Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.
Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.
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DOI：
10.1186/1472-6807-5-15
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发表时间：
2005-08-16
影响因子：
--
通讯作者：
Rekha N
中科院分区：
文献类型：
--
作者：
De S;Krishnadev O;Srinivasan N;Rekha N
如果蛋白质-蛋白质复合物的多肽链在其整个功能寿命中与另一条链结合，则该多肽链被认为是强制性的。这样的链可能不会采用未结合形式的天然折叠。非强制性多肽链与另一条链缔合并在分子刺激下解离。虽然在相互作用界面的构象变化是预期的，非强制性链的整体3-D结构是不变的。本研究的重点是蛋白质-蛋白质复合物，以进一步了解强制性和非强制性接口之间的差异。已知三维结构的复合物中的非强制性链通过其在结合和未结合形式中具有相同折叠的稳定存在来识别。相反，一个强制性的链被检测到它的存在，只有在绑定的形式，没有证据的天然样折叠的链在未绑定的形式。各种界面性质的大量复杂的已知的3-D结构，从而分类进行了比较分析，目的是确定区分这两种类型的接口的结构描述符。我们报告说，强制性和非强制性组件的接口之间的相互作用模式是不同的，强制性链的接触主要是非极性的。与非强制性链（每个接口13 ± 6个触点）相比，强制性链每个接口的触点数量更高（每个接口20 ± 14个触点）。与非强制性链（11.2%）相比，强制性链（16.9%）中主链原子的参与更高。仅在数据集中的强制性蛋白质链中观察到跨亚基的β折叠形成。除此之外，其他特征如残基偏好和界面面积也产生了边际差异，在区分两类界面时，可以将它们统一考虑。这些结果可以是有用的，在区分两种类型的接口中观察到的结构确定在大规模的结构基因组学倡议，特别是对于那些多组分蛋白质组装体的生化表征是不完整的。
A polypeptide chain of a protein-protein complex is said to be obligatory if it is bound to another chain throughout its functional lifetime. Such a chain might not adopt the native fold in the unbound form. A non-obligatory polypeptide chain associates with another chain and dissociates upon molecular stimulus. Although conformational changes at the interaction interface are expected, the overall 3-D structure of the non-obligatory chain is unaltered. The present study focuses on protein-protein complexes to understand further the differences between obligatory and non-obligatory interfaces. A non-obligatory chain in a complex of known 3-D structure is recognized by its stable existence with same fold in the bound and unbound forms. On the contrary, an obligatory chain is detected by its existence only in the bound form with no evidence for the native-like fold of the chain in the unbound form. Various interfacial properties of a large number of complexes of known 3-D structures thus classified are comparatively analyzed with an aim to identify structural descriptors that distinguish these two types of interfaces. We report that the interaction patterns across the interfaces of obligatory and non-obligatory components are different and contacts made by obligatory chains are predominantly non-polar. The obligatory chains have a higher number of contacts per interface (20 ± 14 contacts per interface) than non-obligatory chains (13 ± 6 contacts per interface). The involvement of main chain atoms is higher in the case of obligatory chains (16.9 %) compared to non-obligatory chains (11.2 %). The β-sheet formation across the subunits is observed only among obligatory protein chains in the dataset. Apart from these, other features like residue preferences and interface area produce marginal differences and they may be considered collectively while distinguishing the two types of interfaces. These results can be useful in distinguishing the two types of interfaces observed in structures determined in large-scale in the structural genomics initiatives, especially for those multi-component protein assemblies for which the biochemical characterization is incomplete.
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影响因子：
1.7
作者：
Duan, GL;Smith, VH;Weaver, DF
通讯作者：
Weaver, DF
影响因子：
5.6
作者：
Svensson, C;Teneberg, S;Krengel, U
通讯作者：
Krengel, U
影响因子：
5.6
作者：
Bahadur, RP;Chakrabarti, P;Janin, J
通讯作者：
Janin, J
影响因子：
13.8
作者：
Henrick, K;Thornton, JM
通讯作者：
Thornton, JM
DOI：
10.1073/pnas.181354398
发表时间：
2001-09-11
影响因子：
11.1
作者：
Kuhlman, B;O'Neill, JW;Baker, D
通讯作者：
Baker, D