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Changes in protein structure at the interface accompanying complex formation

机译：伴随复合物形成的界面蛋白质结构的变化

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Protein interactions are essential in all biological processes. The changes brought about in the structure when a free component forms a complex with another molecule need to be characterized for a proper understanding of molecular recognition as well as for the successful implementation of docking algorithms. Here, unbound (U) and bound (B) forms of protein structures from the Protein–Protein Interaction Affinity Database are compared in order to enumerate the changes that occur at the interface atoms/residues in terms of the solvent-accessible surface area (ASA), secondary structure, temperature factors (B factors) and disorder-to-order transitions. It is found that the interface atoms optimize contacts with the atoms in the partner protein, which leads to an increase in their ASA in the bound interface in the majority (69%) of the proteins when compared with the unbound interface, and this is independent of the root-mean-square deviation between the U and B forms. Changes in secondary structure during the transition indicate a likely extension of helices and strands at the expense of turns and coils. A reduction in flexibility during complex formation is reflected in the decrease in B factors of the interface residues on going from the U form to the B form. There is, however, no distinction in flexibility between the interface and the surface in the monomeric structure, thereby highlighting the potential problem of using B factors for the prediction of binding sites in the unbound form for docking another protein. 16% of the proteins have missing (disordered) residues in the U form which are observed (ordered) in the B form, mostly with an irregular conformation; the data set also shows differences in the composition of interface and non-interface residues in the disordered polypeptide segments as well as differences in their surface burial.
机译：蛋白质相互作用在所有生物学过程中都是必不可少的。当自由成分与另一种分子形成复合物时，结构的变化需要加以表征，以正确理解分子识别以及成功实现对接算法。在这里，比较了蛋白质-蛋白质相互作用亲和力数据库中蛋白质结构的未结合（U）和结合（B）形式，以枚举在溶剂可及表面积（ASA）方面发生在界面原子/残基上的变化。 ），二级结构，温度因子（B因子）和无序转换。发现界面原子优化了与伴侣蛋白中原子的接触，与未结合的界面相比，导致大多数（69％）蛋白质的结合界面中的ASA增加，这是独立的U和B形式之间的均方根偏差。过渡过程中二级结构的变化表明，螺旋线和螺旋线可能会延伸，但以匝数和线圈为代价。复合物形成过程中柔韧性的降低反映为界面残基从U型变为B型时B因子的减少。但是，单体结构中的界面和表面之间的柔韧性没有区别，从而突出了潜在的问题，即使用B因子预测未结合形式的结合位点以对接另一种蛋白质。 16％的蛋白质具有U形式的缺失（无序）残基，这些残基以B形式观察（有序），大部分具有不规则构象;该数据集还显示了无序多肽片段中界面残基和非界面残基的组成差异以及其表面掩埋的差异。

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