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Structural changes in DNA-binding proteins on complexation
Nucleic Acids Research ( IF 14.9 ) Pub Date : 2018-03-09 , DOI: 10.1093/nar/gky170
Sayan Poddar 1 , Devlina Chakravarty 2 , Pinak Chakrabarti 1, 2
Affiliation  

Characterization and prediction of the DNA-biding regions in proteins are essential for our understanding of how proteins recognize/bind DNA. We analyze the unbound (U) and the bound (B) forms of proteins from the protein–DNA docking benchmark that contains 66 binary protein–DNA complexes along with their unbound counterparts. Proteins binding DNA undergo greater structural changes on complexation (in particular, those in the enzyme category) than those involved in protein–protein interactions (PPI). While interface atoms involved in PPI exhibit an increase in their solvent-accessible surface area (ASA) in the bound form in the majority of the cases compared to the unbound interface, protein–DNA interactions indicate increase and decrease in equal measure. In 25% structures, the U form has missing residues which are located in the interface in the B form. The missing atoms contribute more toward the buried surface area compared to other interface atoms. Lys, Gly and Arg are prominent in disordered segments that get ordered in the interface on complexation. In going from U to B, there may be an increase in coil and helical content at the expense of turns and strands. Consideration of flexibility cannot distinguish the interface residues from the surface residues in the U form.

中文翻译:

复杂的DNA结合蛋白的结构变化

蛋白质中DNA结合区域的表征和预测对于我们理解蛋白质如何识别/结合DNA至关重要。我们从蛋白质-DNA对接基准中分析了未结合(U)和结合(B)形式的蛋白质,该基准包含66种二元蛋白质-DNA复合物及其未结合的对应物。与蛋白质结合的蛋白质(尤其是酶类别的蛋白质)与结合蛋白质的DNA相比,参与蛋白质-蛋白质相互作用(PPI)的蛋白质发生更大的结构变化。尽管在大多数情况下,与未结合的界面相比,参与PPI的界面原子在结合形式中的溶剂可及表面积(ASA)都有所增加,但蛋白质与DNA的相互作用表明,等量的增加和减少。在25%的结构中,U形式的缺失残基位于B形式的界面中。与其他界面原子相比,缺失的原子对掩埋表面积的贡献更大。Lys,Gly和Arg在无序节段中很突出,这些节段在复合时在界面上有序排列。从U到B时,线圈和螺旋含量可能会增加,但会增加匝数和股数。考虑灵活性时,不能以U形区分界面残基和表面残基。
更新日期:2018-03-09
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