Beyond consensus: Statistical free energies reveal hidden interactions in the design of a TPR motif
Beyond consensus: Statistical free energies reveal hidden interactions in the design of a TPR motif
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DOI：
10.1016/j.jmb.2004.08.026
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发表时间：
2004-10-22
影响因子：
5.6
通讯作者：
Regan, L
中科院分区：
文献类型：
--
作者：
Magliery, TJ;Regan, L
共识设计方法已经成功地用于设计具有特定折叠的蛋白质，而且还用于设计具有特定折叠的耐热样品。在这里，我们考虑如何统计自由能方法可以扩展现有的系统发育设计方法。作为一个例子，我们分析了四肽重复序列（TPR）基序，使用多序列比对来确定TPR中每个位置的重要性。结果提供了超出共识设计单独揭示的信息，特别是在保守性差的位置。一个特别引人注目的发现是，tpr -肽共晶结构显示与配体直接接触的某些残基显示出明显的高变异性。这提示了一种识别配体结合位点的新方法，也表明tpr通常作为配体结合域起作用。利用微扰分析（或统计耦合分析），我们研究了TPR基序中位点间的相互作用。氨基酸残基在低保守位置的相关出现解释了TPR如何实现其接近中性的表面电荷分布，以及为什么从直接共识设计的TPR具有异常高的净电荷。相互作用位点的网络显示，tpr属于两个未被识别的家族，具有与位置7 （Leu或Lys/Arg）的身份相关的不同相互作用集。统计自由能分析提供了比单独的共识更完整的“是什么使TPR成为TPR?”的描述，它提出了扩展和改进蛋白质系统发育设计的一般方法。(C) 2004 Elsevier Ltd.版权所有。
Consensus design methods have been used successfully to engineer proteins with a particular fold, and moreover to engineer thermostable exemplars of particular folds. Here, we consider how a statistical free energy approach can expand upon current methods of phylogenetic design. As an example, we have analyzed the tetratricopeptide repeat (TPR) motif, using multiple sequence alignment to identify the significance of each position in the TPR. The results provide information above and beyond that revealed by consensus design alone, especially at poorly conserved positions. A particularly striking finding is that certain residues, which TPR-peptide co-crystal structures show are in direct contact with the ligand, display a marked hypervariability. This suggests a novel means of identifying ligand-binding sites, and also implies that TPRs generally function as ligand-binding domains. Using perturbation analysis (or statistical coupling analysis), we examined site-site interactions within the TPR motif. Correlated occurrences of amino acid residues at poorly conserved positions explain how TPRs achieve their near-neutral surface charge distributions, and why a TPR designed from straight consensus has an unusually high net charge. Networks of interacting sites revealed that TPRs fall into two unrecognized families with distinct sets of interactions related to the identity of position 7 (Leu or Lys/Arg). Statistical free energy analysis provides a more complete description of "What makes a TPR a TPR?" than consensus alone, and it suggests general approaches to extend and improve the phylogenetic design of proteins. (C) 2004 Elsevier Ltd. All rights reserved.