Hidden dynamic signatures drive substrate selectivity in the disordered phosphoproteome.
Hidden dynamic signatures drive substrate selectivity in the disordered phosphoproteome.
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DOI：
10.1073/pnas.1921473117
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发表时间：
2020-09-22
影响因子：
11.1
通讯作者：
Hilser VJ
中科院分区：
文献类型：
--
作者：
Cho MH;Wrabl JO;Taylor J;Hilser VJ
研究发现，超过40%的真核蛋白质组本质上是无序的，这些无序的片段在磷酸化位点富集，这表明构象异质性可能对激酶的选择性很重要。事实上，依赖于保守序列信息（即“垂直信息”）的经典概念的磷酸化预测程序仅部分有效。我们发现磷酸化位点的构象平衡，其信息嵌入在蛋白质的序列平均能量和结构特性中（即“水平信息”），在区分磷酸化位点和非磷酸化位点方面起着重要作用。事实上，利用水平和垂直信息产生了最先进的磷酸化预测器，其中无序链的构象平衡是主要的贡献者。磷酸化位点在真核生物无序蛋白质组中非常丰富，这表明构象波动在决定激酶与特定底物相互作用的程度方面起着主要作用。在生物物理方面，底物选择性可能不仅取决于激酶与其蛋白质底物之间的结构-化学互补性，还取决于激酶识别或不识别的构象群之间的自由能差。为了验证这一假设，我们开发了一个基于统计热力学的信息学框架，使我们能够通过预测无序蛋白质组中Ser/Thr/Tyr磷酸化位点的能力来探测平衡波动对磷酸化的贡献。该框架的关键是将底物序列信息分解为两种类型：编码保守激酶特异性基元的垂直信息和编码嵌入但通常不明显的位置特异性保护模式的底物构象平衡的水平信息。我们发现构象波动不仅起主要作用，而且是对底物选择性的主要贡献。事实上，区分选择性的主要底物分类器是这些主要单磷酸化位点磷酸化后无序链局部压实变化的大小。除了对蛋白质组磷酸化的结果提供基本的见解外，我们的方法还提供了一种统计热力学策略，用于将任何基于序列的搜索划分为结构化学互补的贡献和构象平衡变化的贡献。
The discovery that more than 40% of the eukaryotic proteome is intrinsically disordered, and that these disordered segments are enriched in phosphorylation sites, suggests that conformational heterogeneity may be important to kinase selectivity. Indeed, phosphorylation prediction programs reliant on classic notions of conserved sequence information (i.e., “vertical information”) are only partially effective. We find that the conformational equilibrium of the phosphorylatable site, whose information is embedded in sequence-averaged energetic and structural properties of the protein (i.e., “horizontal information”), plays a major role in distinguishing phosphorylatable versus nonphosphorylatable sites. In fact, employing both horizontal and vertical information produces a state-of-the-art phosphorylation predictor, wherein the conformational equilibrium of the disordered chain is the dominant contributor. Phosphorylation sites are hyperabundant in the eukaryotic disordered proteome, suggesting that conformational fluctuations play a major role in determining to what extent a kinase interacts with a particular substrate. In biophysical terms, substrate selectivity may be determined not just by the structural–chemical complementarity between the kinase and its protein substrates but also by the free energy difference between the conformational ensembles that are, or are not, recognized by the kinase. To test this hypothesis, we developed a statistical-thermodynamics-based informatics framework, which allows us to probe for the contribution of equilibrium fluctuations to phosphorylation, as evaluated by the ability to predict Ser/Thr/Tyr phosphorylation sites in the disordered proteome. Essential to this framework is a decomposition of substrate sequence information into two types: vertical information encoding conserved kinase specificity motifs and horizontal information encoding substrate conformational equilibrium that is embedded, but often not apparent, within position-specific conservation patterns. We find not only that conformational fluctuations play a major role but also that they are the dominant contribution to substrate selectivity. In fact, the main substrate classifier distinguishing selectivity is the magnitude of change in local compaction of the disordered chain upon phosphorylation of these mostly singly phosphorylated sites. In addition to providing fundamental insights into the consequences of phosphorylation across the proteome, our approach provides a statistical-thermodynamic strategy for partitioning any sequence-based search into contributions from structural–chemical complementarity and those from changes in conformational equilibrium.
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DOI：
10.1073/pnas.89.22.10915
发表时间：
1992-11-15
影响因子：
11.1
作者：
HENIKOFF, S;HENIKOFF, JG
通讯作者：
HENIKOFF, JG
影响因子：
16.6
作者：
Gibbs EB;Lu F;Portz B;Fisher MJ;Medellin BP;Laremore TN;Zhang YJ;Gilmour DS;Showalter SA
通讯作者：
Showalter SA
影响因子：
3.4
作者：
GUY, HR
通讯作者：
GUY, HR
影响因子：
14.9
作者：
Dinkel H;Chica C;Via A;Gould CM;Jensen LJ;Gibson TJ;Diella F
通讯作者：
Diella F
影响因子：
3.4
作者：
Chin, Alexander F.;Toptygin, Dmitri;Hilser, Vincent J.
通讯作者：
Hilser, Vincent J.