helices differs by approximately 50 degrees, resulting in different sets of residues facing the pore. This demonstrates how differences in restraints can have an effect on the model structures generated, and how the violation of these restraints can identify inconsistent experimental data.
通过一种计算方法生成了受磷蛋白五聚体跨膜结构域的分子模型，该方法将系统单点突变的实验测量效应作为建模过程中的指导力。此方法做了以下假设：1）磷蛋白跨膜结构域是一个平行的五螺旋束；2）无干扰突变位置暴露于脂质中，而3）有干扰或部分有干扰的突变则不然。我们的程序所需的计算机时间比系统搜索方法少得多，从而能够快速评估不同实验结果对螺旋排列的影响。在对两个已知结构的螺旋二聚体系统进行的测试计算中研究了该方法的有效性。使用两组独立得出的诱变数据来定义生成磷蛋白模型的限制条件。两个生成的模型都是左手螺旋、高度对称的五聚体。尽管两个模型中的整体束几何形状非常相似，但各个螺旋的方向相差约50度，导致面向孔的残基集不同。这证明了限制条件的差异如何对生成的模型结构产生影响，以及违反这些限制条件如何识别不一致的实验数据。
