The Intrinsic Protein Flexibility of Endogenous Protease Inhibitor TIMP-1 Controls Its Binding Interface and Affects Its Function
The Intrinsic Protein Flexibility of Endogenous Protease Inhibitor TIMP-1 Controls Its Binding Interface and Affects Its Function
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DOI：
10.1021/bi902141x
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发表时间：
2010-07-27
期刊：
影响因子：
2.9
通讯作者：
Sagi, Irit
中科院分区：
文献类型：
--
作者：
Grossman, Moran;Tworowski, Dmitry;Sagi, Irit
蛋白质的柔性被认为在许多生物过程中发挥关键作用，包括抗体亲和力成熟，信号转导和酶催化，但只有有限的信息是关于连接蛋白质动力学与功能的分子细节。在内源性金属蛋白酶组织抑制剂1（TIMP-1）的远端位点处的单点突变使得该临床靶蛋白能够通过仅增加缔合常数而紧密结合并抑制膜型1基质金属蛋白酶（MT 1-MMP）。在2A处确定的该复合物的高分辨率X射线结构不能解释增强结合的机制，并指出蛋白质构象动力学的作用。分子动力学（MD）模拟表明，高亲和力TIMP-1突变体表现出显着降低的结合界面的灵活性和更稳定的氢键网络。这是伴随着重新分配的合奏基板有利的结合构象，适合酶催化位点。显然，主链柔性的降低导致复合物形成时的熵成本降低。这项工作量化的影响，一个单一的点突变的蛋白质构象动力学和功能的TIMP-1。在这里，我们认为，控制内在的蛋白质动力学的MMP内源性抑制剂可用于合理化设计的选择性新的蛋白质抑制剂，这类酶。
Protein flexibility is thought to play key roles in numerous biological processes, including antibody affinity maturation, signal transduction, and enzyme catalysis, yet only limited information is available regarding the molecular details linking protein dynamics with function. A single point mutation at the distal site of the endogenous tissue inhibitor of metalloproteinase 1 (TIMP-1) enables this clinical target protein to tightly bind and inhibit membrane type 1 matrix metalloproteinase (MT1-MMP) by increasing only the association constant. The high-resolution X-ray structure of this complex determined at 2 A could not explain the mechanism of enhanced binding and pointed to a role for protein conformational dynamics. Molecular dynamics (MD) simulations reveal that the high-affinity TIMP-1 mutants exhibit significantly reduced binding interface flexibility and more stable hydrogen bond networks. This was accompanied by a redistribution of the ensemble of substrates to favorable binding conformations that fit the enzyme catalytic site. Apparently, the decrease in backbone flexibility led to a lower entropy cost upon formation of the complex. This work quantifies the effect of a single point mutation on the protein conformational dynamics and function of TIMP-1. Here we argue that controlling the intrinsic protein dynamics of M MP endogenous inhibitors may be utilized for rationalizing the design of selective novel protein inhibitors for this class of enzymes.