Modeling the structure and functional mechanisms of P-glycoprotein

像许多跨膜蛋白一样，通过x射线晶体学测定P-gp的结构已被证明是难以捉摸的，尽管付出了很多努力。这源于形成足够质量的晶体的困难，这些晶体也维持了蛋白质不同部分的天然物理化学环境。因此，代替直接的实验确定，我们努力将所有可用的（通常是间接的）实验数据与基于物理化学的数学方法相结合，以产生一个或多个物理上真实的结构模型。幸运的是，超过三十年的研究已经提供了关于P-gp的丰富信息，从中我们可以获得结构信息。在广泛的范围内，已知该蛋白由两个同源结构域组成，每个结构域都具有六段跨膜成分和核苷酸结合成分。迄今为止，关于P-gp的结构信息最好的两个来源是同源细菌蛋白Sav1866的x射线晶体结构和人类P-gp的低分辨率冷冻电子显微照片。此外，细菌脂质翻转酶MsbA的x射线修正结构有望很快得到，其与P-gp的关系甚至比Sav1866更为密切。因此，我们工作的一个主要重点是利用细菌蛋白的晶体结构作为模板开发人类P-gp的同源模型。虽然Peter Tielemans小组最近发表了这样的模型，但它只是基于P-gp和Sav1866序列的简单比对，不幸的是，这对于跨膜片段总体上没有很好的定义。相反，我们的努力深入研究了密切相关的MDR蛋白家族和ABC转运蛋白超家族中的残基保存模式。这些信息有助于预测哪些残基暴露在膜的核心和头群层，哪些残基排列在孔中，哪些在两个跨膜结构域的界面上。我们目前正在开发同源家族和超家族的大序列比对。这一结果也将有助于确定相关突变的模式，这有助于识别蛋白质三维结构中近端的残基组。最后，我们将检查所得模型与所有实验数据的一致性，例如位点定向诱变，自然发生的多态性和交联数据的影响。如果基于Sav1866模板的模型无法解释实验结果，我们将寻找使其符合的替代构象。另一个重点是根据电子显微镜获得的密度图开发模型。这样做的好处是，结构数据直接来自人类P-gp，即目标蛋白，而不是来自细菌的同源物，后者可能在某种程度上结构不同。这包括人类P-gp的两个跨膜结构域的序列不同，因此在孔的近似双轴周围是不对称的，而细菌同源物只包含一个结构域，因此在膜中形成完美对称的同型二聚体。我们已经联系了发表显微镜数据的小组，并获得了与电子密度相匹配的标准蛋白质螺旋和核苷酸结合结构域的坐标。然而，由于数据的低分辨率，这些模型只指定肽主链，而不是在每个位置残基的类型。为了解决这个问题，我们正在着手进行一个线程项目，该项目预测主链结构上氨基酸序列的正确排列。为此，我们目前正在将我们之前开发的线程软件应用于P-gp蛋白。每个列举的序列与结构的排列将根据若干标准进行评分和排名。如上所述，这将再次测量与实验数据的一致性，不同类型残留物的正确物理化学环境，以及保守残留物和预测簇在空间上是否接近。此外，该分析将包括从残馀接触电位的尺度计算的能量，特别是导出的膜蛋白

Like many transmembrane proteins, determination of the structure of P-gp by X-ray crystallography has proven elusive despite much effort. This stems from the difficulty of forming sufficient-quality crystals that also maintain the native physiochemical environments for the different parts of the protein. Thus, in lieu of the direct, experimental determination, we strive to integrate all available (often indirect) experimental data with physiochemically-based mathematical methods to produce one or more physically realistic models of the structure. Fortunately, over three decades of study has provided a wealth of information about P-gp from which we can gleam structural information. On a broad scale, it is known that the protein is composed of two homologous domains, each with a six-segment transmembrane component and a nucleotide-binding component. To date, the best two sources of structural information about P-gp are an X-ray crystal structure of the homologous bacterial protein Sav1866, and low-resolution cryo-electron micrographs of human P-gp. In addition, the corrected X-ray structure of the bacterial lipid flippase MsbA is expected soon, which is even closely related to P-gp than is Sav1866. Thus, one major focus of our work is to develop a homology model of human P-gp using the crystal structures of the bacterial proteins as templates. While such a model has recently been published by Peter Tielemans group, it was only based on a simple alignment of the P-gp and Sav1866 sequences, and unfortunately, this is overall not well defined for the transmembrane segments. Rather, our efforts go deeper into examining the patterns of residue conservation within the family of closely related MDR proteins and the superfamily of ABC transporters. This information helps predict which residues are exposed to the core and headgroup layers of the membrane, which residues line the pore, and which are at the interfaces of the two transmembrane domains. We are currently in the process of developing a grand sequence alignment of homologous families and the superfamily. The results of this will also enable the determination of patterns of correlated mutations, which help identify groups of residues that are proximal in the 3-dimensional structure of the protein. Finally, we will examine the resultant model for consistency with all the experimental data, such as the effects of site-directed mutagenesis, naturally occurring polymorphisms, and cross-linking data. Where the model based on the Sav1866 template fails to explain the experimental results, we will search for alternate conformations that bring it into compliance. The other major focus is to develop models from the density maps obtained from electron microscopy. This has the advantage that the structural data is directly from human P-gp, the target protein, and not from a bacterial homolog, which likely differs in structure to some degree. This includes the fact that the two transmembrane domains of human P-gp are different in sequence, and thus are asymmetrical around the approximate two-fold axis of the pore, while the bacterial homologs only contain one domain, and thus form perfectly symmetrical homodimers in the membrane. We have already contacted the group that published the microscopy data, and have obtained their coordinates for standard protein helices and nucleotide-binding domains fitted to the electron density. However, due to the low resolution of the data, these models only specify the peptide backbone, and not the type of the residue at each position. To solve this, we are embarking on a threading project, which predicts the correct alignment of the amino acid sequence on the structure of the backbone. To this end, we are currently adapting our previously developed threading software to the P-gp protein. Each enumerated alignment of sequence to structure will be scored and ranked according to a number of criteria. As described above, this will again measure compliance with experimental data, correct physiochemical environments for the different types of residues, and whether conserved residues and predicted clusters are proximal in space. In addition, this analysis will include the calculated energy from scales of residue contact potentials specifically derived for membrane proteins