Toward rational protein crystallization: A Web server for the design of crystallizable protein variants
Toward rational protein crystallization: A Web server for the design of crystallizable protein variants
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DOI：
10.1110/ps.072914007
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发表时间：
2007-08-01
期刊：
影响因子：
8
通讯作者：
Eisenberg, David
中科院分区：
文献类型：
--
作者：
Goldschmidt, Lukasz;Cooper, David R.;Eisenberg, David
生长良好衍射的晶体构成了结构生物学的严重瓶颈。最近提出的“顽固结晶器”的结晶方法是设计表面序列变体，旨在形成可以支撑晶格的分子间接触。这种方法依赖于表面熵减少（SER）的概念，即用具有较低构象熵的残基替换柔性的、暴露于溶剂的残基簇。这种策略最大限度地减少了构象熵的损失。 结晶并使结晶在热力学上有利。该方法已成功用于结晶超过 15 种新型蛋白质，所有这些都是顽固的结晶器。但选择合适的诱变位点并非易事。在此，我们宣布推出一款 Web 服务器，即表面熵减少预测服务器（SERp 服务器），旨在识别可能促进结晶的突变。建议的突变是基于包含以下内容的算法来预测的： 构象熵谱、二级结构预测和序列守恒。次要考虑因素包括侧翼残基的性质和候选突变之间的间隙。虽然设计为使用默认值，但服务器具有许多用户控制的参数，具有相当大的灵活性。其中，我们讨论（1）服务器的方法，（2）如何解释结果，以及（3）选择突变时必须考虑的因素。我们还尝试对标 通过将服务器的预测与成功的 SER 结构进行比较来验证服务器。在大多数情况下，SERp 服务器很容易识别产生突变的结构。该服务器可以通过 http://www.doe-mbi.ucla.edu/Services/SER 访问。
Growing well-diffracting crystals constitutes a serious bottleneck in structural biology. A recently proposed crystallization methodology for "stubborn crystallizers'' is to engineer surface sequence variants designed to form intermolecular contacts that could support a crystal lattice. This approach relies on the concept of surface entropy reduction (SER), i. e., the replacement of clusters of flexible, solvent-exposed residues with residues with lower conformational entropy. This strategy minimizes the loss of conformational entropy upon crystallization and renders crystallization thermodynamically favorable. The method has been successfully used to crystallize more than 15 novel proteins, all stubborn crystallizers. But the choice of suitable sites for mutagenesis is not trivial. Herein, we announce a Web server, the surface entropy reduction prediction server (SERp server), designed to identify mutations that may facilitate crystallization. Suggested mutations are predicted based on an algorithm incorporating a conformational entropy profile, a secondary structure prediction, and sequence conservation. Minor considerations include the nature of flanking residues and gaps between mutation candidates. While designed to be used with default values, the server has many user- controlled parameters allowing for considerable flexibility. Within, we discuss (1) the methodology of the server, (2) how to interpret the results, and (3) factors that must be considered when selecting mutations. We also attempt to benchmark the server by comparing the server's predictions with successful SER structures. In most cases, the structure yielding mutations were easily identified by the SERp server. The server can be accessed at http://www.doe-mbi.ucla.edu/Services/SER.