NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding.
NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding.
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DOI：
10.1039/c4cp00110a
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发表时间：
2014-04-14
期刊：
影响因子：
--
通讯作者：
Veglia G
中科院分区：
文献类型：
--
作者：
Cembran A;Kim J;Gao J;Veglia G
蛋白质作为构象异构体的集合体存在，这些构象异构体分布在类似折叠漏斗的自由能景观上。虽然最稳定的构象占据低能量盆地，但蛋白质功能通常通过占据高能量盆地的低密度构象状态进行。配体结合改变了这些状态的数量，改变了这些构象异构体的分布。了解状态之间的平衡是如何改变配体结合，与其他结合伙伴的相互作用，和/或突变和翻译后修饰是至关重要的解释蛋白质变构信号。在这里，我们提出了一个统计分析的化学位移（CONCISE，COordinated ChemIcal Shifts bEscherichor）的解释蛋白质构象平衡以下的NMR化学位移的线性轨迹。CONCISE使人们能够定量测量与配体滴定相关的群体变化，并估计蛋白质残基对配体结合的反应的聚集程度，给出结构转变的简明视图。CONCISE与热量热和动力学数据的组合允许人们描绘蛋白质的近似构象能量景观。我们用cAMP依赖性蛋白激酶A的催化亚基测试了这种方法，cAMP依赖性蛋白激酶A是一种普遍存在的酶，在核苷酸和假底物结合时经历构象转变。当补充化学位移协方差分析（CHESCA），这种新的方法提供了集体响应和残基特异性的相关性配体结合蛋白质。
Proteins exist as an ensemble of conformers that are distributed on free energy landscapes resembling folding funnels. While the most stable conformers populate low energy basins, protein function is often carried out through low-populated conformational states that occupy high energy basins. Ligand binding shifts the populations of these states, changing the distribution of these conformers. Understanding how the equilibrium among the states is altered upon ligand binding, interaction with other binding partners, and/or mutations and post-translational modifications is of critical importance for explaining allosteric signaling in proteins. Here, we propose a statistical analysis of the chemical shifts (CONCISE, COordiNated ChemIcal Shifts bEhavior) for the interpretation of protein conformational equilibria following linear trajectories of NMR chemical shifts. CONCISE enables one to quantitatively measure the population shifts associated with ligand titrations and estimate the degree of collectiveness of the protein residues’ response to ligand binding, giving a concise view of the structural transitions. The combination of CONCISE with thermocalorimetric and kinetic data allows one to depict a protein’s approximate conformational energy landscape. We tested this method with the catalytic subunit of cAMP-dependent protein kinase A, a ubiquitous enzyme that undergoes conformational transitions upon both nucleotide and pseudo-substrate binding. When complemented with chemical shift covariance analysis (CHESCA), this new method offers both collective response and residue-specific correlations for ligand binding to proteins.
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影响因子：
15
作者：
Arai, Munehito;Ferreon, Josephine C.;Wright, Peter E.
通讯作者：
Wright, Peter E.
DOI：
10.1073/pnas.0610313104
发表时间：
2007-06-05
影响因子：
11.1
作者：
Cavalli, Andrea;Salvatella, Xavier;Vendruscolo, Michele
通讯作者：
Vendruscolo, Michele
影响因子：
13.8
作者：
Csermely, Peter;Palotai, Robin;Nussinov, Ruth
通讯作者：
Nussinov, Ruth
影响因子：
2.8
作者：
BODENHAUSEN, G;RUBEN, DJ
通讯作者：
RUBEN, DJ
DOI：
10.1073/pnas.0709214104
发表时间：
2008-01-15
影响因子：
11.1
作者：
Masterson, Larry R.;Mascioni, Alessandro;Veglia, Gianluigi
通讯作者：
Veglia, Gianluigi