PQS: a protein quaternary structure file server
PQS: a protein quaternary structure file server
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DOI：
10.1016/s0968-0004(98)01253-5
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发表时间：
1998-09-01
影响因子：
13.8
通讯作者：
Thornton, JM
中科院分区：
文献类型：
--
作者：
Henrick, K;Thornton, JM
在处理的7001个晶体学条目中有359个，在第一阶段产生了2895个潜在的二聚体，然后将15%归类为显著晶体堆积的实例。在1994年被接受为可能的二聚体中，19%与其他在线注释不匹配。后者的近一半（190个条目）是伪二聚体溶菌酶（如下所述）。当另一个来源表明PDB条目是单体的或存在于其他寡聚状态时，就会标记不匹配。对于大约18%的可能的同源二聚体，没有可用的注释来与PQS结果进行比较。该测试的全部细节可从PQS网络文档中获得。没有普遍的规则被发现，可以用来区分一个真正的低聚状态和晶体堆积的人工制品明确。由这种自动过程产生的一些二聚体具有Δasa，允许复合物被指定为具有生物学意义，而分子已知是单体。例如，单体T4溶菌酶的结构经常被指定为二聚体；对于T4溶菌酶突变体119L15， Δasa为每条链885 Å2（图2a）。对于这种晶体填充相互作用产生伪二聚体，所涉及的表面可能代表一些未知的生物学功能，如所建议的。更复杂的是，在第一轮中发现但在检查步骤中被拒绝的二聚体有时在PDB条目中被列为真正的二聚体。例如，erabutoxin的二聚体形式6EBX17在二聚体形成时被拒绝，每条链的Δasa仅为290 Å2。在某些情况下，没有现成的在线信息来验证低聚物状态。一些不匹配的发生是因为可用的在线注释是错误的：例如，为r -植红蛋白结构1LIA18生成了十二聚体[A6B6]，而PDB条目将该分子描述为异八聚体。PQS过程也产生复杂的蛋白质-蛋白质排列，可能只有在固体状态下才稳定。一个例子是转录抑制蛋白（rop） 1GTO的24meric组装（Agrawal， V., Predki， P., Regan， L. and Brunger， AT，未发表；PDB条目，1GTO）。该PDB条目具有生物单位的二聚体，并且该过程自动生成作者所描述的存在于晶体结构中的“超稳定螺旋束”（图2b）。发现了几种蛋白酶抑制剂的相关排列，包括丝氨酸蛋白酶抑制剂ci2, 1CIQ (Davis， B., Buckle， AM, de Prat Gay， G. and Fersht， AR，未发表；PDB条目，1CIQ), a [A6B6]
359 from the 7001 crystallographic entries processed, 2895 potential dimers were generated in the first stage, and 15% were then classified as instances of significant crystal packing. Of the 1994 accepted as probable dimers, 19% mismatch some other online annotation. Nearly half of the latter (190 entries) were pseudo-dimeric lysozyme (as described below). A mismatch was flagged when another source indicated that the PDB entry was either monomeric or existed in some other state of oligomerization. For some 18% of the probable homomeric dimers, no annotation was available to compare with the PQS result. Full details of this test are available from the PQS web documentation. No universal rule was found that could be used to differentiate a true oligomeric state and a crystal-packing artefact unambiguously. Some of the dimers generated by this automatic process have a Δasa that allows the complex to be assigned as biologically significant, whereas the molecule is known to be monomeric. For example, structures of monomeric T4 lysozyme are frequently assigned as dimeric; for the T4 lysozyme mutant 119L15, Δasa is 885 Å2 per chain (Fig. 2a). For this type of crystal-packing interaction to give a pseudo-dimer, the surface involved might represent some unknown biological function, as suggested16. A further complication is that dimers found in the first pass but rejected in the check step are sometimes listed as true dimers in the PDB entry. For example, the dimeric form of erabutoxin, 6EBX17, is rejected with an Δasa of only 290 Å2 per chain upon dimer formation. In some cases there is no readily available online information to validate the oligomeric state. Some mismatches occur because the available online annotation is in error: for example, a dodecamer [A6B6] is generated for the R-phycoerythrin structure 1LIA18, while the PDB entry describes the molecule as a hetero-octamer.The PQS procedure also generates complex protein–protein arrangements that might be stable only in the solid state. An example is the 24meric assembly found for the transcription repressor protein (rop), 1GTO (Agrawal, V., Predki, P., Regan, L. and Brunger, AT, unpublished; PDB entry, 1GTO). This PDB entry has a dimer for the biological unit, and the procedure automatically generates what the authors describe as a ‘hyperstable helical bundle’existing in the crystal structure (Fig. 2b). Related arrangements were found for several protease inhibitors, including serine-protease inhibitor ci2, 1CIQ (Davis, B., Buckle, AM, de Prat Gay, G. and Fersht, AR, unpublished; PDB entry, 1CIQ), a [A6B6]