Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain.
Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain.
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DOI：
10.1016/j.jmb.2009.12.052
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发表时间：
2010-03-05
影响因子：
5.6
通讯作者：
McCallum SA
中科院分区：
文献类型：
--
作者：
Sgourakis NG;Patel MM;Garcia AE;Makhatadze GI;McCallum SA
泛素相互作用基序 (UIM) 是一类重要的蛋白质结构域，与泛素或泛素样蛋白相互作用。这些大约 20 个残基长的结构域存在于各种泛素受体蛋白中，并作为细胞内靶标的识别模块，这些靶标可能是单个泛素亚基或多泛素链，连接到各种蛋白质上。先前对 UIM 与泛素之间相互作用的结构研究表明，UIM 采用单个 α 螺旋的扩展结构，包含具有保守序列模式的疏水表面，可与泛素上的关键疏水残基相互作用。鉴于大量的结构研究，关于结构动力学和可塑性的存在和作用的细节令人惊讶地缺乏。为了更好地理解泛素-UIM 识别的结构基础，在与酵母 Vps27 蛋白的 UIM 结构域结合后，对泛素的结构和动力学变化进行了表征。本文报道了旨在研究这些相互作用的泛素-UIM 融合蛋白的溶液结构，并发现其由明确的泛素核心和二分 UIM 螺旋组成。此外，我们还通过 NMR 弛豫研究了对接界面的可塑性以及由于 UIM 结合在皮秒至纳秒和微秒至毫秒蛋白质运动中引起的泛素全局变化。酰胺基团广义有序参数的变化显示出相对于未结合泛素中测定的值而言，UIM-泛素界面处的结构刚性增加的明显趋势。 15N CPMG 弛豫色散测量的分析表明存在两种类型的运动，一种与 UIM 结合界面直接相关，另一种被诱导到蛋白质的远端部分。这项研究证明了蛋白质结构域之间的局部相互作用在皮秒到毫秒的时间尺度上对蛋白质运动产生全局影响的情况。
Ubiquitin-interacting motifs (UIMs) are an important class of protein domains that interact with ubiquitin or ubiquitin-like proteins. These approximately 20 residue-long domains are found in a variety of ubiquitin receptor proteins and serve as recognition modules towards intracellular targets, which may be individual ubiquitin subunits or polyubiquitin chains attached to a variety of proteins. Previous structural studies of the interactions between UIMs with ubiquitin have shown that UIMs adopt an extended structure of a single α-helix, containing a hydrophobic surface with a conserved sequence pattern that interacts with key hydrophobic residues on ubiquitin. In light of this large body of structural studies, details regarding the presence and roles of structural dynamics and plasticity are surprisingly lacking. In order to better understand the structural basis of ubiquitin-UIM recognition, changes in the structure and dynamics of ubiquitin have been characterized upon binding of a UIM domain from the yeast Vps27 protein. The solution structure of a ubiquitin-UIM fusion protein designed to study these interactions is reported here and found to consist of a well-defined ubiquitin core and a bipartite UIM helix. Moreover, we have studied the plasticity of the docking interface as well as global changes in ubiquitin due to UIM binding at the picosecond to nanosecond and microsecond to millisecond protein motions by NMR relaxation. Changes in generalized order parameters of amide groups show a distinct trend toward increased structural rigidity at the UIM-ubiquitin interface relative to values determined in unbound ubiquitin. Analysis of 15N CPMG relaxation dispersion measurements suggest the presence of two types of motions, one directly related to the UIM-binding interface, the other being induced to distal parts of the protein. This study demonstrates a case where localized interactions among protein domains have global effects in protein motions at timescales ranging from picoseconds to milliseconds.
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影响因子：
2.8
作者：
BOYD, J;HOMMEL, U;CAMPBELL, ID
通讯作者：
CAMPBELL, ID
影响因子：
8
作者：
Ermolenko, DN;Richardson, JM;Makhatadze, GI
通讯作者：
Makhatadze, GI
影响因子：
2.2
作者：
CARVER, JP;RICHARDS, RE
通讯作者：
RICHARDS, RE
DOI：
10.1107/s0907444998003254
发表时间：
1998-09-01
期刊：
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
影响因子：
--
作者：
Brunger, AT;Adams, PD;Warren, GL
通讯作者：
Warren, GL
影响因子：
2.9
作者：
FARROW, NA;MUHANDIRAM, R;KAY, LE
通讯作者：
KAY, LE