Nature of allosteric inhibition in glutamate racemase: discovery and characterization of a cryptic inhibitory pocket using atomistic MD simulations and pKa calculations.
Nature of allosteric inhibition in glutamate racemase: discovery and characterization of a cryptic inhibitory pocket using atomistic MD simulations and pKa calculations.
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DOI：
10.1021/jp201037t
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发表时间：
2011-04-07
影响因子：
3.3
通讯作者：
Spies, M. Ashley
中科院分区：
文献类型：
--
作者：
Whalen, Katie L.;Tussey, Kenneth B.;Blanke, Steven R.;Spies, M. Ashley
通过变构来抑制酶是一种鲜为人知的现象，也是对基于结构的药物设计的重大挑战。芽孢杆菌芽胞的主要成分DPA以一种新的变构方式抑制炭疽芽孢杆菌的谷氨酸外消旋酶。谷氨酸消旋酶因其在细菌细胞壁合成中的重要作用，长期以来一直被认为是重要的药物靶标。通过多个对接研究预测了DPA的结合模式，并通过结合位点的定点突变进行了验证，同时结合Blue Native PAGE、分子动力学模拟、自由能和PKA计算阐明了抑制机制。DPA的抑制不仅揭示了一个新的隐蔽结合部位，而且代表了一种变构调节形式，利用了酶构象变化、埋藏残基pKa值的波动和催化之间的相互作用。讨论了未来药物开发的潜力。
Enzyme inhibition via allostery, in which the ligand binds remotely from the active site, is a poorly understood phenomenon, and represents a significant challenge to structure-based drug design. Dipicolinic acid (DPA), a major component of Bacillus spores, is shown to inhibit glutamate racemase from Bacillus anthracis, a monosubstrate/monoproduct enzyme, in a novel allosteric fashion. Glutamate racemase has long been considered an important drug target for its integral role in bacterial cell wall synthesis. The DPA binding mode was predicted via multiple docking studies and validated via site-directed mutagenesis at the binding locus, while the mechanism of inhibition was elucidated with a combination of Blue Native PAGE, molecular dynamics simulations, free energy and pKa calculations. Inhibition by DPA not only reveals a novel cryptic binding site, but also represents a form of allosteric regulation that exploits the interplay between enzyme conformational changes, fluctuations in the pKa values of buried residues and catalysis. The potential for future drug development is discussed.
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影响因子：
2.9
作者：
Mehboob, Shahila;Guo, Liang;Fu, Wentao;Mittal, Anuradha;Yau, Tiffany;Truong, Kent;Johlfs, Mary;Long, Fei;Fung, Leslie W. -M.;Johnson, Michael E.
通讯作者：
Johnson, Michael E.
影响因子：
1.3
作者：
Eastwood, MP;Hardin, C;Wolynes, PG
通讯作者：
Wolynes, PG
DOI：
10.1073/pnas.0404781101
发表时间：
2004-08-24
影响因子：
11.1
作者：
Hardy, JA;Lam, J;Wells, JA
通讯作者：
Wells, JA
影响因子：
7.3
作者：
de Dios, A;Prieto, L;Smith, MC
通讯作者：
Smith, MC
影响因子：
5.6
作者：
Brown, Scott P.;Muchmore, Steven W.
通讯作者：
Muchmore, Steven W.