Toward understanding the mechanism of action of the yeast multidrug resistance transporter Pdr5p: a molecular modeling study.
Toward understanding the mechanism of action of the yeast multidrug resistance transporter Pdr5p: a molecular modeling study.
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DOI：
10.1016/j.jsb.2010.10.012
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发表时间：
2011-02
影响因子：
3
通讯作者：
Xia, Di
中科院分区：
文献类型：
--
作者：
Rutledge, Robert M.;Esser, Lothar;Ma, Jichun;Xia, Di
关键词：
多效耐药蛋白5 （Pdr5p）是一种质膜atp结合盒（ABC）转运蛋白，是酿酒酵母的主要药物外排泵。真菌转运蛋白Pdr5p家族具有许多与其他建模或结晶的ABC转运蛋白明显不同的结构特征，包括反向拓扑结构、非典型的atp结合位点、跨膜部分的序列相似性非常低以及结构域之间的长连接体。这些特征给这些重要转运体的分子建模研究带来了相当大的障碍。在这里，我们报告了基于同源性建模和从头算方法的结合建立了Pdr5p的原子模型，结合了共识跨膜段预测、残基亲脂性和序列熵的信息。已报道的跨膜底物结合口袋中改变耐药性的突变被用于验证模型，而一个改变跨膜和核苷酸结合结构域之间通信模式的突变被用于模型改进。该模型的预测能力在实验中得到了证明，酵母突变体对丙氨酸取代Thr1213和Gln1253的氯霉唑的敏感性增加，这两个基因被预测存在于底物结合口袋中，而不减少质膜中Pdr5p的数量。我们的模型的质量和可靠性在各种方法的背景下讨论用于建模的不同部分的结构。
Pleotropic drug resistant protein 5 (Pdr5p) is a plasma membrane ATP-binding cassette (ABC) transporter and the major drug efflux pump in Saccharomyces cerevisiae. The Pdr5p family of fungal transporters possesses a number of structural features significantly different from other modeled or crystallized ABC transporters, which include a reverse topology, an atypical ATP-binding site, a very low sequence similarity in the transmembrane section and long linkers between domains. These features present a considerable hurdle in molecular modeling studies of these important transporters. Here, we report the creation of an atomic model of Pdr5p based on a combination of homology modeling and ab initio methods, incorporating information from consensus transmembrane segment prediction, residue lipophilicity, and sequence entropy. Reported mutations in the transmembrane substrate-binding pocket that altered drug-resistance were used to validate the model, and one mutation that changed the communication pattern between transmembrane and nucleotide-binding domains was used in model improvement. The predictive power of the model was demonstrated experimentally by the increased sensitivity of yeast mutants to clotrimazole having alanine substitutions for Thr1213 and Gln1253, which are predicted to be in the substrate-binding pocket, without reducing the amount of Pdr5p in the plasma membrane. The quality and reliability of our model are discussed in the context of various approaches used for modeling different parts of the structure.
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Pfam：氏族、网络工具和服务。
影响因子：
14.9
作者：
Finn, Robert D.;Mistry, Jaina;Schuster-Bockler, Benjamin;Griffiths-Jones, Sam;Hollich, Volker;Lassmann, Timo;Moxon, Simon;Marshall, Mhairi;Khanna, Ajay;Durbin, Richard;Eddy, Sean R.;Sonnhammer, Erik L. L.;Bateman, Alex
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Bateman, Alex
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3.6
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作者：
Hanson, L;May, L;Golin, J
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Golin, J
DOI：
10.1073/pnas.0800191105
发表时间：
2008-04-01
影响因子：
11.1
作者：
Ernst, Robert;Kueppers, Petra;Schmitt, Lutz
通讯作者：
Schmitt, Lutz
影响因子：
4.8
作者：
Ferreira-Pereira, A;Marco, S;Rigaud, JL
通讯作者：
Rigaud, JL